diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index ab4ea97b5a1..cf306820c7f 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -2,11 +2,11 @@
     <div class="toolForm">
         <div class="toolFormTitle">
             Citations
-            <button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs" title="Show all in BibTeX format.">
+            <button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format.">
                 <i class="fa fa-pencil-square-o"></i>
                 Show BibTeX
             </button>
-            <button v-else type="button" v-on:click="toggleViewRender" class="btn btn-xs" title="Return to formatted citation list.">
+            <button v-else type="button" v-on:click="toggleViewRender" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list.">
                 <i class="fa fa-times"></i>
                 Hide BibTeX
             </button>
diff --git a/static/scripts/bundled/admin.bundled.js b/static/scripts/bundled/admin.bundled.js
index 16cf74691f7..a590cd288dd 100644
--- a/static/scripts/bundled/admin.bundled.js
+++ b/static/scripts/bundled/admin.bundled.js
@@ -1,7 +1,7 @@
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0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){y.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;o.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),i=t.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(a.go()).then(function(t){i.resolve("ok"===t||"data"===t)}),i},search_features:function(e){var i=this.get("dataset"),n={query:e,hda_ldda:i.get("hda_ldda"),data_type:"features"};return t.getJSON(i.url(),n)},load_data:function(e,i,n,a){var r=this.get("dataset"),o={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:i,resolution:n,hda_ldda:r.get("hda_ldda")};t.extend(o,a);var s=this.get("filters_manager");if(s){for(var l=[],d=s.filters,c=0;c<d.length;c++)l.push(d[c].name);o.filter_cols=JSON.stringify(l)}var u=this,h=t.getJSON(r.url(),o,function(t){t.region=e,u.set_data(e,t)});return this.set_data(e,h),h},get_data:function(t,e,i,n){var a=this.get_elt(t);if(a&&(c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)))return a;for(var r,o,s=this.get("key_ary"),l=this.get("obj_cache"),d=0;d<s.length;d++)if(r=s[d],r.contains(t)&&(o=!0,a=l[r.toString()],c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)&&this.get("can_subset")(a))){if(this.move_key_to_end(r,d),!c.default.is_deferred(a)){var u=this.subset_entry(a,t);this.set_data(t,u),a=u}return a}if(!o&&t.length()<this.attributes.min_region_size){t=t.copy();var h=this.most_recently_added();!h||t.get("start")>h.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,i,n)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,i,n,a,r){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");r===this.DEEP_DATA_REQ?t.extend(a,{start_val:o.data.length+1}):r===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),d=this,c=this.load_data(l,i,n,a),u=t.Deferred();return this.set_data(e,u),t.when(c).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),d.set_data(e,t),u.resolve(t)}),u},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,i,n,a){var r=this._mark_stale(t);return r?(a||(a={}),"bigwig"===r.dataset_type&&(a.num_samples=1e3*n),this.load_data(t,e,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var i=this,n=!0,a=o.map(e.get("chroms_info").chrom_info,function(t){var e=i.get_elt(new S({chrom:t.chrom,start:0,end:t.len}));return e||(n=!1),e});if(n)return a;var r=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){i.add_data(t.data),r.resolve(t.data)}),r},subset_entry:function(t,e){var i={bigwig:function(t,e){return o.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,i){var n=i.get("start")-t.region.get("start");return t.data.slice(n,n+i.length())}},n=t.data;return!t.region.same(e)&&t.dataset_type in i&&(n=i[t.dataset_type](t.data,e)),{region:e,data:n,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new n.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,i,n){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,i,n):{data:null,region:t}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=o.find(this.get_chroms_info(),function(e){return e.chrom===t});return new S({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return o.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),S=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),i=e[0],n=e[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new S({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),i=t.get("chrom"),n=this.get("start"),a=t.get("start"),r=this.get("end"),o=t.get("end");return e&&i&&e!==i?S.overlap_results.DIF_CHROMS:n<a?r<a?S.overlap_results.BEFORE:r<o?S.overlap_results.OVERLAP_START:S.overlap_results.CONTAINS:n>a?n>o?S.overlap_results.AFTER:r<=o?S.overlap_results.CONTAINED_BY:S.overlap_results.OVERLAP_END:r>=o?S.overlap_results.CONTAINS:S.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===S.overlap_results.CONTAINS},overlaps:function(t){return 0===o.intersection([this.compute_overlap(t)],[S.overlap_results.DIF_CHROMS,S.overlap_results.BEFORE,S.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),$=n.Collection.extend({model:S}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new S(t.region))}}),M=n.Collection.extend({model:T}),O=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===o.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),A=n.Collection.extend({model:O}),E=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),z=E.extend(v).extend({defaults:o.extend({},E.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new A(t.tracks));var 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d.append(n("<input />").attr("id",a).attr("name",a).val(s));e.help&&d.append(n("<div class='help'/>").text(e.help))}}),this},render_in_modal:function(t){var e=this,i=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc")},a=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc"),e.update_from_form()},r=function(t){27===(t.keyCode||t.which)?i():13===(t.keyCode||t.which)&&a()};n(window).bind("keypress.check_enter_esc",r),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:t||"Configure",body:this.$el,buttons:{Cancel:i,OK:a}})},update_from_form:function(){var t=this;this.collection.each(function(e,i){if(!e.get("hidden")){var n="param_"+i,a=t.$el.find("#"+n).val();"bool"===e.get("type")&&(a=t.$el.find("#"+n).is(":checked")),e.set_value(a)}})}});e.default={ConfigSetting:c,ConfigSettingCollection:u,ConfigSettingCollectionView:h}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return 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i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,n("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&a.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),a.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),n=a.filter(t.data2,function(i){var n=!1;return a.each(i.tags,function(i){t._match(e.term,i)&&(n=t.matched_tags[i]=!0)}),n||t._match(e.term,i.text)});e.callback({results:n.slice((e.page-1)*i,e.page*i),more:n.length>=e.page*i})},formatResult:function(e){return a.escape(e.text)+'<div class="ui-tags">'+a.reduce(e.tags,function(e,i){return t.matched_tags[i]?e+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search 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t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return t.length>0?t.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(t){var e=this;if(void 0!==t&&(this.$("input").prop("checked",!1),null!==t)){var i=n.isArray(t)?t:[t];a.each(i,function(t){e.$('input[value="'+t+'"]').first().prop("checked",!0)})}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push(n(this).val())}),s.default.isEmpty(t)?null:this.model.get("multiple")?t:t[0]},_messageShow:function(t,e){this.$message.show().removeClass().addClass("ui-message alert alert-"+e).html(t)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(t){var e=s.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=u.extend({initialize:function(t){t.type="radio",u.prototype.initialize.call(this,t)}});var f={};f.View=u.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,u.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return 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a=t.View.extend({initialize:function(e){this.model=e&&e.model||new t.Model(e),this.setElement(i("<div/>").addClass("corner frame")),this.$el.append(i("<div/>").addClass("f-header corner").append(i("<div/>").addClass("f-title")).append(i("<div/>").addClass("f-icon f-close fa fa-close").tooltip({title:"Close",placement:"bottom"}))).append(i("<div/>").addClass("f-content")).append(i("<div/>").addClass("f-resize f-icon corner fa fa-expand").tooltip({title:"Resize"})).append(i("<div/>").addClass("f-cover")),this.$header=this.$(".f-header"),this.$title=this.$(".f-title"),this.$content=this.$(".f-content"),this.render(),this.listenTo(this.model,"change",this.render,this)},render:function(){var t=this,e=this.model.attributes;this.$title.html(e.title||""),this.$header.find(".f-icon-left").remove(),n.each(e.menu,function(e){var a=i("<div/>").addClass("f-icon-left").addClass(e.icon);n.isFunction(e.disabled)&&e.disabled()?a.attr("disabled",!0):a.on("click",function(){e.onclick(t)}).tooltip({title:e.tooltip,placement:"bottom"}),t.$header.append(a)}),e.url?this.$content.html(i("<iframe/>").addClass("f-iframe").attr("scrolling","auto").attr("src",e.url+(-1===e.url.indexOf("?")?"?":"&")+"widget=True")):e.content&&(n.isFunction(e.content)?e.content(t.$content):t.$content.html(e.content))}}),r=t.View.extend({defaultOptions:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_uid:0,frame_list:{},frame_shadow:null,visible:!1,event:{},initialize:function(e){var a=this;this.options=n.defaults(e||{},this.defaultOptions),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(i("<div/>").addClass("galaxy-frame").append(i("<div/>").addClass("frame-background")).append(i("<div/>").addClass("frame-menu frame-scroll-up fa fa-chevron-up fa-2x")).append(i("<div/>").addClass("frame-menu frame-scroll-down fa fa-chevron-down fa-2x"))),this.frame_shadow=new t.View({el:i("<div/>").addClass("corner frame-shadow")}),this.$el.append(this.frame_shadow.$el),this._frameInit(this.frame_shadow,"#frame-shadow"),this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list["#frame-shadow"]=this.frame_shadow,this.visible?this.show():this.hide(),this._panelRefresh(),i(window).resize(function(){a.visible&&a._panelRefresh()})},render:function(){this.$(".frame-scroll-up")[this.top!=this.options.top_min&&"show"||"hide"](),this.$(".frame-scroll-down")[this.top!=this.top_max&&"show"||"hide"]()},add:function(t){if(this.frame_counter>=this.options.frame_max)Galaxy.modal.show({title:"Warning",body:"You have reached the maximum number of allowed frames ("+this.options.frame_max+").",buttons:{Close:function(){Galaxy.modal.hide()}}});else{var e="#frame-"+this.frame_uid++;if(0!==i(e).length)Galaxy.modal.show({title:"Error",body:"This frame already exists. This page might contain multiple frame managers.",buttons:{Close:function(){Galaxy.modal.hide()}}});else{this.top=this.options.top_min;var n=new a(t);this.$el.append(n.$el),t.width=this._toPixelCoord("width",this.options.frame.cols),t.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt(n.$el.css("z-index")),this.frame_list[e]=n,this.frame_counter++,this._frameInit(n,e),this._frameResize(n,{width:t.width,height:t.height}),this._frameInsert(n,{top:0,left:0},!0),!this.visible&&this.show(),this.trigger("add")}}},del:function(t){var e=this,i=t.$el;i.fadeOut("fast",function(){i.remove(),delete e.frame_list[t.id],e.frame_counter--,e._panelRefresh(!0),e._panelAnimationComplete(),e.trigger("remove")})},show:function(){this.visible=!0,this.$el.fadeIn("fast"),this.trigger("show")},hide:function(){this.event.type||(this.visible=!1,this.$el.fadeOut("fast",function(){i(this).hide()}),this.trigger("hide"))},length:function(){return this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(t){i(".tooltip").hide(),this.event.type||((i(t.target).hasClass("f-header")||i(t.target).hasClass("f-title"))&&(this.event.type="drag"),i(t.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(t.preventDefault(),this.event.target=this._frameIdentify(t.target),this.event.xy={x:t.originalEvent.pageX,y:t.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(t){if(this.event.type){var e={x:t.originalEvent.pageX,y:t.originalEvent.pageY},i={x:e.x-this.event.xy.x,y:e.y-this.event.xy.y};this.event.xy=e;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var r={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==r.left&&r.left++,this._frameInsert(this.frame_shadow,r)}}},_eventFrameMouseUp:function(t){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(t){this.event.type||(t.preventDefault(),this.del(this._frameIdentify(t.target)))},_eventHide:function(t){!this.event.type&&this.hide()},_eventPanelScroll:function(t){if(!this.event.type&&this.visible){0!==i(t.srcElement).parents(".frame").length?t.stopPropagation():(t.preventDefault(),this._panelScroll(t.originalEvent.detail?t.originalEvent.detail:t.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(t){this.event.type||(t.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(t){this.event.type||(t.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(t){return this.frame_list["#"+i(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var i="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var i="width"==t||"height"==t?1:-1,n=e*this.options.cell-i*this.options.margin;return"top"==t&&(n+=this.top),n},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var i=this.frame_list[e];if(null!==i.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,i.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(o,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(23),l=a(s),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,s){s=s||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=s.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),l=o(s),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),_=o(p),m=i(51),g=o(m),v=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],o=e.$("#"+t.id+"-section-"+a),s=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){s=!0;break}a==n&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new v(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,o=new v(i.app,{inputs:e});r.add({id:a,$el:o.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=a.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new v(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:v}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),g=r(m),v=i(57),b=r(v);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var o=this.history[i[r]+"_"+this.config[e].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(o)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":o}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": "+t.name,value:t.id,tags:t.tags}),e.history[t.id+"_"+n]=t})}),a.each(this.config,function(t,n){i[t.src]&&e.fields[n].add(i[t.src],function(t,e){return e.hid-t.hid})})},_changeValue:function(){var t=this.model.get("value");if(t&&t.values&&t.values.length>0){var e=[];a.each(t.values,function(t){e.push(t.id)});for(var i=t.values[0].src,n=t.values.length>1,r=0;r<this.config.length;r++){var o=this.fields[r],s=this.config[r];if(s.src==i&&-1!==[n,!0].indexOf(s.multiple)){this.model.set("current",r),o.value(e);break}}}else a.each(this.fields,function(t){t.value(null)})},_handleDrop:function(t){try{var e=this.model.get("data"),i=this.model.get("current"),n=this.config[i],r=this.fields[i],o=JSON.parse(t.originalEvent.dataTransfer.getData("text"))[0],s=o.id,l="dataset"==o.history_content_type?"hda":"hdca",d={id:s,src:l};if(e&&a.findWhere(e[l],d)){if(n.src==l){var c=r.value();c&&n.multiple?-1==c.indexOf(s)&&c.push(s):c=s,r.value(c)}else this.model.set("value",{values:[d]}),this.model.trigger("change:value");this.trigger("change"),this._handleDropStatus("success")}else this._handleDropStatus("danger")}catch(t){this._handleDropStatus("danger")}t.preventDefault()},_handleDropStatus:function(t){var e=this;this.$el.removeClass("ui-dragover").addClass("ui-dragover-"+t),setTimeout(function(){e.$el.removeClass("ui-dragover-"+t)},this.model.get("statustimer"))},_batch:function(t){t.batch=!1;var e=this.model.get("current"),i=this.config[e];if("hdca"==i.src&&!i.multiple){var n=this.history[this.fields[e].value()+"_hdca"];n&&n.map_over_type&&(t.batch=!0)}return i.batch!=h.LINKED&&i.batch!=h.ENABLED||(t.batch=!0,i.batch==h.ENABLED&&"true"===this.button_product.value()&&(t.product=!0)),t}});e.default={View:p}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(43),l=(n(s),i(24)),d=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new u,this.options=t,this.library_select=new o.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new d.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),o=i(24),s=n(o),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new s.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),r.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(56),l=n(s),d=t.View.extend({initialize:function(t){var e=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new 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this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),m=p.extend({initialize:function(t){p.prototype.initialize.call(this,t),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:t.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),g=t.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(t){var e=parent.Galaxy;if(e&&e.modal&&(this.modal=e.modal),e&&e.frame&&(this.frame=e.frame),this.modal&&this.frame){var i=t.model,n=i.get("metadata");if(i.get("file_ext")){if(this.file_ext=i.get("file_ext"),"bed"==this.file_ext){if(!(n.get("chromCol")&&n.get("startCol")&&n.get("endCol")))return void console.log("TabularButtonTrackster : Bed-file metadata incomplete.");this.col.chrom=n.get("chromCol")-1,this.col.start=n.get("startCol")-1,this.col.end=n.get("endCol")-1}if("vcf"==this.file_ext){var 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n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=u.extend({initialize:function(t){t.type="radio",u.prototype.initialize.call(this,t)}});var f={};f.View=u.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,u.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return 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i=t.url_data||{};r.each(t.filters,function(t,e){i["f-"+e]=t}),a.ajax({url:t.url_base+"?"+a.param(i),success:function(i){i.embedded=t.embedded,i.filters=t.filters||{},e.init_grid(i)}})}else this.init_grid(t);else this.setElement("#grid-container"),this.init_grid(t);t.use_panels&&a("#center").css({padding:"10px",overflow:"auto"})},handle_refresh:function(t){t&&a.inArray("history",t)>-1&&window.top.Galaxy&&window.top.Galaxy.currHistoryPanel&&window.top.Galaxy.currHistoryPanel.loadCurrentHistory()},init_grid:function(t){this.grid.set(t);var e=this.grid.attributes;this.allow_title_display&&e.title&&l.default.setWindowTitle(e.title),this.handle_refresh(e.refresh_frames);var i=this.grid.get("url_base");if(i=i.replace(/^.*\/\/[^\/]+/,""),this.grid.set("url_base",i),this.$el.html(h.default.grid(e)),this.$el.find("#grid-table-header").html(h.default.header(e)),this.$el.find("#grid-table-body").html(h.default.body(e)),this.$el.find("#grid-table-footer").html(h.default.footer(e)),e.message){this.$el.find("#grid-message").html(h.default.message(e));var n=this;e.use_hide_message&&setTimeout(function(){n.$el.find("#grid-message").html("")},5e3)}this.init_grid_elements(),this.init_grid_controls(),init_refresh_on_change()},init_grid_controls:function(){var t=this;this.$el.find(".operation-button").each(function(){a(this).off(),a(this).click(function(){return t.submit_operation(this),!1})}),this.$el.find("input[type=text]").each(function(){a(this).off(),a(this).click(function(){a(this).select()}).keyup(function(){a(this).css("font-style","normal")})}),this.$el.find(".sort-link").each(function(){a(this).off(),a(this).click(function(){return 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t.$el.find("#standard-search").slideToggle("fast"),t.$el.find("#advanced-search").slideToggle("fast"),!1})}),this.$el.find("#check_all").off(),this.$el.find("#check_all").on("click",function(){t.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var t=a(this).find("input.grid-row-select-checkbox"),e=a(this).find("span.grid-selected-count"),i=function(){e.text(a(t).filter(":checked").length)};a(t).each(function(){a(this).change(i)}),i()}),0!==this.$el.find(".community_rating_star").length&&this.$el.find(".community_rating_star").rating({});var t=this.grid.attributes,e=this;this.$el.find(".page-link > a").each(function(){a(this).click(function(){return e.set_page(a(this).attr("page_num")),!1})}),this.$el.find(".use-target").each(function(){a(this).click(function(t){return e.execute({href:a(this).attr("href"),target:a(this).attr("target")}),!1})}),0!=t.items.length&&r.each(t.items,function(i,n){var a=e.$("#grid-"+n+"-popup").off(),o=new p.default(a);r.each(t.operations,function(t){e._add_operation(o,t,i)})})},_add_operation:function(t,e,i){var n=this,r=i.operation_config[e.label];r.allowed&&e.allow_popup&&t.addItem({html:e.label,href:r.url_args,target:r.target,confirmation_text:e.confirm,func:function(t){t.preventDefault();var r=a(t.target).html();e.onclick?e.onclick(i.encode_id):n.execute(this.findItemByHtml(r))}})},add_filter_condition:function(t,e){if(""===e)return!1;this.grid.add_filter(t,e,!0);var i=a(h.default.filter_element(t,e)),n=this;i.click(function(){a(this).remove(),n.remove_filter_condition(t,e)}),this.$el.find("#"+t+"-filtering-criteria").append(i),this.go_page_one(),this.execute()},remove_filter_condition:function(t,e){this.grid.remove_filter(t,e),this.go_page_one(),this.execute()},set_sort_condition:function(t){var e=this.grid.get("sort_key"),i=t;-1!==e.indexOf(t)&&"-"!==e.substring(0,1)&&(i="-"+t),this.$el.find(".sort-arrow").remove();var n="-"==i.substring(0,1)?"&uarr;":"&darr;",r=a("<span>"+n+"</span>").addClass("sort-arrow");this.$el.find("#"+t+"-header").append(r),this.grid.set("sort_key",i),this.go_page_one(),this.execute()},set_categorical_filter:function(t,e){var i=this.grid.get("categorical_filters")[t],n=this.grid.get("filters")[t],r=this;this.$el.find("."+t+"-filter").each(function(){var o=a.trim(a(this).text()),s=i[o],l=s[t];if(l==e)a(this).empty(),a(this).addClass("current-filter"),a(this).append(o);else if(l==n){a(this).empty();var d=a('<a href="#">'+o+"</a>");d.click(function(){r.set_categorical_filter(t,l)}),a(this).removeClass("current-filter"),a(this).append(d)}}),this.grid.add_filter(t,e),this.go_page_one(),this.execute()},set_page:function(t){var e=this;this.$el.find(".page-link").each(function(){var i,n=a(this).attr("id"),r=parseInt(n.split("-")[2],10),o=e.grid.get("cur_page");if(r===t)i=a(this).children().text(),a(this).empty(),a(this).addClass("inactive-link"),a(this).text(i);else 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s({collection:n})};e.default={IconButton:a,IconButtonView:r,IconButtonCollection:o,IconButtonMenuView:s,create_icon_buttons_menu:l}}).call(e,i(1),i(2),i(0))},,function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(t){this.options=r.default.merge(t,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(t){this.row.append(n("<th/>").append(t))},appendHeader:function(){this.$thead.append(this.row),this.row=n("<tr/>")},add:function(t,e,i){var a=n("<td/>");e&&a.css("width",e),i&&a.css("text-align",i),this.row.append(a.append(t))},append:function(t,e){this._commit(t,e,!1)},prepend:function(t,e){this._commit(t,e,!0)},get:function(t){return this.$("#"+t)},del:function(t){var e=this.$tbody.find("#"+t);e.length>0&&(e.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(t){if(this.options.selectable){this.before=this.$tbody.find(".current").attr("id"),void 0!==t&&(this.$tbody.find("tr").removeClass("current"),t&&this.$tbody.find("#"+t).addClass("current"));var e=this.$tbody.find(".current").attr("id");return void 0===e?null:(e!=this.before&&this.options.onchange&&this.options.onchange(t),e)}},size:function(){return this.$tbody.find("tr").length},_commit:function(t,e,i){this.del(t),this.row.attr("id",t),i?this.$tbody.prepend(this.row):this.$tbody.append(this.row),e&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return n('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(t){var e=this.value(),i=n(t.target).closest("tr").attr("id");""!=i&&i&&e!=i&&(this.options.onconfirm?this.options.onconfirm(i):this.value(i))},_ondblclick:function(t){var e=this.value();e&&this.options.ondblclick&&this.options.ondblclick(e)},_refresh:function(){0==this.row_count?this.$tmessage.show():this.$tmessage.hide()},_template:function(){return'<div><table class="'+this.options.cls+'"><thead/><tbody/></table><tmessage>'+this.options.content+"</tmessage><div>"}});e.default={View:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){Object.defineProperty(e,"__esModule",{value:!0});var 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i._iterate(t,e)})}})),s=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},l=function t(e,i,r,o){o=n.extend(!0,{},o),a.each(e,function(t){t&&t.type&&t.name&&(o[t.name]=t)});for(var l in e){var d=e[l];d.name=d.name||l;var c=r?r+"|"+d.name:d.name;switch(d.type){case"repeat":a.each(d.cache,function(e,n){t(e,i,c+"_"+n,o)});break;case"conditional":if(d.test_param){i(d.test_param,c+"|"+d.test_param.name,o);var u=s(d,d.test_param.value);-1!=u?t(d.cases[u].inputs,i,c,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+c+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+c+".");break;case"section":t(d.inputs,i,c,o);break;default:i(d,c,o)}}};e.default={Manager:o,visitInputs:l}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0});var a=t.View.extend({initialize:function(e){this.model=e&&e.model||new t.Model(e),this.setElement(i("<div/>").addClass("corner frame")),this.$el.append(i("<div/>").addClass("f-header corner").append(i("<div/>").addClass("f-title")).append(i("<div/>").addClass("f-icon f-close fa fa-close").tooltip({title:"Close",placement:"bottom"}))).append(i("<div/>").addClass("f-content")).append(i("<div/>").addClass("f-resize f-icon corner fa fa-expand").tooltip({title:"Resize"})).append(i("<div/>").addClass("f-cover")),this.$header=this.$(".f-header"),this.$title=this.$(".f-title"),this.$content=this.$(".f-content"),this.render(),this.listenTo(this.model,"change",this.render,this)},render:function(){var t=this,e=this.model.attributes;this.$title.html(e.title||""),this.$header.find(".f-icon-left").remove(),n.each(e.menu,function(e){var a=i("<div/>").addClass("f-icon-left").addClass(e.icon);n.isFunction(e.disabled)&&e.disabled()?a.attr("disabled",!0):a.on("click",function(){e.onclick(t)}).tooltip({title:e.tooltip,placement:"bottom"}),t.$header.append(a)}),e.url?this.$content.html(i("<iframe/>").addClass("f-iframe").attr("scrolling","auto").attr("src",e.url+(-1===e.url.indexOf("?")?"?":"&")+"widget=True")):e.content&&(n.isFunction(e.content)?e.content(t.$content):t.$content.html(e.content))}}),r=t.View.extend({defaultOptions:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_uid:0,frame_list:{},frame_shadow:null,visible:!1,event:{},initialize:function(e){var a=this;this.options=n.defaults(e||{},this.defaultOptions),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(i("<div/>").addClass("galaxy-frame").append(i("<div/>").addClass("frame-background")).append(i("<div/>").addClass("frame-menu frame-scroll-up fa fa-chevron-up fa-2x")).append(i("<div/>").addClass("frame-menu frame-scroll-down fa fa-chevron-down fa-2x"))),this.frame_shadow=new t.View({el:i("<div/>").addClass("corner 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this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(t){i(".tooltip").hide(),this.event.type||((i(t.target).hasClass("f-header")||i(t.target).hasClass("f-title"))&&(this.event.type="drag"),i(t.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(t.preventDefault(),this.event.target=this._frameIdentify(t.target),this.event.xy={x:t.originalEvent.pageX,y:t.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(t){if(this.event.type){var e={x:t.originalEvent.pageX,y:t.originalEvent.pageY},i={x:e.x-this.event.xy.x,y:e.y-this.event.xy.y};this.event.xy=e;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var r={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==r.left&&r.left++,this._frameInsert(this.frame_shadow,r)}}},_eventFrameMouseUp:function(t){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(t){this.event.type||(t.preventDefault(),this.del(this._frameIdentify(t.target)))},_eventHide:function(t){!this.event.type&&this.hide()},_eventPanelScroll:function(t){if(!this.event.type&&this.visible){0!==i(t.srcElement).parents(".frame").length?t.stopPropagation():(t.preventDefault(),this._panelScroll(t.originalEvent.detail?t.originalEvent.detail:t.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(t){this.event.type||(t.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(t){this.event.type||(t.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(t){return this.frame_list["#"+i(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var i="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var i="width"==t||"height"==t?1:-1,n=e*this.options.cell-i*this.options.margin;return"top"==t&&(n+=this.top),n},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var i=this.frame_list[e];if(null!==i.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,i.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(o,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(23),l=a(s),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,s){s=s||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=s.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),l=o(s),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),_=o(p),m=i(51),g=o(m),v=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],o=e.$("#"+t.id+"-section-"+a),s=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){s=!0;break}a==n&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new v(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,o=new v(i.app,{inputs:e});r.add({id:a,$el:o.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=a.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new v(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:v}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),g=r(m),v=i(57),b=r(v);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var o=this.history[i[r]+"_"+this.config[e].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(o)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" 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d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. 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Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){o.append(n("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],o=this.form.data.match(a),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==r)return this.form.highlight(o),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],o=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,o=n-r,s=0;o<=0&&(o=1,s=r-(n-o));var l,d=r+s,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td 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f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var o=t.columns[r];if("advanced"==o.filterable){var s=o.key,l=i[s],d=e[s];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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class="text-filter-form" column_key="'+r+'" action="'+e.url+'" method="get" >';for(u in e.columns){var s=e.columns[u],l=n[s.key];l&&"All"!=l&&(s.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+s.key+'" name="f-'+s.key+'" value="'+l+'"/>')}o+='<span id="'+r+'-filtering-criteria">';var d=n[r];if(d){var c=t.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(r,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(r,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+r+'-filter" name="f-'+r+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+r+'-filtering-criteria">';var m=!1;for(var g in e.categorical_filters[r]){var v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],s.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,q-j,$),void 0!==v&&k>x&&!(j>b||q<v)){var D=Math.max(j,v),I=Math.min(q,b);t.fillRect(D,d+1,I-D,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<I&&(D+=2,I-=2),t.fillRect(D,d+1,I-D,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+g;if(p=f(D),_=f(D+q),o([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=q;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+q):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,s-a)));for(var L=Math.max(D,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=q),g+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=q;break;case"D":$.draw_deletion(p,S,q),g+=q;break;case"I":var V=p-b;if(o([D,D+q],m)){var G=h.slice(v,v+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-s);break;case 1005:break;case 1002:G=G.slice(a-D,D-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(D+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=q}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,q),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];S.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var 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Uint8Array(t.buffer,t.byteOffset+e,a),i,n):s(t,e,i,n,a)}}function s(t,e,i,n,a){for(var r=0;r<a;++r)i[n+r]=t[e+r]}function l(t,e,i){e.set(t,i)}function d(e,i,n,a){e=i?n?new Uint8Array(e,i,n):new Uint8Array(e,i,e.byteLength-i):new Uint8Array(e);var r=new t;r.inflateInit(c,!0),r.next_in=e,r.next_in_index=0,r.avail_in=e.length;for(var s=[],l=0;;){var d=new Uint8Array(32e3);r.next_out=d,r.next_out_index=0,r.avail_out=d.length;var u=r.inflate(h);if(u!=f&&u!=p&&u!=_)throw r.msg;if(0!=r.avail_out){var m=new Uint8Array(d.length-r.avail_out);o(d,0,m,0,d.length-r.avail_out),d=m}if(s.push(d),l+=d.length,u==p||u==_)break}if(a&&(a[0]=(i||0)+r.next_in_index),1==s.length)return s[0].buffer;for(var g=new Uint8Array(l),v=0,b=0;b<s.length;++b){var w=s[b];o(w,0,g,v,w.length),v+=w.length}return g.buffer}var c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),s=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+s,d=e+":"+i+l,c=null,u=null,h='<iframe 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r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof 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this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return 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i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var t=window.Galaxy.config.communication_server_host,e=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:t+":"+e}).success(function(t){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(t){n.css("visibility","hidden")}):n.css("visibility","hidden")}});e.default={View:p}}).call(e,i(1),i(2),i(0))},,,function(t,e,i){"use strict";(function(t){function 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a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},e.redirect?window.location=Galaxy.root+e.redirect+"?"+n.param(a):(t.data.matchModel(i,function(e,i){t.field_list[i].value(e.value)}),e._showMessage(t,success_message))}).fail(function(i){e._showMessage(t,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(t,e){t.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),t.message.update(e)}});e.default={View:d}}).call(e,i(1),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,i){"use strict";(function(t){function e(t){return t&&t.__esModule?t:{default:t}}var n=i(0),a=e(n),r=i(177),o=e(r),s=i(278),l=e(s),d=i(197),c=e(d),u=i(26),h=e(u),f=i(4),p=(e(f),i(61)),_=e(p),m=i(182),g=e(m),v=i(3),b=e(v),w=i(179),y=e(w),x=i(142),k=e(x),C=i(279),S=e(C),$=a.default;window.app=function(e,i){window.Galaxy=new 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v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,q-j,$),void 0!==v&&k>x&&!(j>b||q<v)){var D=Math.max(j,v),I=Math.min(q,b);t.fillRect(D,d+1,I-D,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<I&&(D+=2,I-=2),t.fillRect(D,d+1,I-D,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+g;if(p=f(D),_=f(D+q),o([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=q;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+q):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,s-a)));for(var L=Math.max(D,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=q),g+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=q;break;case"D":$.draw_deletion(p,S,q),g+=q;break;case"I":var V=p-b;if(o([D,D+q],m)){var G=h.slice(v,v+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-s);break;case 1005:break;case 1002:G=G.slice(a-D,D-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(D+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=q}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,q),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];S.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&(S<0||x>$)&&(S=k,$=i<0?x:w,i<0?y:b),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&s.push(l[d]);return a(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return r.topLevelReductionCache=o,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=i>0?0:3e8;t.fromRef&&(s=e);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>s)return a(u)}else u.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<s)return a(u)}else u.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(s+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(o(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=r.exec(n);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};n=n.substring(s[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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e=this;e.options={};for(var n in i.defaultOptions)i.defaultOptions.hasOwnProperty(n)&&(e.options[n]=t.hasOwnProperty(n)?t[n]:i.defaultOptions[n]);return e.options.logLevel=e._parseLevel(e.options.logLevel),e.options.consoleLevel=e._parseLevel(e.options.consoleLevel),e._sending=!1,e._waiting=null,e._postSize=e.options.postSize,e._initCache(),e},i.prototype._initCache=function(){try{this.cache=new a({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(t){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",t]),this.options.logLevel=i.NONE}},i.prototype._parseLevel=function(t){var e=void 0===t?"undefined":r(t);if("number"===e)return t;if("string"===e){var n=t.toUpperCase();if(i.hasOwnProperty(n))return i[n]}throw new Error("Unknown log level: "+t)},i.prototype.emit=function(t,e,i){var n=this;return 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r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof r.consoleLogger.log&&r.consoleLogger.log.apply(r.consoleLogger,s),r)},i.prototype.log=function(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.debug=function(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.info=function(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.warn=function(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.error=function(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.metric=function(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},a.defaultOptions={maxSize:5e3},a.prototype._init=function(t){if(!this._hasStorage())throw new Error("LoggingCache needs localStorage");if(!t.key)throw new Error("LoggingCache needs key for localStorage");return this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return localStorage.setItem(this.key,"[]"),this},a.prototype.stringify=function(t){return JSON.stringify(this.get(t))},a.prototype.print=function(){console.log(JSON.stringify(this._fetchAndParse(),null,"  "))},e.default={MetricsLogger:i,LoggingCache:a}}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(160),s=r(o),l=i(176),d=r(l),c=i(9),u=r(c),h=i(3),f=r(h),p=t.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(e){var i=this;this.config=n.defaults(e.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(t){t.title?(f.default.setWindowTitle(t.title),t.allow_title_display=!1):(f.default.setWindowTitle(),t.allow_title_display=!0),i.center.display(t)},Galaxy.router=this.router=e.Router&&new e.Router(i,e),this.masthead=new s.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(t){var n=t.charAt(0).toUpperCase()+t.slice(1),a=e[n];if(a){var r=new a(i,e);i[r.toString()]=r,i.panels[t]=new d.default.SidePanel({id:t,el:i.$("#"+t),view:r})}}),this.render(),this.router&&t.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var t=this.config.message_box_content||"",e=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+e+"-message").html(t).toggle(!!t).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var t=this.config.inactivity_box_content||"",e=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(t+" ").append(e).toggle(!!t).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var t=this;return n.each(this._panelids,function(e){var i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var t=window.Galaxy.config.communication_server_host,e=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:t+":"+e}).success(function(t){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(t){n.css("visibility","hidden")}):n.css("visibility","hidden")}});e.default={View:p}}).call(e,i(1),i(2),i(0))},,,function(t,e,i){"use strict";(function(t){function 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a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},e.redirect?window.location=Galaxy.root+e.redirect+"?"+n.param(a):(t.data.matchModel(i,function(e,i){t.field_list[i].value(e.value)}),e._showMessage(t,success_message))}).fail(function(i){e._showMessage(t,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(t,e){t.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),t.message.update(e)}});e.default={View:d}}).call(e,i(1),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,i){"use strict";(function(t){function e(t){return t&&t.__esModule?t:{default:t}}var n=i(0),a=e(n),r=i(177),o=e(r),s=i(278),l=e(s),d=i(197),c=e(d),u=i(26),h=e(u),f=i(4),p=(e(f),i(61)),_=e(p),m=i(182),g=e(m),v=i(3),b=e(v),w=i(179),y=e(w),x=i(142),k=e(x),C=i(279),S=e(C),$=a.default;window.app=function(e,i){window.Galaxy=new o.default.GalaxyApp(e,i),Galaxy.debug("admin app");var n=g.default.extend({routes:{"(/)admin(/)users":"show_users","(/)admin(/)roles":"show_roles","(/)admin(/)groups":"show_groups","(/)admin(/)tool_versions":"show_tool_versions","(/)admin(/)quotas":"show_quotas","(/)admin(/)repositories":"show_repositories","(/)admin(/)forms":"show_forms","(/)admin(/)form(/)(:form_id)":"show_form","(/)admin/api_keys":"show_user_api_keys"},authenticate:function(t,e){return Galaxy.user&&Galaxy.user.id&&Galaxy.user.get("is_admin")},show_users:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/users_list",url_data:Galaxy.params,dict_format:!0}))},show_roles:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/roles_list",url_data:Galaxy.params,dict_format:!0}))},show_groups:function(){this.page.display(new h.default({url_base:Galaxy.root+"admin/groups_list",url_data:Galaxy.params,dict_format:!0}))},show_repositories:function(){this.page.display(new 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0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(e,t){return!0},can_subset:function(e){return!1}}),initialize:function(e){y.prototype.initialize.call(this);var t=this.get("init_data");t&&this.add_data(t)},add_data:function(e){this.get("num_elements")<e.length&&this.set("num_elements",e.length);var t=this;o.each(e,function(e){t.set_data(e.region,e)})},data_is_ready:function(){var t=this.get("dataset"),i=e.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:t.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(e){return"pending"!==e}});return 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r=t.get("start");s===this.DEEP_DATA_REQ?e.extend(a,{start_val:o.data.length+1}):s===this.BROAD_DATA_REQ&&(r=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=t.copy().set("start",r),d=this,c=this.load_data(l,i,n,a),u=e.Deferred();return this.set_data(t,u),e.when(c).then(function(e){e.data&&(e.data=o.data.concat(e.data),e.max_low&&(e.max_low=o.max_low),e.message&&(e.message=e.message.replace(/[0-9]+/,e.data.length))),d.set_data(t,e),u.resolve(e)}),u},can_get_more_detailed_data:function(e){var t=this.get_elt(e);return"bigwig"===t.dataset_type&&t.data.length<8e3},get_more_detailed_data:function(e,t,i,n,a){var s=this._mark_stale(e);return s?(a||(a={}),"bigwig"===s.dataset_type&&(a.num_samples=1e3*n),this.load_data(e,t,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(e){var t=this.get_elt(e);return t||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),e.toString()),t.stale=!0,t},get_genome_wide_data:function(t){var i=this,n=!0,a=o.map(t.get("chroms_info").chrom_info,function(e){var t=i.get_elt(new $({chrom:e.chrom,start:0,end:e.len}));return t||(n=!1),t});if(n)return a;var s=e.Deferred();return e.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(e){i.add_data(e.data),s.resolve(e.data)}),s},subset_entry:function(e,t){var i={bigwig:function(e,t){return o.filter(e,function(e){return e[0]>=t.get("start")&&e[0]<=t.get("end")})},refseq:function(t,i){var n=i.get("start")-e.region.get("start");return e.data.slice(n,n+i.length())}},n=e.data;return!e.region.same(t)&&e.dataset_type in i&&(n=i[e.dataset_type](e.data,t)),{region:t,data:n,dataset_type:e.dataset_type}}}),k=x.extend({initialize:function(e){var t=new n.Model;t.urlRoot=e.data_url,this.set("dataset",t)},load_data:function(e,t,i,n){return 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t=e.from_str.split(":"),i=t[0],n=t[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new $({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(e){var t=this.get("chrom"),i=e.get("chrom"),n=this.get("start"),a=e.get("start"),s=this.get("end"),o=e.get("end");return 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this.row_count%2!=0&&i.addClass("dark_row"),t.length===s?n.each(t,function(e,t){i.append(this._renderCell(e,t))},this):t.length>s?(n.each(t.slice(0,s-1),function(e,t){i.append(this._renderCell(e,t))},this),i.append(this._renderCell(t.slice(s-1).join("\t"),s-1))):1===t.length?i.append(this._renderCell(e,0,s)):(n.each(t,function(e,t){i.append(this._renderCell(e,t))},this),n.each(n.range(s-t.length),function(){i.append(a("<td>"))})),this.row_count++,i},_renderChunk:function(e){var t=this.$el.find("table");n.each(e.ck_data.split("\n"),function(e,i){""!==e&&t.append(this._renderRow(e))},this)}}),m=p.extend({initialize:function(e){p.prototype.initialize.call(this,e);var t=n.find(this.$el.parents(),function(e){return"auto"===a(e).css("overflow")});t||(t=window),this.scroll_elt=a(t)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),_=p.extend({initialize:function(e){p.prototype.initialize.call(this,e),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:e.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),g=e.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(e){var t=parent.Galaxy;if(t&&t.modal&&(this.modal=t.modal),t&&t.frame&&(this.frame=t.frame),this.modal&&this.frame){var i=e.model,n=i.get("metadata");if(i.get("file_ext")){if(this.file_ext=i.get("file_ext"),"bed"==this.file_ext){if(!(n.get("chromCol")&&n.get("startCol")&&n.get("endCol")))return void console.log("TabularButtonTrackster : Bed-file metadata incomplete.");this.col.chrom=n.get("chromCol")-1,this.col.start=n.get("startCol")-1,this.col.end=n.get("endCol")-1}if("vcf"==this.file_ext){var 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n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(n("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),h={};h.View=u.extend({initialize:function(e){e.type="radio",u.prototype.initialize.call(this,e)}});var f={};f.View=u.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,u.prototype.initialize.call(this,e)}});var p={};p.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=n("<label/>").addClass("btn btn-default");return 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i=e.url_data||{};s.each(e.filters,function(e,t){i["f-"+t]=e}),a.ajax({url:e.url_base+"?"+a.param(i),success:function(i){i.embedded=e.embedded,i.filters=e.filters||{},t.init_grid(i)}})}else this.init_grid(e);else this.setElement("#grid-container"),this.init_grid(e);e.use_panels&&a("#center").css({padding:"10px",overflow:"auto"})},handle_refresh:function(e){e&&a.inArray("history",e)>-1&&window.top.Galaxy&&window.top.Galaxy.currHistoryPanel&&window.top.Galaxy.currHistoryPanel.loadCurrentHistory()},init_grid:function(e){this.grid.set(e);var t=this.grid.attributes;this.allow_title_display&&t.title&&l.default.setWindowTitle(t.title),this.handle_refresh(t.refresh_frames);var i=this.grid.get("url_base");if(i=i.replace(/^.*\/\/[^\/]+/,""),this.grid.set("url_base",i),this.$el.html(h.default.grid(t)),this.$el.find("#grid-table-header").html(h.default.header(t)),this.$el.find("#grid-table-body").html(h.default.body(t)),this.$el.find("#grid-table-footer").html(h.default.footer(t)),t.message){this.$el.find("#grid-message").html(h.default.message(t));var n=this;t.use_hide_message&&setTimeout(function(){n.$el.find("#grid-message").html("")},5e3)}this.init_grid_elements(),this.init_grid_controls(),init_refresh_on_change()},init_grid_controls:function(){var e=this;this.$el.find(".operation-button").each(function(){a(this).off(),a(this).click(function(){return e.submit_operation(this),!1})}),this.$el.find("input[type=text]").each(function(){a(this).off(),a(this).click(function(){a(this).select()}).keyup(function(){a(this).css("font-style","normal")})}),this.$el.find(".sort-link").each(function(){a(this).off(),a(this).click(function(){return 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e.$el.find("#standard-search").slideToggle("fast"),e.$el.find("#advanced-search").slideToggle("fast"),!1})}),this.$el.find("#check_all").off(),this.$el.find("#check_all").on("click",function(){e.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var e=a(this).find("input.grid-row-select-checkbox"),t=a(this).find("span.grid-selected-count"),i=function(){t.text(a(e).filter(":checked").length)};a(e).each(function(){a(this).change(i)}),i()}),0!==this.$el.find(".community_rating_star").length&&this.$el.find(".community_rating_star").rating({});var e=this.grid.attributes,t=this;this.$el.find(".page-link > a").each(function(){a(this).click(function(){return t.set_page(a(this).attr("page_num")),!1})}),this.$el.find(".use-target").each(function(){a(this).click(function(e){return t.execute({href:a(this).attr("href"),target:a(this).attr("target")}),!1})}),0!=e.items.length&&s.each(e.items,function(i,n){var a=t.$("#grid-"+n+"-popup").off(),o=new p.default(a);s.each(e.operations,function(e){t._add_operation(o,e,i)})})},_add_operation:function(e,t,i){var n=this,s=i.operation_config[t.label];s.allowed&&t.allow_popup&&e.addItem({html:t.label,href:s.url_args,target:s.target,confirmation_text:t.confirm,func:function(e){e.preventDefault();var s=a(e.target).html();t.onclick?t.onclick(i.encode_id):n.execute(this.findItemByHtml(s))}})},add_filter_condition:function(e,t){if(""===t)return!1;this.grid.add_filter(e,t,!0);var i=a(h.default.filter_element(e,t)),n=this;i.click(function(){a(this).remove(),n.remove_filter_condition(e,t)}),this.$el.find("#"+e+"-filtering-criteria").append(i),this.go_page_one(),this.execute()},remove_filter_condition:function(e,t){this.grid.remove_filter(e,t),this.go_page_one(),this.execute()},set_sort_condition:function(e){var t=this.grid.get("sort_key"),i=e;-1!==t.indexOf(e)&&"-"!==t.substring(0,1)&&(i="-"+e),this.$el.find(".sort-arrow").remove();var n="-"==i.substring(0,1)?"&uarr;":"&darr;",s=a("<span>"+n+"</span>").addClass("sort-arrow");this.$el.find("#"+e+"-header").append(s),this.grid.set("sort_key",i),this.go_page_one(),this.execute()},set_categorical_filter:function(e,t){var i=this.grid.get("categorical_filters")[e],n=this.grid.get("filters")[e],s=this;this.$el.find("."+e+"-filter").each(function(){var o=a.trim(a(this).text()),r=i[o],l=r[e];if(l==t)a(this).empty(),a(this).addClass("current-filter"),a(this).append(o);else if(l==n){a(this).empty();var d=a('<a href="#">'+o+"</a>");d.click(function(){s.set_categorical_filter(e,l)}),a(this).removeClass("current-filter"),a(this).append(d)}}),this.grid.add_filter(e,t),this.go_page_one(),this.execute()},set_page:function(e){var t=this;this.$el.find(".page-link").each(function(){var i,n=a(this).attr("id"),s=parseInt(n.split("-")[2],10),o=t.grid.get("cur_page");if(s===e)i=a(this).children().text(),a(this).empty(),a(this).addClass("inactive-link"),a(this).text(i);else 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r({collection:n})};t.default={IconButton:a,IconButtonView:s,IconButtonCollection:o,IconButtonMenuView:r,create_icon_buttons_menu:l}}).call(t,i(1),i(2),i(0))},,function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(e){this.options=s.default.merge(e,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(e){this.row.append(n("<th/>").append(e))},appendHeader:function(){this.$thead.append(this.row),this.row=n("<tr/>")},add:function(e,t,i){var a=n("<td/>");t&&a.css("width",t),i&&a.css("text-align",i),this.row.append(a.append(e))},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){if(this.options.selectable){this.before=this.$tbody.find(".current").attr("id"),void 0!==e&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return void 0===t?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)}},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,i){this.del(e),this.row.attr("id",e),i?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return n('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),i=n(e.target).closest("tr").attr("id");""!=i&&i&&t!=i&&(this.options.onconfirm?this.options.onconfirm(i):this.value(i))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){0==this.row_count?this.$tmessage.show():this.$tmessage.hide()},_template:function(){return'<div><table class="'+this.options.cls+'"><thead/><tbody/></table><tmessage>'+this.options.content+"</tmessage><div>"}});t.default={View:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(function(e){e&&e.__esModule}(s),e.Model.extend({initialize:function(e){this.app=e},checksum:function(){var e="",t=this;return this.app.section.$el.find(".section-row").each(function(){var i=n(this).attr("id"),a=t.app.field_list[i];a&&(e+=i+":"+JSON.stringify(a.value&&a.value())+":"+a.collapsed+";")}),e},create:function(){function e(e,t,n){i.flat_dict[e]=t,a[e]=n,i.app.element_list[t]&&i.app.element_list[t].$el.attr("tour_id",e)}function t(n,a){for(var s in a){var o=a[s];if(o.input){var l=o.input,d=n;switch(""!=n&&(d+="|"),d+=l.name,l.type){case"repeat":var c=[],u=null;for(var h in o){var f=h.indexOf("section-");-1!=f&&(f+="section-".length,c.push(parseInt(h.substr(f))),u||(u=h.substr(0,f)))}c.sort(function(e,t){return e-t});var s=0;for(var p in c)t(d+"_"+s++,o[u+c[p]]);break;case"conditional":var m=i.app.field_list[l.id].value();e(d+"|"+l.test_param.name,l.id,m);var _=r(l,m);-1!=_&&t(d,a[l.id+"-section-"+_]);break;case"section":t(!l.flat&&d||"",o);break;default:var 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i._iterate(e,t)})}})),r=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},l=function e(t,i,s,o){o=n.extend(!0,{},o),a.each(t,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var l in t){var d=t[l];d.name=d.name||l;var c=s?s+"|"+d.name:d.name;switch(d.type){case"repeat":a.each(d.cache,function(t,n){e(t,i,c+"_"+n,o)});break;case"conditional":if(d.test_param){i(d.test_param,c+"|"+d.test_param.name,o);var u=r(d,d.test_param.value);-1!=u?e(d.cases[u].inputs,i,c,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+c+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+c+".");break;case"section":e(d.inputs,i,c,o);break;default:i(d,c,o)}}};t.default={Manager:o,visitInputs:l}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0});var a=e.View.extend({initialize:function(t){this.model=t&&t.model||new e.Model(t),this.setElement(i("<div/>").addClass("corner frame")),this.$el.append(i("<div/>").addClass("f-header corner").append(i("<div/>").addClass("f-title")).append(i("<div/>").addClass("f-icon f-close fa fa-close").tooltip({title:"Close",placement:"bottom"}))).append(i("<div/>").addClass("f-content")).append(i("<div/>").addClass("f-resize f-icon corner fa fa-expand").tooltip({title:"Resize"})).append(i("<div/>").addClass("f-cover")),this.$header=this.$(".f-header"),this.$title=this.$(".f-title"),this.$content=this.$(".f-content"),this.render(),this.listenTo(this.model,"change",this.render,this)},render:function(){var e=this,t=this.model.attributes;this.$title.html(t.title||""),this.$header.find(".f-icon-left").remove(),n.each(t.menu,function(t){var a=i("<div/>").addClass("f-icon-left").addClass(t.icon);n.isFunction(t.disabled)&&t.disabled()?a.attr("disabled",!0):a.on("click",function(){t.onclick(e)}).tooltip({title:t.tooltip,placement:"bottom"}),e.$header.append(a)}),t.url?this.$content.html(i("<iframe/>").addClass("f-iframe").attr("scrolling","auto").attr("src",t.url+(-1===t.url.indexOf("?")?"?":"&")+"widget=True")):t.content&&(n.isFunction(t.content)?t.content(e.$content):e.$content.html(t.content))}}),s=e.View.extend({defaultOptions:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_uid:0,frame_list:{},frame_shadow:null,visible:!1,event:{},initialize:function(t){var a=this;this.options=n.defaults(t||{},this.defaultOptions),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(i("<div/>").addClass("galaxy-frame").append(i("<div/>").addClass("frame-background")).append(i("<div/>").addClass("frame-menu frame-scroll-up fa fa-chevron-up fa-2x")).append(i("<div/>").addClass("frame-menu frame-scroll-down fa fa-chevron-down fa-2x"))),this.frame_shadow=new e.View({el:i("<div/>").addClass("corner 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this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(e){i(".tooltip").hide(),this.event.type||((i(e.target).hasClass("f-header")||i(e.target).hasClass("f-title"))&&(this.event.type="drag"),i(e.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(e.preventDefault(),this.event.target=this._frameIdentify(e.target),this.event.xy={x:e.originalEvent.pageX,y:e.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(e){if(this.event.type){var t={x:e.originalEvent.pageX,y:e.originalEvent.pageY},i={x:t.x-this.event.xy.x,y:t.y-this.event.xy.y};this.event.xy=t;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var s={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==s.left&&s.left++,this._frameInsert(this.frame_shadow,s)}}},_eventFrameMouseUp:function(e){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(e){this.event.type||(e.preventDefault(),this.del(this._frameIdentify(e.target)))},_eventHide:function(e){!this.event.type&&this.hide()},_eventPanelScroll:function(e){if(!this.event.type&&this.visible){0!==i(e.srcElement).parents(".frame").length?e.stopPropagation():(e.preventDefault(),this._panelScroll(e.originalEvent.detail?e.originalEvent.detail:e.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(e){this.event.type||(e.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(e){this.event.type||(e.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(e){return this.frame_list["#"+i(e).closest(".frame").attr("id")]},_frameDragStart:function(e){this._frameFocus(e,!0);var t=this._frameScreen(e);this._frameResize(this.frame_shadow,t),this._frameGrid(this.frame_shadow,e.grid_location),e.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(e){this._frameFocus(e,!1);var t=this._frameScreen(this.frame_shadow);this._frameResize(e,t),this._frameGrid(e,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(e,t){var i="width"==e||"height"==e?1:-1;return"top"==e&&(t-=this.top),parseInt((t+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(e,t){var i="width"==e||"height"==e?1:-1,n=t*this.options.cell-i*this.options.margin;return"top"==e&&(n+=this.top),n},_toGrid:function(e){return{top:this._toGridCoord("top",e.top),left:this._toGridCoord("left",e.left),width:this._toGridCoord("width",e.width),height:this._toGridCoord("height",e.height)}},_toPixel:function(e){return{top:this._toPixelCoord("top",e.top),left:this._toPixelCoord("left",e.left),width:this._toPixelCoord("width",e.width),height:this._toPixelCoord("height",e.height)}},_isCollision:function(e){for(var t in this.frame_list){var i=this.frame_list[t];if(null!==i.grid_location&&function(e,t){return!(e.left>t.left+t.width-1||e.left+e.width-1<t.left||e.top>t.top+t.height-1||e.top+e.height-1<t.top)}(e,i.grid_location))return!0}return!1},_locationRank:function(e){return e.top*this.cols+e.left},_panelRefresh:function(e){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,e)},_panelAnimationComplete:function(){var e=this;i(".frame").promise().done(function(){e._panelScroll(0,!0)})},_panelScroll:function(e,t){var i=this.top-this.options.scroll*e;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var s={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,s,t)}}this.top=i}this.render()},_frameInit:function(e,t){e.id=t,e.screen_location={},e.grid_location={},e.grid_rank=null,e.$el.attr("id",t.substring(1))},_frameInsert:function(e,t,a){var s=this,o=[];e&&(e.grid_location=null,o.push([e,this._locationRank(t)])),n.each(this.frame_list,function(e){null!==e.grid_location&&(e.grid_location=null,o.push([e,e.grid_rank]))}),o.sort(function(e,t){return e[1]<t[1]?-1:e[1]>t[1]?1:0}),n.each(o,function(e){s._framePlace(e[0],a)}),this.top_max=0,n.each(this.frame_list,function(e){null!==e.grid_location&&(s.top_max=Math.max(s.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a<this.options.rows;a++){for(var s=0;s<Math.max(1,this.cols-i.width);s++)if(i.top=a,i.left=s,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(e,i,t):console.log("Grid dimensions exceeded.")},_frameFocus:function(e,t){e.$el.css("z-index",this.frame_z+(t?1:0))},_frameOffset:function(e,t,i){if(e.screen_location.left=t.left,e.screen_location.top=t.top,i){this._frameFocus(e,!0);var n=this;e.$el.animate({top:t.top,left:t.left},"fast",function(){n._frameFocus(e,!1)})}else e.$el.css({top:t.top,left:t.left})},_frameResize:function(e,t){e.$el.css({width:t.width,height:t.height}),e.screen_location.width=t.width,e.screen_location.height=t.height},_frameGrid:function(e,t,i){e.grid_location=t,this._frameOffset(e,this._toPixel(t),i),e.grid_rank=this._locationRank(t)},_frameScreen:function(e){var t=e.screen_location;return{top:t.top,left:t.left,width:t.width,height:t.height}}});t.default={View:s}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({id:s.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(t),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(e){a[e.which]=!1}).on("keydown",function(e){var t=e.which;a[t]=!0,i.model.get("is_workflow")&&a[16]&&52==t?(i.value("$"),event.preventDefault()):8==t||9==t||13==t||37==t||39==t||t>=48&&t<=57&&!a[16]||t>=96&&t<=105||(190==t||110==t)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==t||109==t)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var r=o.step;r||(r=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});t.default={View:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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f=o.default.uid(),p=e("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),m=e("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(e("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(m,d.options,u),h.append(m),t(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=e("<div/>");return i(a,this.model.get("data")),a},_template:function(){return e("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});t.default={View:d}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),m=o(p),_=i(51),g=o(_),v=e.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var e=this;this.$el.empty(),a.each(this.inputs,function(t){e.add(t)})},add:function(e){var t=s.extend(!0,{},e);switch(t.id=e.id=l.default.uid(),this.app.input_list[t.id]=t,t.type){case"conditional":this._addConditional(t);break;case"repeat":this._addRepeat(t);break;case"section":this._addSection(t);break;default:this._addRow(t)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var a in e.cases){var s=e.cases[a],o=t.$("#"+e.id+"-section-"+a),r=!1;for(var l in s.inputs)if(!s.inputs[l].hidden){r=!0;break}a==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var a=new v(this.app,{inputs:e.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var a=e.id+"-section-"+n++,o=new v(i.app,{inputs:t});s.add({id:a,$el:o.$el,ondel:function(){s.del(a),i.app.trigger("change")}})}for(var i=this,n=0,s=new f.default.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),o=a.size(e.cache),r=0;r<Math.max(Math.max(o,e.min||0),e.default||0);r++)t(r<o?e.cache[r]:e.inputs);this.app.model.get("sustain_repeats")&&s.hideOptions();var l=new m.default(this.app,{label:e.title||e.name,help:e.help,field:s});this._append(l.$el,e.id)},_addSection:function(e){var t=new u.default.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new v(this.app,{inputs:e.inputs}).$el),t.append(n("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var a=new m.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(11),d=s(l),c=i(4),u=s(c),h=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(e){e.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:h}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,t.trigger&&t.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var s=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+s)).attr("data-original-title",this.model.get("text_"+s)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(52),u=s(c),h=i(53),f=s(h),p=i(54),m=s(p),_=i(55),g=s(_),v=i(57),w=s(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new u.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],n.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(a.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new w.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new m.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new g.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(22),u=s(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(t),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){t.onchange&&t.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var s in i){var o=this.history[i[s]+"_"+this.config[t].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[s]+"'."),null;a.values.push(o)}return a.values.sort(function(e,t){return e.hid-t.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;a.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),a.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var e=this,t=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[t]?this.config=f[t]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+t+"'."));var i=e.model.get("data"),n=r.default.textify(this.model.get("extensions")),s=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(t,a){e.button_data.push({value:a,icon:t.icon,tooltip:t.tooltip}),e.fields.push(new u.default.View({optional:e.model.get("optional"),multiple:t.multiple,searchable:!t.multiple||i&&i[t.src]&&i[t.src].length>e.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(s[t.src]||"content")+" 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i=this,n=!0,a=o.map(t.get("chroms_info").chrom_info,function(e){var t=i.get_elt(new $({chrom:e.chrom,start:0,end:e.len}));return t||(n=!1),t});if(n)return a;var s=e.Deferred();return e.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(e){i.add_data(e.data),s.resolve(e.data)}),s},subset_entry:function(e,t){var i={bigwig:function(e,t){return o.filter(e,function(e){return e[0]>=t.get("start")&&e[0]<=t.get("end")})},refseq:function(t,i){var n=i.get("start")-e.region.get("start");return e.data.slice(n,n+i.length())}},n=e.data;return!e.region.same(t)&&e.dataset_type in i&&(n=i[e.dataset_type](e.data,t)),{region:t,data:n,dataset_type:e.dataset_type}}}),k=x.extend({initialize:function(e){var t=new n.Model;t.urlRoot=e.data_url,this.set("dataset",t)},load_data:function(e,t,i,n){return 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t=e.from_str.split(":"),i=t[0],n=t[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new $({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(e){var t=this.get("chrom"),i=e.get("chrom"),n=this.get("start"),a=e.get("start"),s=this.get("end"),o=e.get("end");return t&&i&&t!==i?$.overlap_results.DIF_CHROMS:n<a?s<a?$.overlap_results.BEFORE:s<o?$.overlap_results.OVERLAP_START:$.overlap_results.CONTAINS:n>a?n>o?$.overlap_results.AFTER:s<=o?$.overlap_results.CONTAINED_BY:$.overlap_results.OVERLAP_END:s>=o?$.overlap_results.CONTAINS:$.overlap_results.CONTAINED_BY},trim:function(e){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var t=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>t&&(this.attributes.end=t-1)}return this},contains:function(e){return this.compute_overlap(e)===$.overlap_results.CONTAINS},overlaps:function(e){return 0===o.intersection([this.compute_overlap(e)],[$.overlap_results.DIF_CHROMS,$.overlap_results.BEFORE,$.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=n.Collection.extend({model:$}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(e){this.set("region",new $(e.region))}}),M=n.Collection.extend({model:T}),E=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(e){this.set("dataset",new l.default.Dataset(e.dataset));var t=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(e,t){return 0===o.size(e)&&(e={name:t.get("config").get("name").get("value"),color:t.get("config").get("color").get("value")}),e},dataset:function(e){return{id:e.id,hda_ldda:e.get("hda_ldda")}}}}),P=n.Collection.extend({model:E}),O=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return e.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),A=O.extend(v).extend({defaults:o.extend({},O.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(e){this.set("drawables",new P(e.tracks));var t=[];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs)),this.unset("tracks"),this.get("drawables").each(function(e){e.unset("preloaded_data")})},add_tracks:function(e){this.get("drawables").add(e)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(e,t){return{obj_type:"View",prefs:{name:t.get("title"),content_visible:!0},drawables:t.get("drawables")}}}}),D=n.Router.extend({initialize:function(e){this.view=e.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(e){t.navigate(e)})},change_location:function(e){this.view.go_to(e)}});t.default={BackboneTrack:E,BrowserBookmark:T,BrowserBookmarkCollection:M,Cache:y,CanvasManager:b,Genome:C,GenomeDataManager:x,GenomeRegion:$,GenomeRegionCollection:S,GenomeVisualization:A,GenomeReferenceDataManager:k,TrackBrowserRouter:D,Visualization:O,select_datasets:w}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,i){function n(e){e+="";for(var t=/(\d+)(\d{3})/;t.test(e);)e=e.replace(t,"$1,$2");return e}Object.defineProperty(t,"__esModule",{value:!0});var a=function(e){return"promise"in e},s=e.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(e){return!0}},go:function(){var e=i.Deferred(),t=this,n=t.get("ajax_settings"),a=t.get("success_fn"),s=t.get("interval");return function t(){i.ajax(n).success(function(i){a(i)?e.resolve(i):setTimeout(t,s)})}(),e}}),o=function(e){e||(e="#ffffff"),"string"==typeof e&&(e=[e]);for(var 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e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(12),d=s(l),c=e.View.extend({initialize:function(t){var i=this;this.data=[],this.data2=[],this.model=t&&t.model||new e.Model({id:r.default.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,readonly:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(t),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls 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i=t.pageY,a=e.$select.height();e.minHeight=e.minHeight||a,n("#dd-helper").show().on("mousemove",function(t){e.$select.height(Math.max(a+(t.pageY-i),e.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var e=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){e.$select.select2&&e.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var t=[];0!==e.all_button.value()&&a.each(e.model.get("data"),function(e){t.push(e.value)}),e.value(t),e.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(e,t){return!e||""==e||String(t).toUpperCase().indexOf(e.toUpperCase())>=0},_changeData:function(){var e=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:e.model.get("empty_text")}),a.each(this.model.get("data"),function(t){e.data.push(t)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(t,i){e.data2.push({order:i,id:t.value,text:t.label,tags:t.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:e.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(t){e.matched_tags={};var i=e.model.get("pagesize"),n=a.filter(e.data2,function(i){var n=!1;return a.each(i.tags,function(i){e._match(t.term,i)&&(n=e.matched_tags[i]=!0)}),n||e._match(t.term,i.text)});t.callback({results:n.slice((t.page-1)*i,t.page*i),more:n.length>=t.page*i})},formatResult:function(t){return a.escape(t.text)+'<div class="ui-tags">'+a.reduce(t.tags,function(t,i){return e.matched_tags[i]?t+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":t},"")+"</div>"}}),this.$(".select2-container .select2-search 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null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return a.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(n.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){a.each(this.model.get("data"),function(t){t.keep&&!a.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return n.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=n.isArray(e)?e:[e]:n.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(n.isArray(e)){var i=[];a.each(e,function(e){var n=a.findWhere(t.data2,{id:e});n&&i.push(n)}),e=i}else{e=a.findWhere(this.data2,{id:e})}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var e=null;if(this.model.get("searchable")){var t=this.$select.select2("data");t&&(n.isArray(t)?(e=[],t.sort(function(e,t){return e.order-t.order}),a.each(t,function(t){e.push(t.id)})):e=t.id)}else e=this.$select.val();return r.default.isEmpty(e)?null:e}});t.default={View:c}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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d.default.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):a.each(this.model.get("data"),function(t){e.$options.append(n(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=n.isArray(e)?e:[e];a.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(n(this).val())}),r.default.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(e){var t=r.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:t,type:this.model.get("type"),name:this.model.id,value:e.value})).append(n("<label/>").addClass("ui-options-label").attr("for",t).html(e.label))}}),h={};h.View=u.extend({initialize:function(e){e.type="radio",u.prototype.initialize.call(this,e)}});var f={};f.View=u.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,u.prototype.initialize.call(this,e)}});var p={};p.View=c.extend({initialize:function(e){c.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=n("<label/>").addClass("btn btn-default");return e.icon&&t.append(n("<i/>").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(n("<input/>").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),t.default={Base:c,BaseIcons:u,Radio:h,RadioButton:p,Checkbox:f}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(11),l=a(r),d=i(4),c=a(d),u=e.View.extend({initialize:function(e){var t=this;this.options=e,this.name=e.name||"element",this.multiple=e.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:e.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new 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i=n(this._templateRow({id:e.id,name:e.name}));i.on("click",function(){i.remove(),t._refresh()}),i.on("mouseover",function(){i.addClass("portlet-highlight")}),i.on("mouseout",function(){i.removeClass("portlet-highlight")}),this.portlet.append(i),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(e){this.select.update(e)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(e){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(e){return'<div id="'+e.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span class="ui-list-name">'+e.name+"</span></div>"}});t.default={View:u}}).call(t,i(1),i(0))},function(e,t,i){"use strict";var n=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default;s.fn.make_text_editable=function(e){var t="num_cols"in e?e.num_cols:30,i="num_rows"in e?e.num_rows:4,n="use_textarea"in e&&e.use_textarea,a="on_finish"in e?e.on_finish:null,o="help_text"in e?e.help_text:null,r=s(this);return r.addClass("editable-text").click(function(o){if(!(s(this).children(":input").length>0)){r.removeClass("editable-text");var l,d,c=function(e){r.find(":input").remove(),""!==e?r.text(e):r.html("<br>"),r.addClass("editable-text"),a&&a(e)},u="cur_text"in e?e.cur_text:r.text();n?(l=s("<textarea/>").attr({rows:i,cols:t}).text(s.trim(u)).keyup(function(e){27===e.keyCode&&c(u)}),d=s("<button/>").text("Done").click(function(){return c(l.val()),!1})):l=s("<input type='text'/>").attr({value:s.trim(u),size:t}).blur(function(){c(u)}).keyup(function(e){27===e.keyCode?s(this).trigger("blur"):13===e.keyCode&&c(s(this).val()),e.stopPropagation()}),r.text(""),r.append(l),d&&r.append(d),l.focus(),l.select(),o.stopPropagation()}}),o&&r.attr("title",o).tooltip(),r}},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(143),c=o(d),u=i(144),h=o(u),f=i(67),p=o(f);e.ajaxSettings.traditional=!0,t.default=n.View.extend({grid:null,initialize:function(e){this.grid=new c.default,this.dict_format=e.dict_format,this.title=e.title;var t=this;if(window.add_tag_to_grid_filter=function(e,i){var n=e+(void 0!==i&&""!==i?":"+i:"");a("#advanced-search").is(":visible")||(a("#standard-search").slideToggle("fast"),a("#advanced-search").slideToggle("fast")),t.add_filter_condition("tags",n)},this.dict_format)if(this.setElement("<div/>"),e.url_base&&!e.items){var i=e.url_data||{};s.each(e.filters,function(e,t){i["f-"+t]=e}),a.ajax({url:e.url_base+"?"+a.param(i),success:function(i){i.embedded=e.embedded,i.filters=e.filters||{},t.init_grid(i)}})}else this.init_grid(e);else this.setElement("#grid-container"),this.init_grid(e);e.use_panels&&a("#center").css({padding:"10px",overflow:"auto"})},handle_refresh:function(e){e&&a.inArray("history",e)>-1&&window.top.Galaxy&&window.top.Galaxy.currHistoryPanel&&window.top.Galaxy.currHistoryPanel.loadCurrentHistory()},init_grid:function(e){this.grid.set(e);var t=this.grid.attributes;this.allow_title_display&&t.title&&l.default.setWindowTitle(t.title),this.handle_refresh(t.refresh_frames);var i=this.grid.get("url_base");if(i=i.replace(/^.*\/\/[^\/]+/,""),this.grid.set("url_base",i),this.$el.html(h.default.grid(t)),this.$el.find("#grid-table-header").html(h.default.header(t)),this.$el.find("#grid-table-body").html(h.default.body(t)),this.$el.find("#grid-table-footer").html(h.default.footer(t)),t.message){this.$el.find("#grid-message").html(h.default.message(t));var n=this;t.use_hide_message&&setTimeout(function(){n.$el.find("#grid-message").html("")},5e3)}this.init_grid_elements(),this.init_grid_controls(),init_refresh_on_change()},init_grid_controls:function(){var e=this;this.$el.find(".operation-button").each(function(){a(this).off(),a(this).click(function(){return e.submit_operation(this),!1})}),this.$el.find("input[type=text]").each(function(){a(this).off(),a(this).click(function(){a(this).select()}).keyup(function(){a(this).css("font-style","normal")})}),this.$el.find(".sort-link").each(function(){a(this).off(),a(this).click(function(){return e.set_sort_condition(a(this).attr("sort_key")),!1})}),this.$el.find(".text-filter-form").each(function(){a(this).off(),a(this).submit(function(){var t=a(this).attr("column_key"),i=a("#input-"+t+"-filter"),n=i.val();return i.val(""),e.add_filter_condition(t,n),!1})}),this.$el.find(".text-filter-val > a").each(function(){a(this).off(),a(this).click(function(){return a(this).parent().remove(),e.remove_filter_condition(a(this).attr("filter_key"),a(this).attr("filter_val")),!1})}),this.$el.find(".categorical-filter > a").each(function(){a(this).off(),a(this).click(function(){return e.set_categorical_filter(a(this).attr("filter_key"),a(this).attr("filter_val")),!1})}),this.$el.find(".advanced-search-toggle").each(function(){a(this).off(),a(this).click(function(){return 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i="width"==e||"height"==e?1:-1,n=t*this.options.cell-i*this.options.margin;return"top"==e&&(n+=this.top),n},_toGrid:function(e){return{top:this._toGridCoord("top",e.top),left:this._toGridCoord("left",e.left),width:this._toGridCoord("width",e.width),height:this._toGridCoord("height",e.height)}},_toPixel:function(e){return{top:this._toPixelCoord("top",e.top),left:this._toPixelCoord("left",e.left),width:this._toPixelCoord("width",e.width),height:this._toPixelCoord("height",e.height)}},_isCollision:function(e){for(var t in this.frame_list){var i=this.frame_list[t];if(null!==i.grid_location&&function(e,t){return!(e.left>t.left+t.width-1||e.left+e.width-1<t.left||e.top>t.top+t.height-1||e.top+e.height-1<t.top)}(e,i.grid_location))return!0}return!1},_locationRank:function(e){return e.top*this.cols+e.left},_panelRefresh:function(e){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,e)},_panelAnimationComplete:function(){var e=this;i(".frame").promise().done(function(){e._panelScroll(0,!0)})},_panelScroll:function(e,t){var i=this.top-this.options.scroll*e;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var s={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,s,t)}}this.top=i}this.render()},_frameInit:function(e,t){e.id=t,e.screen_location={},e.grid_location={},e.grid_rank=null,e.$el.attr("id",t.substring(1))},_frameInsert:function(e,t,a){var s=this,o=[];e&&(e.grid_location=null,o.push([e,this._locationRank(t)])),n.each(this.frame_list,function(e){null!==e.grid_location&&(e.grid_location=null,o.push([e,e.grid_rank]))}),o.sort(function(e,t){return e[1]<t[1]?-1:e[1]>t[1]?1:0}),n.each(o,function(e){s._framePlace(e[0],a)}),this.top_max=0,n.each(this.frame_list,function(e){null!==e.grid_location&&(s.top_max=Math.max(s.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a<this.options.rows;a++){for(var s=0;s<Math.max(1,this.cols-i.width);s++)if(i.top=a,i.left=s,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(e,i,t):console.log("Grid dimensions exceeded.")},_frameFocus:function(e,t){e.$el.css("z-index",this.frame_z+(t?1:0))},_frameOffset:function(e,t,i){if(e.screen_location.left=t.left,e.screen_location.top=t.top,i){this._frameFocus(e,!0);var n=this;e.$el.animate({top:t.top,left:t.left},"fast",function(){n._frameFocus(e,!1)})}else e.$el.css({top:t.top,left:t.left})},_frameResize:function(e,t){e.$el.css({width:t.width,height:t.height}),e.screen_location.width=t.width,e.screen_location.height=t.height},_frameGrid:function(e,t,i){e.grid_location=t,this._frameOffset(e,this._toPixel(t),i),e.grid_rank=this._locationRank(t)},_frameScreen:function(e){var t=e.screen_location;return{top:t.top,left:t.left,width:t.width,height:t.height}}});t.default={View:s}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({id:s.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(t),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(e){a[e.which]=!1}).on("keydown",function(e){var t=e.which;a[t]=!0,i.model.get("is_workflow")&&a[16]&&52==t?(i.value("$"),event.preventDefault()):8==t||9==t||13==t||37==t||39==t||t>=48&&t<=57&&!a[16]||t>=96&&t<=105||(190==t||110==t)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==t||109==t)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var r=o.step;r||(r=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});t.default={View:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(23),l=a(r),d=l.default.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple="checkbox"==e.type,l.default.BaseIcons.prototype.initialize.call(this,e)},_setValue:function(t){if(l.default.BaseIcons.prototype._setValue.call(this,t),void 0!==t&&null!==t&&this.header_index){var i=this,a=e.isArray(t)?t:[t];n.each(a,function(e){var t=i.header_index[e];n.each(t,function(e){i._setState(e,!0)})})}},_setState:function(e,t){var i=this.$(".button-"+e),n=this.$(".subgroup-"+e);i.data("is_expanded",t),t?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function t(e,t){var i=e.find(".button-"+t);i.on("click",function(){n._setState(t,!i.data("is_expanded"))})}function i(a,s,r){r=r||[];for(var l in s){var d=s[l],c=d.options&&d.options.length>0,u=r.slice(0);n.header_index[d.value]=u.slice(0);var h=e("<div/>");if(c){var f=o.default.uid(),p=e("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),m=e("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(e("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(m,d.options,u),h.append(m),t(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=e("<div/>");return i(a,this.model.get("data")),a},_template:function(){return e("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});t.default={View:d}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(3),l=o(r),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),m=o(p),_=i(51),g=o(_),v=e.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var e=this;this.$el.empty(),a.each(this.inputs,function(t){e.add(t)})},add:function(e){var t=s.extend(!0,{},e);switch(t.id=e.id=l.default.uid(),this.app.input_list[t.id]=t,t.type){case"conditional":this._addConditional(t);break;case"repeat":this._addRepeat(t);break;case"section":this._addSection(t);break;default:this._addRow(t)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var a in e.cases){var s=e.cases[a],o=t.$("#"+e.id+"-section-"+a),r=!1;for(var l in s.inputs)if(!s.inputs[l].hidden){r=!0;break}a==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var a=new v(this.app,{inputs:e.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var a=e.id+"-section-"+n++,o=new v(i.app,{inputs:t});s.add({id:a,$el:o.$el,ondel:function(){s.del(a),i.app.trigger("change")}})}for(var i=this,n=0,s=new f.default.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),o=a.size(e.cache),r=0;r<Math.max(Math.max(o,e.min||0),e.default||0);r++)t(r<o?e.cache[r]:e.inputs);this.app.model.get("sustain_repeats")&&s.hideOptions();var l=new m.default(this.app,{label:e.title||e.name,help:e.help,field:s});this._append(l.$el,e.id)},_addSection:function(e){var t=new u.default.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new v(this.app,{inputs:e.inputs}).$el),t.append(n("<div/>").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var a=new m.default(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});t.default={View:v}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(11),d=s(l),c=i(4),u=s(c),h=e.View.extend({initialize:function(e){this.list={},this.options=r.default.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var t=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),i=new d.default.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:t}});i.append(e.$el),i.$el.addClass("section-row").hide(),this.list[e.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){if(!this.list[e])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),this._refresh()},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(e){e.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});t.default={View:h}}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(t,i){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=i&&i.field||new e.View,this.model=i&&i.model||new e.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,t.trigger&&t.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&-1==e.indexOf("("+t+")")&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var s=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+s)).attr("data-original-title",this.model.get("text_"+s)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(52),u=s(c),h=i(53),f=s(h),p=i(54),m=s(p),_=i(55),g=s(_),v=i(57),w=s(v);t.default=e.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new u.default.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var t=e.data;t||(t=[],n.each(e.options,function(e){t.push({label:e[0],value:e[1]})}));var i=d.default.Select;switch(e.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+e.id,data:t,error_text:e.error_text||"No options available",readonly:e.readonly,multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new d.default.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(e){if(e.options&&e.data)if(e.area=e.multiple,r.default.isEmpty(e.value))e.value=null;else if(a.isArray(e.value)){var t="";for(var i in e.value){if(t+=String(e.value[i]),!e.multiple)break;t+="\n"}e.value=t}return new d.default.Input({id:"field-"+e.id,type:e.type,area:e.area,readonly:e.readonly,placeholder:e.placeholder,datalist:e.datalist,onchange:e.onchange})},_fieldSlider:function(e){return new d.default.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new d.default.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new d.default.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new w.default({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new f.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new m.default.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new g.default.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new d.default.Upload({id:"field-"+e.id,onchange:e.onchange})}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(22),u=s(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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e=this;a.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),a.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var e=this,t=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[t]?this.config=f[t]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+t+"'."));var i=e.model.get("data"),n=r.default.textify(this.model.get("extensions")),s=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(t,a){e.button_data.push({value:a,icon:t.icon,tooltip:t.tooltip}),e.fields.push(new u.default.View({optional:e.model.get("optional"),multiple:t.multiple,searchable:!t.multiple||i&&i[t.src]&&i[t.src].length>e.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(s[t.src]||"content")+" 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e=[];null!==t.library_select.text()&&t.datasets.each(function(t){"file"===t.get("type")&&e.push({value:t.id,label:t.get("name")})}),t.dataset_list.update(e)}),this.on("change",function(){e.onchange&&e.onchange(t.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){t.library_select.trigger("change"),void 0!==t.options.value&&t.value(t.options.value)}})},value:function(e){return this.dataset_list.value(e)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});t.default={View:h}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=n(a),o=i(24),r=n(o),l=e.View.extend({initialize:function(e){var t=this;this.ftpfile_list=new r.default.View({name:"file",optional:e.optional,multiple:e.multiple,onchange:function(){e.onchange&&e.onchange(t.value())}}),this.setElement(this.ftpfile_list.$el),s.default.get({url:Galaxy.root+"api/remote_files",success:function(e){var i=[];for(var n in e)i.push({value:e[n].path,label:e[n].path});t.ftpfile_list.update(i)}})},value:function(e){return this.ftpfile_list.value(e)}});t.default={View:l}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=(n(a),i(4)),o=n(s),r=i(56),l=n(r),d=e.View.extend({initialize:function(e){var t=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){t.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new 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t.default=e,t}(s),r=i(14),l=a(r),d=i(15),c=a(d),u=i(141),h=(a(u),{hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}}),f=e.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new f(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),p=e.Collection.extend({model:f}),m=f.extend({}),_=f.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),g=_.extend({set_value:function(e){this.set("value",parseFloat(e))}}),v=f.extend({get_samples:function(){return o.map(this.get("options"),function(e){return e[0]})}});f.subModelTypes={integer:_,float:g,data:m,select:v};var w=e.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new p(o.map(e.inputs,function(e){return new(f.subModelTypes[e.type]||f)(e)})))},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(e){return e.toJSON()}),t},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return-1!==e.indexOf(t.get("type"))});t.get("inputs").remove(i)},copy:function(t){var i=new w(this.toJSON());if(t){var n=new e.Collection;i.get("inputs").each(function(e){e.get_samples()&&n.push(e)}),i.set("inputs",n)}return i},apply_search_results:function(e){return-1!==o.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(e){var t=this;o.each(o.keys(e),function(i){t.set_input_value(i,e[i])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(e){var t=o.extend({tool_id:this.id,inputs:this.get_inputs_dict()},e),i=n.Deferred(),a=new l.default.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(t),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return n.when(a.go()).then(function(e){i.resolve(new c.default.DatasetCollection(e))}),i}});o.extend(w.prototype,h);var b=(e.View.extend({}),e.Collection.extend({model:w})),y=e.Model.extend(h),x=e.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){o.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var t,i=!0;o.each(this.attributes.elems,function(n){n instanceof y?(t=n,t.hide()):n instanceof w&&n.apply_search_results(e)&&(i=!1,t&&t.show())}),i?this.hide():(this.show(),this.set("open",!0))}});o.extend(x.prototype,h);var k=e.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length<this.attributes.min_chars_for_search)return void this.set("results",null);var t=e;this.timer&&clearTimeout(this.timer),n("#search-clear-btn").hide(),n("#search-spinner").show();var i=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"?q="+t),n.get(i.urlRoot,{q:t},function(e){i.set("results",e),n("#search-spinner").hide(),n("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});o.extend(k.prototype,h);var C=e.Model.extend({initialize:function(t){this.attributes.tool_search=t.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=t.tools,this.attributes.layout=new e.Collection(this.parse(t.layout))},parse:function(e){var t=this,i=function e(i){var n=i.model_class;if(n.indexOf("Tool")===n.length-4)return t.attributes.tools.get(i.id);if("ToolSection"===n){var a=o.map(i.elems,e);return i.elems=a,new x(i)}return"ToolSectionLabel"===n?new y(i):void 0};return o.map(e,i)},clear_search_results:function(){this.get("layout").each(function(e){e instanceof x?e.clear_search_results():e.show()})},apply_search_results:function(){var e=this.get("tool_search").get("results");if(null===e)return void this.clear_search_results();var t=null;this.get("layout").each(function(i){i instanceof y?(t=i,t.hide()):i instanceof w?i.apply_search_results(e)&&t&&t.show():(t=null,i.apply_search_results(e))})}}),$=e.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),S=$.extend({tagName:"div",render:function(){var e=n("<div/>");e.append(A.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(e),this}}),T=$.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(n("<span/>").text(this.model.attributes.text)),this}}),M=$.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){$.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(A.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return o.each(this.model.attributes.elems,function(t){if(t instanceof w){var i=new S({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof y){var n=new T({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),E=e.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(A.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),n("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){if(this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which)return this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),P=e.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new E({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof x){var i=new M({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof w){var n=new S({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof y){var a=new T({model:t});a.render(),e.$el.append(a.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=n(this).attr("class").split(/\s+/)[0],a=e.model.get("tools").get(i);e.trigger("tool_link_click",t,a)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?n("#search-no-results").show():n("#search-no-results").hide()}}),O=e.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(A.tool_form(this.model.toJSON()))}}),A=(e.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new P({collection:this.collection}),this.tool_form_view=new O},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" ','placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />','<a id="search-clear-btn" title="clear search (esc)"> </a>','<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>'].join("")),panel_section:o.template(['<div class="toolSectionTitle" id="title_<%- id %>">','<a href="javascript:void(0)"><span><%- name %></span></a>',"</div>",'<div id="<%- id %>" class="toolSectionBody" style="display: none;">','<div class="toolSectionBg"></div>',"<div>"].join("")),tool_link:o.template(['<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">','<span class="labels">',"<% _.each( labels, function( label ){ %>",'<span class="label label-default label-<%- label %>">',"<%- label %>","</span>","<% }); %>","</span>",'<span class="tool-old-link">',"<%- name %>","</span>"," <%- description %>","</a>"].join("")),tool_form:o.template(['<div class="toolFormTitle"><%- tool.name %> (version <%- tool.version %>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});t.default={ToolParameter:f,IntegerToolParameter:_,SelectToolParameter:v,Tool:w,ToolCollection:b,ToolSearch:k,ToolPanel:C,ToolPanelView:P,ToolFormView:O}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(9),u=s(c),h=i(63),f=s(h),p=i(40),m=s(p),_=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(r.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),r.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),r.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("<input/>").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),r.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new m.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var a in t){var s=t[a],o=this.form.data.match(a),r=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&r){if(!l.optional&&null==s)return this.form.highlight(o),!1;if(s&&s.batch){var d=s.values.length,c=d>0&&s.values[0]&&s.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(e.hid+": "+e.name)))}),s.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("<pre/>").text(JSON.stringify(e,null,4)))}});t.default={View:_}}).call(t,i(1),i(0),i(2))},,function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(e){return-1!==i.indexOf(this.attributes.async_ops,e)},add_filter:function(e,t,i){if(i){var n,a=this.attributes.filters[e];if(null===a||void 0===a)n=t;else if("string"==typeof a)if("All"==a||a==t)n=t;else{var s=[];s[0]=a,s[1]=t,n=s}else n=a,-1===n.indexOf(t)&&n.push(t);this.attributes.filters[e]=n}else this.attributes.filters[e]=t},remove_filter:function(e,t){var n=this.attributes.filters[e];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[e]="";else{var a=i.indexOf(n,t);-1!==a&&(n[a]="")}},get_url_data:function(){var e={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(e.operation=this.attributes.operation),this.attributes.item_ids&&(e.id=this.attributes.item_ids);var t=this;return i.each(i.pairs(t.attributes.filters),function(t){e["f-"+t[0]]=t[1]}),e},get_url:function(e){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(e)}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a);t.default={grid:function(e){var t="";return t=e.embedded?this.grid_header(e)+this.grid_table(e):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(e)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(e),e.info_text&&(t+='<br><div class="toolParamHelp" style="clear: both;">'+e.info_text+"</div>"),t},grid_table:function(e){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(e){var t='<div class="grid-header">';if(e.embedded||(t+="<h2>"+e.title+"</h2>"),e.global_actions){t+='<ul class="manage-table-actions">';var i=e.global_actions.length>=3;i&&(t+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in e.global_actions){var a=e.global_actions[n];t+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(t+="</div>"),t+="</ul>"}return e.insert&&(t+=e.insert),t+=this.grid_filters(e),t+="</div>"},header:function(e){var t="<tr>";e.show_item_checkboxes&&(t+="<th>",e.items.length>0&&(t+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),t+="</th>");for(var i in e.columns){var n=e.columns[i];n.visible&&(t+='<th id="'+n.key+'-header">',n.href?t+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":t+=n.label,t+='<span class="sort-arrow">'+n.extra+"</span></th>")}return t+="</tr>"},body:function(t){var i="",n=0;0==t.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in t.items){var s=t.items[a],o=s.encode_id;i+="<tr ",t.current_item_id==s.id&&(i+='class="current"'),i+=">",t.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var r in t.columns){var l=t.columns[r];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=s.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===e.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",m="";l.attach_popup&&(p="grid-"+a+"-popup",m="menubutton",""!=u&&(m+=" split"),m+=" popup"),i+="<td "+d+">",u?(0!=t.operations.length&&(i+='<div id="'+p+'" class="'+m+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=t.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+m+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(e){var t="";if(e.use_paging&&e.num_pages>1){var i=e.num_page_links,n=e.cur_page_num,a=e.num_pages,s=i/2,o=n-s,r=0;o<=0&&(o=1,r=s-(n-o));var l,d=s+r,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),t+='<tr id="page-links-row">',e.show_item_checkboxes&&(t+="<td></td>"),t+='<td 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f=e.operations[h];f.allow_multiple&&(t+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}t+="</td></tr>"}var p=!1;for(h in e.operations)if(e.operations[h].global_operation){p=!0;break}if(p){t+='<tr><td colspan="100">';for(h in e.operations){var f=e.operations[h];f.global_operation&&(t+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}t+="</td></tr>"}return e.legend&&(t+='<tr><td colspan="100">'+e.legend+"</td></tr>"),t},message:function(e){var t=e.status;return-1!=["success","ok"].indexOf(t)&&(t="done"),'<p><div class="'+t+'message transient-message">'+n.escape(e.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1;for(var s in e.columns){var o=e.columns[s];if("advanced"==o.filterable){var r=o.key,l=i[r],d=t[r];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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v=t.categorical_filters[s][g],w="",b="";for(var y in v)w=y,b=v[y];_&&(o+=" | "),_=!0;var h=n[s];h&&v[s]&&h==b?o+='<span class="categorical-filter '+s+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+s+'-filter"><a href="javascript:void(0);" filter_key="'+w+'" filter_val="'+b+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(e,t){return'<span class="text-filter-val">'+(t=s.default.sanitize(t))+'<a href="javascript:void(0);" filter_key="'+e+'" filter_val="'+t+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(146),l=a(r),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),m=i(26),_=a(m),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var w=null,b=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=e.Model.extend;var x=y.extend({initialize:function(e){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=e},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var e=[];n(".bookmark").each(function(){e.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var t=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,i={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:t},bookmarks:e};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(e){Galaxy.modal.hide(),b.vis_id=e.vis_id,b.has_changes=!1,window.history.pushState({},"",e.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var e=this,t=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(e){o.each(e,function(e){b.add_drawable(l.default.object_from_template(e,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=e.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){e.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){e.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=t,t},add_bookmark:function(e,t,i){var a=n("#right .unified-panel-body"),s=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(s),r=(n("<a href=''/>").text(e).appendTo(o).click(function(){return b.go_to(e),!1}),n("<div/>").text(t).appendTo(s));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){return s.slideUp("fast"),s.remove(),b.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);r.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,s},create_visualization:function(e,t,i,a,s){var r=this,d=new l.default.TracksterView(o.extend(e,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(e){if(t){var n=t.chrom,o=t.start,c=t.end,u=t.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(e[0].chrom)}else d.change_chrom(e[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],r.add_bookmark(f.position,f.annotation,s);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(t){new c.default.TrackBrowserRouter(t),e.history.start()},init_keyboard_nav:function(e){n(document).keyup(function(t){if(!n(t.srcElement).is(":input"))switch(t.which){case 37:e.move_fraction(.25);break;case 38:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()-20);break;case 39:e.move_fraction(-.25);break;case 40:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(e){if(e.has_changes){var t=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(t.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=e.View.extend({initialize:function(){w=new x(Galaxy.root),w.createButtonMenu(),w.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(w.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var e=this,t=p.default.get("dbkey"),i={},n={dbkey:t,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(t||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){e.view_in_saved(n)},"View in new visualization":function(){e.view_new()}}})},view_in_saved:function(e){var t=new _.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:t.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){e.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(e)})}}})},view_existing:function(){var e=galaxy_config.app.viz_config;b=w.create_visualization({container:n("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,!0),this.init_editor()},view_new:function(){var e=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(t){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(t),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){e.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=t.map(function(e){return e[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(e){for(var t='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<e.length;i++)t+='<option value="'+e[i][1]+'">'+e[i][0]+"</option>";return t+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(e,t){n(document).trigger("convert_to_values"),b=w.create_visualization({container:n("#center .unified-panel-body"),name:e,dbkey:t},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){b.add_drawable(l.default.object_from_template(e,b,b))}}),n("#add-bookmark-button").click(function(){var e=b.chrom+":"+b.low+"-"+b.high;return w.add_bookmark(e,"Bookmark description",!0)}),w.init_keyboard_nav(b),n(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});t.default={TracksterUI:x,GalaxyApp:k}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function o(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var r=i(2),l=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(r),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),m=i(148),_=a(m),g=i(149),v=a(g),w=i(150),b=a(w),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),S=a($),T=i(151),M=a(T);i(25);var E=l.extend,P={},O=function(e,t){P[e.attr("id")]=t},A=function(t,i,n,a){n=".group",P[t.attr("id")]=a,t.bind("drag",{handle:"."+i,relative:!0},function(t,i){var a,s,o,r,l,d=(e(this),e(this).parent()),c=d.children(".track,.group"),u=P[e(this).attr("id")];if(s=e(this).parents(n),0!==s.length){o=s.position().top,r=o+s.outerHeight();var h=P[s.attr("id")];if(i.offsetY<o)return e(this).insertBefore(s),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>r)return e(this).insertAfter(s),h.remove_drawable(u),void h.container.add_drawable(u)}for(s=null,l=0;l<c.length;l++)if(a=e(c.get(l)),o=a.position().top,r=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=r)return i.offsetY-o<r-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void P[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=e(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),P[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(e(this).insertBefore(c.get(l)),P[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})},D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",I=["Histogram","Line","Filled","Intensity"],z=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};z.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(e){new S.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],E(z.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var j=function(e,t,i){z.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};E(j.prototype,z.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i<e.length;i++)t=ne(e[i],this.view,this),this.add_drawable(t)},init:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].init()},_draw:function(e){for(var t=0;t<this.drawables.length;t++)this.drawables[t]._draw(e)},to_dict:function(){for(var e=[],t=0;t<this.drawables.length;t++)e.push(this.drawables[t].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:e}},add_drawable:function(e){this.drawables.push(e),e.container=this,this.changed()},add_drawable_before:function(e,t){this.changed();var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,0,e),!0)},replace_drawable:function(e,t,i){var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables[n]=t,i&&e.container_div.replaceWith(t.container_div),this.changed()),n},remove_drawable:function(e){var t=this.drawables.indexOf(e);return-1!==t&&(this.drawables.splice(t,1),e.container=null,this.changed(),!0)},move_drawable:function(e,t){var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(t,0,e),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(e){for(var t,i=this.drawables.slice(0),n=[];0!==i.length;)t=i.shift(),t instanceof e?n.push(t):t.drawables&&(i=i.concat(t.drawables));return n}});var L=function(t,i,n){if(E(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),j.call(this,t,i,n),this.content_div=e("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),A(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};E(L.prototype,z.prototype,j.prototype,{action_icons_def:[z.prototype.action_icons_def[0],z.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},z.prototype.action_icons_def[2]],build_container_div:function(){var t=e("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i<t;i++){if(a=this.drawables[i],a.get_type()!==s){can_composite=!1;break}a instanceof Z&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),e(".tooltip").remove()),o>1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],l[r.name]=[r];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],r.name in l&&l[r.name].push(r);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new b.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].filters_manager=this.saved_filters_managers[e];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var e=0;e<this.drawables.length;e++){var t=this.drawables[e];this.saved_filters_managers.push(t.filters_manager),t.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var e=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,e,!0);e.request_draw()},add_drawable:function(e){j.prototype.add_drawable.call(this,e),this.update_icons()},remove_drawable:function(e){j.prototype.remove_drawable.call(this,e),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var e=E(j.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),e},request_draw:function(e){l.each(this.drawables,function(t){t.request_draw(e)})}});var R=n.View.extend({initialize:function(e){E(e,{obj_type:"View"}),j.call(this,"View",e.container,e),this.chrom=null,this.vis_id=e.vis_id,this.dbkey=e.dbkey,this.stand_alone=void 0===e.stand_alone||e.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:e.name})},render:function(){this.requested_redraw=!1;var t=this.container,i=this;this.top_container=e("<div/>").addClass("top-container").appendTo(t),this.browser_content_div=e("<div/>").addClass("content").appendTo(t),this.bottom_container=e("<div/>").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,i),this.intro_div=e("<div/>").addClass("intro").appendTo(this.viewport_container);e("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(e){l.each(e,function(e){i.add_drawable(ne(e,i,i))})})});this.nav_container=e("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(Z),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new W(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});E(R.prototype,j.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500)}else view.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(p.default.commatize(e)+" - "+p.default.commatize(t)),this.nav_input.val(this.chrom+":"+p.default.commatize(e)+"-"+p.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){t.num=100;var i=this,n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new X(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e('<option value="">Select Chrom/Contig</option>'));for(var s=0,o=i.chrom_data.length;s<o;s++){var r=i.chrom_data[s].chrom,l=e("<option>");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('<option value="previous">Previous 100</option>')),t.next_chroms&&i.chrom_select.append(e('<option value="next">Next 100</option>')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;o<r;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(e){e=e.replace(/,/g,""),e=e.replace(/:|\-/g," ");var t=e.split(/\s+/),i=t[0],n=t[1]?parseInt(t[1],10):void 0,a=t[2]?parseInt(t[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(e){var t=this,i=t.high-t.low;this.move_delta(e*i)},move_delta:function(e){var t=this,i=t.high-t.low;t.low-e<t.max_low?(t.low=t.max_low,t.high=t.max_low+i):t.high-e>t.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){j.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(j.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;l.each(n,function(t){var n=l.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;e<this.max_low&&(e=this.max_low),t>this.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(t=e+this.min_separation),this.low=Math.floor(e),this.high=Math.ceil(t),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(e){var t=e[0],i=e[1];t&&t._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(e){e._draw()})},zoom_in:function(e,t){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;e&&(n=e/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var e=this.high-this.low,t=e/2+this.low,i=e*this.zoom_factor/2;this.low=Math.round(t-i),this.high=Math.round(t+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(e){if(this.overview_drawable){if(this.overview_drawable.dataset.id===e.dataset.id)return;this.overview_viewport.find(".track").remove()}var t=e.copy({content_div:this.overview_viewport}),i=this;t.header_div.hide(),t.is_overview=!0,i.overview_drawable=t,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){e(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var N=C.default.Tool.extend({defaults:{track:null},initialize:function(e){C.default.Tool.prototype.initialize.call(this,e);var t=!0;void 0!==e.tool_state&&void 0!==e.tool_state.hidden&&(t=e.tool_state.hidden),this.set("hidden",t),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(e){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),V=n.View.extend({events:{"change :input":"update_value"},render:function(){var t=this.$el.addClass("param-row"),i=this.model;e("<div>").addClass("param-label").text(i.get("label")).appendTo(t);e("<div/>").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("<div style='clear: both;'/>").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),G=n.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()});e("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(e){var t=new V({model:e});t.render(),n.append(t.$el)}),n.find("input").click(function(){e(this).select()});var a=e("<div>").addClass("param-row").appendTo(n),s=e("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);e("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e<this.params.length;e++)this.params[e].update_value()},run_on_dataset:function(){var e=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:e.id},null,function(t){Galaxy.modal.show({title:e.get("name")+" is Running",body:e.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var e,t=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:t.view.chrom,start:t.view.low,end:t.view.high}),a={target_dataset_id:t.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},s=t,o=i.get("name")+s.tool_region_and_parameters_str(n);if(s.container===view){var r=new L(view,view,{name:t.config.get_value("name")}),l=s.container.replace_drawable(s,r,!1);r.container_div.insertBefore(s.view.content_div.children()[l]),r.add_drawable(s),s.container_div.appendTo(r.content_div),e=r}else e=s.container;var d=new s.constructor(view,e,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(s.mode),d.set_filters_manager(s.filters_manager.copy(d)),d.update_icons(),e.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(e){d.set_dataset(new x.default.Dataset(e)),d.tiles_div.text("Running job."),d.init()})},run:function(t,i,n){t.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(t),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});e.when(a.go()).then(function(e){"no converter"===e?(i.container_div.addClass("error"),i.content_div.text(D)):e.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+e.message)):n(e)})}}),U=function(e,t){v.default.Scaler.call(this,t),this.filter=e};U.prototype.gen_val=function(e){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(e[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var H=function(t,i,n,a,s){this.track=t,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=e("<div class='track-tile'/>").append(a),this.data=s,this.stale=!1};H.prototype.predisplay_actions=function(){};var F=function(e,t,i,n,a){H.call(this,e,t,i,n,a)};F.prototype.predisplay_actions=function(){};var B=function(e,t,i,n,a,s,o,r,l,d,c){H.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};E(B.prototype,H.prototype),B.prototype.predisplay_actions=function(){};var q=function(t,i,a){E(a,{drag_handle_class:"draghandle"}),z.call(this,t,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};E(q.prototype,z.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},z.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},z.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(t){var i="<strong>Tool</strong>:"+t.tool.get("name")+"<br/><strong>Dataset</strong>:"+t.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},s=function(){var i,a=e('select[name="regions"] option:selected').val(),s=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(e(".bookmark"),function(t){return new c.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===a?[s]:"bookmarks"===a?o:[s].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:s}})}},z.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&z.prototype.can_draw.call(this)},build_container_div:function(){return e("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("<div class='track-resize'>");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof W?"LabelTrack":this instanceof X?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof te?"ReadTrack":this instanceof ee?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Z?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("<span/>").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(D)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+t.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("<span/>").text(" ")),a.append(e("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(t,i,n){q.call(this,t,i,n);var a=this;if(A(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new b.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new N(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new G({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};E(Y.prototype,z.prototype,q.prototype,{action_icons_def:q.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();E(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){if(this.can_draw()){var i=t&&t.clear_after,n=this.view.low,a=this.view.high,s=this.view.container.width(),o=this.view.resolution_px_b,r=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=s/(view.max_high-view.max_low),r=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*r),f=Math.floor(n/h),p=[],m=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,t),p.push(u),e.when(u).then(function(e){m.push(e)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var _=this;e.when.apply(e,p).then(function(){_.tiles_div.children(".remove").remove(),m=l.filter(m,function(e){return null!==e}),0!==m.length&&_.postdraw_actions(m,s,o,i)})}},_add_yaxis_label:function(t,i){var n=this,a="max"===t?"top":"bottom",o="max"===t?"max":"min",r="max"===t?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=s(n.config.get_value(r),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=e("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),n.config.set_value(r,s(t,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){if(l.filter(e,function(e){return e instanceof F}).length>0){this.max_height_px=0;var a=this;l.each(e,function(e){e instanceof F||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(e,function(e){return e.has_icons})&&l.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)})},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){n||(n={});var a=n.force,s=n.mode||this.mode,o=1/i,r=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,t),u=a?void 0:r.tile_cache.get_elt(c);if(u)return function(e){return e&&"track"in e}(u)&&r.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var e=l.find(I,function(e){return e===s})?"Coverage":s,i=l.map(d,function(i){return i.data_manager.get_data(t,e,o,r.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(t,s,o,view.reference_track.data_url_extra_params)),i},f=e.Deferred();return r.tile_cache.set_elt(c,f),e.when.apply(e,h()).then(function(){var a,s=h(),o=s;if(l.find(s,function(e){return p.default.is_deferred(e)}))return r.tile_cache.set_elt(c,void 0),void e.when(r.draw_helper(t,i,n)).then(function(e){f.resolve(e)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(s.pop(),t));var u=[],m=[];l.each(d,function(e,t){var n=e.mode,a=o[t];"Auto"===n&&(n=e.get_mode(a),e.update_auto_mode(n)),u.push(n),m.push(e.get_canvas_height(a,n,i,b))});var _,g=r.view.canvas_manager.new_canvas(),v=t.get("start"),w=t.get("end"),b=Math.ceil((w-v)*i)+r.left_offset,y=l.max(m);g.width=b,g.height=n.height||y;var x=g.getContext("2d");x.translate(r.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(e,n){_=e.draw_tile(o[n],x,u[n],t,i,a)}),void 0!==_&&(r.tile_cache.set_elt(c,_),r.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new v.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new F(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+l.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var W=function(e,t){q.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};E(W.prototype,q.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("<div/>").addClass("label-container");s<i.high;){var l=Math.floor((s-i.low)/n*o);r.append(e("<div/>").addClass("pos-label").text(p.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var J=function(e,t,i){if(Y.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=ne(n,e,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(e){(e instanceof Z||e instanceof te)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};E(J.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:j.prototype.to_dict,add_drawable:j.prototype.add_drawable,unpack_drawables:j.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;l.each(this.drawables,function(t){t.visible_height_px=e}),q.prototype.on_resize.call(this)},change_mode:function(e){Y.prototype.change_mode.call(this,e);for(var t=0;t<this.drawables.length;t++)this.drawables[t].change_mode(e)},init:function(){for(var t=[],i=0;i<this.drawables.length;i++)t.push(this.drawables[i].init());var n=this;e.when.apply(e,t).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:z.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var e,t=new L(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)e=this.drawables[i],e.update_icons(),t.add_drawable(e),e.container=t,t.content_div.append(e.container_div);this.container.replace_drawable(this,t,!0);t.request_draw({clear_tile_cache:!0})},before_draw:function(){var e=l.min(l.map(this.drawables,function(e){return e.config.get_value("min_value")})),t=l.max(l.map(this.drawables,function(e){return e.config.get_value("max_value")}));this.config.set_value("min_value",e),this.config.set_value("max_value",t),l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)})},update_all_min_max:function(){var e=this.config.get_value("min_value"),t=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(e,t,i,n){var a,s=-1;for(a=0;a<e.length;a++){var o=e[a].html_elt.find("canvas").height();o>s&&(s=o)}for(a=0;a<e.length;a++){var r=e[a];r.html_elt.find("canvas").height()!==s&&(this.draw_helper(r.region,i,{force:!0,height:s}),r.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var X=function(e){Y.call(this,e,{content_div:e.top_labeltrack},{resize:!1,header:!1}),this.left_offset=e.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};E(X.prototype,z.prototype,Y.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:z.prototype.can_draw,draw_helper:function(e,t,i){var n,a=this.tiles_div.is(":visible"),s=null;return t>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=Y.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l<d;l++)t.fillStyle=this.view.get_base_color(o[l]),t.fillText(o[l],Math.floor(l*a),10);return new H(this,n,a,r,s)}});var K=function(t,i,n){this.mode="Histogram",Y.call(this,t,i,n),this.left_offset=30;var a=this;e.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(e){e&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};E(K.prototype,z.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(e,t,i,n,a){return this._draw_line_track_tile(e,t,i,n,a)},can_subset:function(e){return e.data[1][0]-e.data[0][0]==1},postdraw_actions:function(e,t,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Q=function(e,t,i){this.mode="Heatmap",Y.call(this,e,t,i)};E(Q.prototype,z.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){e.data})},draw_tile:function(e,t,i,n,a){var s=t.canvas;return new v.default.DiagonalHeatmapPainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new H(this,n,a,s,e.data)}});var Z=function(e,t,i){Y.call(this,e,t,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};E(Z.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s,o=this;if(0===l.filter(t,function(e){return e instanceof F}).length){var r={};l.each(l.pluck(t,"incomplete_features"),function(e){l.each(e,function(e){r[e[0]]=e})});var d=this;l.each(t,function(t){var i=l.omit(r,l.map(t.incomplete_features,function(e){return e[0]}));if(i=l.omit(i,l.keys(t.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),s=a.getContext("2d");a.height=Math.max(t.canvas.height,d.get_canvas_height(n,t.mode,t.w_scale,100)),a.width=t.canvas.width,s.drawImage(t.canvas,0,0),s.translate(o.left_offset,0);var c=d.draw_tile(n,s,t.mode,t.region,t.w_scale,t.seq_data);e(t.canvas).replaceWith(e(c.canvas)),t.canvas=a,l.extend(t.other_tiles_features_drawn,r)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(s=0;s<t.length;s++)if(t[s].data.length)for(h=t[s].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(t[0]instanceof B){var m=!0;for(s=0;s<t.length;s++)if(!t[s].all_slotted){m=!1;break}this.action_icons.show_more_rows_icon.toggle(!m)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(e){"Auto"===this.mode&&("no_detail"===e&&(e="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+e+")"))},incremental_slots:function(e,t,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[e];return a&&a.mode===i||(a=new _.default.FeatureSlotter(e,i,100,function(e){return n.measureText(e)}),this.slotters[e]=a),a.slot_features(t)},get_mode:function(e){return"no_detail"===e.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var m=this.filters_manager.filters,_=0,g=e.data.length;_<g;_++){for(var v,w=e.data[_],b=!1,y=0,x=m.length;y<x;y++)if(v=m[y],v.update_attrs(w),!v.keep(w)){b=!0;break}b||(h.push(w),w[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new U(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new U(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,s,function(e){return r.view.get_base_color(e)}),S=null;if(t.fillStyle=this.config.get_value("block_color"),t.font=t.canvas.manager.default_font,t.textAlign="right",e.data){var T=$.draw(t,l.width,l.height,a,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-u}return o?void 0:new B(r,n,a,l,e.data,i,e.message,p,S,incomplete_features,s)}});var ee=function(e,t,i){Y.call(this,e,t,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};E(ee.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(e,t,i,n,a){if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,"Histogram",n,a);var s=this.view;return new this.painter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(e){return s.get_base_color(e)}).draw(t,t.canvas.width,t.canvas.height,a),new H(this,n,a,t.canvas,e.data)},get_canvas_height:function(e,t,i,n){if("bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==e.data.length&&(a=e.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),t).get_required_height(a)},predraw_init:function(){var e=[q.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||e.push(this.dataset.fetch()),e},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s=l.filter(t,function(e){return e instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===s.length&&this.config.get_value("show_labels")&&o&&o.length>1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(e("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var te=function(e,t,i){Z.call(this,e,t,i),this.painter=v.default.ReadPainter,this.update_icons()};E(te.prototype,z.prototype,Y.prototype,Z.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var ie={CompositeTrack:J,DrawableGroup:L,DiagonalHeatmapTrack:Q,FeatureTrack:Z,LineTrack:K,ReadTrack:te,VariantTrack:ee,VcfTrack:ee},ne=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new ie[n](t,i,e)};t.default={TracksterView:R,DrawableGroup:L,LineTrack:K,FeatureTrack:Z,DiagonalHeatmapTrack:Q,ReadTrack:te,VariantTrack:ee,CompositeTrack:J,object_from_template:ne}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(a),o=e.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(e){e.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var e=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),s.each(this.model.action_icons_def,function(t){e.add_action_icon(t.name,t.title,t.css_class,t.on_click_fn,t.prepend,t.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,t,i,a,s,o){var r=this;this.action_icons[e]=n("<a/>").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(function(){a(r.model)}).appendTo(this.icons_div),o&&this.action_icons[e].hide()},set_display_modes:function(e,t){if(e){this.model.display_modes=e,this.model.mode=t||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,s=i.display_modes.length;a<s;a++){var o=i.display_modes[a];n[o]=function(e){return function(){i.change_mode(e)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});t.default={TrackHeaderView:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e,t){this.slot=e,this.feature=t},r=function(e,t,i,n){this.slots={},this.start_end_dct={},this.w_scale=e,this.mode=t,this.include_label="Pack"===t,this.max_rows=i,this.measureText=n};s(r.prototype,{_get_draw_coords:function(e){var t=Math.floor(e[1]*this.w_scale),i=Math.ceil(e[2]*this.w_scale),n=e[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;t-a>=0?(t-=a,"left"):(i+=a,"right")}return[t,i]},_find_slot:function(e){for(var t=e[0],i=e[1],n=0;n<=this.max_rows;n++){var a=!1,s=this.start_end_dct[n];if(void 0!==s)for(var o=0,r=s.length;o<r;o++){var l=s[o];if(i>l[0]&&t<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(e){for(var t,i,n=this.start_end_dct,a=[],s=0,r=0,l=e.length;r<l;r++){t=e[r],i=t[0];var d=this.slots[i];if(d){if(t[1]<d.feature[1]||d.feature[2]<t[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(t),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}s=Math.max(s,this.slots[i].slot)}else a.push(r)}for(var r=0,l=a.length;r<l;r++){t=e[a[r]],i=t[0];var m=this._get_draw_coords(t),_=this._find_slot(m);_>=0&&(void 0===n[_]&&(n[_]=[]),n[_].push(m),this.slots[i]=new o(_,t),s=Math.max(s,_))}return s+1}}),t.default={FeatureSlotter:r}},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=function(e,t){var i=e[0],n=e[1],a=t[0],s=t[1];return i<a?n<=a?1001:n<=s?1003:1002:i>s?1006:n<=s?1005:1004},o=function(e,t){var i=s(e,t);return 1001!==i&&1006!==i},r=function(e,t,i,n,a,s){void 0===s&&(s=4);var o,r=n-t,l=a-i,d=Math.floor(Math.sqrt(r*r+l*l)/s),c=r/d,u=l/d;for(o=0;o<d;o++,t+=c,i+=u)o%2==0&&e.fillRect(t,i,s,1)},l=function(e,t,i,n){var a=t-n/2,s=t+n/2,o=i-Math.sqrt(3*n/2);e.beginPath(),e.moveTo(a,o),e.lineTo(s,o),e.lineTo(t,i),e.lineTo(a,o),e.strokeStyle=this.fillStyle,e.fill(),e.stroke(),e.closePath()},d=function(e){this.default_val=e||1};d.prototype.gen_val=function(e){return this.default_val};var c=function(e){this.incomplete_features=e.incomplete_features,this.feature_mapper=e.feature_mapper},u=function(e,t,i,n,s){this.data=e,this.view_start=t,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=s};u.prototype.default_prefs={},u.prototype.draw=function(e,t,i,n){},u.prototype.get_start_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,-.5)},u.prototype.get_end_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,.5)},u.prototype.get_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,0)},u.prototype._chrom_pos_to_draw_pos=function(e,t,i){return Math.floor(t*(Math.max(0,e-this.view_start)+i))};var h=function(e,t,i,n,a){u.call(this,e,t,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(e,t,i,n){var s=!1,o=this.prefs.min_value,r=this.prefs.max_value,l=r-o,d=i,c=this.view_start,u=this.mode,h=this.data;e.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(e.fillStyle="#aaa",e.fillRect(0,f,t,1)),e.beginPath();var p,m,_;_=h.length>1?a.map(h.slice(0,-1),function(e,t){return Math.ceil((h[t+1][0]-h[t][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,w=parseInt(v.slice(1),16),b=(16711680&w)>>16,y=(65280&w)>>8,x=255&w,k=!1,C=!1,$=0,S=h.length;$<S;$++)if(e.fillStyle=e.strokeStyle=v,k=C=!1,g=_[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(m=h[$][1])){if(m<o?(C=!0,m=o):m>r&&(k=!0,m=r),"Histogram"===u)m=Math.round(m/l*d),e.fillRect(p,f,g,-m);else if("Intensity"===u){var T=(m-o)/l,M=Math.round(b+(255-b)*(1-T)),E=Math.round(y+(255-y)*(1-T)),P=Math.round(x+(255-x)*(1-T));e.fillStyle="rgb("+M+","+E+","+P+")",e.fillRect(p,0,g,d)}else m=Math.round(d-(m-o)/l*d),s?e.lineTo(p,m):(s=!0,"Filled"===u?(e.moveTo(p,d),e.lineTo(p,m)):e.moveTo(p,m));if(e.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===u||"Intensity"===u?O=g:(p-=2,O=4),k&&e.fillRect(p,0,O,3),C&&e.fillRect(p,d-3,O,3)}e.fillStyle=v}else s&&"Filled"===u&&e.lineTo(p,d),s=!1;"Filled"===u?(s&&(e.lineTo(p,f),e.lineTo(0,f)),e.fill()):e.stroke(),e.restore()};var f=function(e){this.feature_positions={},this.slot_height=e,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(e,t,i,n){this.feature_positions[t]||(this.feature_positions[t]=[]),this.feature_positions[t].push({data:e,x_start:i,x_end:n})},f.prototype.get_feature_data=function(e,t){var i,n=Math.floor((t-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;e+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],e>=i.x_start&&e<=i.x_end)return i.data};var p=function(e,t,i,n,a,s,o){u.call(this,e,t,i,n,a),this.alpha_scaler=s||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(e,t){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=e*n),i+this.get_top_padding(t)},get_top_padding:function(e){return 0},draw:function(e,t,i,n,a){var s=this.data,o=this.view_start,r=this.view_end;e.save(),e.fillStyle=this.prefs.block_color,e.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,m=s.length;p<m;p++){var _=s[p],g=_[0],v=_[1],w=_[2],b=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==b)&&v<r&&w>o&&(l=this.draw_element(e,this.mode,_,b,o,r,n,d,t),u.map_feature_data(_,b,l[0],l[1]),(v<o||w>r)&&h.push(_))}return e.restore(),u.y_translation=this.get_top_padding(t),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(e,t,i,n,a,s,o,r,l){return[0,0]}});var m=function(e,t,i,n,a,s,o){p.call(this,e,t,i,n,a,s,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(m.prototype,p.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"no_detail"===e?3:"Squish"===e?5:10},draw_element:function(e,t,i,n,a,s,o,r,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),m=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),_=p,g=m,d=("Dense"===t?0:0+n)*r+this.get_top_padding(l),v=null,w=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(e.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===t&&(n=1),"no_detail"===t)e.fillStyle=b,e.fillRect(p,d+5,m-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),w=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var S,T;if("Squish"===t?(S=1,T=3,$=!1):(S=5,T=9),C){var M,E;"Squish"===t||"Dense"===t?(M=d+Math.floor(1.5)+1,E=1):f?(M=d,E=T):(M+=2.5,E=1),this.draw_background_connector&&("Squish"===t||"Dense"===t?e.fillStyle="#ccc":f?"+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand")):e.fillStyle="#ccc",e.fillRect(p,M,m-p,E));for(var P=0,O=C.length;P<O;P++){var A,D,I=C[P],z=Math.floor(Math.max(0,(I[0]-a-.5)*o)),j=Math.ceil(Math.min(l,Math.max((I[1]-a-.5)*o)));if(!(z>j)){if(e.fillStyle=b,e.fillRect(z,d+(T-S)/2+1,j-z,S),void 0!==v&&k>x&&!(z>w||j<v)){var L=Math.max(z,v),R=Math.min(j,w);e.fillRect(L,d+1,R-L,T),1===C.length&&"Pack"===t&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),L+14<R&&(L+=2,R-=2),e.fillRect(L,d+1,R-L,T))}this.draw_individual_connectors&&A&&this.draw_connector(e,A,D,z,j,d),A=z,D=j}}if("Pack"===t){e.globalAlpha=1,e.fillStyle="white";var N=this.height_scaler.gen_val(i),V=Math.ceil(T*N),G=Math.round((T-V)/2);1!==N&&(e.fillRect(p,M+1,m-p,G),e.fillRect(p,M+T-G+1,m-p,G))}}else e.fillStyle=b,e.fillRect(p,d+1,m-p,T),f&&$&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),e.fillRect(p,d+1,m-p,T));e.globalAlpha=1,h&&"Pack"===t&&c>a&&(e.fillStyle=y,0===a&&p-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,m+2,d+8,this.max_label_length),g+=e.measureText(h).width+2):(e.textAlign="right",e.fillText(h,p-2,d+8,this.max_label_length),_-=e.measureText(h).width+2))}return e.globalAlpha=1,[_,g]}});var _=function(e,t,i,n,a,s,o,r,l){p.call(this,e,t,i,n,a,s,o),this.ref_seq=r?r.data:null,this.base_color_fn=l};a.extend(_.prototype,p.prototype,{get_row_height:function(){var e,t=this.mode;return"Dense"===t?e=10:"Squish"===t?e=5:(e=10,this.prefs.show_insertions&&(e*=2)),e},_parse_cigar:function(e){var t="MIDNSHP=X",i=[[0,0]],n=i[0],s=0,o=a.map(e.match(/[0-9]+[MIDNSHP=X]/g),function(e){var a=parseInt(e.slice(0,-1),10),o=e.slice(-1);return"N"===o?0!==n[1]&&(n=[s+a,s+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,s+=a),[t.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(e,t,i,n,a,r,d,c,u,h){var f=function(e){return Math.floor(Math.max(0,(e-a-.5)*i))};e.textAlign="center";var p,m,_=[a,r],g=0,v=0,w=Math.round(i/2),b=e.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===t,C=k?9:3,$=n+1,S=new x(e,C,i,t),T=[],M=[],E=this._parse_cigar(c);c=E.cigar,T=E.blocks;for(var P=0;P<T.length;P++){var O=T[P];o([d+O[0],d+O[1]],_)&&(p=f(d+O[0]),m=f(d+O[1]),p===m&&(m+=1),e.fillStyle=y,e.fillRect(p,$,m-p,C))}for(var A=0,D=c.length;A<D;A++){var I=c[A],z="MIDNSHP=X"[I[0]],j=I[1],L=d+g;if(p=f(L),m=f(L+j),o([L,L+j],_))switch(p===m&&(m+=1),z){case"H":case"S":case"P":break;case"M":g+=j;break;case"=":case"X":var R="";"X"===z?R=h.slice(v,v+j):this.ref_seq&&(R=this.ref_seq.slice(Math.max(0,L-a),Math.min(L-a+j,r-a)));for(var N=Math.max(L,a),V=0;V<R.length;V++)if(R&&!this.prefs.show_differences||"X"===z){var G=Math.floor(Math.max(0,(N+V-a)*i));e.fillStyle=this.base_color_fn(R[V]),k&&i>b?e.fillText(R[V],G,n+9):i>.05&&e.fillRect(G-w,$,Math.max(1,Math.round(i)),C)}"X"===z&&(v+=j),g+=j;break;case"N":e.fillStyle="#ccc",e.fillRect(p,$+(C-1)/2,m-p,1),g+=j;break;case"D":S.draw_deletion(p,$,j),g+=j;break;case"I":var U=p-w;if(o([L,L+j],_)){var H=h.slice(v,v+j);if(this.prefs.show_insertions){var F=p-(m-p)/2;if(("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b){switch(e.fillStyle="yellow",e.fillRect(F-w,n-9,m-p,9),M[M.length]={type:"triangle",data:[U,n+4,5]},e.fillStyle="#ccc",s([L,L+j],_)){case 1003:H=H.slice(a-L);break;case 1004:H=H.slice(0,L-r);break;case 1005:break;case 1002:H=H.slice(a-L,L-r)}for(var V=0,B=H.length;V<B;V++){var G=Math.floor(Math.max(0,(L+V-a)*i));e.fillText(H[V],G-(m-p)/2,n)}}else e.fillStyle="yellow",e.fillRect(F,n+("Dense"!==this.mode?2:5),m-p,"Dense"!==t?3:9)}else("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b&&M.push({type:"text",data:[H.length,U,n+9]})}v+=j}else g=function(e,t,i){return-1!=="M=NXD".indexOf(t)&&(e+=i),e}(g,z,j),v=function(e,t,i){return-1!=="IX".indexOf(t)&&(e+=i),e}(v,z,j)}e.fillStyle="yellow";for(var q,Y,W,P=0;P<M.length;P++)q=M[P],Y=q.type,W=q.data,"text"===Y?(e.save(),e.font="bold "+e.font,e.fillText(W[0],W[1],W[2]),e.restore()):"triangle"===Y&&l(e,W[0],W[1],W[2])},draw_element:function(e,t,i,n,a,s,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),m=("Dense"===t?0:0+n)*l,_="Pack"===t?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=s&&i[4][2]?this.draw_read(e,t,o,m,a,s,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=s&&i[5][2]?this.draw_read(e,t,o,m,a,s,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),w=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&w>v){e.fillStyle="#ccc";var b=m+1+(_-1)/2;r(e,v,b,w,b)}}else this.draw_read(e,t,o,m,a,s,c,i[4],i[5],i[6]);return"Pack"===t&&c>=a&&"."!==h&&(e.fillStyle=this.prefs.label_color,0===a&&f-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,p+2,m+9,this.max_label_length)):(e.textAlign="right",e.fillText(h,f-2,m+9,this.max_label_length))),[0,0]}});var g=function(e,t,i,n,a,s,o){m.call(this,e,t,i,n,a,s,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,m.prototype,{calculate_longest_feature_length:function(){for(var e=0,t=0,i=this.data.length;t<i;t++){var n=this.data[t],a=n[1],s=n[2];e=Math.max(e,s-a)}return e},get_top_padding:function(e){var t=this.view_end-this.view_start,i=e/t;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(e,t,i,n,a,s){var o=(i+n)/2,r=n-o;Math.PI;r>0&&(e.beginPath(),e.arc(o,s,n-o,Math.PI,0),e.stroke())}});var v=function(e,t){Array.isArray(e)?this.rgb=e:6==e.length?this.rgb=e.match(/.{2}/g).map(function(e){return parseInt(e,16)}):7==e.length?this.rgb=e.substring(1,7).match(/.{2}/g).map(function(e){return parseInt(e,16)}):this.rgb=e.split("").map(function(e){return parseInt(e+e,16)}),this.alpha="number"==typeof t?t:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(e){return Math.round(e)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},toHSL:function(){var e,t,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,s=this.alpha,o=Math.max(i,n,a),r=Math.min(i,n,a),l=(o+r)/2,d=o-r;if(o===r)e=t=0;else{switch(t=l>.5?d/(2-o-r):d/(o+r),o){case i:e=(n-a)/d+(n<a?6:0);break;case n:e=(a-i)/d+2;break;case a:e=(i-n)/d+4}e/=6}return{h:360*e,s:t,l:l,a:s}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},mix:function(e,t){var i=this,n=t,a=2*n-1,s=i.toHSL().a-e.toHSL().a,o=((a*s==-1?a:(a+s)/(1+a*s))+1)/2,r=1-o,l=[i.rgb[0]*o+e.rgb[0]*r,i.rgb[1]*o+e.rgb[1]*r,i.rgb[2]*o+e.rgb[2]*r],d=i.alpha*n+e.alpha*(1-n);return new v(l,d)}};var w=function(e,t,i,n){this.start_color=new v(e),this.end_color=new v(t),this.start_value=i,this.end_value=n,this.value_range=n-i};w.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e=(e-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-e).toCSS()};var b=function(e,t,i,n,a){this.positive_ramp=new w(t,i,0,a),this.negative_ramp=new 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g=0,v=f.length;g<v;g++)a=f[g],s=_(a[1]),o=_(a[2]),r=_(a[4]),l=_(a[5]),d=a[6],e.fillStyle=m.map_value(d),e.fillRect(s,r,o-s,l-r);e.restore()};var x=function(e,t,i,n){this.ctx=e,this.row_height=t,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=e.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(e,t,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;t+=.5*(this.row_height-n),this.ctx.fillRect(e,t,i*this.px_per_base,n)}});var k=function(e,t,i,n,a,s){u.call(this,e,t,i,n,a),this.base_color_fn=s,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"Squish"===e?5:10},get_required_height:function(e){var t=this.prefs.summary_height;return e>1&&this.prefs.show_sample_data&&(t+=this.divider_height+e*this.get_row_height()),t},draw:function(e,t,i,n){e.save();var s,o,r,l,d,c,u,h,f,p,m,_=function(e,t){var i=e.length,n=t.length,a=0,s=1,o=null;return"-"===t?(o="deletion",s=e.length):0===e.indexOf(t)&&i>n?(o="deletion",s=i-n,a=n):0===t.indexOf(e)&&i<n&&(o="insertion",s=n-i,a=n),null!==o?{type:o,start:a,len:s}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,w="Squish"===this.mode?5:10,b=n<.1?w:"Squish"===this.mode?3:9,y=!0,k=new x(e,w,n,this.mode);1===v&&(w=b=n<e.canvas.manager.char_width_px?this.prefs.summary_height:w,k.row_height=w,y=!1),this.prefs.show_sample_data&&y&&(e.fillStyle="#F3F3F3",e.globalAlpha=1,e.fillRect(0,this.prefs.summary_height-this.divider_height,t,this.divider_height)),e.textAlign="center";for(var C=0;C<this.data.length;C++)if(s=this.data[C],o=s[1],r=s[3],l=[s[4].split(",")],d=s[7].split(","),c=s.slice(8),l=a.map(a.flatten(l),function(e){var t={type:"snp",value:e,start:0},i=_(r,e);return a.extend(t,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(e.fillStyle="#999999",e.globalAlpha=1,m=0;m<l.length;m++)for(h=this.get_start_draw_pos(o+l[m].start,n),e.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,m=0;m<l.length;m++){e.fillStyle="deletion"===l[m].type?"black":this.base_color_fn(l[m].value);var $=c/d.length,S=Math.ceil(this.prefs.summary_height*$);e.fillRect(h,f-S,g,S),f-=S}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,m=0;m<d.length;m++,f+=w)if(p=d[m]?d[m].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],e.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],e.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;e.fillStyle=this.base_color_fn(T),k.draw_details?e.fillText(T,this.get_draw_pos(o,n),f+w):e.fillRect(h,f+1,g,b)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}e.restore()}}),t.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:m,ReadPainter:_,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e){this.manager=null,this.name=e.name,this.index=e.index,this.tool_id=e.tool_id,this.tool_exp_name=e.tool_exp_name};s(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var r=function(t,i,n){return e("<a/>").attr("href","javascript:void(0);").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(t){o.call(this,t),this.low="low"in t?t.low:-Number.MAX_VALUE,this.high="high"in t?t.high:Number.MAX_VALUE,this.min="min"in t?t.min:Number.MAX_VALUE,this.max="max"in t?t.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=e("<div/>").addClass("filter-row slider-row");var n=e("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(e("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),e("<span/>").text(this.low+"-"+this.high)),s=e("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=e("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=e("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(e,t){i.slide(e,t)},change:function(e,t){i.control_element.slider("option","slide").call(i.control_element,e,t)}}),i.slider=i.control_element,i.slider_label=a,function(t,i,n){t.click(function(){var t=i.text(),a=parseFloat(n.slider("option","max")),s=a<=1?4:a<=1e6?a.toString().length:6,o=!1,r=e(this).parents(".slider-row");r.addClass("input"),n.slider("option","values")&&(s=2*s+1,o=!0),i.text(""),e("<input type='text'/>").attr("size",s).attr("maxlength",s).attr("value",t).appendTo(i).focus().select().click(function(e){e.stopPropagation()}).blur(function(){e(this).remove(),i.text(t),r.removeClass("input")}).keyup(function(t){if(27===t.keyCode)e(this).trigger("blur");else if(13===t.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),s=function(e){return isNaN(e)||e>a||e<i},l=e(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],s(l[0])||s(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this)}else if(l=parseFloat(l),s(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this);n.slider(o?"values":"value",l),r.removeClass("input")}})})}(s,a,i.control_element);var d=e("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=r("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=r("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),e("<div style='clear: both;'/>").appendTo(i.parent_div)};s(l.prototype,{to_dict:function(){var e=o.prototype.to_dict.call(this);return s(e,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(e,t){return t-e<=2?.01:1},slide:function(e,t){var i=t.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(e){return e.length>this.index},_keep_val:function(e){return isNaN(e)||e>=this.low&&e<=this.high},keep:function(e){if(!this.applies_to(e))return!0;var t=e[this.index];if(t instanceof Array){for(var i=!0,n=0;n<t.length;n++)if(!this._keep_val(t[n])){i=!1;break}return i}return this._keep_val(e[this.index])},update_attrs:function(e){var t=!1;if(!this.applies_to(e))return t;var i=e[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),t=!0),a>this.max&&(this.max=Math.ceil(a),t=!0)}return t},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var e=this.slider.slider("option","min"),t=this.slider.slider("option","max");(this.min<e||this.max>t)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(t,i){if(this.track=t,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=e("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).bind("keydown",function(e){e.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),s=("height_filter"in i?i.height_filter:null),o=i.filters,r=0;r<o.length;r++)"number"===o[r].type?(n=new l(o[r]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===s&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=e("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;e("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};s(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var e,t={},i=[],n=0;n<this.filters.length;n++)e=this.filters[n],i.push(e.to_dict());return t.filters=i,t.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,t.height_filter=this.height_filter?this.height_filter.name:null,t.visible=this.parent_div.is(":visible"),t},copy:function(e){for(var t=new d(e),i=0;i<this.filters.length;i++)t.add_filter(this.filters[i].copy());return t},add_filter:function(e){e.manager=this,this.parent_div.append(e.parent_div),this.filters.push(e)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var e=0;e<this.filters.length;e++){this.filters[e].update_ui_elt()}},clear_filters:function(){for(var e=0;e<this.filters.length;e++){var t=this.filters[e];t.slider.slider("option","values",[t.min,t.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var t,i,n=(function(e,t,i){return t in e||(e[t]=i),e[t]}),a={},s=0;s<this.filters.length;s++)t=this.filters[s],t.tool_id&&(t.min!==t.low&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" >= "+t.low),t.max!==t.high&&(i=n(a,t.tool_id,[]),i[i.length]=t.tool_exp_name+" <= "+t.high));var o=[];for(var r in a)o[o.length]=[r,a[r]];!function t(i,n){var a=n[0],s=a[0],o=a[1],r="("+o.join(") and (")+")",l={cond:r,input:i,target_dataset_id:i,tool_id:s};n=n.slice(1),e.getJSON(run_tool_url,l,function(e){e.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+s,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):t(e.dataset_id,n)})}(this.track.dataset_id,o)}}),t.default={FiltersManager:d,NumberFilter:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(13),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=i(152),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=a.default.GenomeDataManager.extend({load_data:function(t,i,n,a){var s=e.Deferred();this.set_data(t,s);var r=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new e.Deferred;return e.when(o.makeBwg(r)).then(function(i,n){e.when(i.readWigData(t.get("chrom"),t.get("start"),t.get("end"))).then(function(e){var i=[],n={max:Number.MIN_VALUE};e.forEach(function(e){n.max!==e.min-1&&(i.push([n.max+1,0]),i.push([e.min-2,0])),i.push([e.min-1,e.score]),i.push([e.max,e.score]),n=e});var a={data:i,region:t,dataset_type:"bigwig"};l.set_data(t,a),s.resolve(a)})}),s}});t.default={BBIDataManager:r}}).call(t,i(0))},function(e,t,i){(function(n){var a,s;a=[i(153),i(154),i(155)],void 0!==(s=function(e,t){"use strict";function i(){}function a(e){e&&(this.id=e)}function s(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function o(e,t,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:e,timeout:5e3,beforeSend:function(e){e.setRequestHeader("Range","bytes="+t+"-"+(t+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function r(e,t){return e[t]+e[t+1]*y+e[t+2]*x+e[t+3]*k+e[t+4]*C}function l(){}function d(e,t,i,n){this.bwg=e,this.cirTreeOffset=t,this.cirTreeLength=i,this.isSummary=n}function c(e){var t=n.Deferred(),i=new l;return i.url=e,n.when(o(i.url,0,512)).then(function(e){if(!e)return t.resolve(null,"Couldn't fetch file");var a=e,s=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=s[0]+y*s[1]+x*s[2]+k*s[3];if(d==g)i.type="bigwig";else{if(d!=w)return d==v||d==b?t.resolve(null,"Currently don't support big-endian BBI files"):t.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=r(s,8),i.unzoomedDataOffset=r(s,16),i.unzoomedIndexOffset=r(s,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=r(s,36),i.totalSummaryOffset=r(s,44),i.uncompressBufSize=l[13],i.extHeaderOffset=r(s,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=r(s,24*c+72),f=r(s,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(e){return i.schema=e,t.resolve(i)})})}),t}function u(e,t,i,n,a){this.bbi=e,this.type=t,this.fieldCount=i,this.offset=n,this.field=a}var h=e.Range,f=e.union,p=e.intersection,m=t.inflateBuffer,_=t.arrayCopy,g=2291137574,v=654086024,w=2273964779,b=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var e=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var t=this.unzoomedDataOffset;return t=t+4-(t-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,t-this.chromTreeOffset)).then(function(t){var i=new Uint8Array(t),n=new Int16Array(t),a=new Int32Array(t),s=(a[0],a[1],a[2]),o=(a[3],r(i,16),function(t){var a=i[t],l=n[t/2+1];t+=4;for(var d=0;d<l;++d)if(0===a){t+=s;var c=r(i,t);t+=8,c-=e.chromTreeOffset,o(c)}else{for(var u="",h=0;h<s;++h){var f=i[t++];0!==f&&(u+=String.fromCharCode(f))}var p=i[t+3]<<24|i[t+2]<<16|i[t+1]<<8|i[t+0];i[t+7],i[t+6],i[t+5],i[t+4],t+=8,e.chromsToIDs[u]=p,0===u.indexOf("chr")&&(e.chromsToIDs[u.substr(3)]=p),e.idsToChroms[p]=u,e.maxID=Math.max(e.maxID,p)}});o(32)})},d.prototype.readWigData=function(e,t,i){var n=this.bwg.chromsToIDs[e];return void 0===n?[]:this.readWigDataById(n,t,i)},d.prototype.readWigDataById=function(e,t,i){var a=this,s=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var r=new Int32Array(a.cirHeader);a.cirBlockSize=r[1],n.when(a.readWigDataById(e,t,i)).then(function(e){s.resolve(e)})}),s;var l=[],d=0,c=(Date.now(),function(n,a,s,o){return(e<0||n==e)&&a<=i&&s>=t}),u=function(e,t){if(a.bwg.instrument&&console.log("level="+t+"; offset="+e+"; time="+(0|Date.now())),d+=e.length,1==e.length&&e[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return m(a.cachedCirRoot,0,t),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}));for(var i,o=4+32*a.cirBlockSize,r=0;r<e.length;++r){var u=new h(e[r],e[r]+o);i=i?f(i,u):u}for(var _=i.ranges(),g=0;g<_.length;++g){var v=_[g];p(e,v,t)}},p=function(e,t,i,r){t.max(),t.min();n.when(o(a.bwg.url,t.min(),t.max()-t.min())).then(function(o){for(var r=0;r<e.length;++r)t.contains(e[r])&&(m(o,e[r]-t.min(),i),e[r]-a.cirTreeOffset==48&&e[r]-t.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}))})},m=function(n,a,s){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16),y=r(o,a+24);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&l.push({offset:b,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&x.push(b),a+=24}x.length>0&&u(x,s+1)}};return u([a.cirTreeOffset+48],1),s},d.prototype.fetchFeatures=function(e,t){var a=this,s=n.Deferred();if(t.sort(function(e,t){return(0|e.offset)-(0|t.offset)}),0===t.length)return[];var r=[],l=function(e,t,n,s){s||(s={});var o=new i;o._chromId=e,o.segment=a.bwg.idsToChroms[e],o.min=t,o.max=n,o.type=a.bwg.type;for(var l in s)o[l]=s[l];r.push(o)},d=function(){if(0===t.length){Date.now();return s.resolve(r)}var i=t[0];if(i.data)a.parseFeatures(i.data,l,e),t.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<t.length&&t[h].offset==c+u;)u+=t[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(e){for(var i=0,n=0;i<u;){var s,o=t[n];if(a.bwg.uncompressBufSize>0)s=m(e,i+2,o.size-2);else{var r=new Uint8Array(o.size);_(new Uint8Array(e,i,o.size),0,r,0,o.size),s=r.buffer}o.data=s,i+=o.size,++n}d()})}};return d(),s},d.prototype.parseFeatures=function(e,t,i){var s=new Uint8Array(e);if(this.isSummary)for(var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),d=e.byteLength/32,c=0;c<d;++c){var u=r[8*c],m=r[8*c+1],_=r[8*c+2],g=r[8*c+3],v=(l[8*c+4],l[8*c+5]),w=l[8*c+6];l[8*c+7];if(i(u,m+1,_)){var b={type:"bigwig",score:w/g,maxScore:v};"bigbed"==this.bwg.type&&(b.type="density"),t(u,m+1,_,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(e),r=new Int32Array(e),l=new Float32Array(e),u=r[0],y=r[1],x=(r[2],r[3]),k=r[4],C=s[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var S=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&t(u,T,M,{score:S})}else if(2==C)for(var c=0;c<d;++c){var m=r[2*c+6]+1,_=m+k-1,S=l[2*c+7];i(u,m,_)&&t(u,m,_,{score:S})}else if(1==C)for(var c=0;c<d;++c){var m=r[3*c+6]+1,_=r[3*c+7],S=l[3*c+8];m>_&&(m=_),i(u,m,_)&&t(u,m,_,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var E=0,P=this.bwg.definedFieldCount,O=this.bwg.schema;E<s.length;){var u=s[E+3]<<24|s[E+2]<<16|s[E+1]<<8|s[E+0],m=s[E+7]<<24|s[E+6]<<16|s[E+5]<<8|s[E+4],_=s[E+11]<<24|s[E+10]<<16|s[E+9]<<8|s[E+8];E+=12;for(var A="";;){var D=s[E++];if(0==D)break;A+=String.fromCharCode(D)}var I,z={};if(I=A.length>0?A.split("\t"):[],I.length>0&&P>3&&(z.label=I[0]),I.length>1&&P>4){var S=parseInt(I[1]);isNaN(S)||(z.score=S)}if(I.length>2&&P>5&&(z.orientation=I[2]),I.length>5&&P>8){var j=I[5];$.test(j)&&(z.itemRgb="rgb("+j+")")}if(I.length>P-3&&O)for(var L=P-3;L<I.length;++L)z[O.fields[L+3].name]=I[L];if(i(u,m+1,_,I))if(P<12)t(u,m+1,_,z);else{var R=0|I[3],N=0|I[4],V=0|I[6],G=I[7].split(","),U=I[8].split(",");if(z.exonFrames){var H=z.exonFrames.split(",");z.exonFrames=void 0}z.type="transcript";var F=new a;for(var B in z)F[B]=z[B];if(F.id=I[0],F.segment=this.bwg.idsToChroms[u],F.min=m+1,F.max=_,F.notes=[],z.groups=[F],I.length>9){var q=z.geneName||I[9],Y=q;I.length>10&&(Y=I[10]),z.geneName2&&(Y=z.geneName2);var W=n.extend({},F);W.id=q,W.label=Y,W.type="gene",z.groups.push(W)}for(var J=[],X=0;X<V;++X){var K=(0|U[X])+m,Q=K+(0|G[X]),Z=new h(K,Q);J.push(Z)}for(var ee=f(J),te=ee.ranges(),ie=0;ie<te.length;++ie){var ne=te[ie];t(u,ne.min()+1,ne.max(),z)}if(N>R){var ae="+"==z.orientation?new h(R,N+3):new h(R-3,N),se=p(ee,ae);if(se){z.type="translation";for(var oe=se.ranges(),re=0,le=0;oe[0].min()>te[le].max();)le++;for(var ie=0;ie<oe.length;++ie){var de=ie;"-"==z.orientation&&(de=oe.length-ie-1);var ne=oe[de];if(z.readframe=re,H){var ce=parseInt(H[de+le]);"number"==typeof ce&&ce>=0&&ce<=2&&(z.readframe=ce,z.readframeExplicit=!0)}var ue=ne.max()-ne.min();re=(re+ue)%3,t(u,ne.min()+1,ne.max(),z)}}}}}}},d.prototype.getFirstAdjacent=function(e,t,i,n){var a=this.bwg.chromsToIDs[e];if(void 0===a)return n([]);this.getFirstAdjacentById(a,t,i,n)},d.prototype.getFirstAdjacentById=function(e,t,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(e,t,i,n)});var s=null,o=-1,l=-1,d=0,c=(Date.now(),function(e,t){d+=e.length;for(var i,n=4+32*a.cirBlockSize,s=0;s<e.length;++s){var o=new h(e[s],e[s]+n);i=i?f(i,o):o}for(var r=i.ranges(),l=0;l<r.length;++l){var c=r[l];u(e,c,t)}}),u=function(o,r,l,c){r.max(),r.min();a.bwg.data.slice(r.min(),r.max()-r.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(r.contains(o[u])&&(p(c,o[u]-r.min(),l),0==--d)){if(!s)return i>0&&(0!=e||t>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(e!=a.bwg.maxID||t<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,s,o){return i<0&&(n<e||s<t)||i>0&&(n>e||a>t)},[s],function(e){for(var t=null,a=-1,s=-1,o=0;o<e.length;++o){var r=e[o],l=r._chromId,d=r.min,c=r.max;(null==t||i<0&&(l>a||c>s)||i>0&&(l<a||d<s))&&(t=r,s=i<0?c:d,a=l)}return n(null!=t?[t]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),m=h[d],_=f[d/2+1];if(d+=4,0!=m)for(var g=0;g<_;++g){var v=d/4,w=p[v],b=p[v+1],y=p[v+2],x=p[v+3],k=r(h,d+16),C=r(h,d+24);(i<0&&(w<e||w==e&&b<=t)||i>0&&(y>e||y==e&&x>=t))&&(/_random/.exec(a.bwg.idsToChroms[w])||(null==s||i<0&&(y>o||y==o&&x>l)||i>0&&(w<o||w==o&&b<l))&&(s={offset:k,size:C},l=i<0?x:b,o=i<0?y:w)),d+=32}else{for(var $=-1,S=-1,g=0;g<_;++g){var v=d/4,w=p[v],b=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(w<e||w==e&&b<=t)&&y>=e||i>0&&(y>e||y==e&&x>=t)&&w<=e)&&($<0||x>S)&&($=k,S=i<0?x:b,i<0?y:w),d+=24}$>=0&&c([$],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(e,t,i){var n,a=i-t;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var s=0;s<this.zoomLevels.length;s++)if(a/this.zoomLevels[s].reduction<25e3){n=this.getZoomedView(s);break}return n.readWigData(e,t,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var e=4e3;this.zoomLevels[0]&&(e=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,e,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(e){var t=this.zoomLevels[e];return t.view||(t.view=new d(this,t.indexOffset,4e3,!0)),t.view},l.prototype._tsFetch=function(e,t,i,n,a){var s=this;if(!(e>=this.zoomLevels.length-1)){var o;return o=e<0?this.getUnzoomedView():this.getZoomedView(e),o.readWigDataById(t,i,n,a)}if(this.topLevelReductionCache){for(var r=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==t&&r.push(l[d]);return a(r)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return s.topLevelReductionCache=o,s._tsFetch(e,t,i,n,a)})},l.prototype.thresholdSearch=function(e,t,i,n,a){function s(){if(0==l.length)return a(null);l.sort(function(e,t){var n=e.zoom-t.zoom;return 0!=n?n:(n=e.chrOrd-t.chrOrd,0!=n?n:e.min-t.min*i)});var e=l.splice(0,1)[0];o._tsFetch(e.zoom,e.chr,e.min,e.max,function(o){var r=i>0?0:3e8;e.fromRef&&(r=t);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(e.zoom<0){if(u.min>r)return a(u)}else u.max>r&&l.push({chr:e.chr,chrOrd:e.chrOrd,zoom:e.zoom-2,min:u.min,max:u.max,fromRef:e.fromRef})}else if(c>n)if(e.zoom<0){if(u.max<r)return a(u)}else u.min<r&&l.push({chr:e.chr,chrOrd:e.chrOrd,zoom:e.zoom-2,min:u.min,max:u.max,fromRef:e.fromRef})}s()})}i=i<0?-1:1;for(var o=this,r=this.chromsToIDs[e],l=[{chrOrd:0,chr:r,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(r+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}s()},l.prototype.getAutoSQL=function(e){if(!this.asOffset)return e(null);n.when(o(this.url,this.asOffset,2048)).then(function(t){for(var i=new Uint8Array(t),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var s=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,r=s.exec(n);if(r){var l={declType:r[1],name:r[2],comment:r[4],fields:[]};n=n.substring(r[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return e(l)}})},l.prototype.getExtraIndices=function(e){var t=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return e(null);this.data.slice(this.extHeaderOffset,64).fetch(function(i){if(!i)return e(null,"Couldn't fetch extension header");var n=new Uint8Array(i),a=new Int16Array(i),s=(new Int32Array(i),a[0],a[1]),o=r(n,4);if(0==s)return e(null);t.data.slice(o,20*s).fetch(function(i){if(!i)return e(null,"Couldn't fetch index info");for(var n=new Uint8Array(i),a=new Int16Array(i),o=(new Int32Array(i),[]),l=0;l<s;++l){var d=a[10*l],c=a[10*l+1],h=r(n,20*l+4),f=a[10*l+8],p=new u(t,d,c,h,f);o.push(p)}e(o)})})},u.prototype.lookup=function(e,t){var i=this;this.bbi.data.slice(this.offset,32).fetch(function(n){function a(n){i.bbi.data.slice(n,4+d*(c+u)).fetch(function(n){var o=new Uint8Array(n),l=new Uint16Array(n),d=(new Uint32Array(n),o[0]),h=l[1],f=4;if(0!=d){for(var p=0;p<h;++p){for(var m="",_=0;_<c;++_){var g=o[f++];0!=g&&(m+=String.fromCharCode(g))}if(m==e){var v=r(o,f),w=s(o,f+8);return i.bbi.getUnzoomedView().fetchFeatures(function(t,n,a,s){if(s&&s.length>i.field-3)return s[i.field-3]==e},[{offset:v,size:w}],t)}f+=u}return t([])}for(var b=null,p=0;p<h;++p){for(var m="",_=0;_<c;++_){var g=o[f++];0!=g&&(m+=String.fromCharCode(g))}var y=r(o,f);if(f+=8,e.localeCompare(m)<0&&b)return void a(b);b=y}a(b)})}var o=new Uint8Array(n),l=(new Int16Array(n),new Int32Array(n)),d=(l[0],l[1]),c=l[2],u=l[3];r(o,16);a(i.offset+32)})},{makeBwg:c}}.apply(t,a))&&(e.exports=s)}).call(t,i(0))},function(e,t,i){var n,a;n=[],void 0!==(a=function(){"use strict";function e(e,t){if("number"!=typeof e||"number"!=typeof t)throw"Bad range "+e+","+t;this._min=e,this._max=t}function t(e){var t=e.sort(o),i=[],n=t.shift();t.forEach(function(e){e._min<=n._max?e._max>n._max&&(n._max=e._max):(i.push(n),n=e)}),i.push(n),this._ranges=i}function i(e,i){return e instanceof t||(e instanceof Array||(e=[e]),e=new t(e)),i&&e.insertRange(i),e}function n(i,n){for(var a=i.ranges(),s=n.ranges(),o=a.length,r=s.length,l=0,d=0,c=[];l<o&&d<r;){var i=a[l],n=s[d],u=Math.max(i.min(),n.min()),h=Math.min(i.max(),n.max());h>=u&&c.push(new e(u,h)),i.max()>n.max()?++d:++l}return 0==c.length?null:1==c.length?c[0]:new t(c)}function a(e){for(var t=0,i=e.ranges(),n=0;n<i.length;++n){var a=i[n];t+=a.max()-a.min()+1}return t}function s(e,t){return e.min()<t.min()?-1:e.min()>t.min()?1:e.max()<t.max()?-1:t.max()>e.max()?1:0}function o(e,t){return e._min<t._min?-1:e._min>t._min?1:e._max<t._max?-1:t._max>e._max?1:0}return e.prototype.min=function(){return this._min},e.prototype.max=function(){return this._max},e.prototype.contains=function(e){return e>=this._min&&e<=this._max},e.prototype.isContiguous=function(){return!0},e.prototype.ranges=function(){return[this]},e.prototype._pushRanges=function(e){e.push(this)},e.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},t.prototype.min=function(){return this._ranges[0].min()},t.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},t.prototype.lower_bound=function(e){var t=this.ranges();if(e>this.max())return t.length;if(e<this.min())return 0;for(var i=0,n=t.length-1;i<=n;){var a=Math.floor((i+n)/2);if(e>t[a]._max)i=a+1;else{if(!(e<t[a]._min))return a;n=a-1}}return i},t.prototype.contains=function(e){var t=this.lower_bound(e);return!!(t<this._ranges.length&&this._ranges[t].contains(e))},t.prototype.insertRange=function(e){var t=this.lower_bound(e._min);if(t===this._ranges.length)return void this._ranges.push(e);var i=this.ranges();if(e._max<i[t]._min)return void this._ranges.splice(t,0,e);i[t]._min<e._min&&(e._min=i[t]._min);for(var n=t+1;n<i.length&&i[n]._min<=e._max;)n++;n--,i[n]._max>e._max&&(e._max=i[n]._max),this._ranges.splice(t,n-t+1,e)},t.prototype.isContiguous=function(){return this._ranges.length>1},t.prototype.ranges=function(){return this._ranges},t.prototype._pushRanges=function(e){for(var t=0;t<this._ranges.length;++t)e.push(this._ranges[t])},t.prototype.toString=function(){for(var e="",t=0;t<this._ranges.length;++t)t>0&&(e+=","),e+=this._ranges[t].toString();return e},{Range:e,union:i,intersection:n,coverage:a,rangeOver:s,_rangeOrder:o}}.apply(t,n))&&(e.exports=a)},function(e,t,i){var n,a;n=[],void 0!==(a=function(){function e(){}function t(){this.was=[0]}function i(e,t,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=t,this.mode=g,this.reset(e,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function s(e,t,i,n,a){return e[0]=v,t[0]=w,i[0]=b,n[0]=y,f}function o(e,t,i,n,a){if(0!=a){if(!e)throw"Undef src";if(!i)throw"Undef dest";0==t&&a==e.length?l(e,i,n):E?l(e.subarray(t,t+a),i,n):1==e.BYTES_PER_ELEMENT&&a>100?l(new 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e||(e=c),i&&(i=!1),this.istate=new t,this.istate.inflateInit(this,i?-e:e)},e.prototype.inflate=function(e){return null==this.istate?-2:this.istate.inflate(this,e)},e.prototype.inflateEnd=function(){if(null==this.istate)return-2;var e=istate.inflateEnd(this);return this.istate=null,e},e.prototype.inflateSync=function(){return istate.inflateSync(this)},e.prototype.inflateSetDictionary=function(e,t){return istate.inflateSetDictionary(this,e,t)},t.prototype.inflateReset=function(e){return null==e||null==e.istate?-2:(e.total_in=e.total_out=0,e.msg=null,e.istate.mode=0!=e.istate.nowrap?7:0,e.istate.blocks.reset(e,null),f)},t.prototype.inflateEnd=function(e){return null!=this.blocks&&this.blocks.free(e),this.blocks=null,f},t.prototype.inflateInit=function(e,t){return e.msg=null,this.blocks=null,nowrap=0,t<0&&(t=-t,nowrap=1),t<8||t>15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<<t),this.inflateReset(e),f)},t.prototype.inflate=function(e,t){var i,n;if(null==e||null==e.istate||null==e.next_in)return-2;for(t=4==t?m:f,i=m;;)switch(e.istate.mode){case 0:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,8!=(15&(e.istate.method=e.next_in[e.next_in_index++]))){e.istate.mode=13,e.msg="unknown compression method",e.istate.marker=5;break}if(8+(e.istate.method>>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<<e.istate.wbits&&(a=(1<<e.istate.wbits)-1,n=i-a),e.istate.blocks.set_dictionary(t,n,a),e.istate.mode=7,f)};var S=[0,0,255,255];t.prototype.inflateSync=function(e){var t,i,n,a,s;if(null==e||null==e.istate)return-2;if(13!=e.istate.mode&&(e.istate.mode=13,e.istate.marker=0),0==(t=e.avail_in))return m;for(i=e.next_in_index,n=e.istate.marker;0!=t&&n<4;)e.next_in[i]==S[n]?n++:n=0!=e.next_in[i]?0:4-n,i++,t--;return e.total_in+=i-e.next_in_index,e.next_in_index=i,e.avail_in=t,e.istate.marker=n,4!=n?-3:(a=e.total_in,s=e.total_out,this.inflateReset(e),e.total_in=a,e.total_out=s,e.istate.mode=7,f)},t.prototype.inflateSyncPoint=function(e){return null==e||null==e.istate||null==e.istate.blocks?-2:e.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(e,t){t&&(t[0]=this.check),6==this.mode&&this.codes.free(e),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(e.adler=this.check=e._adler.adler32(0,null,0,0))},i.prototype.proc=function(e,t){var i,n,a,r,l,d,c;for(r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),m=[],v=[];s(u,h,m,v,e),this.codes.init(u[0],h[0],m[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(t=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var w=0;w<i;w++)this.blens[w]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,b,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&_[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&_[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(w=18==y?7:y-14,b=18==y?11:3;a<i+w;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(n>>>=i,a-=i,b+=n&_[w],n>>>=w,a-=w,w=this.index,i=this.table,w+b>258+(31&i)+(i>>5&31)||16==y&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);y=16==y?this.blens[w-1]:0;do{this.blens[w++]=y}while(0!=--b);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),m=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,m,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,m[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);mode=12;case 8:return t=p,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);case 9:return t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);default:return t=-2,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}},i.prototype.free=function(e){this.reset(e,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(e,t,i){o(e,t,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(e,t){var i,n,a;return n=e.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.len+=c&_[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.dist+=c&_[n],c>>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);e.window[r++]=e.window[d++],l--,d==e.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,e.window[r++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,e.read!=e.write)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);this.mode=8;case 8:return i=p,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 9:return i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);default:return i=-2,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i)}},n.prototype.free=function(e){},n.prototype.inflate_fast=function(e,t,i,n,a,s,r,l){var d,c,u,h,m,g,v,w,b,y,x,k,C,$,S,T;v=l.next_in_index,w=l.avail_in,m=r.bitb,g=r.bitk,b=r.write,y=b<r.read?r.read-b-1:r.end-b,x=_[e],k=_[t];do{for(;g<20;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if(d=m&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(m&_[h]),m>>=h,g-=h;g<15;)w--,m|=(255&l.next_in[v++])<<g,g+=8;for(d=m&k,c=a,u=s,T=3*(u+d),h=c[T];;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if($=c[T+2]+(m&_[h]),m>>=h,g-=h,y-=C,b>=$)S=b-$,r.window[b++]=r.window[S++],r.window[b++]=r.window[S++],C-=2;else{S=b-$;do{S+=r.end}while(S<0);if(h=r.end-S,C>h){if(C-=h,b-S>0&&h>b-S)do{r.window[b++]=r.window[S++]}while(0!=--h);else o(r.window,S,r.window,b,h),b+=h,S+=h,h=0;S=0}}do{r.window[b++]=r.window[S++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3;d+=c[T+2],d+=m&_[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3);if(d+=c[T+2],d+=m&_[h],T=3*(u+d),0==(h=c[T])){m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--;break}}else m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--}while(y>=258&&w>=10);return C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,f},a.prototype.huft_build=function(e,t,i,n,a,s,r,l,d,c,h){var p,_,g,v,w,b,y,x,k,C,$,S,T,M,E;C=0,w=i;do{this.c[e[t+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return r[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(y=b,x<b&&(x=b),w=15;0!=w&&0==this.c[w];w--);for(g=w,x>w&&(x=w),l[0]=x,M=1<<b;b<w;b++,M<<=1)if((M-=this.c[b])<0)return-3;if((M-=this.c[w])<0)return-3;for(this.c[w]+=M,this.x[1]=b=0,C=1,T=2;0!=--w;)this.x[T]=b+=this.c[C],T++,C++;w=0,C=0;do{0!=(b=e[t+C])&&(this.v[this.x[b]++]=w),C++}while(++w<i);for(i=this.x[g],this.x[0]=w=0,C=0,v=-1,S=-x,this.u[0]=0,$=0,E=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>S+x;){if(v++,S+=x,E=g-S,E=E>x?x:E,(_=1<<(b=y-S))>p+1&&(_-=p+1,T=y,b<E))for(;++b<E&&!((_<<=1)<=this.c[++T]);)_-=this.c[T];if(E=1<<b,this.hn[0]+E>u)return-3;this.u[v]=$=this.hn[0],this.hn[0]+=E,0!=v?(this.x[v]=w,this.r[0]=b,this.r[1]=x,b=w>>>S-x,this.r[2]=$-this.u[v-1]-b,o(this.r,0,d,3*(this.u[v-1]+b),3)):r[0]=$}for(this.r[1]=y-S,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=s[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),_=1<<y-S,b=w>>>S;b<E;b+=_)o(this.r,0,d,3*($+b),3);for(b=1<<y-1;0!=(w&b);b>>>=1)w^=b;for(w^=b,k=(1<<S)-1;(w&k)!=this.x[v];)v--,S-=x,k=(1<<S)-1}return 0!=M&&1!=g?m:f},a.prototype.inflate_trees_bits=function(e,t,i,n,a){var s;return this.initWorkArea(19),this.hn[0]=0,s=this.huft_build(e,0,19,19,null,null,i,t,n,this.hn,this.v),-3==s?a.msg="oversubscribed dynamic bit lengths tree":s!=m&&0!=t[0]||(a.msg="incomplete dynamic bit lengths tree",s=-3),s},a.prototype.inflate_trees_dynamic=function(e,t,i,n,a,s,o,r,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,e,257,x,k,s,n,r,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,e,t,0,C,$,o,a,r,this.hn,this.v),d!=f||0==a[0]&&e>257?(-3==d?l.msg="oversubscribed distance tree":d==m?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(e){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(e),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<e&&(this.v=new Int32Array(e));for(var t=0;t<e;t++)this.v[t]=0;for(var t=0;t<16;t++)this.c[t]=0;for(var t=0;t<3;t++)this.r[t]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),E="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(t,n))&&(e.exports=a)},function(e,t,i){(function(n){var a,s,o;!function(n,r){s=[i(0)],a=r,void 0!==(o="function"==typeof a?a.apply(t,s):a)&&(e.exports=o)}(0,function(e){var t=e.ajaxSettings;t.responseFields.native="responseNative",t.converters["* native"]=!0;var i={},a=0,s={0:200,1223:204},o={},r=n.ajaxSettings.xhr();window.ActiveXObject&&e(window).on("unload",function(){for(var e in o)o[e]()}),i.cors=!!r&&"withCredentials"in r,i.ajax=r=!!r,e.ajaxTransport("native",function(e){var t;if(i.cors||r&&!e.crossDomain)return{send:function(i,n){var r,l=e.xhr(),d=++a,c={};if(l.open(e.type,e.url,e.async,e.username,e.password),e.xhrFields)for(r in 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t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=(a(s),i(1)),r=a(o),l=i(8),d=n(l),c=i(7),u=n(c),h=r.Model.extend(d.default.LoggableMixin).extend({_logNamespace:"user",urlRoot:function(){return Galaxy.root+"api/users"},defaults:{id:null,username:"("+(0,u.default)("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(e){this.log("User.initialize:",e),this.on("loaded",function(e,t){this.log(this+" has loaded:",e,t)}),this.on("change",function(e,t){this.log(this+" has changed:",e,t.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(e,t){e=e||h.CURRENT_ID_STR,t=t||{};var i=this,n=t.success;return t.success=function(e,t){i.trigger("loaded",e,t),n&&n(e,t)},e===h.CURRENT_ID_STR&&(t.url=this.urlRoot+"/"+h.CURRENT_ID_STR),r.Model.prototype.fetch.call(this,t)},clearSessionStorage:function(){for(var e in sessionStorage)0===e.indexOf("history:")?sessionStorage.removeItem(e):"history-panel"===e&&sessionStorage.removeItem(e)},toString:function(){var e=[this.get("username")];return this.get("id")&&(e.unshift(this.get("id")),e.push(this.get("email"))),"User("+e.join(":")+")"}});h.CURRENT_ID_STR="current",h.getCurrentUserFromApi=function(e){var t=new h;return t.loadFromApi(h.CURRENT_ID_STR,e),t};r.Collection.extend(d.default.LoggableMixin).extend({model:h,urlRoot:function(){return Galaxy.root+"api/users"}});t.default={User:h}},,function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(161)),r=a(o),l=i(163),d=a(l),c=i(164),u=a(c),h=e.View.extend({initialize:function(e){var t=this;this.options=e,this.setElement(this._template()),this.$navbarBrandLink=this.$(".navbar-brand-link"),this.$navbarBrandImage=this.$(".navbar-brand-image"),this.$navbarBrandTitle=this.$(".navbar-brand-title"),this.$navbarTabs=this.$(".navbar-tabs"),this.$quoteMeter=this.$(".quota-meter-container"),this.collection=new r.default.Collection,this.collection.on("add",function(e){t.$navbarTabs.append(new r.default.Tab({model:e}).render().$el)}).on("reset",function(){t.$navbarTabs.empty()}).on("dispatch",function(e){t.collection.each(function(t){e(t)})}).fetch(this.options),Galaxy.frame=this.frame=new d.default({collection:this.collection}),Galaxy.quotaMeter=this.quotaMeter=new u.default.UserQuotaMeter({model:Galaxy.user,el:this.$quoteMeter}),n(window).on("click",function(e){var t=n(e.target).closest("a[download]");1==t.length&&(0===n("iframe[id=download]").length&&n("body").append(n("<iframe/>").attr("id","download").hide()),n("iframe[id=download]").attr("src",t.attr("href")),e.preventDefault())}).on("beforeunload",function(){var e="";if(t.collection.each(function(t){var i=t.get("onbeforeunload")&&t.get("onbeforeunload")();i&&(e+=i+" ")}),""!==e)return e})},render:function(){return this.$navbarBrandTitle.html("Galaxy "+(this.options.brand&&"/ "+this.options.brand||"")),this.$navbarBrandLink.attr("href",this.options.logo_url),this.$navbarBrandImage.attr("src",this.options.logo_src),this.quotaMeter.render(),this},_template:function(){return'<div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div class="navbar-header"><div class="navbar-tabs"/></div><div class="navbar-brand"><a class="navbar-brand-link"><img class="navbar-brand-image"/><span class="navbar-brand-title"/></a></div><div class="quota-meter-container"/><div class="navbar-icons"/></div>'}});t.default={View:h}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(162),l=o(r),d=i(40),c=o(d),u=i(7),h=o(u),f=i(3),p=o(f),m=e.Collection.extend({model:e.Model.extend({defaults:{visible:!0,target:"_parent"}}),fetch:function(e){e=e||{},this.reset();var t=new l.default.GenericNavView;this.add(t.render()),this.add({id:"analysis",title:(0,h.default)("Analyze Data"),url:"",tooltip:(0,h.default)("Analysis home view")}),this.add({id:"workflow",title:(0,h.default)("Workflow"),tooltip:(0,h.default)("Chain tools into workflows"),disabled:!Galaxy.user.id,url:"workflows/list"}),this.add({id:"shared",title:(0,h.default)("Shared Data"),url:"library/index",tooltip:(0,h.default)("Access published resources"),menu:[{title:(0,h.default)("Data Libraries"),url:"library/list"},{title:(0,h.default)("Histories"),url:"histories/list_published"},{title:(0,h.default)("Workflows"),url:"workflows/list_published"},{title:(0,h.default)("Visualizations"),url:"visualizations/list_published"},{title:(0,h.default)("Pages"),url:"pages/list_published"}]}),this.add({id:"visualization",title:(0,h.default)("Visualization"),url:"visualizations/list",tooltip:(0,h.default)("Visualize datasets"),disabled:!Galaxy.user.id,menu:[{title:(0,h.default)("New Track Browser"),url:"visualization/trackster",target:"_frame"},{title:(0,h.default)("Saved Visualizations"),url:"visualizations/list",target:"_frame"},{title:(0,h.default)("Interactive Environments"),url:"visualization/gie_list",target:"galaxy_main"}]}),c.default.add({url:"api/webhooks/masthead/all",callback:function(e){n(document).ready(function(){n.each(e.models,function(e,t){var i=t.toJSON();if(i.activate){var n={id:i.name,icon:i.config.icon,url:i.config.url,tooltip:i.config.tooltip,onclick:i.config.function&&new Function(i.config.function)};Galaxy.page?Galaxy.page.masthead.collection.add(n):Galaxy.masthead&&Galaxy.masthead.collection.add(n),p.default.appendScriptStyle(i)}})})}}),Galaxy.user.get("is_admin")&&this.add({id:"admin",title:(0,h.default)("Admin"),url:"admin",tooltip:(0,h.default)("Administer this Galaxy"),cls:"admin-only"});var i={id:"help",title:(0,h.default)("Help"),tooltip:(0,h.default)("Support, contact, and community"),menu:[{title:(0,h.default)("Support"),url:e.support_url,target:"_blank"},{title:(0,h.default)("Search"),url:e.search_url,target:"_blank"},{title:(0,h.default)("Mailing Lists"),url:e.mailing_lists,target:"_blank"},{title:(0,h.default)("Videos"),url:e.screencasts_url,target:"_blank"},{title:(0,h.default)("Wiki"),url:e.wiki_url,target:"_blank"},{title:(0,h.default)("How to Cite Galaxy"),url:e.citation_url,target:"_blank"},{title:(0,h.default)("Interactive Tours"),url:"tours"}]};e.terms_url&&i.menu.push({title:(0,h.default)("Terms and Conditions"),url:e.terms_url,target:"_blank"}),e.biostar_url&&i.menu.unshift({title:(0,h.default)("Ask a question"),url:"biostar/biostar_question_redirect",target:"_blank"}),e.biostar_url&&i.menu.unshift({title:(0,h.default)("Galaxy Biostar"),url:e.biostar_url_redirect,target:"_blank"}),this.add(i);var s={};s=Galaxy.user.id?{id:"user",title:(0,h.default)("User"),cls:"loggedin-only",tooltip:(0,h.default)("Account and saved data"),menu:[{title:(0,h.default)("Logged in as")+" "+Galaxy.user.get("email")},{title:(0,h.default)("Preferences"),url:"user"},{title:(0,h.default)("Custom Builds"),url:"custom_builds"},{title:(0,h.default)("Logout"),url:"user/logout?session_csrf_token="+Galaxy.session_csrf_token,target:"_top",divider:!0},{title:(0,h.default)("Saved Histories"),url:"histories/list",target:"_top"},{title:(0,h.default)("Saved Datasets"),url:"datasets/list",target:"_top"},{title:(0,h.default)("Saved Pages"),url:"pages/list",target:"_top"}]}:e.allow_user_creation?{id:"user",title:(0,h.default)("Login or Register"),cls:"loggedout-only",tooltip:(0,h.default)("Account registration or login"),menu:[{title:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},{title:(0,h.default)("Register"),url:"user/create",target:"galaxy_main",noscratchbook:!0}]}:{id:"user",title:(0,h.default)("Login"),cls:"loggedout-only",tooltip:(0,h.default)("Login"),url:"user/login",target:"galaxy_main",noscratchbook:!0},this.add(s);var o=this.get(e.active_view);return o&&o.set("active",!0),(new a.Deferred).resolve().promise()}}),_=e.View.extend({initialize:function(e){this.model=e.model,this.setElement(this._template()),this.$dropdown=this.$(".dropdown"),this.$toggle=this.$(".dropdown-toggle"),this.$menu=this.$(".dropdown-menu"),this.$note=this.$(".dropdown-note"),this.listenTo(this.model,"change",this.render,this)},events:{"click .dropdown-toggle":"_toggleClick"},render:function(){var e=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa "+this.model.get("icon")).addClass(this.model.get("toggle")&&"toggle").attr("target",this.model.get("target")).attr("href",this.model.get("url")).attr("title",this.model.get("tooltip")).tooltip("destroy"),this.model.get("tooltip")&&this.$toggle.tooltip({placement:"bottom"}),this.$dropdown.removeClass().addClass("dropdown").addClass(this.model.get("disabled")&&"disabled").addClass(this.model.get("active")&&"active"),this.model.get("menu")&&this.model.get("show_menu")?(this.$menu.show(),n("#dd-helper").show().off().on("click",function(){n("#dd-helper").hide(),e.model.set("show_menu",!1)})):(e.$menu.hide(),n("#dd-helper").hide()),this.$menu.empty().removeClass("dropdown-menu"),this.model.get("menu")&&(s.each(this.model.get("menu"),function(t){e.$menu.append(e._buildMenuItem(t)),t.divider&&e.$menu.append(n("<li/>").addClass("divider"))}),e.$menu.addClass("dropdown-menu"),e.$toggle.append(n("<b/>").addClass("caret"))),this},_buildMenuItem:function(e){var t=this;return e=s.defaults(e||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),e.url=t._formatUrl(e.url),n("<li/>").append(n("<a/>").attr("href",e.url).attr("target",e.target).html(e.title).on("click",function(i){i.preventDefault(),t.model.set("show_menu",!1),e.onclick?e.onclick():Galaxy.frame.add(e)}))},_toggleClick:function(e){var t=this,i=this.model;if(e.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(e){i.id!==e.id&&e.get("menu")&&e.set("show_menu",!1)}),i.get("disabled")){var a=function(e,t){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+t).html(e)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){t.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(e){return"string"==typeof e&&-1===e.indexOf("//")&&"/"!=e.charAt(0)?Galaxy.root+e:e},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});t.default={Collection:m,Tab:_}}).call(t,i(1),i(0),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(9),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(e){var t=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),r=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+r,d=t+":"+i+l,c=null,u=null,h='<iframe class="f-iframe fade in communication-iframe" src="'+d+'"> </iframe>';return n(".chat-modal").length>0&&n(".chat-modal").remove(),o.modal=new s.default.View({body:h,height:350,width:600,closing_events:!0,title_separator:!1,cls:"ui-modal chat-modal"}),o.modal.show(),c=n(".chat-modal .modal-header"),u=n(".chat-modal .modal-body"),c.addClass("modal-header-body"),u.addClass("modal-header-body"),c.find("h4").remove(),c.removeAttr("min-height padding border"),c.append('<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i><i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i><i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>'),n(".close-modal").click(function(e){n(".chat-modal").css("display","none")}),n(".expand-compress-modal").click(function(e){n(".expand-compress-modal").hasClass("fa-expand")?(n(".chat-modal .modal-dialog").width("1000px"),n(".chat-modal 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u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new r.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),a=t[n];if(a){var s=new a(i,t);i[s.toString()]=s,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:s})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='<label 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e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(0),s=n(a),o=i(61),r=n(o),l=i(4),d=n(l),c=s.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),c.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=r.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3);!function(e){e&&e.__esModule}(s);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),a.each(this.options.parameters,function(t){var i=n("<div/>").addClass("upload-"+t.id+" upload-icon-button 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To upload some files, log in to the FTP server at <strong>"+t.ftp_upload_site+"</strong> using your Galaxy credentials.",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}).set(t),this.collection=this.model.get("collection"),this.setElement(this._template()),this.$content=this.$(".upload-ftp-content"),this.$wait=this.$(".upload-ftp-wait"),this.$help=this.$(".upload-ftp-help"),this.$number=this.$(".upload-ftp-number"),this.$disk=this.$(".upload-ftp-disk"),this.$body=this.$(".upload-ftp-body"),this.$warning=this.$(".upload-ftp-warning"),this.$select=this.$(".upload-ftp-select-all"),this.render()},render:function(){var e=this;this.$wait.show(),this.$content.hide(),this.$warning.hide(),this.$help.hide(),n.ajax({url:Galaxy.root+"api/remote_files",method:"GET",success:function(t){e.model.set("ftp_files",t),e._index(),e._renderTable()},error:function(){e._renderTable()}})},_renderTable:function(){var e=this,t=this.model.get("ftp_files");if(this.rows=[],t&&t.length>0){this.$body.empty();var i=0;a.each(t,function(t){e.rows.push(e._renderRow(t)),i+=t.size}),this.$number.html(t.length+" files"),this.$disk.html(o.default.bytesToString(i,!0)),this.collection&&(this.$("._has_collection").show(),this.$select.addClass(this.model.get("class_add")).off().on("click",function(){e._all()}),this._refresh()),this.$content.show()}else this.$warning.show();this.model.get("help_enabled")&&this.$help.show(),this.$wait.hide()},_renderRow:function(e){var t=this,i=this.model.attributes,a=n(this._templateRow(e)),s=a.find(".icon");if(this.$body.append(a),this.collection){var o=this.ftp_index[e.path];s.addClass(void 0===o?i.class_add:i.class_remove),a.on("click",function(){t._switch(s,e),t._refresh()})}else a.on("click",function(){i.onchange(e)});return s},_index:function(){var e=this;this.ftp_index={},this.collection&&this.collection.each(function(t){"ftp"==t.get("file_mode")&&(e.ftp_index[t.get("file_path")]=t.id)})},_all:function(){var e=this.model.attributes,t=this.model.get("ftp_files"),i=this.$select.hasClass(e.class_add);for(var n in t){var a=t[n],s=this.ftp_index[a.path];(void 0===s&&i||void 0!==s&&!i)&&this._switch(this.rows[n],a)}this._refresh()},_switch:function(e,t){e.removeClass();var i=this.model.attributes,n=this.ftp_index[t.path];if(void 0===n){var a=i.onadd(t);e.addClass(i.class_remove),this.ftp_index[t.path]=a}else i.onremove(n),e.addClass(i.class_add),this.ftp_index[t.path]=void 0},_refresh:function(){var e=a.reduce(this.ftp_index,function(e,t){return void 0!==t&&e++,e},0);this.$select.removeClass(),0==e?this.$select.addClass(this.model.get("class_add")):this.$select.addClass(e==this.rows.length?this.model.get("class_remove"):this.model.get("class_partial"))},_templateRow:function(e){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+a.escape(e.path)+'</td><td class="ftp-size">'+o.default.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_template:function(){return'<div class="'+this.model.get("cls")+'"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">'+this.model.get("help_text")+'</div><div class="upload-ftp-content"><span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(165)),r=a(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new r.default.View({placement:e.placement||"bottom",container:e.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."}})}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. 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y=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['<a class="name" title="',(0,b.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,b.default)("Remove this dataset from the list"),'">',(0,b.default)("Discard"),"</button>"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,b.default)("Enter a new name for the element"),":\n(",(0,b.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,b.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:y,collectionClass:d.default.HistoryDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for 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e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset"!==e.history_content_type?(0,b.default)("is not a dataset"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,b.default)("has been deleted or purged"):null:(0,b.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(a(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content 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";return t+='<a class="cancel-create" href="javascript:void(0);">'+(0,b.default)("Cancel")+"</a> ",t+=(0,b.default)("or"),t+=' <a class="reset" href="javascript:void(0);">'+(0,b.default)("start over")+"</a>.",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:(0,b.default)("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,b.default)("An error occurred");if(e.xhr){var n=e.xhr,a=e.message;0===n.readyState&&0===n.status?i+=": "+(0,b.default)("Galaxy could not be reached and may be updating.")+(0,b.default)(" Try again in a few minutes."):n.responseJSON?i+=":<br /><pre>"+JSON.stringify(n.responseJSON)+"</pre>":i+=": "+a}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart 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i=e.offset(),n=e.scrollTop(),a=t-i.top,s=i.top+e.outerHeight()-t;a>=0&&a<this.autoscrollDist?e.scrollTop(n-2):s>=0&&s<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestElement:function(e){for(var t=this.$(".collection-elements li.collection-element").toArray(),i=0;i<t.length;i++){var n=a(t[i]),s=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(s+o>e&&s-o<e)return n}return a()},_dropElements:function(e){e.originalEvent&&(e=e.originalEvent),e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestElement(e.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".collection-elements .collection-element").last()),this._syncOrderToDom(),!1},_syncOrderToDom:function(){var e=this,t=[];this.$(".collection-elements .collection-element").each(function(){var i=a(this).attr("data-element-id"),s=n.findWhere(e.workingElements,{id:i});s?t.push(s):console.error("missing element: 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class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,b.default)("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',(0,b.default)("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',(0,b.default)("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',(0,b.default)("Create list"),"</button>","</div>","</div>"].join("")),helpContent:n.template(["<p>",(0,b.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"</p>","<ul>","<li>",(0,b.default)(["Rename elements in the list by clicking on ",'<i data-target=".collection-element .name">the existing name</i>.'].join("")),"</li>","<li>",(0,b.default)(["Discard elements from the final created list by clicking on the ",'<i data-target=".collection-element .discard">"Discard"</i> button.'].join("")),"</li>","<li>",(0,b.default)(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'<i data-target=".collection-element">them</i> and you can then move those selected by dragging the ',"entire group. 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"),(0,b.default)("Would you like to "),'<a class="reset" href="javascript:void(0)">',(0,b.default)("start over"),"</a>?","</li>"].join("")),invalidInitial:n.template(['<div class="header flex-row no-flex">','<div class="alert alert-warning" style="display: block">','<span class="alert-message">',"<% if( _.size( problems ) ){ %>",(0,b.default)("The following selections could not be included due to problems"),":","<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>","<% } else if( _.size( elements ) < 1 ){ %>",(0,b.default)("No datasets were selected"),".","<% } %>","<br />",(0,b.default)("At least one element is needed for the collection"),". ",(0,b.default)("You may need to "),'<a class="cancel-create" href="javascript:void(0)">',(0,b.default)("cancel"),"</a> ",(0,b.default)("and reselect new elements"),".","</span>","</div>","</div>",'<div class="footer flex-row no-flex">','<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',(0,b.default)("Cancel"),"</button>","</div>","</div>","</div>"].join(""))}),toString:function(){return"ListCollectionCreator"}}),k=function(e,t,i){var a,o=s.Deferred(),r=Galaxy.modal||new g.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),a=new i(t),r.show({title:t.title||(0,b.default)("Create a collection"),body:a.$el,width:"80%",height:"100%",closing_events:!0}),a.render(),window._collectionCreator=a,o},C=function(e,t){return t=t||{},t.title=(0,b.default)("Create a collection from a list of datasets"),k(e,t,x)};t.default={DatasetCollectionElementView:y,ListCollectionCreator:x,collectionCreatorModal:k,listCollectionCreatorModal:C,createListCollection:r}}).call(t,i(1),i(2),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(189),s=n(a),o=i(206),r=n(o),l=i(7),d=(n(l),r.default.HistoryContentMixin),c=s.default.DatasetCollection,u=c.extend(d).extend({defaults:e.extend(e.clone(c.prototype.defaults),{history_content_type:"dataset_collection",model_class:"HistoryDatasetCollectionAssociation"}),save:function(e,t){return this.isNew()&&(t=t||{},t.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),c.prototype.save.call(this,e,t)},toString:function(){return"History"+c.prototype.toString.call(this)}});t.default={HistoryDatasetCollection:u}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return 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this.attributes.collection_type.indexOf(":")>0?v:m},initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){var t=this.collectionClass();this.debug(this+"._createElementsModel",t,this.get("elements"),this.elements);var i=this.get("elements")||[];this.unset("elements",{silent:!0});var n=this;return e.each(i,function(t,i){e.extend(t,{parent_hdca_id:n.get("id")})}),this.elements=new t(i),this.elements},toJSON:function(){var e=n.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=n.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?a.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){return"DatasetCollection("+[this.get("id"),this.get("name")||this.get("element_identifier")].join(",")+")"}}),g=_.extend(d.default.mixin(u,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),u.constructor.call(this,e,t)},toString:function(){return["NestedDCDCE(",this.object?""+this.object:this.get("element_identifier"),")"].join("")}})),v=f.extend({model:g,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}});t.default={DatasetCollection:_}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.default={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",subworkflow:"fa-sitemap fa-rotate-270",pause:"fa-pause"}},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(192),l=o(r),d=i(193),c=(o(d),i(213)),u=o(c),h=i(3),f=o(h),p=i(8),m=o(p),_=i(7),g=o(_),v=e.Model.extend(m.default.LoggableMixin).extend(m.default.mixin(m.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:l.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,a){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,n.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,g.default)("(empty)")},toJSON:function(){return a.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:s.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,a){var s;try{s=new Date(a.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=s||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var a={history_id:this.id};e&&(a.current=!0),t&&(a.name=t),i||(a.all_datasets=!1),a.view="dev-detailed";var s=this,o=n.post(this.urlRoot,a);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,b=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return a.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),a.defaults(t,i)},fetchFirst:function(e){var t=this,i=s.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:a.extend(a.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,a.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,a){var s=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){s.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:b}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(213),r=s(o),l=i(214),d=s(l),c=i(188),u=s(c),h=i(193),f=s(h),p=i(253),m=s(p),_=i(8),g=s(_),v=i(215),w=s(v),b=r.default.PaginatedCollection,y=b.extend(g.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync add":this.trackJobStates}),t=t||{},b.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var e=this;this.each(function(t){if(!t.has("job_states_summary")&&"dataset_collection"===t.attributes.history_content_type){var i=t.attributes.job_source_type,n=t.attributes.job_source_id;if(i){e.jobStateSummariesCollection.add({id:n,model:i,history_id:e.history_id,collection_id:t.attributes.id});var a=e.jobStateSummariesCollection.get(n);t.jobStatesSummary=a}}})},model:function(e,t){return"dataset"===e.history_content_type?new d.default.HistoryDatasetAssociation(e,t):"dataset_collection"===e.history_content_type?new u.default.HistoryDatasetCollection(e,t):{validationError:"Unknown history_content_type: "+e.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(e){this.stopPolling(),this.historyId=e,e&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new m.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=e,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(e){return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(b.prototype.comparators),{name:g.default.buildComparator("name",{ascending:!0}),"name-dsc":g.default.buildComparator("name",{ascending:!1}),hid:g.default.buildComparator("hid",{ascending:!1}),"hid-asc":g.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,a=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,a){var s=i.get(t[n]);return s?e.concat(s):e},[]),i.ajaxQueue("save",a,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new w.default.AjaxQueue(n.slice().reverse().map(function(n,a){var s=e.isString(t)?n[t]:t;return function(){return s.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var r=e.extend(e.clone(t),{view:"summary",keys:l,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){s.fetch.call(s,r).fail(a.reject).done(function(e){a.notify(e,o,n),e.length!==o?(s.allFetched=!0,a.resolve(e,o,n)):i(n+o)})})}t=t||{};var a=n.Deferred(),s=this,o=t.limitPerCall||s.limitPerProgressiveFetch,r=d.default.HistoryDatasetAssociation.prototype.searchAttributes,l=r.join(",");return i(),a},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,a,s;e.isString(t)?(i=t,s="hda",a="dataset"):(i=t.id,s={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",a="hdca"===s?"dataset_collection":"dataset");var o=this,r=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:s,type:a})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,r,{},"Error copying contents",{type:a,id:i,source:s})});return r},createHDCA:function(e,t,i,n,a){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(a)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=a.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:y}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(8),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return s.storageKeyPrefix+e},get:function(e){return new s({id:s.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(s.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:s}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(8),l=o(r),d=i(7),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:l.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:l.default.wrapTemplate(['<div class="subtitle"></div>']),details:l.default.wrapTemplate(['<div class="details"></div>'])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['<div class="details">',"</div>"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(194),l=o(r),d=i(166),c=o(d),u=i(175),h=o(u),f=i(8),p=o(f),m=i(7),_=o(m),g=l.default.ListItemView,v=g.extend({_logNamespace:"dataset",className:g.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),g.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return 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this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),P=e.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new E({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof x){var i=new M({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof w){var n=new S({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof y){var a=new T({model:t});a.render(),e.$el.append(a.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=n(this).attr("class").split(/\s+/)[0],a=e.model.get("tools").get(i);e.trigger("tool_link_click",t,a)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?n("#search-no-results").show():n("#search-no-results").hide()}}),O=e.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(A.tool_form(this.model.toJSON()))}}),A=(e.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new P({collection:this.collection}),this.tool_form_view=new O},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" ','placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />','<a id="search-clear-btn" title="clear search (esc)"> </a>','<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>'].join("")),panel_section:o.template(['<div class="toolSectionTitle" id="title_<%- id %>">','<a href="javascript:void(0)"><span><%- name %></span></a>',"</div>",'<div id="<%- id %>" class="toolSectionBody" style="display: none;">','<div class="toolSectionBg"></div>',"<div>"].join("")),tool_link:o.template(['<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">','<span class="labels">',"<% _.each( labels, function( label ){ %>",'<span class="label label-default label-<%- label %>">',"<%- label %>","</span>","<% }); %>","</span>",'<span class="tool-old-link">',"<%- name %>","</span>"," <%- description %>","</a>"].join("")),tool_form:o.template(['<div class="toolFormTitle"><%- tool.name %> (version <%- tool.version %>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});t.default={ToolParameter:f,IntegerToolParameter:_,SelectToolParameter:v,Tool:w,ToolCollection:b,ToolSearch:k,ToolPanel:C,ToolPanelView:P,ToolFormView:O}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(4),d=s(l),c=i(9),u=s(c),h=i(63),f=s(h),p=i(40),m=s(p),_=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(r.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),r.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),r.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("<input/>").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),r.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new m.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var a in t){var s=t[a],o=this.form.data.match(a),r=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&r){if(!l.optional&&null==s)return this.form.highlight(o),!1;if(s&&s.batch){var d=s.values.length,c=d>0&&s.values[0]&&s.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(e.hid+": "+e.name)))}),s.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("<pre/>").text(JSON.stringify(e,null,4)))}});t.default={View:_}}).call(t,i(1),i(0),i(2))},,function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(e){return-1!==i.indexOf(this.attributes.async_ops,e)},add_filter:function(e,t,i){if(i){var n,a=this.attributes.filters[e];if(null===a||void 0===a)n=t;else if("string"==typeof a)if("All"==a||a==t)n=t;else{var s=[];s[0]=a,s[1]=t,n=s}else n=a,-1===n.indexOf(t)&&n.push(t);this.attributes.filters[e]=n}else this.attributes.filters[e]=t},remove_filter:function(e,t){var n=this.attributes.filters[e];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[e]="";else{var a=i.indexOf(n,t);-1!==a&&(n[a]="")}},get_url_data:function(){var e={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(e.operation=this.attributes.operation),this.attributes.item_ids&&(e.id=this.attributes.item_ids);var t=this;return i.each(i.pairs(t.attributes.filters),function(t){e["f-"+t[0]]=t[1]}),e},get_url:function(e){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(e)}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(3),s=function(e){return e&&e.__esModule?e:{default:e}}(a);t.default={grid:function(e){var t="";return t=e.embedded?this.grid_header(e)+this.grid_table(e):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(e)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(e),e.info_text&&(t+='<br><div class="toolParamHelp" style="clear: both;">'+e.info_text+"</div>"),t},grid_table:function(e){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(e){var t='<div class="grid-header">';if(e.embedded||(t+="<h2>"+e.title+"</h2>"),e.global_actions){t+='<ul class="manage-table-actions">';var i=e.global_actions.length>=3;i&&(t+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in e.global_actions){var a=e.global_actions[n];t+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(t+="</div>"),t+="</ul>"}return e.insert&&(t+=e.insert),t+=this.grid_filters(e),t+="</div>"},header:function(e){var t="<tr>";e.show_item_checkboxes&&(t+="<th>",e.items.length>0&&(t+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),t+="</th>");for(var i in e.columns){var n=e.columns[i];n.visible&&(t+='<th id="'+n.key+'-header">',n.href?t+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":t+=n.label,t+='<span class="sort-arrow">'+n.extra+"</span></th>")}return t+="</tr>"},body:function(t){var i="",n=0;0==t.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in t.items){var s=t.items[a],o=s.encode_id;i+="<tr ",t.current_item_id==s.id&&(i+='class="current"'),i+=">",t.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var r in t.columns){var l=t.columns[r];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=s.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===e.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",m="";l.attach_popup&&(p="grid-"+a+"-popup",m="menubutton",""!=u&&(m+=" split"),m+=" popup"),i+="<td "+d+">",u?(0!=t.operations.length&&(i+='<div id="'+p+'" class="'+m+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=t.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+m+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(e){var t="";if(e.use_paging&&e.num_pages>1){var i=e.num_page_links,n=e.cur_page_num,a=e.num_pages,s=i/2,o=n-s,r=0;o<=0&&(o=1,r=s-(n-o));var l,d=s+r,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),t+='<tr id="page-links-row">',e.show_item_checkboxes&&(t+="<td></td>"),t+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(t+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var u=o;u<c+1;u++)u==e.cur_page_num?t+='<span class="page-link inactive-link" id="page-link-'+u+'">'+u+"</span>":t+='<span class="page-link" id="page-link-'+u+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+u+'">'+u+"</a></span>";c<a&&(t+='...<span class="page-link" id="page-link-'+a+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+a+'">'+a+"</a></span>"),t+="</span>",t+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(e.show_item_checkboxes){t+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var h in e.operations){var f=e.operations[h];f.allow_multiple&&(t+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}t+="</td></tr>"}var p=!1;for(h in e.operations)if(e.operations[h].global_operation){p=!0;break}if(p){t+='<tr><td colspan="100">';for(h in e.operations){var f=e.operations[h];f.global_operation&&(t+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}t+="</td></tr>"}return e.legend&&(t+='<tr><td colspan="100">'+e.legend+"</td></tr>"),t},message:function(e){var t=e.status;return-1!=["success","ok"].indexOf(t)&&(t="done"),'<p><div class="'+t+'message transient-message">'+n.escape(e.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1;for(var s in e.columns){var o=e.columns[s];if("advanced"==o.filterable){var r=o.key,l=i[r],d=t[r];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div id="standard-search" style="display: '+c+';"><table><tr><td style="padding: 0;"><table>';for(var s in e.columns){var o=e.columns[s];"standard"==o.filterable&&(u+=this.grid_column_filter(e,o))}u+="</table></td></tr><tr><td>",a&&(u+='<a href="" class="advanced-search-toggle">Advanced Search</a>'),u+="</td></tr></table></div>",u+='<div id="advanced-search" style="display: '+n+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var s in e.columns){var o=e.columns[s];"advanced"==o.filterable&&(u+=this.grid_column_filter(e,o))}return u+="</table></div>"},grid_column_filter:function(t,i){var n=(t.default_filter_dict,t.filters),a=i.label,s=i.key;"advanced"==i.filterable&&(a=a.toLowerCase());var o="<tr>";if("advanced"==i.filterable&&(o+='<td align="left" style="padding-left: 10px">'+a+":</td>"),o+='<td style="padding-bottom: 1px;">',i.is_text){o+='<form class="text-filter-form" column_key="'+s+'" action="'+t.url+'" method="get" >';for(u in t.columns){var r=t.columns[u],l=n[r.key];l&&"All"!=l&&(r.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+r.key+'" name="f-'+r.key+'" value="'+l+'"/>')}o+='<span id="'+s+'-filtering-criteria">';var d=n[s];if(d){var c=e.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(s,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(s,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var m=p.length;m<20&&(m=20),m+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+s+'-filter" name="f-'+s+'" type="text" placeholder="'+p+'" size="'+m+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+s+'-filtering-criteria">';var _=!1;for(var g in t.categorical_filters[s]){var v=t.categorical_filters[s][g],w="",b="";for(var y in v)w=y,b=v[y];_&&(o+=" | "),_=!0;var h=n[s];h&&v[s]&&h==b?o+='<span class="categorical-filter '+s+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+s+'-filter"><a href="javascript:void(0);" filter_key="'+w+'" filter_val="'+b+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(e,t){return'<span class="text-filter-val">'+(t=s.default.sanitize(t))+'<a href="javascript:void(0);" filter_key="'+e+'" filter_val="'+t+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(2),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(146),l=a(r),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),m=i(26),_=a(m),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var w=null,b=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=e.Model.extend;var x=y.extend({initialize:function(e){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=e},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var e=[];n(".bookmark").each(function(){e.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var t=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,i={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:t},bookmarks:e};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(e){Galaxy.modal.hide(),b.vis_id=e.vis_id,b.has_changes=!1,window.history.pushState({},"",e.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var e=this,t=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(e){o.each(e,function(e){b.add_drawable(l.default.object_from_template(e,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=e.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){e.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){e.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=t,t},add_bookmark:function(e,t,i){var a=n("#right .unified-panel-body"),s=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(s),r=(n("<a href=''/>").text(e).appendTo(o).click(function(){return b.go_to(e),!1}),n("<div/>").text(t).appendTo(s));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){return s.slideUp("fast"),s.remove(),b.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);r.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,s},create_visualization:function(e,t,i,a,s){var r=this,d=new l.default.TracksterView(o.extend(e,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(e){if(t){var n=t.chrom,o=t.start,c=t.end,u=t.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(e[0].chrom)}else d.change_chrom(e[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],r.add_bookmark(f.position,f.annotation,s);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(t){new c.default.TrackBrowserRouter(t),e.history.start()},init_keyboard_nav:function(e){n(document).keyup(function(t){if(!n(t.srcElement).is(":input"))switch(t.which){case 37:e.move_fraction(.25);break;case 38:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()-20);break;case 39:e.move_fraction(-.25);break;case 40:Math.round(e.viewport_container.height()/15);e.viewport_container.scrollTop(e.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(e){if(e.has_changes){var t=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(t.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=e.View.extend({initialize:function(){w=new x(Galaxy.root),w.createButtonMenu(),w.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(w.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var e=this,t=p.default.get("dbkey"),i={},n={dbkey:t,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(t||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){e.view_in_saved(n)},"View in new visualization":function(){e.view_new()}}})},view_in_saved:function(e){var t=new _.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:t.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){e.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(e)})}}})},view_existing:function(){var e=galaxy_config.app.viz_config;b=w.create_visualization({container:n("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,!0),this.init_editor()},view_new:function(){var e=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(t){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(t),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){e.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=t.map(function(e){return e[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(e){for(var t='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<e.length;i++)t+='<option value="'+e[i][1]+'">'+e[i][0]+"</option>";return t+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(e,t){n(document).trigger("convert_to_values"),b=w.create_visualization({container:n("#center .unified-panel-body"),name:e,dbkey:t},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){b.add_drawable(l.default.object_from_template(e,b,b))}}),n("#add-bookmark-button").click(function(){var e=b.chrom+":"+b.low+"-"+b.high;return w.add_bookmark(e,"Bookmark description",!0)}),w.init_keyboard_nav(b),n(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});t.default={TracksterUI:x,GalaxyApp:k}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function o(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var r=i(2),l=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(r),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),m=i(148),_=a(m),g=i(149),v=a(g),w=i(150),b=a(w),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),S=a($),T=i(151),M=a(T);i(25);var E=l.extend,P={},O=function(e,t){P[e.attr("id")]=t},A=function(t,i,n,a){n=".group",P[t.attr("id")]=a,t.bind("drag",{handle:"."+i,relative:!0},function(t,i){var a,s,o,r,l,d=(e(this),e(this).parent()),c=d.children(".track,.group"),u=P[e(this).attr("id")];if(s=e(this).parents(n),0!==s.length){o=s.position().top,r=o+s.outerHeight();var h=P[s.attr("id")];if(i.offsetY<o)return e(this).insertBefore(s),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>r)return e(this).insertAfter(s),h.remove_drawable(u),void h.container.add_drawable(u)}for(s=null,l=0;l<c.length;l++)if(a=e(c.get(l)),o=a.position().top,r=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=r)return i.offsetY-o<r-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void P[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=e(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),P[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(e(this).insertBefore(c.get(l)),P[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})},D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",I=["Histogram","Line","Filled","Intensity"],z=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};z.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(e){new S.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],E(z.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var j=function(e,t,i){z.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};E(j.prototype,z.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i<e.length;i++)t=ne(e[i],this.view,this),this.add_drawable(t)},init:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].init()},_draw:function(e){for(var t=0;t<this.drawables.length;t++)this.drawables[t]._draw(e)},to_dict:function(){for(var e=[],t=0;t<this.drawables.length;t++)e.push(this.drawables[t].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:e}},add_drawable:function(e){this.drawables.push(e),e.container=this,this.changed()},add_drawable_before:function(e,t){this.changed();var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,0,e),!0)},replace_drawable:function(e,t,i){var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables[n]=t,i&&e.container_div.replaceWith(t.container_div),this.changed()),n},remove_drawable:function(e){var t=this.drawables.indexOf(e);return-1!==t&&(this.drawables.splice(t,1),e.container=null,this.changed(),!0)},move_drawable:function(e,t){var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(t,0,e),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(e){for(var t,i=this.drawables.slice(0),n=[];0!==i.length;)t=i.shift(),t instanceof e?n.push(t):t.drawables&&(i=i.concat(t.drawables));return n}});var L=function(t,i,n){if(E(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),j.call(this,t,i,n),this.content_div=e("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),A(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};E(L.prototype,z.prototype,j.prototype,{action_icons_def:[z.prototype.action_icons_def[0],z.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},z.prototype.action_icons_def[2]],build_container_div:function(){var t=e("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i<t;i++){if(a=this.drawables[i],a.get_type()!==s){can_composite=!1;break}a instanceof Z&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),e(".tooltip").remove()),o>1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],l[r.name]=[r];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)r=a.filters_manager.filters[n],r.name in l&&l[r.name].push(r);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new b.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e<this.drawables.length;e++)this.drawables[e].filters_manager=this.saved_filters_managers[e];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var e=0;e<this.drawables.length;e++){var t=this.drawables[e];this.saved_filters_managers.push(t.filters_manager),t.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var e=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,e,!0);e.request_draw()},add_drawable:function(e){j.prototype.add_drawable.call(this,e),this.update_icons()},remove_drawable:function(e){j.prototype.remove_drawable.call(this,e),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var e=E(j.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),e},request_draw:function(e){l.each(this.drawables,function(t){t.request_draw(e)})}});var R=n.View.extend({initialize:function(e){E(e,{obj_type:"View"}),j.call(this,"View",e.container,e),this.chrom=null,this.vis_id=e.vis_id,this.dbkey=e.dbkey,this.stand_alone=void 0===e.stand_alone||e.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:e.name})},render:function(){this.requested_redraw=!1;var t=this.container,i=this;this.top_container=e("<div/>").addClass("top-container").appendTo(t),this.browser_content_div=e("<div/>").addClass("content").appendTo(t),this.bottom_container=e("<div/>").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,i),this.intro_div=e("<div/>").addClass("intro").appendTo(this.viewport_container);e("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(e){l.each(e,function(e){i.add_drawable(ne(e,i,i))})})});this.nav_container=e("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(Z),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new W(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});E(R.prototype,j.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500)}else view.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(p.default.commatize(e)+" - "+p.default.commatize(t)),this.nav_input.val(this.chrom+":"+p.default.commatize(e)+"-"+p.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){t.num=100;var i=this,n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new X(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e('<option value="">Select Chrom/Contig</option>'));for(var s=0,o=i.chrom_data.length;s<o;s++){var r=i.chrom_data[s].chrom,l=e("<option>");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('<option value="previous">Previous 100</option>')),t.next_chroms&&i.chrom_select.append(e('<option value="next">Next 100</option>')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;o<r;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(e){e=e.replace(/,/g,""),e=e.replace(/:|\-/g," ");var t=e.split(/\s+/),i=t[0],n=t[1]?parseInt(t[1],10):void 0,a=t[2]?parseInt(t[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(e){var t=this,i=t.high-t.low;this.move_delta(e*i)},move_delta:function(e){var t=this,i=t.high-t.low;t.low-e<t.max_low?(t.low=t.max_low,t.high=t.max_low+i):t.high-e>t.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){j.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(j.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;l.each(n,function(t){var n=l.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;e<this.max_low&&(e=this.max_low),t>this.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(t=e+this.min_separation),this.low=Math.floor(e),this.high=Math.ceil(t),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(e){var t=e[0],i=e[1];t&&t._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(e){e._draw()})},zoom_in:function(e,t){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;e&&(n=e/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var e=this.high-this.low,t=e/2+this.low,i=e*this.zoom_factor/2;this.low=Math.round(t-i),this.high=Math.round(t+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(e){if(this.overview_drawable){if(this.overview_drawable.dataset.id===e.dataset.id)return;this.overview_viewport.find(".track").remove()}var t=e.copy({content_div:this.overview_viewport}),i=this;t.header_div.hide(),t.is_overview=!0,i.overview_drawable=t,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){e(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var N=C.default.Tool.extend({defaults:{track:null},initialize:function(e){C.default.Tool.prototype.initialize.call(this,e);var t=!0;void 0!==e.tool_state&&void 0!==e.tool_state.hidden&&(t=e.tool_state.hidden),this.set("hidden",t),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(e){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),V=n.View.extend({events:{"change :input":"update_value"},render:function(){var t=this.$el.addClass("param-row"),i=this.model;e("<div>").addClass("param-label").text(i.get("label")).appendTo(t);e("<div/>").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("<div style='clear: both;'/>").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),G=n.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()});e("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(e){var t=new V({model:e});t.render(),n.append(t.$el)}),n.find("input").click(function(){e(this).select()});var a=e("<div>").addClass("param-row").appendTo(n),s=e("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);e("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e<this.params.length;e++)this.params[e].update_value()},run_on_dataset:function(){var e=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:e.id},null,function(t){Galaxy.modal.show({title:e.get("name")+" is Running",body:e.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var e,t=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:t.view.chrom,start:t.view.low,end:t.view.high}),a={target_dataset_id:t.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},s=t,o=i.get("name")+s.tool_region_and_parameters_str(n);if(s.container===view){var r=new L(view,view,{name:t.config.get_value("name")}),l=s.container.replace_drawable(s,r,!1);r.container_div.insertBefore(s.view.content_div.children()[l]),r.add_drawable(s),s.container_div.appendTo(r.content_div),e=r}else e=s.container;var d=new s.constructor(view,e,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(s.mode),d.set_filters_manager(s.filters_manager.copy(d)),d.update_icons(),e.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(e){d.set_dataset(new x.default.Dataset(e)),d.tiles_div.text("Running job."),d.init()})},run:function(t,i,n){t.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(t),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});e.when(a.go()).then(function(e){"no converter"===e?(i.container_div.addClass("error"),i.content_div.text(D)):e.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+e.message)):n(e)})}}),U=function(e,t){v.default.Scaler.call(this,t),this.filter=e};U.prototype.gen_val=function(e){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(e[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var H=function(t,i,n,a,s){this.track=t,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=e("<div class='track-tile'/>").append(a),this.data=s,this.stale=!1};H.prototype.predisplay_actions=function(){};var F=function(e,t,i,n,a){H.call(this,e,t,i,n,a)};F.prototype.predisplay_actions=function(){};var B=function(e,t,i,n,a,s,o,r,l,d,c){H.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};E(B.prototype,H.prototype),B.prototype.predisplay_actions=function(){};var q=function(t,i,a){E(a,{drag_handle_class:"draghandle"}),z.call(this,t,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};E(q.prototype,z.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},z.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},z.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(t){var i="<strong>Tool</strong>:"+t.tool.get("name")+"<br/><strong>Dataset</strong>:"+t.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},s=function(){var i,a=e('select[name="regions"] option:selected').val(),s=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(e(".bookmark"),function(t){return new c.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===a?[s]:"bookmarks"===a?o:[s].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:s}})}},z.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&z.prototype.can_draw.call(this)},build_container_div:function(){return e("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("<div class='track-resize'>");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof W?"LabelTrack":this instanceof X?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof te?"ReadTrack":this instanceof ee?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Z?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("<span/>").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(D)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+t.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("<span/>").text(" ")),a.append(e("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(t,i,n){q.call(this,t,i,n);var a=this;if(A(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new b.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new N(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new G({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};E(Y.prototype,z.prototype,q.prototype,{action_icons_def:q.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();E(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){if(this.can_draw()){var i=t&&t.clear_after,n=this.view.low,a=this.view.high,s=this.view.container.width(),o=this.view.resolution_px_b,r=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=s/(view.max_high-view.max_low),r=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*r),f=Math.floor(n/h),p=[],m=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,t),p.push(u),e.when(u).then(function(e){m.push(e)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var _=this;e.when.apply(e,p).then(function(){_.tiles_div.children(".remove").remove(),m=l.filter(m,function(e){return null!==e}),0!==m.length&&_.postdraw_actions(m,s,o,i)})}},_add_yaxis_label:function(t,i){var n=this,a="max"===t?"top":"bottom",o="max"===t?"max":"min",r="max"===t?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=s(n.config.get_value(r),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=e("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),n.config.set_value(r,s(t,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){if(l.filter(e,function(e){return e instanceof F}).length>0){this.max_height_px=0;var a=this;l.each(e,function(e){e instanceof F||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(e,function(e){return e.has_icons})&&l.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)})},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){n||(n={});var a=n.force,s=n.mode||this.mode,o=1/i,r=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,t),u=a?void 0:r.tile_cache.get_elt(c);if(u)return function(e){return e&&"track"in e}(u)&&r.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var e=l.find(I,function(e){return e===s})?"Coverage":s,i=l.map(d,function(i){return i.data_manager.get_data(t,e,o,r.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(t,s,o,view.reference_track.data_url_extra_params)),i},f=e.Deferred();return r.tile_cache.set_elt(c,f),e.when.apply(e,h()).then(function(){var a,s=h(),o=s;if(l.find(s,function(e){return p.default.is_deferred(e)}))return r.tile_cache.set_elt(c,void 0),void e.when(r.draw_helper(t,i,n)).then(function(e){f.resolve(e)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(s.pop(),t));var u=[],m=[];l.each(d,function(e,t){var n=e.mode,a=o[t];"Auto"===n&&(n=e.get_mode(a),e.update_auto_mode(n)),u.push(n),m.push(e.get_canvas_height(a,n,i,b))});var _,g=r.view.canvas_manager.new_canvas(),v=t.get("start"),w=t.get("end"),b=Math.ceil((w-v)*i)+r.left_offset,y=l.max(m);g.width=b,g.height=n.height||y;var x=g.getContext("2d");x.translate(r.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(e,n){_=e.draw_tile(o[n],x,u[n],t,i,a)}),void 0!==_&&(r.tile_cache.set_elt(c,_),r.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new v.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new F(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+l.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var W=function(e,t){q.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};E(W.prototype,q.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("<div/>").addClass("label-container");s<i.high;){var l=Math.floor((s-i.low)/n*o);r.append(e("<div/>").addClass("pos-label").text(p.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var J=function(e,t,i){if(Y.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=ne(n,e,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(e){(e instanceof Z||e instanceof te)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};E(J.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:j.prototype.to_dict,add_drawable:j.prototype.add_drawable,unpack_drawables:j.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;l.each(this.drawables,function(t){t.visible_height_px=e}),q.prototype.on_resize.call(this)},change_mode:function(e){Y.prototype.change_mode.call(this,e);for(var t=0;t<this.drawables.length;t++)this.drawables[t].change_mode(e)},init:function(){for(var t=[],i=0;i<this.drawables.length;i++)t.push(this.drawables[i].init());var n=this;e.when.apply(e,t).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:z.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var e,t=new L(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)e=this.drawables[i],e.update_icons(),t.add_drawable(e),e.container=t,t.content_div.append(e.container_div);this.container.replace_drawable(this,t,!0);t.request_draw({clear_tile_cache:!0})},before_draw:function(){var e=l.min(l.map(this.drawables,function(e){return e.config.get_value("min_value")})),t=l.max(l.map(this.drawables,function(e){return e.config.get_value("max_value")}));this.config.set_value("min_value",e),this.config.set_value("max_value",t),l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)})},update_all_min_max:function(){var e=this.config.get_value("min_value"),t=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",e),i.config.set_value("max_value",t)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(e,t,i,n){var a,s=-1;for(a=0;a<e.length;a++){var o=e[a].html_elt.find("canvas").height();o>s&&(s=o)}for(a=0;a<e.length;a++){var r=e[a];r.html_elt.find("canvas").height()!==s&&(this.draw_helper(r.region,i,{force:!0,height:s}),r.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var X=function(e){Y.call(this,e,{content_div:e.top_labeltrack},{resize:!1,header:!1}),this.left_offset=e.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};E(X.prototype,z.prototype,Y.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:z.prototype.can_draw,draw_helper:function(e,t,i){var n,a=this.tiles_div.is(":visible"),s=null;return t>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=Y.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l<d;l++)t.fillStyle=this.view.get_base_color(o[l]),t.fillText(o[l],Math.floor(l*a),10);return new H(this,n,a,r,s)}});var K=function(t,i,n){this.mode="Histogram",Y.call(this,t,i,n),this.left_offset=30;var a=this;e.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(e){e&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};E(K.prototype,z.prototype,Y.prototype,{display_modes:I,build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(e,t,i,n,a){return this._draw_line_track_tile(e,t,i,n,a)},can_subset:function(e){return e.data[1][0]-e.data[0][0]==1},postdraw_actions:function(e,t,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Q=function(e,t,i){this.mode="Heatmap",Y.call(this,e,t,i)};E(Q.prototype,z.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){e.data})},draw_tile:function(e,t,i,n,a){var s=t.canvas;return new v.default.DiagonalHeatmapPainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new H(this,n,a,s,e.data)}});var Z=function(e,t,i){Y.call(this,e,t,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};E(Z.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s,o=this;if(0===l.filter(t,function(e){return e instanceof F}).length){var r={};l.each(l.pluck(t,"incomplete_features"),function(e){l.each(e,function(e){r[e[0]]=e})});var d=this;l.each(t,function(t){var i=l.omit(r,l.map(t.incomplete_features,function(e){return e[0]}));if(i=l.omit(i,l.keys(t.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),s=a.getContext("2d");a.height=Math.max(t.canvas.height,d.get_canvas_height(n,t.mode,t.w_scale,100)),a.width=t.canvas.width,s.drawImage(t.canvas,0,0),s.translate(o.left_offset,0);var c=d.draw_tile(n,s,t.mode,t.region,t.w_scale,t.seq_data);e(t.canvas).replaceWith(e(c.canvas)),t.canvas=a,l.extend(t.other_tiles_features_drawn,r)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(s=0;s<t.length;s++)if(t[s].data.length)for(h=t[s].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(t[0]instanceof B){var m=!0;for(s=0;s<t.length;s++)if(!t[s].all_slotted){m=!1;break}this.action_icons.show_more_rows_icon.toggle(!m)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(e){"Auto"===this.mode&&("no_detail"===e&&(e="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+e+")"))},incremental_slots:function(e,t,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[e];return a&&a.mode===i||(a=new _.default.FeatureSlotter(e,i,100,function(e){return n.measureText(e)}),this.slotters[e]=a),a.slot_features(t)},get_mode:function(e){return"no_detail"===e.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var m=this.filters_manager.filters,_=0,g=e.data.length;_<g;_++){for(var v,w=e.data[_],b=!1,y=0,x=m.length;y<x;y++)if(v=m[y],v.update_attrs(w),!v.keep(w)){b=!0;break}b||(h.push(w),w[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new U(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new U(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,s,function(e){return r.view.get_base_color(e)}),S=null;if(t.fillStyle=this.config.get_value("block_color"),t.font=t.canvas.manager.default_font,t.textAlign="right",e.data){var T=$.draw(t,l.width,l.height,a,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-u}return o?void 0:new B(r,n,a,l,e.data,i,e.message,p,S,incomplete_features,s)}});var ee=function(e,t,i){Y.call(this,e,t,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};E(ee.prototype,z.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(z.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(e,t,i,n,a){if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,"Histogram",n,a);var s=this.view;return new this.painter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(e){return s.get_base_color(e)}).draw(t,t.canvas.width,t.canvas.height,a),new H(this,n,a,t.canvas,e.data)},get_canvas_height:function(e,t,i,n){if("bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==e.data.length&&(a=e.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),t).get_required_height(a)},predraw_init:function(){var e=[q.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||e.push(this.dataset.fetch()),e},postdraw_actions:function(t,i,n,a){Y.prototype.postdraw_actions.call(this,t,i,n,a);var s=l.filter(t,function(e){return e instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===s.length&&this.config.get_value("show_labels")&&o&&o.length>1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(e("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var te=function(e,t,i){Z.call(this,e,t,i),this.painter=v.default.ReadPainter,this.update_icons()};E(te.prototype,z.prototype,Y.prototype,Z.prototype,{build_config_params:function(){return l.union(z.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var ie={CompositeTrack:J,DrawableGroup:L,DiagonalHeatmapTrack:Q,FeatureTrack:Z,LineTrack:K,ReadTrack:te,VariantTrack:ee,VcfTrack:ee},ne=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new ie[n](t,i,e)};t.default={TracksterView:R,DrawableGroup:L,LineTrack:K,FeatureTrack:Z,DiagonalHeatmapTrack:Q,ReadTrack:te,VariantTrack:ee,CompositeTrack:J,object_from_template:ne}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(a),o=e.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(e){e.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var e=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),s.each(this.model.action_icons_def,function(t){e.add_action_icon(t.name,t.title,t.css_class,t.on_click_fn,t.prepend,t.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,t,i,a,s,o){var r=this;this.action_icons[e]=n("<a/>").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(function(){a(r.model)}).appendTo(this.icons_div),o&&this.action_icons[e].hide()},set_display_modes:function(e,t){if(e){this.model.display_modes=e,this.model.mode=t||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,s=i.display_modes.length;a<s;a++){var o=i.display_modes[a];n[o]=function(e){return function(){i.change_mode(e)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});t.default={TrackHeaderView:o}}).call(t,i(1),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e,t){this.slot=e,this.feature=t},r=function(e,t,i,n){this.slots={},this.start_end_dct={},this.w_scale=e,this.mode=t,this.include_label="Pack"===t,this.max_rows=i,this.measureText=n};s(r.prototype,{_get_draw_coords:function(e){var t=Math.floor(e[1]*this.w_scale),i=Math.ceil(e[2]*this.w_scale),n=e[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;t-a>=0?(t-=a,"left"):(i+=a,"right")}return[t,i]},_find_slot:function(e){for(var t=e[0],i=e[1],n=0;n<=this.max_rows;n++){var a=!1,s=this.start_end_dct[n];if(void 0!==s)for(var o=0,r=s.length;o<r;o++){var l=s[o];if(i>l[0]&&t<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(e){for(var t,i,n=this.start_end_dct,a=[],s=0,r=0,l=e.length;r<l;r++){t=e[r],i=t[0];var d=this.slots[i];if(d){if(t[1]<d.feature[1]||d.feature[2]<t[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(t),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}s=Math.max(s,this.slots[i].slot)}else a.push(r)}for(var r=0,l=a.length;r<l;r++){t=e[a[r]],i=t[0];var m=this._get_draw_coords(t),_=this._find_slot(m);_>=0&&(void 0===n[_]&&(n[_]=[]),n[_].push(m),this.slots[i]=new o(_,t),s=Math.max(s,_))}return s+1}}),t.default={FeatureSlotter:r}},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=function(e,t){var i=e[0],n=e[1],a=t[0],s=t[1];return i<a?n<=a?1001:n<=s?1003:1002:i>s?1006:n<=s?1005:1004},o=function(e,t){var i=s(e,t);return 1001!==i&&1006!==i},r=function(e,t,i,n,a,s){void 0===s&&(s=4);var o,r=n-t,l=a-i,d=Math.floor(Math.sqrt(r*r+l*l)/s),c=r/d,u=l/d;for(o=0;o<d;o++,t+=c,i+=u)o%2==0&&e.fillRect(t,i,s,1)},l=function(e,t,i,n){var a=t-n/2,s=t+n/2,o=i-Math.sqrt(3*n/2);e.beginPath(),e.moveTo(a,o),e.lineTo(s,o),e.lineTo(t,i),e.lineTo(a,o),e.strokeStyle=this.fillStyle,e.fill(),e.stroke(),e.closePath()},d=function(e){this.default_val=e||1};d.prototype.gen_val=function(e){return this.default_val};var c=function(e){this.incomplete_features=e.incomplete_features,this.feature_mapper=e.feature_mapper},u=function(e,t,i,n,s){this.data=e,this.view_start=t,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=s};u.prototype.default_prefs={},u.prototype.draw=function(e,t,i,n){},u.prototype.get_start_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,-.5)},u.prototype.get_end_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,.5)},u.prototype.get_draw_pos=function(e,t){return this._chrom_pos_to_draw_pos(e,t,0)},u.prototype._chrom_pos_to_draw_pos=function(e,t,i){return Math.floor(t*(Math.max(0,e-this.view_start)+i))};var h=function(e,t,i,n,a){u.call(this,e,t,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(e,t,i,n){var s=!1,o=this.prefs.min_value,r=this.prefs.max_value,l=r-o,d=i,c=this.view_start,u=this.mode,h=this.data;e.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(e.fillStyle="#aaa",e.fillRect(0,f,t,1)),e.beginPath();var p,m,_;_=h.length>1?a.map(h.slice(0,-1),function(e,t){return Math.ceil((h[t+1][0]-h[t][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,w=parseInt(v.slice(1),16),b=(16711680&w)>>16,y=(65280&w)>>8,x=255&w,k=!1,C=!1,$=0,S=h.length;$<S;$++)if(e.fillStyle=e.strokeStyle=v,k=C=!1,g=_[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(m=h[$][1])){if(m<o?(C=!0,m=o):m>r&&(k=!0,m=r),"Histogram"===u)m=Math.round(m/l*d),e.fillRect(p,f,g,-m);else if("Intensity"===u){var T=(m-o)/l,M=Math.round(b+(255-b)*(1-T)),E=Math.round(y+(255-y)*(1-T)),P=Math.round(x+(255-x)*(1-T));e.fillStyle="rgb("+M+","+E+","+P+")",e.fillRect(p,0,g,d)}else m=Math.round(d-(m-o)/l*d),s?e.lineTo(p,m):(s=!0,"Filled"===u?(e.moveTo(p,d),e.lineTo(p,m)):e.moveTo(p,m));if(e.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===u||"Intensity"===u?O=g:(p-=2,O=4),k&&e.fillRect(p,0,O,3),C&&e.fillRect(p,d-3,O,3)}e.fillStyle=v}else s&&"Filled"===u&&e.lineTo(p,d),s=!1;"Filled"===u?(s&&(e.lineTo(p,f),e.lineTo(0,f)),e.fill()):e.stroke(),e.restore()};var f=function(e){this.feature_positions={},this.slot_height=e,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(e,t,i,n){this.feature_positions[t]||(this.feature_positions[t]=[]),this.feature_positions[t].push({data:e,x_start:i,x_end:n})},f.prototype.get_feature_data=function(e,t){var i,n=Math.floor((t-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;e+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],e>=i.x_start&&e<=i.x_end)return i.data};var p=function(e,t,i,n,a,s,o){u.call(this,e,t,i,n,a),this.alpha_scaler=s||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(e,t){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=e*n),i+this.get_top_padding(t)},get_top_padding:function(e){return 0},draw:function(e,t,i,n,a){var s=this.data,o=this.view_start,r=this.view_end;e.save(),e.fillStyle=this.prefs.block_color,e.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,m=s.length;p<m;p++){var _=s[p],g=_[0],v=_[1],w=_[2],b=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==b)&&v<r&&w>o&&(l=this.draw_element(e,this.mode,_,b,o,r,n,d,t),u.map_feature_data(_,b,l[0],l[1]),(v<o||w>r)&&h.push(_))}return e.restore(),u.y_translation=this.get_top_padding(t),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(e,t,i,n,a,s,o,r,l){return[0,0]}});var m=function(e,t,i,n,a,s,o){p.call(this,e,t,i,n,a,s,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(m.prototype,p.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"no_detail"===e?3:"Squish"===e?5:10},draw_element:function(e,t,i,n,a,s,o,r,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),m=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),_=p,g=m,d=("Dense"===t?0:0+n)*r+this.get_top_padding(l),v=null,w=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(e.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===t&&(n=1),"no_detail"===t)e.fillStyle=b,e.fillRect(p,d+5,m-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),w=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var S,T;if("Squish"===t?(S=1,T=3,$=!1):(S=5,T=9),C){var M,E;"Squish"===t||"Dense"===t?(M=d+Math.floor(1.5)+1,E=1):f?(M=d,E=T):(M+=2.5,E=1),this.draw_background_connector&&("Squish"===t||"Dense"===t?e.fillStyle="#ccc":f?"+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand")):e.fillStyle="#ccc",e.fillRect(p,M,m-p,E));for(var P=0,O=C.length;P<O;P++){var A,D,I=C[P],z=Math.floor(Math.max(0,(I[0]-a-.5)*o)),j=Math.ceil(Math.min(l,Math.max((I[1]-a-.5)*o)));if(!(z>j)){if(e.fillStyle=b,e.fillRect(z,d+(T-S)/2+1,j-z,S),void 0!==v&&k>x&&!(z>w||j<v)){var L=Math.max(z,v),R=Math.min(j,w);e.fillRect(L,d+1,R-L,T),1===C.length&&"Pack"===t&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),L+14<R&&(L+=2,R-=2),e.fillRect(L,d+1,R-L,T))}this.draw_individual_connectors&&A&&this.draw_connector(e,A,D,z,j,d),A=z,D=j}}if("Pack"===t){e.globalAlpha=1,e.fillStyle="white";var N=this.height_scaler.gen_val(i),V=Math.ceil(T*N),G=Math.round((T-V)/2);1!==N&&(e.fillRect(p,M+1,m-p,G),e.fillRect(p,M+T-G+1,m-p,G))}}else e.fillStyle=b,e.fillRect(p,d+1,m-p,T),f&&$&&("+"===f?e.fillStyle=e.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand_inv")),e.fillRect(p,d+1,m-p,T));e.globalAlpha=1,h&&"Pack"===t&&c>a&&(e.fillStyle=y,0===a&&p-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,m+2,d+8,this.max_label_length),g+=e.measureText(h).width+2):(e.textAlign="right",e.fillText(h,p-2,d+8,this.max_label_length),_-=e.measureText(h).width+2))}return e.globalAlpha=1,[_,g]}});var _=function(e,t,i,n,a,s,o,r,l){p.call(this,e,t,i,n,a,s,o),this.ref_seq=r?r.data:null,this.base_color_fn=l};a.extend(_.prototype,p.prototype,{get_row_height:function(){var e,t=this.mode;return"Dense"===t?e=10:"Squish"===t?e=5:(e=10,this.prefs.show_insertions&&(e*=2)),e},_parse_cigar:function(e){var t="MIDNSHP=X",i=[[0,0]],n=i[0],s=0,o=a.map(e.match(/[0-9]+[MIDNSHP=X]/g),function(e){var a=parseInt(e.slice(0,-1),10),o=e.slice(-1);return"N"===o?0!==n[1]&&(n=[s+a,s+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,s+=a),[t.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(e,t,i,n,a,r,d,c,u,h){var f=function(e){return Math.floor(Math.max(0,(e-a-.5)*i))};e.textAlign="center";var p,m,_=[a,r],g=0,v=0,w=Math.round(i/2),b=e.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===t,C=k?9:3,$=n+1,S=new x(e,C,i,t),T=[],M=[],E=this._parse_cigar(c);c=E.cigar,T=E.blocks;for(var P=0;P<T.length;P++){var O=T[P];o([d+O[0],d+O[1]],_)&&(p=f(d+O[0]),m=f(d+O[1]),p===m&&(m+=1),e.fillStyle=y,e.fillRect(p,$,m-p,C))}for(var A=0,D=c.length;A<D;A++){var I=c[A],z="MIDNSHP=X"[I[0]],j=I[1],L=d+g;if(p=f(L),m=f(L+j),o([L,L+j],_))switch(p===m&&(m+=1),z){case"H":case"S":case"P":break;case"M":g+=j;break;case"=":case"X":var R="";"X"===z?R=h.slice(v,v+j):this.ref_seq&&(R=this.ref_seq.slice(Math.max(0,L-a),Math.min(L-a+j,r-a)));for(var N=Math.max(L,a),V=0;V<R.length;V++)if(R&&!this.prefs.show_differences||"X"===z){var G=Math.floor(Math.max(0,(N+V-a)*i));e.fillStyle=this.base_color_fn(R[V]),k&&i>b?e.fillText(R[V],G,n+9):i>.05&&e.fillRect(G-w,$,Math.max(1,Math.round(i)),C)}"X"===z&&(v+=j),g+=j;break;case"N":e.fillStyle="#ccc",e.fillRect(p,$+(C-1)/2,m-p,1),g+=j;break;case"D":S.draw_deletion(p,$,j),g+=j;break;case"I":var U=p-w;if(o([L,L+j],_)){var H=h.slice(v,v+j);if(this.prefs.show_insertions){var F=p-(m-p)/2;if(("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b){switch(e.fillStyle="yellow",e.fillRect(F-w,n-9,m-p,9),M[M.length]={type:"triangle",data:[U,n+4,5]},e.fillStyle="#ccc",s([L,L+j],_)){case 1003:H=H.slice(a-L);break;case 1004:H=H.slice(0,L-r);break;case 1005:break;case 1002:H=H.slice(a-L,L-r)}for(var V=0,B=H.length;V<B;V++){var G=Math.floor(Math.max(0,(L+V-a)*i));e.fillText(H[V],G-(m-p)/2,n)}}else e.fillStyle="yellow",e.fillRect(F,n+("Dense"!==this.mode?2:5),m-p,"Dense"!==t?3:9)}else("Pack"===t||"Auto"===this.mode)&&void 0!==h&&i>b&&M.push({type:"text",data:[H.length,U,n+9]})}v+=j}else g=function(e,t,i){return-1!=="M=NXD".indexOf(t)&&(e+=i),e}(g,z,j),v=function(e,t,i){return-1!=="IX".indexOf(t)&&(e+=i),e}(v,z,j)}e.fillStyle="yellow";for(var q,Y,W,P=0;P<M.length;P++)q=M[P],Y=q.type,W=q.data,"text"===Y?(e.save(),e.font="bold "+e.font,e.fillText(W[0],W[1],W[2]),e.restore()):"triangle"===Y&&l(e,W[0],W[1],W[2])},draw_element:function(e,t,i,n,a,s,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),m=("Dense"===t?0:0+n)*l,_="Pack"===t?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=s&&i[4][2]?this.draw_read(e,t,o,m,a,s,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=s&&i[5][2]?this.draw_read(e,t,o,m,a,s,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),w=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&w>v){e.fillStyle="#ccc";var b=m+1+(_-1)/2;r(e,v,b,w,b)}}else this.draw_read(e,t,o,m,a,s,c,i[4],i[5],i[6]);return"Pack"===t&&c>=a&&"."!==h&&(e.fillStyle=this.prefs.label_color,0===a&&f-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,p+2,m+9,this.max_label_length)):(e.textAlign="right",e.fillText(h,f-2,m+9,this.max_label_length))),[0,0]}});var g=function(e,t,i,n,a,s,o){m.call(this,e,t,i,n,a,s,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,m.prototype,{calculate_longest_feature_length:function(){for(var e=0,t=0,i=this.data.length;t<i;t++){var n=this.data[t],a=n[1],s=n[2];e=Math.max(e,s-a)}return e},get_top_padding:function(e){var t=this.view_end-this.view_start,i=e/t;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(e,t,i,n,a,s){var o=(i+n)/2,r=n-o;Math.PI;r>0&&(e.beginPath(),e.arc(o,s,n-o,Math.PI,0),e.stroke())}});var v=function(e,t){Array.isArray(e)?this.rgb=e:6==e.length?this.rgb=e.match(/.{2}/g).map(function(e){return parseInt(e,16)}):7==e.length?this.rgb=e.substring(1,7).match(/.{2}/g).map(function(e){return parseInt(e,16)}):this.rgb=e.split("").map(function(e){return parseInt(e+e,16)}),this.alpha="number"==typeof t?t:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(e){return Math.round(e)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},toHSL:function(){var e,t,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,s=this.alpha,o=Math.max(i,n,a),r=Math.min(i,n,a),l=(o+r)/2,d=o-r;if(o===r)e=t=0;else{switch(t=l>.5?d/(2-o-r):d/(o+r),o){case i:e=(n-a)/d+(n<a?6:0);break;case n:e=(a-i)/d+2;break;case a:e=(i-n)/d+4}e/=6}return{h:360*e,s:t,l:l,a:s}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(e){return e=Math.round(e),e=(e>255?255:e<0?0:e).toString(16),1===e.length?"0"+e:e}).join("")},mix:function(e,t){var i=this,n=t,a=2*n-1,s=i.toHSL().a-e.toHSL().a,o=((a*s==-1?a:(a+s)/(1+a*s))+1)/2,r=1-o,l=[i.rgb[0]*o+e.rgb[0]*r,i.rgb[1]*o+e.rgb[1]*r,i.rgb[2]*o+e.rgb[2]*r],d=i.alpha*n+e.alpha*(1-n);return new v(l,d)}};var w=function(e,t,i,n){this.start_color=new v(e),this.end_color=new v(t),this.start_value=i,this.end_value=n,this.value_range=n-i};w.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e=(e-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-e).toCSS()};var b=function(e,t,i,n,a){this.positive_ramp=new w(t,i,0,a),this.negative_ramp=new w(t,e,0,-n),this.start_value=n,this.end_value=a};b.prototype.map_value=function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e>=0?this.positive_ramp.map_value(e):this.negative_ramp.map_value(-e)};var y=function(e,t,i,n,a){u.call(this,e,t,i,n,a);var s,o;if(void 0===this.prefs.min_value){var r=1/0;for(s=0,o=this.data.length;s<o;s++)r=Math.min(r,this.data[s][6]);this.prefs.min_value=r}if(void 0===this.prefs.max_value){var l=-1/0;for(s=0,o=this.data.length;s<o;s++)l=Math.max(l,this.data[s][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(e,t,i,n){var a,s,o,r,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),m=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),_=function(e){return(e-h)*n};e.save(),e.rotate(-45*Math.PI/180),e.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],s=_(a[1]),o=_(a[2]),r=_(a[4]),l=_(a[5]),d=a[6],e.fillStyle=m.map_value(d),e.fillRect(s,r,o-s,l-r);e.restore()};var x=function(e,t,i,n){this.ctx=e,this.row_height=t,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=e.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(e,t,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;t+=.5*(this.row_height-n),this.ctx.fillRect(e,t,i*this.px_per_base,n)}});var k=function(e,t,i,n,a,s){u.call(this,e,t,i,n,a),this.base_color_fn=s,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var e=this.mode;return"Dense"===e?10:"Squish"===e?5:10},get_required_height:function(e){var t=this.prefs.summary_height;return e>1&&this.prefs.show_sample_data&&(t+=this.divider_height+e*this.get_row_height()),t},draw:function(e,t,i,n){e.save();var s,o,r,l,d,c,u,h,f,p,m,_=function(e,t){var i=e.length,n=t.length,a=0,s=1,o=null;return"-"===t?(o="deletion",s=e.length):0===e.indexOf(t)&&i>n?(o="deletion",s=i-n,a=n):0===t.indexOf(e)&&i<n&&(o="insertion",s=n-i,a=n),null!==o?{type:o,start:a,len:s}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,w="Squish"===this.mode?5:10,b=n<.1?w:"Squish"===this.mode?3:9,y=!0,k=new x(e,w,n,this.mode);1===v&&(w=b=n<e.canvas.manager.char_width_px?this.prefs.summary_height:w,k.row_height=w,y=!1),this.prefs.show_sample_data&&y&&(e.fillStyle="#F3F3F3",e.globalAlpha=1,e.fillRect(0,this.prefs.summary_height-this.divider_height,t,this.divider_height)),e.textAlign="center";for(var C=0;C<this.data.length;C++)if(s=this.data[C],o=s[1],r=s[3],l=[s[4].split(",")],d=s[7].split(","),c=s.slice(8),l=a.map(a.flatten(l),function(e){var t={type:"snp",value:e,start:0},i=_(r,e);return a.extend(t,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(e.fillStyle="#999999",e.globalAlpha=1,m=0;m<l.length;m++)for(h=this.get_start_draw_pos(o+l[m].start,n),e.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,m=0;m<l.length;m++){e.fillStyle="deletion"===l[m].type?"black":this.base_color_fn(l[m].value);var $=c/d.length,S=Math.ceil(this.prefs.summary_height*$);e.fillRect(h,f-S,g,S),f-=S}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,m=0;m<d.length;m++,f+=w)if(p=d[m]?d[m].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],e.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],e.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;e.fillStyle=this.base_color_fn(T),k.draw_details?e.fillText(T,this.get_draw_pos(o,n),f+w):e.fillRect(h,f+1,g,b)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}e.restore()}}),t.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:m,ReadPainter:_,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=a.extend,o=function(e){this.manager=null,this.name=e.name,this.index=e.index,this.tool_id=e.tool_id,this.tool_exp_name=e.tool_exp_name};s(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var r=function(t,i,n){return e("<a/>").attr("href","javascript:void(0);").attr("title",t).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(t){o.call(this,t),this.low="low"in t?t.low:-Number.MAX_VALUE,this.high="high"in t?t.high:Number.MAX_VALUE,this.min="min"in t?t.min:Number.MAX_VALUE,this.max="max"in t?t.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=e("<div/>").addClass("filter-row slider-row");var n=e("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(e("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),e("<span/>").text(this.low+"-"+this.high)),s=e("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=e("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=e("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(e,t){i.slide(e,t)},change:function(e,t){i.control_element.slider("option","slide").call(i.control_element,e,t)}}),i.slider=i.control_element,i.slider_label=a,function(t,i,n){t.click(function(){var t=i.text(),a=parseFloat(n.slider("option","max")),s=a<=1?4:a<=1e6?a.toString().length:6,o=!1,r=e(this).parents(".slider-row");r.addClass("input"),n.slider("option","values")&&(s=2*s+1,o=!0),i.text(""),e("<input type='text'/>").attr("size",s).attr("maxlength",s).attr("value",t).appendTo(i).focus().select().click(function(e){e.stopPropagation()}).blur(function(){e(this).remove(),i.text(t),r.removeClass("input")}).keyup(function(t){if(27===t.keyCode)e(this).trigger("blur");else if(13===t.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),s=function(e){return isNaN(e)||e>a||e<i},l=e(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],s(l[0])||s(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this)}else if(l=parseFloat(l),s(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),e(this);n.slider(o?"values":"value",l),r.removeClass("input")}})})}(s,a,i.control_element);var d=e("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=r("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=r("Use filter for data 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i=t.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(e){return e.length>this.index},_keep_val:function(e){return isNaN(e)||e>=this.low&&e<=this.high},keep:function(e){if(!this.applies_to(e))return!0;var t=e[this.index];if(t instanceof Array){for(var i=!0,n=0;n<t.length;n++)if(!this._keep_val(t[n])){i=!1;break}return i}return this._keep_val(e[this.index])},update_attrs:function(e){var t=!1;if(!this.applies_to(e))return t;var i=e[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),t=!0),a>this.max&&(this.max=Math.ceil(a),t=!0)}return t},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var e=this.slider.slider("option","min"),t=this.slider.slider("option","max");(this.min<e||this.max>t)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(t,i){if(this.track=t,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=e("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).bind("keydown",function(e){e.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),s=("height_filter"in i?i.height_filter:null),o=i.filters,r=0;r<o.length;r++)"number"===o[r].type?(n=new 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t.filters=i,t.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,t.height_filter=this.height_filter?this.height_filter.name:null,t.visible=this.parent_div.is(":visible"),t},copy:function(e){for(var t=new d(e),i=0;i<this.filters.length;i++)t.add_filter(this.filters[i].copy());return t},add_filter:function(e){e.manager=this,this.parent_div.append(e.parent_div),this.filters.push(e)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var e=0;e<this.filters.length;e++){this.filters[e].update_ui_elt()}},clear_filters:function(){for(var e=0;e<this.filters.length;e++){var t=this.filters[e];t.slider.slider("option","values",[t.min,t.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var t,i,n=(function(e,t,i){return t in 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Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):t(e.dataset_id,n)})}(this.track.dataset_id,o)}}),t.default={FiltersManager:d,NumberFilter:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(13),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=i(152),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=a.default.GenomeDataManager.extend({load_data:function(t,i,n,a){var s=e.Deferred();this.set_data(t,s);var r=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new e.Deferred;return e.when(o.makeBwg(r)).then(function(i,n){e.when(i.readWigData(t.get("chrom"),t.get("start"),t.get("end"))).then(function(e){var i=[],n={max:Number.MIN_VALUE};e.forEach(function(e){n.max!==e.min-1&&(i.push([n.max+1,0]),i.push([e.min-2,0])),i.push([e.min-1,e.score]),i.push([e.max,e.score]),n=e});var a={data:i,region:t,dataset_type:"bigwig"};l.set_data(t,a),s.resolve(a)})}),s}});t.default={BBIDataManager:r}}).call(t,i(0))},function(e,t,i){(function(n){var a,s;a=[i(153),i(154),i(155)],void 0!==(s=function(e,t){"use strict";function i(){}function a(e){e&&(this.id=e)}function s(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function o(e,t,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:e,timeout:5e3,beforeSend:function(e){e.setRequestHeader("Range","bytes="+t+"-"+(t+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function r(e,t){return e[t]+e[t+1]*y+e[t+2]*x+e[t+3]*k+e[t+4]*C}function l(){}function d(e,t,i,n){this.bwg=e,this.cirTreeOffset=t,this.cirTreeLength=i,this.isSummary=n}function c(e){var t=n.Deferred(),i=new l;return i.url=e,n.when(o(i.url,0,512)).then(function(e){if(!e)return t.resolve(null,"Couldn't fetch file");var a=e,s=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=s[0]+y*s[1]+x*s[2]+k*s[3];if(d==g)i.type="bigwig";else{if(d!=w)return 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l.prototype.readChromTree=function(){var e=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var t=this.unzoomedDataOffset;return t=t+4-(t-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,t-this.chromTreeOffset)).then(function(t){var i=new Uint8Array(t),n=new Int16Array(t),a=new Int32Array(t),s=(a[0],a[1],a[2]),o=(a[3],r(i,16),function(t){var a=i[t],l=n[t/2+1];t+=4;for(var d=0;d<l;++d)if(0===a){t+=s;var c=r(i,t);t+=8,c-=e.chromTreeOffset,o(c)}else{for(var u="",h=0;h<s;++h){var f=i[t++];0!==f&&(u+=String.fromCharCode(f))}var p=i[t+3]<<24|i[t+2]<<16|i[t+1]<<8|i[t+0];i[t+7],i[t+6],i[t+5],i[t+4],t+=8,e.chromsToIDs[u]=p,0===u.indexOf("chr")&&(e.chromsToIDs[u.substr(3)]=p),e.idsToChroms[p]=u,e.maxID=Math.max(e.maxID,p)}});o(32)})},d.prototype.readWigData=function(e,t,i){var n=this.bwg.chromsToIDs[e];return void 0===n?[]:this.readWigDataById(n,t,i)},d.prototype.readWigDataById=function(e,t,i){var a=this,s=n.Deferred();if(!this.cirHeader)return 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r=0;r<e.length;++r)t.contains(e[r])&&(m(o,e[r]-t.min(),i),e[r]-a.cirTreeOffset==48&&e[r]-t.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}))})},m=function(n,a,s){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16),y=r(o,a+24);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&l.push({offset:b,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var m=a/4,_=c[m],g=c[m+1],v=c[m+2],w=c[m+3],b=r(o,a+16);(e<0||_<e||_==e&&g<=i)&&(e<0||v>e||v==e&&w>=t)&&x.push(b),a+=24}x.length>0&&u(x,s+1)}};return u([a.cirTreeOffset+48],1),s},d.prototype.fetchFeatures=function(e,t){var a=this,s=n.Deferred();if(t.sort(function(e,t){return(0|e.offset)-(0|t.offset)}),0===t.length)return[];var r=[],l=function(e,t,n,s){s||(s={});var o=new i;o._chromId=e,o.segment=a.bwg.idsToChroms[e],o.min=t,o.max=n,o.type=a.bwg.type;for(var l in 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e||(e=c),i&&(i=!1),this.istate=new t,this.istate.inflateInit(this,i?-e:e)},e.prototype.inflate=function(e){return null==this.istate?-2:this.istate.inflate(this,e)},e.prototype.inflateEnd=function(){if(null==this.istate)return-2;var e=istate.inflateEnd(this);return this.istate=null,e},e.prototype.inflateSync=function(){return istate.inflateSync(this)},e.prototype.inflateSetDictionary=function(e,t){return istate.inflateSetDictionary(this,e,t)},t.prototype.inflateReset=function(e){return null==e||null==e.istate?-2:(e.total_in=e.total_out=0,e.msg=null,e.istate.mode=0!=e.istate.nowrap?7:0,e.istate.blocks.reset(e,null),f)},t.prototype.inflateEnd=function(e){return null!=this.blocks&&this.blocks.free(e),this.blocks=null,f},t.prototype.inflateInit=function(e,t){return e.msg=null,this.blocks=null,nowrap=0,t<0&&(t=-t,nowrap=1),t<8||t>15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<<t),this.inflateReset(e),f)},t.prototype.inflate=function(e,t){var i,n;if(null==e||null==e.istate||null==e.next_in)return-2;for(t=4==t?m:f,i=m;;)switch(e.istate.mode){case 0:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,8!=(15&(e.istate.method=e.next_in[e.next_in_index++]))){e.istate.mode=13,e.msg="unknown compression method",e.istate.marker=5;break}if(8+(e.istate.method>>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<<e.istate.wbits&&(a=(1<<e.istate.wbits)-1,n=i-a),e.istate.blocks.set_dictionary(t,n,a),e.istate.mode=7,f)};var S=[0,0,255,255];t.prototype.inflateSync=function(e){var t,i,n,a,s;if(null==e||null==e.istate)return-2;if(13!=e.istate.mode&&(e.istate.mode=13,e.istate.marker=0),0==(t=e.avail_in))return m;for(i=e.next_in_index,n=e.istate.marker;0!=t&&n<4;)e.next_in[i]==S[n]?n++:n=0!=e.next_in[i]?0:4-n,i++,t--;return e.total_in+=i-e.next_in_index,e.next_in_index=i,e.avail_in=t,e.istate.marker=n,4!=n?-3:(a=e.total_in,s=e.total_out,this.inflateReset(e),e.total_in=a,e.total_out=s,e.istate.mode=7,f)},t.prototype.inflateSyncPoint=function(e){return null==e||null==e.istate||null==e.istate.blocks?-2:e.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(e,t){t&&(t[0]=this.check),6==this.mode&&this.codes.free(e),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(e.adler=this.check=e._adler.adler32(0,null,0,0))},i.prototype.proc=function(e,t){var i,n,a,r,l,d,c;for(r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),m=[],v=[];s(u,h,m,v,e),this.codes.init(u[0],h[0],m[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(t=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var w=0;w<i;w++)this.blens[w]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,b,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&_[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&_[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(w=18==y?7:y-14,b=18==y?11:3;a<i+w;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<<a,a+=8}if(n>>>=i,a-=i,b+=n&_[w],n>>>=w,a-=w,w=this.index,i=this.table,w+b>258+(31&i)+(i>>5&31)||16==y&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);y=16==y?this.blens[w-1]:0;do{this.blens[w++]=y}while(0!=--b);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),m=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,m,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,m[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,t=this.inflate_flush(e,t),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);mode=12;case 8:return t=p,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);case 9:return t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);default:return t=-2,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}},i.prototype.free=function(e){this.reset(e,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(e,t,i){o(e,t,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(e,t){var i,n,a;return n=e.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==m&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r<e.read?e.read-r-1:e.end-r,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.len+=c&_[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&_[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u<n;){if(0==o)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,o--,c|=(255&t.next_in[h++])<<u,u+=8}this.dist+=c&_[n],c>>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);e.window[r++]=e.window[d++],l--,d==e.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l&&(e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,r==e.end&&0!=e.read&&(r=0,l=r<e.read?e.read-r-1:e.end-r),0==l)))return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);i=f,e.window[r++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r<e.read?e.read-r-1:e.end-r,e.read!=e.write)return e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);this.mode=8;case 8:return i=p,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 9:return i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);default:return i=-2,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i)}},n.prototype.free=function(e){},n.prototype.inflate_fast=function(e,t,i,n,a,s,r,l){var d,c,u,h,m,g,v,w,b,y,x,k,C,$,S,T;v=l.next_in_index,w=l.avail_in,m=r.bitb,g=r.bitk,b=r.write,y=b<r.read?r.read-b-1:r.end-b,x=_[e],k=_[t];do{for(;g<20;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if(d=m&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(m&_[h]),m>>=h,g-=h;g<15;)w--,m|=(255&l.next_in[v++])<<g,g+=8;for(d=m&k,c=a,u=s,T=3*(u+d),h=c[T];;){if(m>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)w--,m|=(255&l.next_in[v++])<<g,g+=8;if($=c[T+2]+(m&_[h]),m>>=h,g-=h,y-=C,b>=$)S=b-$,r.window[b++]=r.window[S++],r.window[b++]=r.window[S++],C-=2;else{S=b-$;do{S+=r.end}while(S<0);if(h=r.end-S,C>h){if(C-=h,b-S>0&&h>b-S)do{r.window[b++]=r.window[S++]}while(0!=--h);else o(r.window,S,r.window,b,h),b+=h,S+=h,h=0;S=0}}do{r.window[b++]=r.window[S++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3;d+=c[T+2],d+=m&_[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,-3);if(d+=c[T+2],d+=m&_[h],T=3*(u+d),0==(h=c[T])){m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--;break}}else m>>=c[T+1],g-=c[T+1],r.window[b++]=c[T+2],y--}while(y>=258&&w>=10);return C=l.avail_in-w,C=g>>3<C?g>>3:C,w+=C,v-=C,g-=C<<3,r.bitb=m,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=b,f},a.prototype.huft_build=function(e,t,i,n,a,s,r,l,d,c,h){var p,_,g,v,w,b,y,x,k,C,$,S,T,M,E;C=0,w=i;do{this.c[e[t+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return r[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(y=b,x<b&&(x=b),w=15;0!=w&&0==this.c[w];w--);for(g=w,x>w&&(x=w),l[0]=x,M=1<<b;b<w;b++,M<<=1)if((M-=this.c[b])<0)return-3;if((M-=this.c[w])<0)return-3;for(this.c[w]+=M,this.x[1]=b=0,C=1,T=2;0!=--w;)this.x[T]=b+=this.c[C],T++,C++;w=0,C=0;do{0!=(b=e[t+C])&&(this.v[this.x[b]++]=w),C++}while(++w<i);for(i=this.x[g],this.x[0]=w=0,C=0,v=-1,S=-x,this.u[0]=0,$=0,E=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>S+x;){if(v++,S+=x,E=g-S,E=E>x?x:E,(_=1<<(b=y-S))>p+1&&(_-=p+1,T=y,b<E))for(;++b<E&&!((_<<=1)<=this.c[++T]);)_-=this.c[T];if(E=1<<b,this.hn[0]+E>u)return-3;this.u[v]=$=this.hn[0],this.hn[0]+=E,0!=v?(this.x[v]=w,this.r[0]=b,this.r[1]=x,b=w>>>S-x,this.r[2]=$-this.u[v-1]-b,o(this.r,0,d,3*(this.u[v-1]+b),3)):r[0]=$}for(this.r[1]=y-S,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=s[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),_=1<<y-S,b=w>>>S;b<E;b+=_)o(this.r,0,d,3*($+b),3);for(b=1<<y-1;0!=(w&b);b>>>=1)w^=b;for(w^=b,k=(1<<S)-1;(w&k)!=this.x[v];)v--,S-=x,k=(1<<S)-1}return 0!=M&&1!=g?m:f},a.prototype.inflate_trees_bits=function(e,t,i,n,a){var s;return this.initWorkArea(19),this.hn[0]=0,s=this.huft_build(e,0,19,19,null,null,i,t,n,this.hn,this.v),-3==s?a.msg="oversubscribed dynamic bit lengths tree":s!=m&&0!=t[0]||(a.msg="incomplete dynamic bit lengths tree",s=-3),s},a.prototype.inflate_trees_dynamic=function(e,t,i,n,a,s,o,r,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,e,257,x,k,s,n,r,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,e,t,0,C,$,o,a,r,this.hn,this.v),d!=f||0==a[0]&&e>257?(-3==d?l.msg="oversubscribed distance tree":d==m?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(e){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(e),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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n={id:i.name,icon:i.config.icon,url:i.config.url,tooltip:i.config.tooltip,onclick:i.config.function&&new Function(i.config.function)};Galaxy.page?Galaxy.page.masthead.collection.add(n):Galaxy.masthead&&Galaxy.masthead.collection.add(n),p.default.appendScriptStyle(i)}})})}}),Galaxy.user.get("is_admin")&&this.add({id:"admin",title:(0,h.default)("Admin"),url:"admin",tooltip:(0,h.default)("Administer this Galaxy"),cls:"admin-only"});var i={id:"help",title:(0,h.default)("Help"),tooltip:(0,h.default)("Support, contact, and community"),menu:[{title:(0,h.default)("Support"),url:e.support_url,target:"_blank"},{title:(0,h.default)("Search"),url:e.search_url,target:"_blank"},{title:(0,h.default)("Mailing Lists"),url:e.mailing_lists,target:"_blank"},{title:(0,h.default)("Videos"),url:e.screencasts_url,target:"_blank"},{title:(0,h.default)("Wiki"),url:e.wiki_url,target:"_blank"},{title:(0,h.default)("How to Cite Galaxy"),url:e.citation_url,target:"_blank"},{title:(0,h.default)("Interactive 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e=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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e=s.defaults(e||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),e.url=t._formatUrl(e.url),n("<li/>").append(n("<a/>").attr("href",e.url).attr("target",e.target).html(e.title).on("click",function(i){i.preventDefault(),t.model.set("show_menu",!1),e.onclick?e.onclick():Galaxy.frame.add(e)}))},_toggleClick:function(e){var t=this,i=this.model;if(e.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(e){i.id!==e.id&&e.get("menu")&&e.set("show_menu",!1)}),i.get("disabled")){var a=function(e,t){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+t).html(e)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){t.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(e){return"string"==typeof e&&-1===e.indexOf("//")&&"/"!=e.charAt(0)?Galaxy.root+e:e},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});t.default={Collection:m,Tab:_}}).call(t,i(1),i(0),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(9),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(e){var t=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),r=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+r,d=t+":"+i+l,c=null,u=null,h='<iframe 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r.default.View({visible:!1}),this.setElement(this.frames.$el),this.buttonActive=e.collection.add({id:"enable-scratchbook",icon:"fa-th",tooltip:(0,m.default)("Enable/Disable Scratchbook"),onclick:function(){t.active=!t.active,t.buttonActive.set({toggle:t.active,show_note:t.active,note_cls:t.active&&"fa fa-check"}),!t.active&&t.frames.hide()},onbeforeunload:function(){if(t.frames.length()>0)return"You opened "+t.frames.length()+" frame(s) which will be lost."}}),this.buttonLoad=e.collection.add({id:"show-scratchbook",icon:"fa-eye",tooltip:(0,m.default)("Show/Hide Scratchbook"),show_note:!0,visible:!1,onclick:function(e){t.frames.visible?t.frames.hide():t.frames.show()}}),this.frames.on("add remove",function(){this.visible&&0==this.length()&&this.hide(),t.buttonLoad.set({note:this.length(),visible:this.length()>0})}).on("show hide ",function(){t.buttonLoad.set({toggle:this.visible,icon:this.visible&&"fa-eye"||"fa-eye-slash"})}),this.history_cache={}},addDataset:function(e){var 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t=this;if(t.options.patchExisting&&e)for(var i in e)e.hasOwnProperty(i)&&(t[i]=e[i])},s.prototype._initLogger=function(e){var t=this;if(t.config.debug){e.consoleLogger=e.consoleLogger||console,e.consoleLevel=e.consoleLevel||m.default.MetricsLogger.ALL;try{e.consoleNamespaceWhitelist=localStorage.getItem(b).split(",")}catch(e){}try{e.consoleFlattenMessages="true"==localStorage.getItem("galaxy:debug:flatten")}catch(e){}console.log(e.consoleFlattenMessages)}return t.logger=new m.default.MetricsLogger(e),t.emit={},["log","debug","info","warn","error","metric"].map(function(e){t.emit[e]=function(i){t.logger.emit(e,arguments[0],Array.prototype.slice.call(arguments,1))}}),t.config.debug&&(u.default.LoggableMixin.logger=t.logger),t},s.prototype._initLocale=function(e){var t=this;return t.debug("_initLocale:",e),t.localize=w.default,window._l=t.localize,t},s.prototype._initUser=function(e){var t=this;return t.debug("_initUser:",e),t.user=new 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u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new r.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),a=t[n];if(a){var s=new a(i,t);i[s.toString()]=s,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:s})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return a(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=a("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=a("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?a.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='<label class="prompt">'+(0,l.default)("Tags")+"</label>",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return'<input class="tags-input" value="'+this.tagsToCSV()+'"/>'},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t='<span class="label label-info">'+e+"</span>";i.push(t)}),0===i.length&&i.push("<img src="+t+' class="add-tag-button" title="Add tags"/>'),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(0),s=n(a),o=i(61),r=n(o),l=i(4),d=n(l),c=s.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),c.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=r.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3);!function(e){e&&e.__esModule}(s);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),a.each(this.options.parameters,function(t){var i=n("<div/>").addClass("upload-"+t.id+" upload-icon-button fa").addClass(e.model.get(t.id)&&e.options.class_check||e.options.class_uncheck).on("click",function(){e.model.get("enabled")&&e.model.set(t.id,!e.model.get(t.id))});e.$table.append(n("<tr/>").append(n("<td/>").append(i)).append(n("<td/>").append(t.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=function(e){return e&&e.__esModule?e:{default:e}}(s);t.default=e.View.extend({initialize:function(t){this.model=new e.Model({cls:"upload-ftp",class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",help_enabled:!0,help_text:"This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>"+t.ftp_upload_site+"</strong> using your Galaxy credentials.",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}).set(t),this.collection=this.model.get("collection"),this.setElement(this._template()),this.$content=this.$(".upload-ftp-content"),this.$wait=this.$(".upload-ftp-wait"),this.$help=this.$(".upload-ftp-help"),this.$number=this.$(".upload-ftp-number"),this.$disk=this.$(".upload-ftp-disk"),this.$body=this.$(".upload-ftp-body"),this.$warning=this.$(".upload-ftp-warning"),this.$select=this.$(".upload-ftp-select-all"),this.render()},render:function(){var e=this;this.$wait.show(),this.$content.hide(),this.$warning.hide(),this.$help.hide(),n.ajax({url:Galaxy.root+"api/remote_files",method:"GET",success:function(t){e.model.set("ftp_files",t),e._index(),e._renderTable()},error:function(){e._renderTable()}})},_renderTable:function(){var e=this,t=this.model.get("ftp_files");if(this.rows=[],t&&t.length>0){this.$body.empty();var i=0;a.each(t,function(t){e.rows.push(e._renderRow(t)),i+=t.size}),this.$number.html(t.length+" files"),this.$disk.html(o.default.bytesToString(i,!0)),this.collection&&(this.$("._has_collection").show(),this.$select.addClass(this.model.get("class_add")).off().on("click",function(){e._all()}),this._refresh()),this.$content.show()}else this.$warning.show();this.model.get("help_enabled")&&this.$help.show(),this.$wait.hide()},_renderRow:function(e){var t=this,i=this.model.attributes,a=n(this._templateRow(e)),s=a.find(".icon");if(this.$body.append(a),this.collection){var o=this.ftp_index[e.path];s.addClass(void 0===o?i.class_add:i.class_remove),a.on("click",function(){t._switch(s,e),t._refresh()})}else a.on("click",function(){i.onchange(e)});return s},_index:function(){var e=this;this.ftp_index={},this.collection&&this.collection.each(function(t){"ftp"==t.get("file_mode")&&(e.ftp_index[t.get("file_path")]=t.id)})},_all:function(){var e=this.model.attributes,t=this.model.get("ftp_files"),i=this.$select.hasClass(e.class_add);for(var n in t){var a=t[n],s=this.ftp_index[a.path];(void 0===s&&i||void 0!==s&&!i)&&this._switch(this.rows[n],a)}this._refresh()},_switch:function(e,t){e.removeClass();var i=this.model.attributes,n=this.ftp_index[t.path];if(void 0===n){var a=i.onadd(t);e.addClass(i.class_remove),this.ftp_index[t.path]=a}else i.onremove(n),e.addClass(i.class_add),this.ftp_index[t.path]=void 0},_refresh:function(){var e=a.reduce(this.ftp_index,function(e,t){return void 0!==t&&e++,e},0);this.$select.removeClass(),0==e?this.$select.addClass(this.model.get("class_add")):this.$select.addClass(e==this.rows.length?this.model.get("class_remove"):this.model.get("class_partial"))},_templateRow:function(e){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+a.escape(e.path)+'</td><td class="ftp-size">'+o.default.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_template:function(){return'<div class="'+this.model.get("cls")+'"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">'+this.model.get("help_text")+'</div><div class="upload-ftp-content"><span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=(a(s),i(165)),r=a(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new r.default.View({placement:e.placement||"bottom",container:e.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."}})}).call(t,i(1),i(2))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},t),a=n.data;if(a.error_message)return void n.error(a.error_message);var s=new FormData;for(var o in a.payload)s.append(o,a.payload[o]);var r=0;for(var o in a.files){var l=a.files[o];s.append(l.name,l.file,l.file.name),r+=l.file.size}if(r>1048576*n.maxfilesize)return void n.error(n.error_filesize);var d=new XMLHttpRequest;d.open("POST",n.url,!0),d.setRequestHeader("Accept","application/json"),d.setRequestHeader("Cache-Control","no-cache"),d.setRequestHeader("X-Requested-With","XMLHttpRequest"),d.onreadystatechange=function(){if(d.readyState==d.DONE){var t=null,i="";if(d.responseText)try{t=e.parseJSON(d.responseText),i=t.err_msg}catch(e){t=d.responseText,i=t}if(d.status<200||d.status>299){var a=d.statusText;403==d.status?a=n.error_login:0==d.status?a=n.error_server:a||(a=n.error_default),n.error(a+" ("+d.status+"). 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t.name===e.name&&t.size===e.size}).length&&(e.duplicate=!0)}),t.each(e,function(e){e.duplicate||(i=String(p++),f[i]=e,h.announce(i,f[i]),m++)}),i}}function a(e){f[e]&&(delete f[e],m--)}function s(){if(0==m||g)return g=!1,_=!1,void h.complete();_=!0;var e=-1;for(var t in f){e=t;break}f[e];a(e),i.uploadpost({url:h.url,data:h.initialize(e),success:function(t){h.success(e,t),s()},error:function(t){h.error(e,t),s()},progress:function(t){h.progress(e,t)}})}function o(){v.dialog()}function r(e){for(e in f)a(e)}function l(){_||(_=!0,s())}function d(){g=!0}function c(e){return h=i.extend({},h,e)}function u(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var h=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),f={},p=0,m=0,_=!1,g=!1,v=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:a,start:l,stop:d,reset:r,configure:c,compatible:u}}}(e)}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}function r(e,t){var i=e.toJSON();return C(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var l=i(188),d=o(l),c=i(166),u=o(c),h=i(8),f=o(h),p=i(207),m=o(p),_=i(9),g=o(_),v=i(208),w=(o(v),i(7)),b=o(w);i(209);var y=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['<a class="name" title="',(0,b.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,b.default)("Remove this dataset from the list"),'">',(0,b.default)("Discard"),"</button>"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,b.default)("Enter a new name for the element"),":\n(",(0,b.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,b.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:y,collectionClass:d.default.HistoryDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;n.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset"!==e.history_content_type?(0,b.default)("is not a dataset"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,b.default)("has been deleted or purged"):null:(0,b.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(a(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content 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";return t+='<a class="cancel-create" href="javascript:void(0);">'+(0,b.default)("Cancel")+"</a> ",t+=(0,b.default)("or"),t+=' <a class="reset" href="javascript:void(0);">'+(0,b.default)("start over")+"</a>.",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:(0,b.default)("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,b.default)("An error occurred");if(e.xhr){var n=e.xhr,a=e.message;0===n.readyState&&0===n.status?i+=": "+(0,b.default)("Galaxy could not be reached and may be updating.")+(0,b.default)(" Try again in a few minutes."):n.responseJSON?i+=":<br /><pre>"+JSON.stringify(n.responseJSON)+"</pre>":i+=": "+a}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend   .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(e){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(e){e.preventDefault();var t=this.$list();this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestElement(e.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=a('<div class="element-drop-placeholder"></div>');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),a=t-i.top,s=i.top+e.outerHeight()-t;a>=0&&a<this.autoscrollDist?e.scrollTop(n-2):s>=0&&s<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestElement:function(e){for(var t=this.$(".collection-elements li.collection-element").toArray(),i=0;i<t.length;i++){var n=a(t[i]),s=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(s+o>e&&s-o<e)return n}return a()},_dropElements:function(e){e.originalEvent&&(e=e.originalEvent),e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestElement(e.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".collection-elements .collection-element").last()),this._syncOrderToDom(),!1},_syncOrderToDom:function(){var e=this,t=[];this.$(".collection-elements .collection-element").each(function(){var i=a(this).attr("data-element-id"),s=n.findWhere(e.workingElements,{id:i});s?t.push(s):console.error("missing element: ",i)}),this.workingElements=t,this._renderList()},_elementDragstart:function(e,t){t.select(!0),this.$dragging=this.$(".collection-elements .collection-element.selected")},_elementDragend:function(e,t){a(".element-drop-placeholder").remove(),this.$dragging=null},templates:n.extend({},m.default.CollectionCreatorMixin._creatorTemplates,{header:n.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',(0,b.default)("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',(0,b.default)("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" ','title="',(0,b.default)("Close and show more help"),'" aria-hidden="true">&times;</button>','<span class="alert-message"></span>',"</div>"].join("")),middle:n.template(['<div class="collection-elements-controls">','<a class="reset" href="javascript:void(0);" ','title="',(0,b.default)("Undo all 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class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,b.default)("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',(0,b.default)("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',(0,b.default)("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',(0,b.default)("Create list"),"</button>","</div>","</div>"].join("")),helpContent:n.template(["<p>",(0,b.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"</p>","<ul>","<li>",(0,b.default)(["Rename elements in the list by clicking on ",'<i data-target=".collection-element .name">the existing name</i>.'].join("")),"</li>","<li>",(0,b.default)(["Discard elements from the final created list by clicking on the ",'<i data-target=".collection-element .discard">"Discard"</i> button.'].join("")),"</li>","<li>",(0,b.default)(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'<i data-target=".collection-element">them</i> and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the <i data-target=".clear-selected">"Clear selected"</i> link.'].join("")),"</li>","<li>",(0,b.default)(['Click the <i data-target=".reset">"Start over"</i> link to begin again as if you had just opened ',"the interface."].join("")),"</li>","<li>",(0,b.default)(['Click the <i data-target=".cancel-create">"Cancel"</i> button to exit the interface.'].join("")),"</li>","</ul><br />","<p>",(0,b.default)(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>.'].join("")),"</p>"].join("")),invalidElements:n.template([(0,b.default)("The following selections could not be included due to problems:"),"<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>"].join("")),noElementsLeft:n.template(['<li class="no-elements-left-message">',(0,b.default)("No elements left! "),(0,b.default)("Would you like to "),'<a class="reset" href="javascript:void(0)">',(0,b.default)("start over"),"</a>?","</li>"].join("")),invalidInitial:n.template(['<div class="header flex-row no-flex">','<div class="alert alert-warning" style="display: block">','<span class="alert-message">',"<% if( _.size( problems ) ){ %>",(0,b.default)("The following selections could not be included due to problems"),":","<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>","<% } else if( _.size( elements ) < 1 ){ %>",(0,b.default)("No datasets were selected"),".","<% } %>","<br />",(0,b.default)("At least one element is needed for the collection"),". ",(0,b.default)("You may need to "),'<a class="cancel-create" href="javascript:void(0)">',(0,b.default)("cancel"),"</a> ",(0,b.default)("and reselect new elements"),".","</span>","</div>","</div>",'<div class="footer flex-row no-flex">','<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',(0,b.default)("Cancel"),"</button>","</div>","</div>","</div>"].join(""))}),toString:function(){return"ListCollectionCreator"}}),k=function(e,t,i){var a,o=s.Deferred(),r=Galaxy.modal||new g.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),a=new i(t),r.show({title:t.title||(0,b.default)("Create a collection"),body:a.$el,width:"80%",height:"100%",closing_events:!0}),a.render(),window._collectionCreator=a,o},C=function(e,t){return t=t||{},t.title=(0,b.default)("Create a collection from a list of 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e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(205),r=s(o),l=i(8),d=s(l),c=i(7),u=(s(c),{defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return e.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",n.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}}),h=n.Model.extend(d.default.LoggableMixin).extend(u).extend({_logNamespace:"collections"}),f=n.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"collections",model:h,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),p=r.default.DatasetAssociation.extend(d.default.mixin(u,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas 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this.attributes.collection_type.indexOf(":")>0?v:m},initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){var t=this.collectionClass();this.debug(this+"._createElementsModel",t,this.get("elements"),this.elements);var i=this.get("elements")||[];this.unset("elements",{silent:!0});var n=this;return e.each(i,function(t,i){e.extend(t,{parent_hdca_id:n.get("id")})}),this.elements=new t(i),this.elements},toJSON:function(){var e=n.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=n.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?a.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){return"DatasetCollection("+[this.get("id"),this.get("name")||this.get("element_identifier")].join(",")+")"}}),g=_.extend(d.default.mixin(u,{constructor:function(e,t){this.debug("\t 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t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,g.default)("(empty)")},toJSON:function(){return a.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:s.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,a){var s;try{s=new Date(a.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=s||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var a={history_id:this.id};e&&(a.current=!0),t&&(a.name=t),i||(a.all_datasets=!1),a.view="dev-detailed";var s=this,o=n.post(this.urlRoot,a);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,b=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return a.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),a.defaults(t,i)},fetchFirst:function(e){var t=this,i=s.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:a.extend(a.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,a.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,a){var s=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){s.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:b}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(213),r=s(o),l=i(214),d=s(l),c=i(188),u=s(c),h=i(193),f=s(h),p=i(253),m=s(p),_=i(8),g=s(_),v=i(215),w=s(v),b=r.default.PaginatedCollection,y=b.extend(g.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync add":this.trackJobStates}),t=t||{},b.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var e=this;this.each(function(t){if(!t.has("job_states_summary")&&"dataset_collection"===t.attributes.history_content_type){var i=t.attributes.job_source_type,n=t.attributes.job_source_id;if(i){e.jobStateSummariesCollection.add({id:n,model:i,history_id:e.history_id,collection_id:t.attributes.id});var a=e.jobStateSummariesCollection.get(n);t.jobStatesSummary=a}}})},model:function(e,t){return"dataset"===e.history_content_type?new d.default.HistoryDatasetAssociation(e,t):"dataset_collection"===e.history_content_type?new u.default.HistoryDatasetCollection(e,t):{validationError:"Unknown history_content_type: "+e.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(e){this.stopPolling(),this.historyId=e,e&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new m.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=e,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(e){return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(b.prototype.comparators),{name:g.default.buildComparator("name",{ascending:!0}),"name-dsc":g.default.buildComparator("name",{ascending:!1}),hid:g.default.buildComparator("hid",{ascending:!1}),"hid-asc":g.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,a=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,a){var s=i.get(t[n]);return s?e.concat(s):e},[]),i.ajaxQueue("save",a,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new w.default.AjaxQueue(n.slice().reverse().map(function(n,a){var s=e.isString(t)?n[t]:t;return function(){return s.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var r=e.extend(e.clone(t),{view:"summary",keys:l,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){s.fetch.call(s,r).fail(a.reject).done(function(e){a.notify(e,o,n),e.length!==o?(s.allFetched=!0,a.resolve(e,o,n)):i(n+o)})})}t=t||{};var a=n.Deferred(),s=this,o=t.limitPerCall||s.limitPerProgressiveFetch,r=d.default.HistoryDatasetAssociation.prototype.searchAttributes,l=r.join(",");return i(),a},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,a,s;e.isString(t)?(i=t,s="hda",a="dataset"):(i=t.id,s={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",a="hdca"===s?"dataset_collection":"dataset");var o=this,r=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:s,type:a})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,r,{},"Error copying contents",{type:a,id:i,source:s})});return r},createHDCA:function(e,t,i,n,a){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(a)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=a.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:y}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(8),a=function(e){return e&&e.__esModule?e:{default:e}}(n),s=a.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return s.storageKeyPrefix+e},get:function(e){return new s({id:s.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(s.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:s}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(8),l=o(r),d=i(7),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:l.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:l.default.wrapTemplate(['<div class="subtitle"></div>']),details:l.default.wrapTemplate(['<div class="details"></div>'])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['<div class="details">',"</div>"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(194),l=o(r),d=i(166),c=o(d),u=i(175),h=o(u),f=i(8),p=o(f),m=i(7),_=o(m),g=l.default.ListItemView,v=g.extend({_logNamespace:"dataset",className:g.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),g.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return g.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,_.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,_.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,_.default)("This dataset is not yet viewable");else{t.title=(0,_.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return s(this.templates.noAccess(this.model.toJSON(),this));var e=g.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=s('<div class="detail-messages"></div>'),n=t.model.toJSON();return e.each(t.templates.detailMessages,function(e){i.append(s(e(n,t)))}),i},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case c.default.NOT_VIEWABLE:return[];case c.default.OK:case c.default.FAILED_METADATA:case c.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,h.default)({title:(0,_.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:e.isEmpty(this.model.get("meta_files"))?s(['<a class="download-btn icon-btn" ','href="',this.model.urls.download,'" title="'+(0,_.default)("Download")+'" download>','<span class="fa fa-floppy-o"></span>',"</a>"].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return s(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+(0,_.default)("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+t.download+'" download>',(0,_.default)("Download dataset"),"</a></li>",e.map(this.model.get("meta_files"),function(e){return['<li><a href="',t.meta_download+e.file_type,'">',(0,_.default)("Download")," ",e.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:e.extend(e.clone(g.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){return"DatasetListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=e.extend({},g.prototype.templates.warnings,{failed_metadata:p.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',(0,_.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,_.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,_.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,_.default)("This dataset has been deleted"),"</div>","<% } %>"])}),i=p.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),n=p.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,_.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),a={};a[c.default.OK]=a[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,_.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,_.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),a[c.default.NEW]=p.default.wrapTemplate(["<div>",(0,_.default)("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset"),a[c.default.NOT_VIEWABLE]=p.default.wrapTemplate(["<div>",(0,_.default)("You do not have permission to view this dataset"),"</div>"],"dataset"),a[c.default.DISCARDED]=p.default.wrapTemplate(["<div>",(0,_.default)("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),a[c.default.QUEUED]=p.default.wrapTemplate(["<div>",(0,_.default)("This job is waiting to run"),"</div>"],"dataset"),a[c.default.RUNNING]=p.default.wrapTemplate(["<div>",(0,_.default)("This job is currently running"),"</div>"],"dataset"),a[c.default.UPLOAD]=p.default.wrapTemplate(["<div>",(0,_.default)("This dataset is currently uploading"),"</div>"],"dataset"),a[c.default.SETTING_METADATA]=p.default.wrapTemplate(["<div>",(0,_.default)("Metadata is being auto-detected"),"</div>"],"dataset"),a[c.default.PAUSED]=p.default.wrapTemplate(["<div>",(0,_.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),a[c.default.ERROR]=p.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',(0,_.default)("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),a[c.default.EMPTY]=p.default.wrapTemplate(["<div>",(0,_.default)("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),a.unknown=p.default.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var s={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',(0,_.default)("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},o=p.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return e.extend({},g.prototype.templates,{warnings:t,details:i,noAccess:n,summaries:a,detailMessages:s,displayApplications:o})}(),t.default={DatasetListItemView:v}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(194),r=s(o),l=i(195),d=s(l),c=i(8),u=s(c),h=i(7),f=s(h),p=r.default.FoldoutListItemView,m=r.default.ListItemView,_=p.extend({className:p.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,p.prototype.initialize.call(this,e)},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,i){e.has(t.changed,"deleted")?this.render():e.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=e.extend({},p.prototype.templates.warnings,{error:u.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","</div>","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,f.default)("This collection has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,f.default)("This collection has been deleted"),"</div>","<% } %>"])}),i=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection"),n=u.default.wrapTemplate(['<div class="subtitle">','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<%        if( collection.collection_type === "list" ){ %>',(0,f.default)("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,f.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,f.default)("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,f.default)("a list of <%- countText %>dataset lists"),"<% } %>","</div>"],"collection");return e.extend({},p.prototype.templates,{warnings:t,titleBar:i,subtitle:n})}();var g=m.extend({className:m.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),m.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return e.extend({},m.prototype.templates,{titleBar:t})}();var v=d.default.DatasetListItemView.extend({className:d.default.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),d.default.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):a.when()},toString:function(){return"DatasetDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var w=_.extend({className:_.prototype.className+" dataset-collection-element",_swapNewRender:function(e){_.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:_,DCEListItemView:g,DatasetDCEListItemView:v,NestedDCDCEListItemView:w}}).call(t,i(2),i(0),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(20),o=a(s),r=i(4),l=a(r),d=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.url=this.model.get("url"),this.redirect=this.model.get("redirect"),this.setElement("<div/>"),this.render()},render:function(){var e=this;n.ajax({url:Galaxy.root+this.url,type:"GET"}).done(function(t){var i=n.extend({},e.model.attributes,t),a=new o.default({title:i.title,message:i.message,status:i.status||"warning",icon:i.icon,inputs:i.inputs,buttons:{submit:new l.default.Button({tooltip:i.submit_tooltip,title:i.submit_title||"Save",icon:i.submit_icon||"fa-save",cls:"btn btn-primary ui-clear-float",onclick:function(){e._submit(a)}})}});e.$el.empty().append(a.$el)}).fail(function(t){e.$el.empty().append(new l.default.Message({message:"Failed to load resource "+e.url+".",status:"danger",persistent:!0}).$el)})},_submit:function(e){var t=this;n.ajax({url:Galaxy.root+t.url,data:JSON.stringify(e.data.create()),type:"PUT",contentType:"application/json"}).done(function(i){var a={};i.id?a.id=i.id:a={message:i.message,status:"success",persistent:!1},t.redirect?window.location=Galaxy.root+t.redirect+"?"+n.param(a):(e.data.matchModel(i,function(t,i){e.field_list[i].value(t.value)}),t._showMessage(e,success_message))}).fail(function(i){t._showMessage(e,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(e,t){e.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),e.message.update(t)}});t.default={View:d}}).call(t,i(1),i(0))},,,,,,,,function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(166),r=s(o),l=i(8),d=s(l),c=i(7),u=s(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:r.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
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t=e.Model.prototype.toJSON.call(this);return n.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=n.contains(r.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var i=this;return e.Model.prototype.fetch.call(this,t).always(function(){i._generateUrls()})},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},save:function(t,i){return i=i||{},i.wait=!!n.isUndefined(i.wait)||i.wait,e.Model.prototype.save.call(this,t,i)},delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?a.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return a.when();e=e||{},e.url=this.urls.purge;var t=this,i=a.ajax(e);return i.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),i.fail(function(i,n,a){var s=(0,u.default)("Unable to purge dataset");i.responseJSON&&i.responseJSON.error?s=i.responseJSON.error:-1!==i.responseText.indexOf("Removal of datasets by users is not allowed in this Galaxy instance")&&(s="Removal of datasets by users is not allowed in this Galaxy instance"),i.responseText=s,t.trigger("error",t,i,e,(0,u.default)(s),{error:s})}),i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=a.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=e.call(a,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:a})}),l.always(function(e){s.push(e),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(166),s=(n(a),i(8)),o=(n(s),i(7)),r=(n(o),{defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id");return""+this.urlRoot+t+"/contents/"+e+"s/"+i},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}});t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i={_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_changeHideOriginals:function(e){this.hideOriginals=this.$(".hide-originals").prop("checked")},_changeName:function(e){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(e){13!==e.keyCode||this.blocking||this._clickCreate()},_getName:function(){return 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Please try again in a few minutes.")+" "+h,(0,u.default)("Cannot connect to Galaxy"))}function l(e,t,i,n,a){return n=n||f,n+=" "+h,a=a||(0,u.default)("An error occurred"),s(n,a,d(e,t,i))}function d(e,t,i){return{raven:n.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:n.result(Galaxy.config,"version_major"),xhr:n.omit(t,n.functions(t)),options:n.omit(i,"xhr"),url:n.result(Galaxy.lastAjax,"url"),data:n.result(Galaxy.lastAjax,"data"),model:n.result(e,"toJSON",""+e),user:n.omit(n.result(Galaxy.user,"toJSON"),"email")}}Object.defineProperty(t,"__esModule",{value:!0});var c=i(7),u=function(e){return e&&e.__esModule?e:{default:e}}(c),h=(0,u.default)("Please contact a Galaxy administrator if the problem persists."),f=(0,u.default)("An error occurred while updating information with the server."),p=(0,u.default)("The following information can assist the developers in finding the source of the error:");t.default={errorModal:s,offlineErrorModal:o,badGatewayErrorModal:r,ajaxErrorModal:l}}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var a=i(2),s=n(a),o=i(1),r=n(o),l=i(8),d=function(e){return e&&e.__esModule?e:{default:e}}(l),c=r.Collection.extend({initialize:function(e,t){r.Collection.prototype.initialize.call(this,e,t),this.setOrder(t.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),Galaxy.debug("fetch options:",e),r.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(e){e=s.clone(e)||{};var t=this;e.traditional=!0,e.data=e.data||t._buildFetchData(e),Galaxy.debug("data:",e.data);var i=this._buildFetchFilters(e);return Galaxy.debug("filters:",i),s.isEmpty(i)||s.extend(e.data,this._fetchFiltersToAjaxData(i)),Galaxy.debug("data:",e.data),e},_buildFetchData:function(e){var t={};return this.order&&(t.order=this.order),s.defaults(s.pick(e,this._fetchParams),t)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(e){return s.clone(e.filters||{})},_fetchFiltersToAjaxData:function(e){var t={q:[],qv:[]};return s.each(e,function(e,i){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(i),t.qv.push(e))}),t},reset:function(e,t){return this.allFetched=!1,r.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:d.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":d.default.buildComparator("update_time",{ascending:!0}),create_time:d.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":d.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var i=this,n=i.comparators[e];if(s.isUndefined(n))throw new Error("unknown order: "+e);if(n!==i.comparator)return i.order=e,i.comparator=n,t.silent||i.trigger("changed-order",t),i}}),u=c.extend({limitPerPage:500,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=s.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?s.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(s.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=s.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=s.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t<n)&&(i.allFetched=!0,i.trigger("all-fetched",this))})},fetchAll:function(e){e=e||{};var t=this;return e=s.pick(e,"silent"),e.filters={},t.fetch(e).done(function(){t.allFetched=!0,t.trigger("all-fetched",t)})}});t.default={ControlledFetchCollection:c,PaginatedCollection:u,InfinitelyScrollingCollection:h}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(205),s=n(a),o=i(206),r=n(o),l=i(8),d=n(l),c=i(7),u=(n(c),s.default.DatasetAssociation),h=r.default.HistoryContentMixin,f=u.extend(d.default.mixin(h,{defaults:e.extend({},u.prototype.defaults,h.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));t.default={HistoryDatasetAssociation:f}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function i(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function n(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression 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this.deferred.always(e)}},{key:"progress",value:function(e){return this.deferred.progress(e)}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(),l=function(e){function t(e){a(this,t);var n=i(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e));return n.names={},n}return n(t,e),o(t,[{key:"add",value:function(e){if(!e.hasOwnProperty("name")||!e.hasOwnProperty("fn"))throw new Error('NamedAjaxQueue.add requires an object with both "name" and "fn": '+JSON.stringify(e));if(!this.names.hasOwnProperty(e.name))return this.names[e.name]=!0,s(t.prototype.__proto__||Object.getPrototypeOf(t.prototype),"add",this).call(this,e.fn)}},{key:"clear",value:function(){return this.names={},this}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(r);t.default={AjaxQueue:r,NamedAjaxQueue:l}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(194),r=s(o),l=i(256),d=s(l),c=i(8),u=s(c),h=i(7),f=s(h);i(217);var p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:r.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,a){console.error(e,t,i,n,a)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,a){this.trigger("error",e,t,i,n,a)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=a(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=a(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=a(['<div class="list-action-menu btn-group">','<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,f.default)("For all selected"),"...","</button>",'<ul class="dropdown-menu pull-right" role="menu">',"</ul>","</div>"].join("")),s=i.map(function(e){var t=['<li><a href="javascript:void(0);">',e.html,"</a></li>"].join("");return a(t).click(function(t){return t.preventDefault(),e.func(t)})});return n.find("ul").append(s),t.replaceWith(n),n},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){return t._createItemView(e)}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(n.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return n.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=n.extend(this._getItemViewOptions(e),{model:e}),a=new t(i);return this._setUpItemViewListeners(a),a},_destroyItemView:function(e){this.stopListening(e),this.views=n.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:n.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){n.each(this.views,function(e){e.expand()})},collapseAll:function(){n.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(-1!==s){var o=n._createItemView(e);return a(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,s),e()}]),o}},_attachView:function(e,t,i){i=!!n.isUndefined(i)||i,t=t||0;var a=this;return a.views.splice(t,0,e),a._insertIntoListAt(t,a._renderItemView$el(e).hide()),a.trigger("view:attached",e),i?e.$el.slideDown(a.fxSpeed,function(){a.trigger("view:attached:rendered")}):(e.$el.show(),a.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var s=this,o=n.find(s.views,function(t){return t.model===e});if(o)return s.views=n.without(s.views,o),s.trigger("view:removed",o),a({}).queue("fx",[function(e){o.$el.fadeOut(s.fxSpeed,e)},function(e){o.remove(),s.trigger("view:removed:rendered"),s.views.length?e():s._renderEmptyMessage().fadeIn(s.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i<n?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(e){return e.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:n.bind(this._firstSearch,this),onsearch:n.bind(this.searchItems,this),onclear:n.bind(this.clearSearch,this)}),e},_firstSearch:function(e){return this.log("onFirstSearch",e),this.searchItems(e)},searchItems:function(e,t){if(this.log("searchItems",e,this.searchFor,t),!t&&this.searchFor===e)return this;this.searchFor=e,this.renderItems(),this.trigger("search:searching",e,this);var i=this.$("> .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]),controls:u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- view.title %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=a(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- model.name %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function a(){return['<input type="text" name="',t.name,'" placeholder="',t.placeholder,'" ','class="search-query ',t.classes,'" ',"/>"].join("")}var l=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===s.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===s.default.type(t)&&(t=s.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(a()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===l&&t.escWillClear)i.call(this,e);else{var a=o(this).val();(e.which===d||t.minSearchLen&&a.length>=t.minSearchLen)&&n.call(this,e,a)}}).val(t.initialVal)}(),function(){return o(['<span class="search-clear fa fa-times-circle" ','title="',r("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o(['<span class="search-loading fa fa-spinner fa-spin" ','title="',r("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}()]))}var a=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=s.default,r=window._l||function(e){return e};s.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(195),s=n(a),o=i(8),r=n(o),l=i(219),d=n(l),c=i(7),u=n(c),h=s.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+"</span>\n            </div>\n            </br>\n            "+d.default.nametagTemplate(t)+"\n        </div>\n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:r.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,u.default)("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function i(t){return 0==t.indexOf("name:")?'<span class="label label-info">'+e.escape(t.slice(5))+"</span>":""}function n(t){return'<span class="nametags">'+e.sortBy(e.uniq(t.tags)).map(i).join("")+"</span>"}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(166),s=n(a),o=i(196),r=n(o),l=i(221),d=n(l),c=i(8),u=(n(c),i(219)),h=n(u),f=i(7),p=n(f),m=r.default.DCListItemView,_=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?s.default.OK:s.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e,t=this.model,i=t.get("element_count"),n=t.get("job_source_type"),a=this.model.get("collection_type");e="list"==a?"list":"paired"==a?"dataset pair":"list:paired"==a?"list of pairs":"nested list";var s="";1==i?s=" with 1 item":i&&(s=" with "+i+" items");var o=t.jobStatesSummary,r=""+e+s;if(n&&"Job"!=n){if(o&&o.hasDetails()){var l=o.new(),d=l?null:o.jobCount();if(l)return'\n                        <div class="progress state-progress">\n                            <span class="note">Creating jobs.<span class="blinking">..</span></span>\n                            <div class="progress-bar info" style="width:100%">\n                        </div>';if(o.errored()){return"a "+e+" with "+o.numInError()+" / "+d+" jobs in error"}if(o.terminal())return"a "+r;var c=o.states().running||0,u=o.states().ok||0,h=u/(1*d),f=c/(1*d),p=1-h-f;return'\n                        <div class="progress state-progress">\n                            <span class="note">'+(d&&d>1?d+" jobs":"a job")+" generating a "+e+'</span>\n                            <div class="progress-bar ok" style="width:'+100*h+'%"></div>\n                            <div class="progress-bar running" style="width:'+100*f+'%"></div>\n                            <div class="progress-bar new" style="width:'+100*p+'%">\n                        </div>'}return'\n                    <div class="progress state-progress">\n                        <span class="note">Loading job data for '+e+'.<span class="blinking">..</span></span>\n                        <div class="progress-bar info" style="width:100%">\n                    </div>'}return"a "+r},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+'</span>\n            </div>\n            <div class="state-description">\n            </div>\n            '+h.default.nametagTemplate(t)+"\n        </div>\n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:_}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(216),s=n(a),o=i(189),r=(n(o),i(196)),l=n(r),d=i(8),c=n(d),u=i(7),h=n(u),f=s.default.ModelListPanel,p=f.extend({_logNamespace:"collections",className:f.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:l.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){f.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return l.default.NestedDCDCEListItemView.extend({foldoutPanelClass:p})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=f.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return f.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});p.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',(0,h.default)("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',(0,h.default)("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,h.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,h.default)("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,h.default)("a list of dataset lists"),"<% } %>","</div>","</div>",'<div class="tags-display"></div>','<div class="actions">','<a class="download-btn icon-btn" ','href="<%- view.downloadUrl %>','" title="" download="" data-original-title="Download Collection">','<span class="fa fa-floppy-o"></span>',"</a>","</div>","</div>"],"collection");return e.extend(e.clone(f.prototype.templates),{controls:t})}(),t.default={CollectionView:p}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(166),o=a(s),r=i(195),l=a(r),d=i(181),c=a(d),u=i(223),h=a(u),f=i(175),p=a(f),m=i(8),_=a(m),g=i(7),v=a(g),w=l.default.DatasetListItemView,b=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),a={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(a.disabled=!0,i?a.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(a.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(a.disabled=!0,a.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(a)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,a=function(t){var a='<div id="thdiv-'+e+'" class="toolhelp">';t.name&&t.help?(a+="<strong>Tool help for "+t.name+"</strong><hr/>",a+=t.help):a+="<strong>Tool help is unavailable for this dataset.</strong><hr/>",a+="</div>",i.$el.find(".details").append(n.parseHTML(a))},s=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){a(e)}).fail(function(){a({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){s(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});b.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:_.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',(0,v.default)("An error occurred setting the metadata for this dataset"),'<br /><a href="<%- dataset.urls.edit %>" target="_top">',(0,v.default)("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:_.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,v.default)("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',(0,v.default)("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',(0,v.default)("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")}),i=_.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-link icon-btn" href="<%- visualizations[0].href %>"',' target="<%- visualizations[0].target %>" title="',(0,v.default)("Visualize in"),' <%- visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown icon-btn">','<a data-toggle="dropdown" title="',(0,v.default)("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%- visualization.href %>"',' target="<%- visualization.target %>">',"<%- visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:b}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),o=a(s),r=i(7),l=a(r);i(25);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var 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e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:(0,c.default)("All workflows"),href:"workflow"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflows/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['<div class="toolTitle">','<a href="',this.root,e.href,'" target="galaxy_main">',e.title,"</a>","</div>"].join("")},_templateAllWorkflow:function(e){return['<div class="toolTitle">','<a href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_templateWorkflowLink:function(e){return['<div class="toolTitle">','<a class="'+e.cls+' " href="',Galaxy.root,e.href,'">',e.title,"</a>","</div>"].join("")},_template:function(){return['<div class="toolMenuContainer">','<div class="toolMenu" style="display: none">','<div 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If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=s.default.merge(e,this.options),this.ui_button=new u.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;s.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:i<n?-1:0}),t.options.datatypes_disable_auto||t.list_extensions.unshift(t.options.auto)}}),s.default.get({url:Galaxy.root+"api/genomes",success:function(e){for(var i in e)t.list_genomes.push({id:e[i][1],text:e[i][0]});t.list_genomes.sort(function(e,i){return e.id==t.options.default_genome?-1:i.id==t.options.default_genome?1:e.text>i.text?1:e.text<i.text?-1:0})}})},show:function(){var e=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model)return void window.setTimeout(function(){e.show()},500);this.current_user=Galaxy.user.id,this.modal||(this.tabs=new d.default.View,this.default_view=new f.default(this),this.tabs.add({id:"regular",title:"Regular",$el:this.default_view.$el}),this.composite_view=new m.default(this),this.tabs.add({id:"composite",title:"Composite",$el:this.composite_view.$el}),this.collection_view=new g.default(this),this.tabs.add({id:"collection",title:"Collection",$el:this.collection_view.$el}),this.modal=new r.default.View({title:"Download from web or upload from disk",body:this.tabs.$el,height:this.options.height,width:this.options.width,closing_events:!0,title_separator:!1})),this.modal.show()},currentHistory:function(){return this.current_user&&Galaxy.currHistoryPanel.model.get("id")},currentFtp:function(){return this.current_user&&this.options.ftp_upload_site},toData:function(e,t){var i={payload:{tool_id:"upload1",history_id:t||this.currentHistory(),inputs:{}},files:[],error_message:null};if(e&&e.length>0){var n={file_count:e.length,dbkey:e[0].get("genome","?"),file_type:e[0].get("extension","auto")};for(var a in e){var s=e[a];if(s.set("status","running"),!(s.get("file_size")>0)){i.error_message="Upload content incomplete.",s.set("status","error"),s.set("info",i.error_message);break}var o="files_"+a+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=s.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=s.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=s.get("genome",null),n[o+"file_type"]=s.get("extension",null),s.get("file_mode")){case"new":n[o+"url_paste"]=s.get("url_paste");break;case"ftp":n[o+"ftp_files"]=s.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:s.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(1))},function(e,t,i){"use strict";(function(e,i){Object.defineProperty(t,"__esModule",{value:!0});var n=e.View.extend({initialize:function(t){var n=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load 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e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(244),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(245),x=s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local file",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new x.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new c.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&a.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Type (set all):</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139),p=s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});var a=this.app.select_genome.value(),s=this.app.select_extension.value();this.select_genome=new p.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:a,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new p.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:s,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:a,extension:s}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-extension" style="float: left;"/>&nbsp;&nbsp<div class="upload-extension-info upload-icon-button fa fa-search"/></td><td><div class="upload-genome"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(e){this.$container=e.$container,this.collection=e.collection,this.new_content=e.new_content,this.max=e.max||50,this.content_list={},this.$message=i("<div/>").addClass("ui-limitloader").append("...only the first "+this.max+" entries are visible."),this.$container.append(this.$message),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add",this._refresh,this),this.listenTo(this.collection,"remove",this._remove,this)},_done:function(){var e=n.size(this.content_list)>this.max;return this.$message[e?"show":"hide"](),e},_reset:function(){n.each(this.content_list,function(e){e.remove()}),this.content_list={},this.$message.hide()},_remove:function(e){var t=e.id,i=this.content_list[t];i&&(i.remove(),delete this.content_list[t]),this._refresh()},_refresh:function(){if(!this._done())for(var e in this.collection.models){var t=this.collection.models[e];this.content_list[t.id];if(!this.content_list[t.id]){var i=this.new_content(t);if(this.content_list[t.id]=i,this._done())break}}}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(247),c=s(d),u=i(185),h=s(u),f=i(165),p=(s(f),i(139)),m=s(p),_=i(4),g=s(_);t.default=e.View.extend({collection:new l.default.Collection,initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new g.default.Button({title:"Start",onclick:function(){t._eventStart()}}),this.btnClose=new g.default.Button({title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=n.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&n.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){new h.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new m.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new c.default(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),a.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_template:function(){return'<div class="upload-view-composite"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th/><th/><th>Description</th><th>Name</th><th>Size</th><th>Settings</th><th>Status</th></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Composite Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome/Build:</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(183),d=s(l),c=i(184),u=s(c),h=i(165),f=s(h),p=i(4),m=s(p),_=i(139);s(_);i(186),t.default=e.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new m.default.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new f.default.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new f.default.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(a.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(r.default.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){e.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){"new"==this.model.get("file_mode")?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(r.default.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new u.default({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new d.default(this).$el),this.settings.show())},_template:function(){return'<tr class="upload-row"><td><div class="upload-source"/><div class="upload-text-column"><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-status"/></td><td><div class="upload-file-desc upload-title"/></td><td><div class="upload-file-name upload-title"/></td><td><div class="upload-file-size upload-size"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=(s(o),i(180)),l=s(r),d=i(249),c=s(d),u=i(184),h=s(u),f=i(185),p=s(f),m=i(165),_=s(m),g=i(139),v=s(g),w=i(4),b=s(w),y=i(187);s(y);i(186),t.default=e.View.extend({upload_size:0,collection:new l.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new b.default.Button({id:"btn-local",title:"Choose local files",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new b.default.Button({id:"btn-ftp",title:"Choose FTP files",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new b.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new b.default.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnBuild=new b.default.Button({id:"btn-build",title:"Build",onclick:function(){t._eventBuild()}}),this.btnStop=new b.default.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new b.default.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new b.default.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new _.default.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new v.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:a(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new v.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new l.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(i);var n=new c.default(this,{model:i});this.$(".upload-table > tbody:first").append(n.$el),this._updateScreen(),n.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=n.pluck(t.outputs,"hid"),a=this.collection.get(e);a.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,a.get("file_size"))),this.upload_completed+=100*a.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];n.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=n.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new h.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),a(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,a=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[a?"enable":"disable"](),this.btnFtp[a?"enable":"disable"](),this.btnCreate[a?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title-compressed">Collection Type:</span><span class="upload-footer-collection-type"/><span class="upload-footer-title-compressed">File Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title-compressed">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(1),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(180),d=(s(l),i(183)),c=s(d),u=i(165),h=s(u),f=i(139);s(f);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new h.default.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var e=this.model.attributes;this.$title.html(a.escape(e.file_name)),this.$size.html(r.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(r.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c.default(this).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title-extended"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(1),i(0),i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),s=n(a),o=i(251),r=n(o),l=i(252),d=n(l),c=i(7),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return['<div id="current-history-panel" class="history-panel middle"/>'].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t,i){return n.clone(m).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),r=a(o),l=i(211),d=a(l),c=i(8),u=(a(c),i(7)),h=a(u),f=i(40),p=a(f),m=[{html:(0,h.default)("History Lists"),header:!0},{html:(0,h.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,h.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,h.default)("Current History"),header:!0,anon:!0},{html:(0,h.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,h.default)("Copy History"),func:function(){(0,d.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Share or Publish"),href:"history/sharing"},{html:(0,h.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,h.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,h.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,h.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,h.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,h.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,h.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Purge Deleted Datasets"),confirm:(0,h.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,h.default)("Downloads"),header:!0},{html:(0,h.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,h.default)("Other Actions"),header:!0},{html:(0,h.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(t){var i=[];e.each(t.models,function(e,t){var n=t.toJSON();n.activate&&i.push({html:(0,h.default)(n.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,h.default)("Webhooks"),header:!0}),e.merge(m,i))}});var _=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,a=s(i,n,Galaxy.root);return new r.default(e,a)};t.default=_}).call(t,i(0),i(2))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(191),r=(s(o),i(254)),l=s(r),d=i(8),c=s(d),u=i(7),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,m=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'<a class="uploader-link" href="javascript:void(0)">',(0,h.default)("load your own data"),"</a>",(0,h.default)(" or "),'<a class="get-data-link" href="javascript:void(0)">',(0,h.default)("get data from an external source"),"</a>"].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):a.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):a.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="quota-message errormessage">',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:m}}).call(t,i(2),i(0),i(0))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(1),a=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),s=i(215),o=function(e){return e&&e.__esModule?e:{default:e}}(s),r=["new","queued","running"],l=["error","deleted"],d=a.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(l)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var i in e)if((t[e[i]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),i=0;for(var n in e)i+=t[e[n]]||0;return i},numInError:function(){return this.numWithStates(l)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(r)},jobCount:function(){var e=this.states(),t=0;for(var i in e)t+=e[i];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),c=a.Collection.extend({model:d,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var e=this.models.filter(function(e){return!e.terminal()}),t=e.map(function(e){return e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(255),r=s(o),l=i(192),d=(s(l),i(166)),c=(s(d),i(214)),u=s(c),h=i(257),f=s(h),p=i(258),m=s(p),_=i(181),g=s(_),v=i(223),w=s(v),b=i(187),y=s(b),x=i(261),k=s(x),C=i(262),$=s(C),S=i(175),T=s(S),M=i(67),E=(s(M),i(8)),P=s(E),O=i(7),A=s(O);i(25);var D=r.default.HistoryView,I=D.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},D.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return D.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return D.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return D.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html("<i>"+(0,A.default)("loading...")+"</i>")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=D.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=D.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new g.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,A.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,D.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,A.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,A.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,A.default)("Permanently delete datasets"),func:function(){if(confirm((0,A.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,A.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,A.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,A.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,a=this,t=t||a.getSelectedModels(),i=i||!1;"list"==e?n=y.default.createListCollection:"paired"==e?n=k.default.createPairCollection:"list:paired"==e?n=$.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){a.model.refresh()})},_getItemViewOptions:function(e){var t=D.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(D.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["<i>",(0,A.default)("Searching "),i,"/",this.model.contentsShown(),"</i>"].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),a("<div/>").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),a("<div/>").addClass("history-drop-target-help").text((0,A.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});I.prototype.templates=function(){var e=P.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'<span class="shown-count">',"<%- shown %> ",(0,A.default)("shown"),"</span>","<% } %>","<% if( history.contents_active.deleted ){ %>",'<span class="deleted-count">',"<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>","<% } else { %>","<%- history.contents_active.deleted %> ",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("deleted"),"</a>","<% } %>","</span>","<% } %>","<% if( history.contents_active.hidden ){ %>",'<span class="hidden-count">',"<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>","<%- history.contents_active.hidden %> ",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hidden"),"</a>","<% } %>","</span>","<% } %>"],"history"),t=P.default.wrapTemplate([(0,A.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("hide deleted"),"</a>, ","<% } else { %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,A.default)("show deleted"),"</a>, ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("hide hidden"),"</a>","<% } else { %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,A.default)("show hidden"),"</a>","<% } %>","<% } %>"],"history");return n.extend(n.clone(D.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:I}}).call(t,i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(216),o=a(s),r=i(191),l=a(r),d=i(192),c=a(d),u=i(193),h=(a(u),i(218)),f=a(h),p=i(220),m=a(p),_=i(158),g=(a(_),i(212)),v=a(g),w=i(175),b=a(w),y=i(8),x=a(y),k=i(7),C=a(k);i(217);var $=o.default.ModelListPanel,S=$.extend({_logNamespace:"history",HDAViewClass:f.default.HDAListItemView,HDCAViewClass:m.default.HDCAListItemView,collectionClass:c.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:$.prototype.className+" history-panel",emptyMsg:(0,C.default)("This history is empty"),noneFoundMsg:(0,C.default)("No matching datasets found"),searchPlaceholder:(0,C.default)("search datasets"),initialize:function(e){$.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return $.prototype.freeModel.call(this),this.model&&this.model.stopPolling(),this},_setUpListeners:function(){$.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,a){this.errorHandler(e,t,i,n,a)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(t,i,n){var a=this;return n=e.extend(n||{silent:!0}),this.info("loadHistory:",t,i,n),this.setModel(new l.default.History({id:t})),n.silent=!0,this.trigger("loading"),this.model.fetchWithContents(i,n).always(function(){a.render(),a.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):n.when()},_setUpCollectionListeners:function(){return $.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(t,i,a){var s=n('<div class="loading-indicator"/>');this.$el.html(s.text(t).slideDown(e.isUndefined(i)?this.fxSpeed:i))},_hideLoadingIndicator:function(t){this.$(".loading-indicator").slideUp(e.isUndefined(t)?this.fxSpeed+200:t,function(){n(this).remove()})},_buildNewRender:function(){var e=$.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,b.default)({title:(0,C.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),n())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('<div class="contents-loading-indicator"><span class="fa fa-2x fa-spinner fa-spin"/></div>'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls 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d=a[i];if(this.debug(s+":"+l.name),this.debug(i+":"+d.name),n[s]!==a[i]&&(o=e.match.call(this,e.preprocessMatch.call(this,{matchTo:l,possible:d,index:i,bestMatch:o})),this.debug("bestMatch:",JSON.stringify(o,null,"  ")),1===o.score)){this.debug("breaking early due to perfect match");break}}var c=e.scoreThreshold.call(this);if(this.debug("scoreThreshold:",c),this.debug("bestMatch.score:",o.score),o.score>=c?r.push(e.createPair.call(this,{listA:n,indexA:s,listB:a,indexB:o.index})):s+=1,!n.length||!a.length)return r}return this.debug("paired:",JSON.stringify(r,null,"  ")),this.debug("autopair _strategy ---------------------------"),r}}function l(e,t){var i=e.toJSON();return y(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(263),c=o(d),u=i(208),h=o(u),f=i(207),p=o(f),m=i(8),_=o(m),g=i(7),v=o(g);i(209);var w=e.View.extend(_.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<span class="forward-dataset-name flex-column"><%- pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%- pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%- pair.reverse.name %></span>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),b=e.View.extend(_.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpCommonSettings(e),this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(e){return e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,a){e(n,t)&&i[a].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,a){if(n===a)return n;var s=Math.floor((a-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[s].name);if(o<0)return i(n,s);if(o>0)return i(s+1,a);for(;t.unpaired[s]&&t.unpaired[s].name===e.name;)s++;return s}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:r({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",a=0,s=0;a<e.length&&a<t.length&&e[a]===t[a];)i+=e[a],a+=1;if(a===e.length)return e;if(a===t.length)return t;for(a=e.length-1,s=t.length-1;a>=0&&s>=0&&e[a]===t[s];)n=[e[a],n].join(""),a-=1,s-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var a=this._createPair(e,t,i.name);return this.paired.push(a),this.unpaired=n.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",a),a},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,a=t.name,s=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),a.replace(new RegExp(this.filters[1]),""));if(i){var o=s.lastIndexOf(".");if(o>0){var r=s.slice(o,s.length);s=s.replace(r,""),n=n.replace(r,""),a=a.replace(r,"")}}return s||n+" & "+a},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=n.without(this.paired,e),this._addToUnpaired(e.forward),this._addToUnpaired(e.reverse),t.silent||this.trigger("pair:unpair",[e]),e},unpairAll:function(){for(var e=[];this.paired.length;)e.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",e)},_pairToJSON:function(e,t){return t=t||"hda",{collection_type:"paired",src:"new_collection",name:e.name,element_identifiers:[{name:"forward",id:e.forward.id,src:t},{name:"reverse",id:e.reverse.id,src:t}]}},createList:function(e){var t=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",s={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:n.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return t.blocking=!0,a.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(s)}).always(function(){t.blocking=!1}).fail(function(e,i,n){t._ajaxErrHandler(e,i,n)}).done(function(e,i,n){t.trigger("collection:created",e,i,n),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,i,n)})},_ajaxErrHandler:function(e,t,i){this.error(e,t,i);var n=this,a=(0,v.default)("An error occurred while creating this collection");e&&(0===e.readyState&&0===e.status?a+=": "+(0,v.default)("Galaxy could not be reached and may be updating.")+(0,v.default)(" Try again in a few minutes."):e.responseJSON?a+="<br /><pre>"+JSON.stringify(e.responseJSON)+"</pre>":a+=": "+i),n._showAlert(a,"alert-danger")},render:function(e,t){return this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(s(this.templates.helpContent()));return this._renderFilters(),i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),i},_renderUnpaired:function(e,t){var i,n,a=this,s=[],o=this._splitByFilters();return this.$(".forward-column .title").text([o[0].length,(0,v.default)("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-o[0].length)),this.$(".reverse-column .title").text([o[1].length,(0,v.default)("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-o[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=o[1].map(function(e,t){return void 0!==o[0][t]&&o[0][t]!==e&&s.push(a._renderPairButton()),a._renderUnpairedDataset(e)}),i=o[0].map(function(e){return a._renderUnpairedDataset(e)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(s)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(e){return["(",e," ",(0,v.default)("filtered out"),")"].join("")},_renderUnpairedDataset:function(e){return s("<li/>").attr("id","dataset-"+e.id).addClass("dataset unpaired").attr("draggable",!0).addClass(e.selected?"selected":"").append(s("<span/>").addClass("dataset-name").text(e.name)).data("dataset",e)},_renderPairButton:function(){return s("<li/>").addClass("dataset unpaired").append(s("<span/>").addClass("dataset-name").text((0,v.default)("Pair these datasets")))},_renderUnpairedEmpty:function(){var e=s('<div class="empty-message"></div>').text("("+(0,v.default)("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(e),e},_renderUnpairedNotShown:function(){var e=s('<div class="empty-message"></div>').text("("+(0,v.default)("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(e),e},_adjUnpairedOnScrollbar:function(){var e=this.$(".unpaired-columns").last(),t=this.$(".unpaired-columns .reverse-column .dataset").first();if(t.length){var i=e.offset().left+e.outerWidth(),n=t.offset().left+t.outerWidth(),a=Math.floor(i)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",a>0?a:0)}},_renderPaired:function(e,t){if(this.$(".paired-column-title .title").text([this.paired.length,(0,v.default)("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(e,t){var n=new w({pair:e});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',(0,v.default)("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var e=s('<div class="empty-message"></div>').text("("+(0,v.default)("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(e),e},footerSettings:{".hide-originals":"hideOriginals",".remove-extensions":"removeExtensions"},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(e){function t(e,t){return['<button class="filter-choice btn" ','data-forward="',e,'" data-reverse="',t,'">',(0,v.default)("Forward"),": ",e,", ",(0,v.default)("Reverse"),": ",t,"</button>"].join("")}var i=s(n.template(['<div class="choose-filters">','<div class="help">',(0,v.default)("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",n.values(this.commonFilters).map(function(e){return t(e[0],e[1])}).join(""),"</div>"].join(""))({}));return this.$(e).popover({container:".collection-creator",placement:"bottom",html:!0,content:i})},_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_setUpBehaviors:function(){return this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("pair:new",function(){this._renderUnpaired(),this._renderPaired(),this.$(".paired-columns").scrollTop(8e6)}),this.on("pair:unpair",function(e){this._renderUnpaired(),this._renderPaired(),this.splitView()}),this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()],this.metric("filter-change",this.filters),this._renderFilters(),this._renderUnpaired()}),this.on("autopair",function(){this._renderUnpaired(),this._renderPaired();var e,t=null;this.paired.length?(t="alert-success",e=this.paired.length+" "+(0,v.default)("pairs created"),this.unpaired.length||(e+=": "+(0,v.default)("all datasets have been successfully paired"),this.hideUnpaired(),this.$(".collection-name").focus())):e=(0,v.default)(["Could not automatically create any pairs from the given dataset names.","You may want to choose or enter different filters and try auto-pairing again.","Close this message using the X on the right to view more help."].join(" ")),this._showAlert(e,t)}),this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(e){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(e){s(e.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(e){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(e){s(e.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend   .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(e){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},_clickShowOnlyUnpaired:function(e){this.$(".paired-columns").is(":visible")?this.hidePaired():this.splitView()},_clickShowOnlyPaired:function(e){this.$(".unpaired-columns").is(":visible")?this.hideUnpaired():this.splitView()},hideUnpaired:function(e,t){this.unpairedPanelHidden=!0,this.pairedPanelHidden=!1,this._renderMiddle(e,t)},hidePaired:function(e,t){this.unpairedPanelHidden=!1,this.pairedPanelHidden=!0,this._renderMiddle(e,t)},splitView:function(e,t){return this.unpairedPanelHidden=this.pairedPanelHidden=!1,this._renderMiddle(e,t),this},_clickUnpairAll:function(e){this.metric("unpairAll"),this.unpairAll()},_clickAutopair:function(e){var t=this.autoPair();this.metric("autopair",t.length,this.unpaired.length),this.trigger("autopair")},_clickFilterChoice:function(e){var t=s(e.currentTarget);this.$(".forward-unpaired-filter input").val(t.data("forward")),this.$(".reverse-unpaired-filter input").val(t.data("reverse")),this._hideChooseFilters(),this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide"),this.$(".popover").css("display","none")},_clearFilters:function(e){this.$(".forward-unpaired-filter input").val(""),this.$(".reverse-unpaired-filter input").val(""),this.trigger("filter-change")},_clickUnpairedDataset:function(e){return e.stopPropagation(),this.toggleSelectUnpaired(s(e.currentTarget))},toggleSelectUnpaired:function(e,t){t=t||{};var i=e.data("dataset"),n=void 0!==t.force?t.force:!e.hasClass("selected");return e.length&&void 0!==i?(n?(e.addClass("selected"),t.waitToPair||this.pairAllSelected()):e.removeClass("selected"),e):e},pairAllSelected:function(e){e=e||{};var t=this,i=[],n=[],a=[];return t.$(".unpaired-columns .forward-column .dataset.selected").each(function(){i.push(s(this).data("dataset"))}),t.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){n.push(s(this).data("dataset"))}),i.length=n.length=Math.min(i.length,n.length),i.forEach(function(e,i){try{a.push(t._pair(e,n[i],{silent:!0}))}catch(e){t.error(e)}}),a.length&&!e.silent&&this.trigger("pair:new",a),a},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(e){if(e.shiftKey){var t=this,i=s(e.target).addClass("selected"),n=function(e){t.$(e.target).filter(".dataset").addClass("selected")};i.parent().on("mousemove",n),s(document).one("mouseup",function(e){i.parent().off("mousemove",n),t.pairAllSelected()})}},_clickPairRow:function(e){var t=s(e.currentTarget).index(),i=s(".unpaired-columns .forward-column .dataset").eq(t).data("dataset"),n=s(".unpaired-columns .reverse-column .dataset").eq(t).data("dataset");this._pair(i,n)},_startPartitionDrag:function(e){function t(e){n.$(".flexible-partition-drag").css("color",""),s("body").css("cursor","").unbind("mousemove",i)}function i(e){var t=e.pageY-a;n.adjPartition(t)||s("body").trigger("mouseup"),n._adjUnpairedOnScrollbar(),a+=t}var n=this,a=e.pageY;s("body").css("cursor","ns-resize"),n.$(".flexible-partition-drag").css("color","black"),s("body").mousemove(i),s("body").one("mouseup",t)},adjPartition:function(e){var t=this.$(".unpaired-columns"),i=this.$(".paired-columns"),n=parseInt(t.css("height"),10),a=parseInt(i.css("height"),10);n=Math.max(10,n+e),a-=e;var s=e<0;if(s){if(this.unpairedPanelHidden)return!1;if(n<=10)return this.hideUnpaired(),!1}else this.unpairedPanelHidden&&(t.show(),this.unpairedPanelHidden=!1);if(s)this.pairedPanelHidden&&(i.show(),this.pairedPanelHidden=!1);else{if(this.pairedPanelHidden)return!1;if(a<=15)return this.hidePaired(),!1}return t.css({height:n+"px",flex:"0 0 auto"}),!0},selectPair:function(e){e.stopPropagation(),s(e.currentTarget).toggleClass("selected")},clearSelectedPaired:function(e){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(e){e.stopPropagation();var t=s(e.currentTarget),i=t.parent().parent(),n=i.index(".dataset.paired"),a=this.paired[n],o=prompt("Enter a new name for the pair:",a.name);o&&(a.name=o,a.customizedName=!0,t.text(a.name))},_clickUnpair:function(e){var t=Math.floor(s(e.currentTarget).index(".unpair-btn"));this._unpair(this.paired[t])},_dragoverPairedColumns:function(e){e.preventDefault();var t=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestPairedDatasetLi(e.originalEvent.clientY);s(".element-drop-placeholder").remove();var n=s('<div class="element-drop-placeholder"></div>');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),a=t-i.top,s=i.top+e.outerHeight()-t;a>=0&&a<this.autoscrollDist?e.scrollTop(n-2):s>=0&&s<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestPairedDatasetLi:function(e){for(var t=this.$(".paired-columns .column-datasets li").toArray(),i=0;i<t.length;i++){var n=s(t[i]),a=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(a+o>e&&a-o<e)return n}return s()},_dropPairedColumns:function(e){e.preventDefault(),e.dataTransfer.dropEffect="move";var 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diff --git a/static/scripts/bundled/login.bundled.js b/static/scripts/bundled/login.bundled.js
index 3048787cbdf..f070fe75032 100644
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+++ b/static/scripts/bundled/login.bundled.js
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fa").addClass(t.icon),this.$title.addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right")}}),c=o.extend({$menu:null,initialize:function(e){this.model=e&&e.model||new t.Model({id:"",title:"",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(e),this.collection=new t.Collection,this.setElement(n("<div/>").append(this.$root=n("<div/>").append(this.$icon=n("<i/>")).append(this.$title=n("<span/>")))),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"change add remove reset",this.render,this),this.render()},render:function(){var t=this,e=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(e.cls).attr("id",e.id).css({display:e.visible&&this.collection.where({visible:!0}).length>0?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:e.tooltip,placement:"bottom"}).off("click").on("click",function(t){n(".tooltip").hide(),t.preventDefault(),e.onclick&&e.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.removeClass().addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=n("<ul/>").addClass("menu dropdown-menu").addClass("pull-"+t.model.get("pull")).attr("role","menu"),this.$el.append(this.$menu)),this.collection.each(function(e){var i=e.attributes;if(i.visible){var a=n("<a/>").addClass("dropdown-item").attr({href:i.href,target:i.target}).append(n("<i/>").addClass("fa").addClass(i.icon).css("display",i.icon?"inline-block":"none")).append(i.title).on("click",function(t){i.onclick&&(t.preventDefault(),i.onclick())});t.$menu.append(n("<li/>").append(a)),i.divider&&t.$menu.append(n("<li/>").addClass("divider"))}})},addMenu:function(t){this.collection.add(r.default.merge(t,{title:"",target:"",href:"",onclick:null,divider:!1,visible:!0,icon:null,cls:"button-menu btn-group"}))}});e.default={ButtonDefault:o,ButtonLink:s,ButtonIcon:d,ButtonCheck:l,ButtonMenu:c}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return 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e=[];r.$("input.grid-row-select-checkbox[name=id]:checked").each(function(){window.console.log(t(this).val()),e[e.length]=t.ajax({url:Galaxy.root+"api/datasets/"+t(this).val(),dataType:"json",data:{data_type:"track_config",hda_ldda:"histories"==r.current()?"hda":"ldda"}})}),t.when.apply(t,e).then(function(){var e=arguments[0]instanceof Array?t.map(arguments,function(t){return t[0]}):[arguments[0]];i(e)}),Galaxy.modal.hide()}}})},w=function(t){this.default_font=void 0!==t?t:"9px Monaco, Lucida Console, 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e=this.attributes.obj_cache,i=this.attributes.key_ary,n=t.toString(),a=o.indexOf(i,function(t){return t.toString()===n});return-1!==a&&(e[n].stale?(i.splice(a,1),delete e[n]):this.move_key_to_end(t,a)),e[n]},set_elt:function(t,e){var i=this.attributes.obj_cache,n=this.attributes.key_ary,a=t.toString(),r=this.attributes.num_elements;if(!i[a]){if(n.length>=r){delete i[n.shift().toString()]}n.push(t)}return i[a]=e,e},move_key_to_end:function(t,e){this.attributes.key_ary.splice(e,1),this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){y.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;o.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),i=t.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(a.go()).then(function(t){i.resolve("ok"===t||"data"===t)}),i},search_features:function(e){var i=this.get("dataset"),n={query:e,hda_ldda:i.get("hda_ldda"),data_type:"features"};return t.getJSON(i.url(),n)},load_data:function(e,i,n,a){var r=this.get("dataset"),o={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:i,resolution:n,hda_ldda:r.get("hda_ldda")};t.extend(o,a);var s=this.get("filters_manager");if(s){for(var l=[],d=s.filters,c=0;c<d.length;c++)l.push(d[c].name);o.filter_cols=JSON.stringify(l)}var u=this,h=t.getJSON(r.url(),o,function(t){t.region=e,u.set_data(e,t)});return this.set_data(e,h),h},get_data:function(t,e,i,n){var a=this.get_elt(t);if(a&&(c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)))return a;for(var r,o,s=this.get("key_ary"),l=this.get("obj_cache"),d=0;d<s.length;d++)if(r=s[d],r.contains(t)&&(o=!0,a=l[r.toString()],c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)&&this.get("can_subset")(a))){if(this.move_key_to_end(r,d),!c.default.is_deferred(a)){var u=this.subset_entry(a,t);this.set_data(t,u),a=u}return a}if(!o&&t.length()<this.attributes.min_region_size){t=t.copy();var h=this.most_recently_added();!h||t.get("start")>h.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,i,n)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,i,n,a,r){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");r===this.DEEP_DATA_REQ?t.extend(a,{start_val:o.data.length+1}):r===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),d=this,c=this.load_data(l,i,n,a),u=t.Deferred();return this.set_data(e,u),t.when(c).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),d.set_data(e,t),u.resolve(t)}),u},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,i,n,a){var r=this._mark_stale(t);return r?(a||(a={}),"bigwig"===r.dataset_type&&(a.num_samples=1e3*n),this.load_data(t,e,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var i=this,n=!0,a=o.map(e.get("chroms_info").chrom_info,function(t){var e=i.get_elt(new S({chrom:t.chrom,start:0,end:t.len}));return e||(n=!1),e});if(n)return a;var r=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){i.add_data(t.data),r.resolve(t.data)}),r},subset_entry:function(t,e){var i={bigwig:function(t,e){return o.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,i){var n=i.get("start")-t.region.get("start");return t.data.slice(n,n+i.length())}},n=t.data;return!t.region.same(e)&&t.dataset_type in i&&(n=i[t.dataset_type](t.data,e)),{region:e,data:n,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new n.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,i,n){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,i,n):{data:null,region:t}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=o.find(this.get_chroms_info(),function(e){return e.chrom===t});return new S({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return o.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),S=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),i=e[0],n=e[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new S({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),i=t.get("chrom"),n=this.get("start"),a=t.get("start"),r=this.get("end"),o=t.get("end");return e&&i&&e!==i?S.overlap_results.DIF_CHROMS:n<a?r<a?S.overlap_results.BEFORE:r<o?S.overlap_results.OVERLAP_START:S.overlap_results.CONTAINS:n>a?n>o?S.overlap_results.AFTER:r<=o?S.overlap_results.CONTAINED_BY:S.overlap_results.OVERLAP_END:r>=o?S.overlap_results.CONTAINS:S.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===S.overlap_results.CONTAINS},overlaps:function(t){return 0===o.intersection([this.compute_overlap(t)],[S.overlap_results.DIF_CHROMS,S.overlap_results.BEFORE,S.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),$=n.Collection.extend({model:S}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new S(t.region))}}),M=n.Collection.extend({model:T}),O=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===o.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),A=n.Collection.extend({model:O}),E=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),z=E.extend(v).extend({defaults:o.extend({},E.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new A(t.tracks));var e=[];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs)),this.unset("tracks"),this.get("drawables").each(function(t){t.unset("preloaded_data")})},add_tracks:function(t){this.get("drawables").add(t)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(t,e){return{obj_type:"View",prefs:{name:e.get("title"),content_visible:!0},drawables:e.get("drawables")}}}}),R=n.Router.extend({initialize:function(t){this.view=t.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var e=this;e.view.on("navigate",function(t){e.navigate(t)})},change_location:function(t){this.view.go_to(t)}});e.default={BackboneTrack:O,BrowserBookmark:T,BrowserBookmarkCollection:M,Cache:y,CanvasManager:w,Genome:C,GenomeDataManager:x,GenomeRegion:S,GenomeRegionCollection:$,GenomeVisualization:z,GenomeReferenceDataManager:k,TrackBrowserRouter:R,Visualization:E,select_datasets:b}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,i){function n(t){t+="";for(var e=/(\d+)(\d{3})/;e.test(t);)t=t.replace(e,"$1,$2");return t}Object.defineProperty(e,"__esModule",{value:!0});var a=function(t){return"promise"in t},r=t.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(t){return!0}},go:function(){var t=i.Deferred(),e=this,n=e.get("ajax_settings"),a=e.get("success_fn"),r=e.get("interval");return function e(){i.ajax(n).success(function(i){a(i)?t.resolve(i):setTimeout(e,r)})}(),t}}),o=function(t){t||(t="#ffffff"),"string"==typeof t&&(t=[t]);for(var 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o=i(9),s=(r(o),i(45)),l=(r(s),i(41)),d=r(l),c=t.Model.extend({}),u=t.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var t=new c;n.each(n.keys(this.attributes),function(e){if(0===e.indexOf("metadata_")){var i=e.split("metadata_")[1];t.set(i,this.attributes[e]),delete this.attributes[e]}},this),this.set("metadata",t,{silent:!0})},get_metadata:function(t){return 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i.set("default_value",e)}},{from_models_and_saved_values:function(t,e){return e&&(t=o.map(t,function(t){return o.extend({},t,{value:e[t.key]})})),new u(t)}}),h=t.View.extend({className:"config-settings-view",render:function(){var t=this.$el;return this.collection.each(function(e,i){if(!e.get("hidden")){var a="param_"+i,r=e.get("type"),s=e.get("value"),d=n("<div class='form-row' />").appendTo(t);if(d.append(n("<label />").attr("for",a).text(e.get("label")+":")),"bool"===r)d.append(n('<input type="checkbox" />').attr("id",a).attr("name",a).attr("checked",s));else if("text"===r)d.append(n('<input type="text"/>').attr("id",a).val(s).click(function(){n(this).select()}));else if("select"===r){var c=n("<select />").attr("id",a);o.each(e.get("options"),function(t){n("<option/>").text(t.label).attr("value",t.value).appendTo(c)}),c.val(s),d.append(c)}else if("color"===r){var u=n("<div/>").appendTo(d),h=n("<input />").attr("id",a).attr("name",a).val(s).css("float","left").appendTo(u).click(function(t){n(".tooltip").removeClass("in");var e=n(this).siblings(".tooltip").addClass("in");e.css({left:n(this).position().left+n(this).width()+5,top:n(this).position().top-n(e).height()/2+n(this).height()/2}).show(),e.click(function(t){t.stopPropagation()}),n(document).bind("click.color-picker",function(){e.hide(),n(document).unbind("click.color-picker")}),t.stopPropagation()}),f=n("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),p=n("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),_=n("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(p),m=(n("<div class='tooltip-arrow'></div>").appendTo(p),n.farbtastic(_,{width:100,height:100,callback:h,color:s}));u.append(n("<div/>").css("clear","both")),function(t){f.click(function(){t.setColor(l.default.get_random_color())})}(m)}else d.append(n("<input />").attr("id",a).attr("name",a).val(s));e.help&&d.append(n("<div class='help'/>").text(e.help))}}),this},render_in_modal:function(t){var e=this,i=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc")},a=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc"),e.update_from_form()},r=function(t){27===(t.keyCode||t.which)?i():13===(t.keyCode||t.which)&&a()};n(window).bind("keypress.check_enter_esc",r),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:t||"Configure",body:this.$el,buttons:{Cancel:i,OK:a}})},update_from_form:function(){var t=this;this.collection.each(function(e,i){if(!e.get("hidden")){var n="param_"+i,a=t.$el.find("#"+n).val();"bool"===e.get("type")&&(a=t.$el.find("#"+n).is(":checked")),e.set_value(a)}})}});e.default={ConfigSetting:c,ConfigSettingCollection:u,ConfigSettingCollectionView:h}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(12),d=r(l),c=t.View.extend({initialize:function(e){var i=this;this.data=[],this.data2=[],this.model=e&&e.model||new t.Model({id:s.default.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,readonly:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(e),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=n("<select/>")).append(this.$dropdown=n("<div/>")).append(this.$resize=n("<div/>").append(this.$resize_icon=n("<i/>"))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(e){var i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,n("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&a.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),a.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),n=a.filter(t.data2,function(i){var n=!1;return a.each(i.tags,function(i){t._match(e.term,i)&&(n=t.matched_tags[i]=!0)}),n||t._match(e.term,i.text)});e.callback({results:n.slice((e.page-1)*i,e.page*i),more:n.length>=e.page*i})},formatResult:function(e){return a.escape(e.text)+'<div class="ui-tags">'+a.reduce(e.tags,function(e,i){return t.matched_tags[i]?e+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search 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null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(t){return a.findWhere(this.data,{value:t})},text:function(){var t=this._getValue(),e=this.exists(n.isArray(t)?t[0]:t);return e?e.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(t,e){a.each(this.model.get("data"),function(e){e.keep&&!a.findWhere(t,{value:e.value})&&t.push(e)}),e&&t&&t.sort(e),this.model.set("data",t)},update:function(t){this.model.set("data",t)},setOnChange:function(t){this.model.set("onchange",t)},length:function(){return n.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(t){var e=this;if(null!==t&&void 0!==t||(t="__null__"),this.model.get("multiple")?t=n.isArray(t)?t:[t]:n.isArray(t)&&(t=t.length>0?t[0]:"__null__"),this.model.get("searchable")){if(n.isArray(t)){var i=[];a.each(t,function(t){var n=a.findWhere(e.data2,{id:t});n&&i.push(n)}),t=i}else{t=a.findWhere(this.data2,{id:t})}this.$select.select2("data",t)}else this.$select.val(t)},_getValue:function(){var t=null;if(this.model.get("searchable")){var e=this.$select.select2("data");e&&(n.isArray(e)?(t=[],e.sort(function(t,e){return t.order-e.order}),a.each(e,function(e){t.push(e.id)})):t=e.id)}else t=this.$select.val();return s.default.isEmpty(t)?null:t}});e.default={View:c}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(12),d=r(l),c=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({visible:!0,data:[],id:s.default.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(e),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var t=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=n("<div/>")).append(this.$menu=n("<div/>").addClass("ui-options-menu")).append(this.$options=n(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new d.default.ButtonCheck({onclick:function(){t.$("input").prop("checked",0!==t.all_button.value()),t.value(t._getValue()),t.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(t){this.model.set("data",t)},_changeData:function(){var t=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):a.each(this.model.get("data"),function(e){t.$options.append(n(t._templateOption(e)).addClass("ui-option").tooltip({title:e.tooltip,placement:"bottom"}))});var t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return 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n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=u.extend({initialize:function(t){t.type="radio",u.prototype.initialize.call(this,t)}});var f={};f.View=u.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,u.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return t.icon&&e.append(n("<i/>").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(n("<input/>").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),e.default={Base:c,BaseIcons:u,Radio:h,RadioButton:p,Checkbox:f}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(11),l=a(s),d=i(4),c=a(d),u=t.View.extend({initialize:function(t){var e=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:t.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new 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i=n(this._templateRow({id:t.id,name:t.name}));i.on("click",function(){i.remove(),e._refresh()}),i.on("mouseover",function(){i.addClass("portlet-highlight")}),i.on("mouseout",function(){i.removeClass("portlet-highlight")}),this.portlet.append(i),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(t){this.select.update(t)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(t){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(t){return'<div id="'+t.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span class="ui-list-name">'+t.name+"</span></div>"}});e.default={View:u}}).call(e,i(1),i(0))},function(t,e,i){"use strict";var n=i(0),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=a.default;r.fn.make_text_editable=function(t){var e="num_cols"in t?t.num_cols:30,i="num_rows"in t?t.num_rows:4,n="use_textarea"in t&&t.use_textarea,a="on_finish"in t?t.on_finish:null,o="help_text"in t?t.help_text:null,s=r(this);return s.addClass("editable-text").click(function(o){if(!(r(this).children(":input").length>0)){s.removeClass("editable-text");var l,d,c=function(t){s.find(":input").remove(),""!==t?s.text(t):s.html("<br>"),s.addClass("editable-text"),a&&a(t)},u="cur_text"in t?t.cur_text:s.text();n?(l=r("<textarea/>").attr({rows:i,cols:e}).text(r.trim(u)).keyup(function(t){27===t.keyCode&&c(u)}),d=r("<button/>").text("Done").click(function(){return c(l.val()),!1})):l=r("<input 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this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(t){i(".tooltip").hide(),this.event.type||((i(t.target).hasClass("f-header")||i(t.target).hasClass("f-title"))&&(this.event.type="drag"),i(t.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(t.preventDefault(),this.event.target=this._frameIdentify(t.target),this.event.xy={x:t.originalEvent.pageX,y:t.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(t){if(this.event.type){var e={x:t.originalEvent.pageX,y:t.originalEvent.pageY},i={x:e.x-this.event.xy.x,y:e.y-this.event.xy.y};this.event.xy=e;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var r={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==r.left&&r.left++,this._frameInsert(this.frame_shadow,r)}}},_eventFrameMouseUp:function(t){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(t){this.event.type||(t.preventDefault(),this.del(this._frameIdentify(t.target)))},_eventHide:function(t){!this.event.type&&this.hide()},_eventPanelScroll:function(t){if(!this.event.type&&this.visible){0!==i(t.srcElement).parents(".frame").length?t.stopPropagation():(t.preventDefault(),this._panelScroll(t.originalEvent.detail?t.originalEvent.detail:t.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(t){this.event.type||(t.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(t){this.event.type||(t.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(t){return this.frame_list["#"+i(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var i="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var i="width"==t||"height"==t?1:-1,n=e*this.options.cell-i*this.options.margin;return"top"==t&&(n+=this.top),n},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var i=this.frame_list[e];if(null!==i.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,i.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(o,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(23),l=a(s),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,s){s=s||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=s.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),l=o(s),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),_=o(p),m=i(51),g=o(m),v=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],o=e.$("#"+t.id+"-section-"+a),s=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){s=!0;break}a==n&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new v(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,o=new v(i.app,{inputs:e});r.add({id:a,$el:o.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=a.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new v(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:v}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),g=r(m),v=i(57),b=r(v);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var o=this.history[i[r]+"_"+this.config[e].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(o)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":o}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": 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a=i(3),r=(n(a),i(4)),o=n(r),s=i(43),l=(n(s),i(24)),d=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new u,this.options=t,this.library_select=new o.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new d.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),o=i(24),s=n(o),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new s.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),r.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(56),l=n(s),d=t.View.extend({initialize:function(t){var e=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new o.default.Input({type:"password"}),this.setElement(this._template(t)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(t){var e=this;l.default.openFileBrowser({successCallback:function(t){e.value(t.destination+"^"+t.token)}})},_template:function(t){return'<div class="ui-gs-select-file"><div class="ui-gs-browse-field"><span class="ui-gs-browse-button" /><span class="ui-gs-filename-textbox" /></div><div class="ui-gs-token-field"><span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span><span class="ui-gs-token-textbox" /></div></div>'},value:function(t){if(void 0===t)return this._getValue();this._setValue(t)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(t){t&&(values=t.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});e.default={View:d}}).call(e,i(1))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0}),e.default={openFileBrowser:function(t){var e=window.Galaxy.config.genomespace_ui_url,i=e+"upload/loadUrlToGenomespace.html?getLocation=true",n=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=t.successCallback,window.addEventListener("message",function(t){successCalBack(t.data)},!1),n.focus(),null!=t.errorCallback&&(n.setCallbackOnGSUploadError=config.errorCallback)}}},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default=t.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},initialize:function(t){this.options=r.default.merge(t,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var 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a("<div/>").append(a("<div/>").addClass("portlet-header").append(a("<div/>").addClass("portlet-operations")).append(a("<div/>").addClass("portlet-title").append(a("<i/>").addClass("portlet-title-icon")).append(a("<span/>").addClass("portlet-title-text")))).append(a("<div/>").addClass("portlet-content").append(a("<div/>").addClass("portlet-body")).append(a("<div/>").addClass("portlet-buttons"))).append(a("<div/>").addClass("portlet-backdrop"))}});e.default={View:c}}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(e){this.model=e&&e.model||new t.Model({id:r.default.uid(),title:"",icon:"",cls:"btn btn-default",wait:!1,wait_text:"Sending...",wait_cls:"btn 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a=n("<a/>").addClass("dropdown-item").attr({href:i.href,target:i.target}).append(n("<i/>").addClass("fa").addClass(i.icon).css("display",i.icon?"inline-block":"none")).append(i.title).on("click",function(t){i.onclick&&(t.preventDefault(),i.onclick())});t.$menu.append(n("<li/>").append(a)),i.divider&&t.$menu.append(n("<li/>").addClass("divider"))}})},addMenu:function(t){this.collection.add(r.default.merge(t,{title:"",target:"",href:"",onclick:null,divider:!1,visible:!0,icon:null,cls:"button-menu btn-group"}))}});e.default={ButtonDefault:o,ButtonLink:s,ButtonIcon:d,ButtonCheck:l,ButtonMenu:c}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return 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e=this.attributes.obj_cache,i=this.attributes.key_ary,n=t.toString(),a=o.indexOf(i,function(t){return t.toString()===n});return-1!==a&&(e[n].stale?(i.splice(a,1),delete e[n]):this.move_key_to_end(t,a)),e[n]},set_elt:function(t,e){var i=this.attributes.obj_cache,n=this.attributes.key_ary,a=t.toString(),r=this.attributes.num_elements;if(!i[a]){if(n.length>=r){delete i[n.shift().toString()]}n.push(t)}return i[a]=e,e},move_key_to_end:function(t,e){this.attributes.key_ary.splice(e,1),this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:o.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){y.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;o.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),i=t.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(a.go()).then(function(t){i.resolve("ok"===t||"data"===t)}),i},search_features:function(e){var i=this.get("dataset"),n={query:e,hda_ldda:i.get("hda_ldda"),data_type:"features"};return t.getJSON(i.url(),n)},load_data:function(e,i,n,a){var r=this.get("dataset"),o={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:i,resolution:n,hda_ldda:r.get("hda_ldda")};t.extend(o,a);var s=this.get("filters_manager");if(s){for(var l=[],d=s.filters,c=0;c<d.length;c++)l.push(d[c].name);o.filter_cols=JSON.stringify(l)}var u=this,h=t.getJSON(r.url(),o,function(t){t.region=e,u.set_data(e,t)});return this.set_data(e,h),h},get_data:function(t,e,i,n){var a=this.get_elt(t);if(a&&(c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)))return a;for(var r,o,s=this.get("key_ary"),l=this.get("obj_cache"),d=0;d<s.length;d++)if(r=s[d],r.contains(t)&&(o=!0,a=l[r.toString()],c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)&&this.get("can_subset")(a))){if(this.move_key_to_end(r,d),!c.default.is_deferred(a)){var u=this.subset_entry(a,t);this.set_data(t,u),a=u}return a}if(!o&&t.length()<this.attributes.min_region_size){t=t.copy();var h=this.most_recently_added();!h||t.get("start")>h.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,i,n)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,i,n,a,r){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");r===this.DEEP_DATA_REQ?t.extend(a,{start_val:o.data.length+1}):r===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),d=this,c=this.load_data(l,i,n,a),u=t.Deferred();return this.set_data(e,u),t.when(c).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),d.set_data(e,t),u.resolve(t)}),u},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,i,n,a){var r=this._mark_stale(t);return r?(a||(a={}),"bigwig"===r.dataset_type&&(a.num_samples=1e3*n),this.load_data(t,e,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var i=this,n=!0,a=o.map(e.get("chroms_info").chrom_info,function(t){var e=i.get_elt(new S({chrom:t.chrom,start:0,end:t.len}));return e||(n=!1),e});if(n)return a;var r=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){i.add_data(t.data),r.resolve(t.data)}),r},subset_entry:function(t,e){var i={bigwig:function(t,e){return o.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,i){var n=i.get("start")-t.region.get("start");return t.data.slice(n,n+i.length())}},n=t.data;return!t.region.same(e)&&t.dataset_type in i&&(n=i[t.dataset_type](t.data,e)),{region:e,data:n,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new n.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,i,n){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,i,n):{data:null,region:t}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=o.find(this.get_chroms_info(),function(e){return e.chrom===t});return new S({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return o.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),S=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),i=e[0],n=e[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new S({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),i=t.get("chrom"),n=this.get("start"),a=t.get("start"),r=this.get("end"),o=t.get("end");return e&&i&&e!==i?S.overlap_results.DIF_CHROMS:n<a?r<a?S.overlap_results.BEFORE:r<o?S.overlap_results.OVERLAP_START:S.overlap_results.CONTAINS:n>a?n>o?S.overlap_results.AFTER:r<=o?S.overlap_results.CONTAINED_BY:S.overlap_results.OVERLAP_END:r>=o?S.overlap_results.CONTAINS:S.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===S.overlap_results.CONTAINS},overlaps:function(t){return 0===o.intersection([this.compute_overlap(t)],[S.overlap_results.DIF_CHROMS,S.overlap_results.BEFORE,S.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),$=n.Collection.extend({model:S}),T=n.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new S(t.region))}}),M=n.Collection.extend({model:T}),O=n.Model.extend(v).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new 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d.append(n("<input />").attr("id",a).attr("name",a).val(s));e.help&&d.append(n("<div class='help'/>").text(e.help))}}),this},render_in_modal:function(t){var e=this,i=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc")},a=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc"),e.update_from_form()},r=function(t){27===(t.keyCode||t.which)?i():13===(t.keyCode||t.which)&&a()};n(window).bind("keypress.check_enter_esc",r),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:t||"Configure",body:this.$el,buttons:{Cancel:i,OK:a}})},update_from_form:function(){var t=this;this.collection.each(function(e,i){if(!e.get("hidden")){var n="param_"+i,a=t.$el.find("#"+n).val();"bool"===e.get("type")&&(a=t.$el.find("#"+n).is(":checked")),e.set_value(a)}})}});e.default={ConfigSetting:c,ConfigSettingCollection:u,ConfigSettingCollectionView:h}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return 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i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,n("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&a.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),a.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),n=a.filter(t.data2,function(i){var n=!1;return a.each(i.tags,function(i){t._match(e.term,i)&&(n=t.matched_tags[i]=!0)}),n||t._match(e.term,i.text)});e.callback({results:n.slice((e.page-1)*i,e.page*i),more:n.length>=e.page*i})},formatResult:function(e){return a.escape(e.text)+'<div class="ui-tags">'+a.reduce(e.tags,function(e,i){return t.matched_tags[i]?e+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search 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null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(t){return a.findWhere(this.data,{value:t})},text:function(){var t=this._getValue(),e=this.exists(n.isArray(t)?t[0]:t);return e?e.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(t,e){a.each(this.model.get("data"),function(e){e.keep&&!a.findWhere(t,{value:e.value})&&t.push(e)}),e&&t&&t.sort(e),this.model.set("data",t)},update:function(t){this.model.set("data",t)},setOnChange:function(t){this.model.set("onchange",t)},length:function(){return 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t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return t.length>0?t.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(t){var e=this;if(void 0!==t&&(this.$("input").prop("checked",!1),null!==t)){var i=n.isArray(t)?t:[t];a.each(i,function(t){e.$('input[value="'+t+'"]').first().prop("checked",!0)})}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push(n(this).val())}),s.default.isEmpty(t)?null:this.model.get("multiple")?t:t[0]},_messageShow:function(t,e){this.$message.show().removeClass().addClass("ui-message alert alert-"+e).html(t)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(t){var e=s.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=u.extend({initialize:function(t){t.type="radio",u.prototype.initialize.call(this,t)}});var f={};f.View=u.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,u.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return 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a=t.View.extend({initialize:function(e){this.model=e&&e.model||new t.Model(e),this.setElement(i("<div/>").addClass("corner frame")),this.$el.append(i("<div/>").addClass("f-header corner").append(i("<div/>").addClass("f-title")).append(i("<div/>").addClass("f-icon f-close fa fa-close").tooltip({title:"Close",placement:"bottom"}))).append(i("<div/>").addClass("f-content")).append(i("<div/>").addClass("f-resize f-icon corner fa fa-expand").tooltip({title:"Resize"})).append(i("<div/>").addClass("f-cover")),this.$header=this.$(".f-header"),this.$title=this.$(".f-title"),this.$content=this.$(".f-content"),this.render(),this.listenTo(this.model,"change",this.render,this)},render:function(){var t=this,e=this.model.attributes;this.$title.html(e.title||""),this.$header.find(".f-icon-left").remove(),n.each(e.menu,function(e){var a=i("<div/>").addClass("f-icon-left").addClass(e.icon);n.isFunction(e.disabled)&&e.disabled()?a.attr("disabled",!0):a.on("click",function(){e.onclick(t)}).tooltip({title:e.tooltip,placement:"bottom"}),t.$header.append(a)}),e.url?this.$content.html(i("<iframe/>").addClass("f-iframe").attr("scrolling","auto").attr("src",e.url+(-1===e.url.indexOf("?")?"?":"&")+"widget=True")):e.content&&(n.isFunction(e.content)?e.content(t.$content):t.$content.html(e.content))}}),r=t.View.extend({defaultOptions:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_uid:0,frame_list:{},frame_shadow:null,visible:!1,event:{},initialize:function(e){var a=this;this.options=n.defaults(e||{},this.defaultOptions),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(i("<div/>").addClass("galaxy-frame").append(i("<div/>").addClass("frame-background")).append(i("<div/>").addClass("frame-menu frame-scroll-up fa fa-chevron-up fa-2x")).append(i("<div/>").addClass("frame-menu frame-scroll-down fa fa-chevron-down fa-2x"))),this.frame_shadow=new t.View({el:i("<div/>").addClass("corner frame-shadow")}),this.$el.append(this.frame_shadow.$el),this._frameInit(this.frame_shadow,"#frame-shadow"),this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list["#frame-shadow"]=this.frame_shadow,this.visible?this.show():this.hide(),this._panelRefresh(),i(window).resize(function(){a.visible&&a._panelRefresh()})},render:function(){this.$(".frame-scroll-up")[this.top!=this.options.top_min&&"show"||"hide"](),this.$(".frame-scroll-down")[this.top!=this.top_max&&"show"||"hide"]()},add:function(t){if(this.frame_counter>=this.options.frame_max)Galaxy.modal.show({title:"Warning",body:"You have reached the maximum number of allowed frames ("+this.options.frame_max+").",buttons:{Close:function(){Galaxy.modal.hide()}}});else{var e="#frame-"+this.frame_uid++;if(0!==i(e).length)Galaxy.modal.show({title:"Error",body:"This frame already exists. This page might contain multiple frame managers.",buttons:{Close:function(){Galaxy.modal.hide()}}});else{this.top=this.options.top_min;var n=new a(t);this.$el.append(n.$el),t.width=this._toPixelCoord("width",this.options.frame.cols),t.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt(n.$el.css("z-index")),this.frame_list[e]=n,this.frame_counter++,this._frameInit(n,e),this._frameResize(n,{width:t.width,height:t.height}),this._frameInsert(n,{top:0,left:0},!0),!this.visible&&this.show(),this.trigger("add")}}},del:function(t){var e=this,i=t.$el;i.fadeOut("fast",function(){i.remove(),delete e.frame_list[t.id],e.frame_counter--,e._panelRefresh(!0),e._panelAnimationComplete(),e.trigger("remove")})},show:function(){this.visible=!0,this.$el.fadeIn("fast"),this.trigger("show")},hide:function(){this.event.type||(this.visible=!1,this.$el.fadeOut("fast",function(){i(this).hide()}),this.trigger("hide"))},length:function(){return this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(t){i(".tooltip").hide(),this.event.type||((i(t.target).hasClass("f-header")||i(t.target).hasClass("f-title"))&&(this.event.type="drag"),i(t.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(t.preventDefault(),this.event.target=this._frameIdentify(t.target),this.event.xy={x:t.originalEvent.pageX,y:t.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(t){if(this.event.type){var e={x:t.originalEvent.pageX,y:t.originalEvent.pageY},i={x:e.x-this.event.xy.x,y:e.y-this.event.xy.y};this.event.xy=e;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var r={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==r.left&&r.left++,this._frameInsert(this.frame_shadow,r)}}},_eventFrameMouseUp:function(t){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(t){this.event.type||(t.preventDefault(),this.del(this._frameIdentify(t.target)))},_eventHide:function(t){!this.event.type&&this.hide()},_eventPanelScroll:function(t){if(!this.event.type&&this.visible){0!==i(t.srcElement).parents(".frame").length?t.stopPropagation():(t.preventDefault(),this._panelScroll(t.originalEvent.detail?t.originalEvent.detail:t.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(t){this.event.type||(t.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(t){this.event.type||(t.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(t){return this.frame_list["#"+i(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var i="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var i="width"==t||"height"==t?1:-1,n=e*this.options.cell-i*this.options.margin;return"top"==t&&(n+=this.top),n},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var i=this.frame_list[e];if(null!==i.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,i.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(o,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(23),l=a(s),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,s){s=s||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=s.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),l=o(s),d=i(4),c=(o(d),i(11)),u=o(c),h=i(49),f=o(h),p=i(50),_=o(p),m=i(51),g=o(m),v=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],o=e.$("#"+t.id+"-section-"+a),s=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){s=!0;break}a==n&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new v(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,o=new v(i.app,{inputs:e});r.add({id:a,$el:o.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=a.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new v(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:v}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),g=r(m),v=i(57),b=r(v);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var o=this.history[i[r]+"_"+this.config[e].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(o)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":o}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": "+t.name,value:t.id,tags:t.tags}),e.history[t.id+"_"+n]=t})}),a.each(this.config,function(t,n){i[t.src]&&e.fields[n].add(i[t.src],function(t,e){return e.hid-t.hid})})},_changeValue:function(){var t=this.model.get("value");if(t&&t.values&&t.values.length>0){var e=[];a.each(t.values,function(t){e.push(t.id)});for(var i=t.values[0].src,n=t.values.length>1,r=0;r<this.config.length;r++){var o=this.fields[r],s=this.config[r];if(s.src==i&&-1!==[n,!0].indexOf(s.multiple)){this.model.set("current",r),o.value(e);break}}}else a.each(this.fields,function(t){t.value(null)})},_handleDrop:function(t){try{var e=this.model.get("data"),i=this.model.get("current"),n=this.config[i],r=this.fields[i],o=JSON.parse(t.originalEvent.dataTransfer.getData("text"))[0],s=o.id,l="dataset"==o.history_content_type?"hda":"hdca",d={id:s,src:l};if(e&&a.findWhere(e[l],d)){if(n.src==l){var c=r.value();c&&n.multiple?-1==c.indexOf(s)&&c.push(s):c=s,r.value(c)}else this.model.set("value",{values:[d]}),this.model.trigger("change:value");this.trigger("change"),this._handleDropStatus("success")}else this._handleDropStatus("danger")}catch(t){this._handleDropStatus("danger")}t.preventDefault()},_handleDropStatus:function(t){var e=this;this.$el.removeClass("ui-dragover").addClass("ui-dragover-"+t),setTimeout(function(){e.$el.removeClass("ui-dragover-"+t)},this.model.get("statustimer"))},_batch:function(t){t.batch=!1;var e=this.model.get("current"),i=this.config[e];if("hdca"==i.src&&!i.multiple){var n=this.history[this.fields[e].value()+"_hdca"];n&&n.map_over_type&&(t.batch=!0)}return i.batch!=h.LINKED&&i.batch!=h.ENABLED||(t.batch=!0,i.batch==h.ENABLED&&"true"===this.button_product.value()&&(t.product=!0)),t}});e.default={View:p}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(43),l=(n(s),i(24)),d=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new u,this.options=t,this.library_select=new o.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new d.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),o=i(24),s=n(o),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new s.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),r.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(56),l=n(s),d=t.View.extend({initialize:function(t){var e=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new 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v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(D.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var q=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),D.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(q.prototype,j.prototype,D.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){D.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){D.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(D.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),D.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){D.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(D.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new q(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new q(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:q,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:q,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),D=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>D)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,D-j,$),void 0!==v&&k>x&&!(j>b||D<v)){var q=Math.max(j,v),I=Math.min(D,b);t.fillRect(q,d+1,I-q,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),q+14<I&&(q+=2,I-=2),t.fillRect(q,d+1,I-q,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,D,d),z=j,R=D}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],D=P[1],q=d+g;if(p=f(q),_=f(q+D),o([q,q+D],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=D;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+D):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,q-a),Math.min(q-a+D,s-a)));for(var L=Math.max(q,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=D),g+=D;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=D;break;case"D":$.draw_deletion(p,S,D),g+=D;break;case"I":var V=p-b;if(o([q,q+D],m)){var G=h.slice(v,v+D);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([q,q+D],m)){case 1003:G=G.slice(a-q);break;case 1004:G=G.slice(0,q-s);break;case 1005:break;case 1002:G=G.slice(a-q,q-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(q+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=D}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,D),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,D)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var D=P[5];S.test(D)&&(j.itemRgb="rgb("+D+")")}if(P.length>A-3&&E)for(var q=A-3;q<P.length;++q)j[E.fields[q+3].name]=P[q];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=p[v+4]<<32|p[v+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&(S<0||x>$)&&(S=k,$=i<0?x:w,i<0?y:b),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&s.push(l[d]);return a(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return r.topLevelReductionCache=o,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=i>0?0:3e8;t.fromRef&&(s=e);for(var d=0;d<o.length;++d){var c,u=o[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>s)return a(u)}else u.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<s)return a(u)}else u.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(s+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(o(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=r.exec(n);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};n=n.substring(s[0]);for(var d=o.exec(n);null!=d;d=o.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,o;!function(n,s){r=[i(0)],a=s,void 0!==(o="function"==typeof a?a.apply(e,r):a)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},o={},s=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),i.cors=!!s&&"withCredentials"in s,i.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(i.cors||s&&!t.crossDomain)return{send:function(i,n){var s,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in 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t=this.model.get("tool_search").get("results");t&&0===t.length?n("#search-no-results").show():n("#search-no-results").hide()}}),E=t.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(z.tool_form(this.model.toJSON()))}}),z=(t.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new A({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),n("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" 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%>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});e.default={ToolParameter:f,IntegerToolParameter:m,SelectToolParameter:v,Tool:b,ToolCollection:w,ToolSearch:k,ToolPanel:C,ToolPanelView:A,ToolFormView:E}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(9),u=r(c),h=i(63),f=r(h),p=i(40),_=r(p),m=t.View.extend({initialize:function(t){var e=this;this.modal=parent.Galaxy.modal||new u.default.View,this.form=new f.default(s.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(t,i){var a=i.model.attributes,r="",o={},l=a.job_id;l?r=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),s.default.get({url:r,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),e._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),t.resolve()},error:function(e,r){var o=e&&e.err_msg||"Uncaught error.";401==r?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new d.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},postchange:function(t,e){var i={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:n.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),s.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:i,success:function(i){e.update(i),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(t){var e=this,i=t.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var i=this,r={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(r))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){o.append(n("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],o=this.form.data.match(a),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==r)return this.form.highlight(o),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],o=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,o=n-r,s=0;o<=0&&(o=1,s=r-(n-o));var l,d=r+s,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(e+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var u=o;u<c+1;u++)u==t.cur_page_num?e+='<span class="page-link inactive-link" id="page-link-'+u+'">'+u+"</span>":e+='<span class="page-link" id="page-link-'+u+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+u+'">'+u+"</a></span>";c<a&&(e+='...<span class="page-link" id="page-link-'+a+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+a+'">'+a+"</a></span>"),e+="</span>",e+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(t.show_item_checkboxes){e+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var h in t.operations){var f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var o=t.columns[r];if("advanced"==o.filterable){var s=o.key,l=i[s],d=e[s];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div id="standard-search" style="display: '+c+';"><table><tr><td style="padding: 0;"><table>';for(var r in t.columns){var o=t.columns[r];"standard"==o.filterable&&(u+=this.grid_column_filter(t,o))}u+="</table></td></tr><tr><td>",a&&(u+='<a href="" class="advanced-search-toggle">Advanced Search</a>'),u+="</td></tr></table></div>",u+='<div id="advanced-search" style="display: '+n+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var r in t.columns){var o=t.columns[r];"advanced"==o.filterable&&(u+=this.grid_column_filter(t,o))}return u+="</table></div>"},grid_column_filter:function(e,i){var n=(e.default_filter_dict,e.filters),a=i.label,r=i.key;"advanced"==i.filterable&&(a=a.toLowerCase());var o="<tr>";if("advanced"==i.filterable&&(o+='<td align="left" style="padding-left: 10px">'+a+":</td>"),o+='<td style="padding-bottom: 1px;">',i.is_text){o+='<form class="text-filter-form" column_key="'+r+'" action="'+e.url+'" method="get" >';for(u in e.columns){var s=e.columns[u],l=n[s.key];l&&"All"!=l&&(s.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+s.key+'" name="f-'+s.key+'" value="'+l+'"/>')}o+='<span id="'+r+'-filtering-criteria">';var d=n[r];if(d){var c=t.type(d);if("string"==c&&"All"!=d&&(o+=this.filter_element(r,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),o+=this.filter_element(r,h)}}o+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+r+'-filter" name="f-'+r+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+r+'-filtering-criteria">';var m=!1;for(var g in e.categorical_filters[r]){var v=e.categorical_filters[r][g],b="",w="";for(var y in v)b=y,w=v[y];m&&(o+=" | "),m=!0;var h=n[r];h&&v[r]&&h==w?o+='<span class="categorical-filter '+r+'-filter current-filter">'+g+"</span>":o+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+g+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(146),l=a(s),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),g=i(3),v=a(g);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){v.default.cssLoadFile("static/style/jquery.rating.css"),v.default.cssLoadFile("static/style/autocomplete_tagging.css"),v.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),v.default.cssLoadFile("static/style/library.css"),v.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){o.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),o=n("<div/>").addClass("position").appendTo(r),s=(n("<a href=''/>").text(t).appendTo(o).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var s=this,d=new l.default.TracksterView(o.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,o=e.start,c=e.end,u=e.overview;n&&void 0!==o&&c?d.change_chrom(n,o,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],s.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function o(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var s=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),g=i(149),v=a(g),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),S=i(21),$=a(S),T=i(151),M=a(T);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,o,s,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){o=r.position().top,s=o+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<o)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>s)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),o=a.position().top,s=o+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=o&&i.offsetY<=s)return i.offsetY-o<s-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=$.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new $.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(D.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var q=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),D.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(q.prototype,j.prototype,D.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),o=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],l[s.name]=[s];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)s=a.filters_manager.filters[n],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===o&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){D.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){D.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(D.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var I=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),D.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=$.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,o=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(o),n.current_height=e.clientY,n.current_x=n.offsetX;var s=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,s=i.viewport_container.width();i.update_location(Math.round(a/s*o)+i.low,Math.round(r/s*o)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),o=i.high-i.low,s=i.viewport_container.width(),l=i.low;i.low=Math.round(a/s*o)+l,i.high=Math.round(r/s*o)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(I.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,o=i.chrom_data.length;r<o;r++){var s=i.chrom_data[r].chrom,l=t("<option>");l.text(s),l.val(s),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var o=0,s=a.drawables.length;o<s;o++){var l=a.drawables[o];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){D.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(D.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),N=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new N({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,o=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var s=new q(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,s,!1);s.container_div.insertBefore(r.view.content_div.children()[l]),s.add_drawable(r),r.container_div.appendTo(s.content_div),t=s}else t=r.container;var d=new r.constructor(view,t,{name:o,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),V=function(t,e){v.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,o,s,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?o:[r].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new L(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new B({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,o=r/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*s),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,o,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,o,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(s),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(s,r(e,1)),i()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,o=1/i,s=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:s.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&s.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,o,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),o=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=o[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,g=s.view.canvas_manager.new_canvas(),v=e.get("start"),b=e.get("end"),w=Math.ceil((b-v)*i)+s.left_offset,y=l.max(_);g.width=w,g.height=n.height||y;var x=g.getContext("2d");x.translate(s.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(o[n],x,u[n],e,i,a)}),void 0!==m&&(s.tile_cache.set_elt(c,m),s.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new v.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,o=this.view.container.width(),s=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(s)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new q(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var o=t[a].html_elt.find("canvas").height();o>r&&(r=o)}for(a=0;a<t.length;a++){var s=t[a];s.html_elt.find("canvas").height()!==r&&(this.draw_helper(s.region,i,{force:!0,height:r}),s.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),o=r.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=o.length;l<d;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*a),10);return new G(this,n,a,s,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new v.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=v.default.ArcLinkedFeaturePainter:this.painter=v.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,o=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(o.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,u=o.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,o){var s=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,g=t.data.length;m<g;m++){for(var v,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(v=_[y],v.update_attrs(b),!v.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,S=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return s.view.get_base_color(t)}),$=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=S.draw(e,l.width,l.height,a,f);$=T.feature_mapper,incomplete_features=T.incomplete_features,$.translation=-u}return o?void 0:new F(s,n,a,l,t.data,i,t.message,p,$,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=v.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),o=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var d=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=v.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:q,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:I,DrawableGroup:q,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,o){var s=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var o=i.display_modes[a];n[o]=function(t){return function(){i.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var o=0,s=r.length;o<s;o++){var l=r[o];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,s=0,l=t.length;s<l;s++){e=t[s],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(s)}for(var s=0,l=a.length;s<l;s++){e=t[a[s]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new o(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:s}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},o=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},s=function(t,e,i,n,a,r){void 0===r&&(r=4);var o,s=n-e,l=a-i,d=Math.floor(Math.sqrt(s*s+l*l)/r),c=s/d,u=l/d;for(o=0;o<d;o++,e+=c,i+=u)o%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,o=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,o),t.lineTo(r,o),t.lineTo(e,i),t.lineTo(a,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+o/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var g,v=this.prefs.block_color||this.prefs.color,b=parseInt(v.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,S=0,$=h.length;S<$;S++)if(t.fillStyle=t.strokeStyle=v,k=C=!1,g=m[S],p=Math.floor((h[S][0]-c-.5)*n),null!==(_=h[S][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,g,-_);else if("Intensity"===u){var T=(_-o)/l,M=Math.round(w+(255-w)*(1-T)),O=Math.round(y+(255-y)*(1-T)),A=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,g,d)}else _=Math.round(d-(_-o)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=g:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=v}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,o){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=o||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],g=m[0],v=m[1],b=m[2],w=a&&void 0!==a[g]?a[g].slot:null;("Dense"===this.mode||null!==w)&&v<s&&b>o&&(l=this.draw_element(t,this.mode,m,w,o,s,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(v<o||b>s)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,o,s,l){return[0,0]}});var _=function(t,e,i,n,a,r,o){p.call(this,t,e,i,n,a,r,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,o,s,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*o))),m=p,g=_,d=("Dense"===e?0:0+n)*s+this.get_top_padding(l),v=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var $,T;if("Squish"===e?($=1,T=3,S=!1):($=5,T=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=T):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*o)),D=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*o)));if(!(j>D)){if(t.fillStyle=w,t.fillRect(j,d+(T-$)/2+1,D-j,$),void 0!==v&&k>x&&!(j>b||D<v)){var q=Math.max(j,v),I=Math.min(D,b);t.fillRect(q,d+1,I-q,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),q+14<I&&(q+=2,I-=2),t.fillRect(q,d+1,I-q,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,D,d),z=j,R=D}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(i),N=Math.ceil(T*L),B=Math.round((T-N)/2);1!==L&&(t.fillRect(p,M+1,_-p,B),t.fillRect(p,M+T-B+1,_-p,B))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,T),f&&S&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,T));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),g+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,g]}});var m=function(t,e,i,n,a,r,o,s,l){p.call(this,t,e,i,n,a,r,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,o=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(o)&&(n[1]+=a,r+=a),[e.indexOf(o),a]});return{blocks:i,cigar:o}},draw_read:function(t,e,i,n,a,s,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,s],g=0,v=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,S=n+1,$=new x(t,C,i,e),T=[],M=[],O=this._parse_cigar(c);c=O.cigar,T=O.blocks;for(var A=0;A<T.length;A++){var E=T[A];o([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,S,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],D=P[1],q=d+g;if(p=f(q),_=f(q+D),o([q,q+D],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":g+=D;break;case"=":case"X":var I="";"X"===j?I=h.slice(v,v+D):this.ref_seq&&(I=this.ref_seq.slice(Math.max(0,q-a),Math.min(q-a+D,s-a)));for(var L=Math.max(q,a),N=0;N<I.length;N++)if(I&&!this.prefs.show_differences||"X"===j){var B=Math.floor(Math.max(0,(L+N-a)*i));t.fillStyle=this.base_color_fn(I[N]),k&&i>w?t.fillText(I[N],B,n+9):i>.05&&t.fillRect(B-b,S,Math.max(1,Math.round(i)),C)}"X"===j&&(v+=D),g+=D;break;case"N":t.fillStyle="#ccc",t.fillRect(p,S+(C-1)/2,_-p,1),g+=D;break;case"D":$.draw_deletion(p,S,D),g+=D;break;case"I":var V=p-b;if(o([q,q+D],m)){var G=h.slice(v,v+D);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[V,n+4,5]},t.fillStyle="#ccc",r([q,q+D],m)){case 1003:G=G.slice(a-q);break;case 1004:G=G.slice(0,q-s);break;case 1005:break;case 1002:G=G.slice(a-q,q-s)}for(var N=0,F=G.length;N<F;N++){var B=Math.floor(Math.max(0,(q+N-a)*i));t.fillText(G[N],B-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,V,n+9]})}v+=D}else g=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(g,j,D),v=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(v,j,D)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,o,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*o,(c-a-.5)*o)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*o))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var g=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,o,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,o,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),b=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&b>v){t.fillStyle="#ccc";var w=_+1+(m-1)/2;s(t,v,w,b,w)}}else this.draw_read(t,e,o,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var g=function(t,e,i,n,a,r,o){_.call(this,t,e,i,n,a,r,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(g.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var o=(i+n)/2,s=n-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,r,n-o,Math.PI,0),t.stroke())}});var v=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};v.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,o=Math.max(i,n,a),s=Math.min(i,n,a),l=(o+s)/2,d=o-s;if(o===s)t=e=0;else{switch(e=l>.5?d/(2-o-s):d/(o+s),o){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,o=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,s=1-o,l=[i.rgb[0]*o+t.rgb[0]*s,i.rgb[1]*o+t.rgb[1]*s,i.rgb[2]*o+t.rgb[2]*s],d=i.alpha*n+t.alpha*(1-n);return new v(l,d)}};var b=function(t,e,i,n){this.start_color=new v(t),this.end_color=new v(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,o;if(void 0===this.prefs.min_value){var s=1/0;for(r=0,o=this.data.length;r<o;r++)s=Math.min(s,this.data[r][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,o=this.data.length;r<o;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,o,s,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var g=0,v=f.length;g<v;g++)a=f[g],r=m(a[1]),o=m(a[2]),s=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,s,o-r,l-s);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,o,s,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,o=null;return"-"===e?(o="deletion",r=t.length):0===t.indexOf(e)&&i>n?(o="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(o="insertion",r=n-i,a=n),null!==o?{type:o,start:a,len:r}:{}},g=Math.max(1,Math.floor(n)),v=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===v&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],o=r[1],s=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(s,t);return a.extend(e,i)}),!(o<this.view_start||o>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(o+l[_].start,n),t.fillRect(h,0,g,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var S=c/d.length,$=Math.ceil(this.prefs.summary_height*S);t.fillRect(h,f-$,g,$),f-=$}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(o+u.start,n),"snp"===u.type){var T=u.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,n),f+b):t.fillRect(h,f+1,g,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:g,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),n.slider("option","values")&&(r=2*r+1,o=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(o?"values":"value",l),s.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),o=i.filters,s=0;s<o.length;s++)"number"===o[s].type?(n=new l(o[s]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in a)o[o.length]=[s,a[s]];!function e(i,n){var a=n[0],r=a[0],o=a[1],s="("+o.join(") and (")+")",l={cond:s,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:s}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(o(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),o=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==g)i.type="bigwig";else{if(d!=b)return d==v||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=o[2],i.numZoomLevels=o[3],i.chromTreeOffset=s(r,8),i.unzoomedDataOffset=s(r,16),i.unzoomedIndexOffset=s(r,24),i.fieldCount=o[16],i.definedFieldCount=o[17],i.asOffset=s(r,36),i.totalSummaryOffset=s(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=s(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=s(r,24*c+72),f=s(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,g=2291137574,v=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,S=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),o=(a[3],s(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=s(i,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});o(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(o(a.bwg.url,this.cirTreeOffset,48)).then(function(o){a.cirHeader=o;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,o){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,o=4+32*a.cirBlockSize,s=0;s<t.length;++s){var u=new h(t[s],t[s]+o);i=i?f(i,u):u}for(var m=i.ranges(),g=0;g<m.length;++g){var v=m[g];p(t,v,e)}},p=function(t,e,i,s){e.max(),e.min();n.when(o(a.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),i),t[s]-a.cirTreeOffset==48&&t[s]-e.min()==0&&(a.cachedCirRoot=o),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var o=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=o[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16),y=s(o,a+24);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],g=c[_+1],v=c[_+2],b=c[_+3],w=s(o,a+16);(t<0||m<t||m==t&&g<=i)&&(t<0||v>t||v==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,n,r){r||(r={});var o=new i;o._chromId=t,o.segment=a.bwg.idsToChroms[t],o.min=e,o.max=n,o.type=a.bwg.type;for(var l in r)o[l]=r[l];s.push(o)},d=function(){if(0===e.length){Date.now();return r.resolve(s)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(o(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,o=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,o.size-2);else{var s=new Uint8Array(o.size);m(new Uint8Array(t,i,o.size),0,s,0,o.size),r=s.buffer}o.data=r,i+=o.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=s[8*c],_=s[8*c+1],m=s[8*c+2],g=s[8*c+3],v=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/g,maxScore:v};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=s[0],y=s[1],x=(s[2],s[3]),k=s[4],C=r[20],d=o[11];if(3==C)for(var c=0;c<d;++c){var $=l[c+6],T=y+c*x+1,M=y+c*x+k;i(u,T,M)&&e(u,T,M,{score:$})}else if(2==C)for(var c=0;c<d;++c){var _=s[2*c+6]+1,m=_+k-1,$=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:$})}else if(1==C)for(var c=0;c<d;++c){var _=s[3*c+6]+1,m=s[3*c+7],$=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:$})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var $=parseInt(P[1]);isNaN($)||(j.score=$)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var D=P[5];S.test(D)&&(j.itemRgb="rgb("+D+")")}if(P.length>A-3&&E)for(var q=A-3;q<P.length;++q)j[E.fields[q+3].name]=P[q];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var I=0|P[3],L=0|P[4],N=0|P[6],B=P[7].split(","),V=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<N;++W){var K=(0|V[W])+_,Z=K+(0|B[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(L>I){var at="+"==j.orientation?new h(I,L+3):new h(I-3,L),rt=p(tt,at);if(rt){j.type="translation";for(var ot=rt.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var it=0;it<ot.length;++it){var dt=it;"-"==j.orientation&&(dt=ot.length-it-1);var nt=ot[dt];if(j.readframe=st,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();st=(st+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,o=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var o=new h(t[r],t[r]+n);i=i?f(i,o):o}for(var s=i.ranges(),l=0;l<s.length;++l){var c=s[l];u(t,c,e)}}),u=function(o,s,l,c){s.max(),s.min();a.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var u=0;u<o.length;++u)if(s.contains(o[u])&&(p(c,o[u]-s.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,o){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,d=s.min,c=s.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=s,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var g=0;g<m;++g){var v=d/4,b=p[v],w=p[v+1],y=p[v+2],x=p[v+3],k=s(h,d+16),C=s(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>o||y==o&&x>l)||i>0&&(b<o||b==o&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,o=i<0?y:b)),d+=32}else{for(var S=-1,$=-1,g=0;g<m;++g){var 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e=0;e<this._ranges.length;++e)t.push(this._ranges[e])},e.prototype.toString=function(){for(var t="",e=0;e<this._ranges.length;++e)e>0&&(t+=","),t+=this._ranges[e].toString();return t},{Range:t,union:i,intersection:n,coverage:a,rangeOver:r,_rangeOrder:o}}.apply(e,n))&&(t.exports=a)},function(t,e,i){var n,a;n=[],void 0!==(a=function(){function t(){}function e(){this.was=[0]}function i(t,e,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=e,this.mode=g,this.reset(t,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function r(t,e,i,n,a){return t[0]=v,e[0]=b,i[0]=w,n[0]=y,f}function o(t,e,i,n,a){if(0!=a){if(!t)throw"Undef src";if(!i)throw"Undef dest";0==e&&a==t.length?l(t,i,n):O?l(t.subarray(e,e+a),i,n):1==t.BYTES_PER_ELEMENT&&a>100?l(new 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c=15,u=1440,h=0,f=0,p=1,_=-5,m=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],g=0,v=9,b=5,w=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],y=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],S=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,i){return t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var $=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==$[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=g,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,s,l,d,c;for(s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case g:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];r(u,h,_,v,t),this.codes.init(u[0],h[0],_[0],0,v[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,d,i),s+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}this.blens[T[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=g;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){o(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,d,c=0,u=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,u=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==o)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,o--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=s-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);t.window[s++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);i=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,s,l){var d,c,u,h,_,g,v,b,w,y,x,k,C,S,$,T;v=l.next_in_index,b=l.avail_in,_=s.bitb,g=s.bitk,w=s.write,y=w<s.read?s.read-w-1:s.end-w,x=m[t],k=m[e];do{for(;g<20;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(d=_&x,c=i,u=n,T=3*(u+d),0!=(h=c[T]))for(;;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15,C=c[T+2]+(_&m[h]),_>>=h,g-=h;g<15;)b--,_|=(255&l.next_in[v++])<<g,g+=8;for(d=_&k,c=a,u=r,T=3*(u+d),h=c[T];;){if(_>>=c[T+1],g-=c[T+1],0!=(16&h)){for(h&=15;g<h;)b--,_|=(255&l.next_in[v++])<<g,g+=8;if(S=c[T+2]+(_&m[h]),_>>=h,g-=h,y-=C,w>=S)$=w-S,s.window[w++]=s.window[$++],s.window[w++]=s.window[$++],C-=2;else{$=w-S;do{$+=s.end}while($<0);if(h=s.end-$,C>h){if(C-=h,w-$>0&&h>w-$)do{s.window[w++]=s.window[$++]}while(0!=--h);else o(s.window,$,s.window,w,h),w+=h,$+=h,h=0;$=0}}do{s.window[w++]=s.window[$++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3;d+=c[T+2],d+=_&m[h],T=3*(u+d),h=c[T]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,-3);if(d+=c[T+2],d+=_&m[h],T=3*(u+d),0==(h=c[T])){_>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--;break}}else _>>=c[T+1],g-=c[T+1],s.window[w++]=c[T+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=g>>3<C?g>>3:C,b+=C,v-=C,g-=C<<3,s.bitb=_,s.bitk=g,l.avail_in=b,l.total_in+=v-l.next_in_index,l.next_in_index=v,s.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,d,c,h){var p,m,g,v,b,w,y,x,k,C,S,$,T,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(g=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,T=2;0!=--b;)this.x[T]=w+=this.c[C],T++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[g],this.x[0]=b=0,C=0,v=-1,$=-x,this.u[0]=0,S=0,O=0;y<=g;y++)for(p=this.c[y];0!=p--;){for(;y>$+x;){if(v++,$+=x,O=g-$,O=O>x?x:O,(m=1<<(w=y-$))>p+1&&(m-=p+1,T=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++T]);)m-=this.c[T];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=O,0!=v?(this.x[v]=b,this.r[0]=w,this.r[1]=x,w=b>>>$-x,this.r[2]=S-this.u[v-1]-w,o(this.r,0,d,3*(this.u[v-1]+w),3)):s[0]=S}for(this.r[1]=y-$,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-$,w=b>>>$;w<O;w+=m)o(this.r,0,d,3*(S+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<$)-1;(b&k)!=this.x[v];)v--,$-=x,k=(1<<$)-1}return 0!=M&&1!=g?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,o,s,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,s,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,S,o,a,s,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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t=r.defaults(t||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),t.url=e._formatUrl(t.url),n("<li/>").append(n("<a/>").attr("href",t.url).attr("target",t.target).html(t.title).on("click",function(i){i.preventDefault(),e.model.set("show_menu",!1),t.onclick?t.onclick():Galaxy.frame.add(t)}))},_toggleClick:function(t){var e=this,i=this.model;if(t.preventDefault(),n(".tooltip").hide(),i.trigger("dispatch",function(t){i.id!==t.id&&t.get("menu")&&t.set("show_menu",!1)}),i.get("disabled")){var a=function(t,e){return n("<div/>").append(n("<a/>").attr("href",Galaxy.root+e).html(t)).html()};this.$toggle.popover&&this.$toggle.popover("destroy"),this.$toggle.popover({html:!0,placement:"bottom",content:"Please "+a("login","user/login?use_panels=True")+" or "+a("register","user/create?use_panels=True")+" to use this feature."}).popover("show"),setTimeout(function(){e.$toggle.popover("destroy")},5e3)}else i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),o=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),s=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+s,d=e+":"+i+l,c=null,u=null,h='<iframe 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a={container:e,name:i.get("title"),id:i.id,dbkey:i.get("dbkey"),stand_alone:!1},r=i.get("latest_revision"),o=r.config.view.drawables;n.each(o,function(t){t.dataset={hda_ldda:t.hda_ldda,id:t.dataset_id}}),view=t.create_visualization(a,r.config.viewport,r.config.view.drawables,r.config.bookmarks,!1)}};e.add(a)})},add:function(t){if("_blank"==t.target)window.open(t.url);else if("_top"==t.target||"_parent"==t.target||"_self"==t.target)window.location=t.url;else if(!this.active||t.noscratchbook){var e=a(window.parent.document).find("#galaxy_main");"galaxy_main"==t.target||"center"==t.target?0===e.length?window.location=t.url+(-1==t.url.indexOf("?")?"?":"&")+"use_panels=True":e.attr("src",t.url):window.location=t.url}else this.frames.add(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var 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_.default.MetricsLogger(t),e.emit={},["log","debug","info","warn","error","metric"].map(function(t){e.emit[t]=function(i){e.logger.emit(t,arguments[0],Array.prototype.slice.call(arguments,1))}}),e.config.debug&&(u.default.LoggableMixin.logger=e.logger),e},r.prototype._initLocale=function(t){var e=this;return e.debug("_initLocale:",t),e.localize=b.default,window._l=e.localize,e},r.prototype._initUser=function(t){var e=this;return e.debug("_initUser:",t),e.user=new f.default.User(t),e.user.logger=e.logger,e},r.prototype._setUpListeners=function(){var e=this;return e.lastAjax={},t(document).bind("ajaxSend",function(t,i,n){var a=n.data;try{a=JSON.parse(a)}catch(t){}e.lastAjax={url:location.href.slice(0,-1)+n.url,data:a}}),e},r.prototype.debugging=function(t){var e=this;try{if(void 0===t)return"true"===localStorage.getItem("galaxy:debug");if(t)return localStorage.setItem("galaxy:debug",!0),!0;localStorage.removeItem("galaxy:debug"),e.debuggingNamespaces(null)}catch(t){console.log((0,b.default)("localStorage not available for debug flag retrieval"))}return!1},r.prototype.debuggingNamespaces=function(t){var e=this;try{if(void 0===t){var i=localStorage.getItem(w);return"string"==typeof i?i.split(","):[]}null===t?localStorage.removeItem(w):localStorage.setItem(w,t);var n=e.debuggingNamespaces();return e.logger&&(e.logger.options.consoleNamespaceWhitelist=n),n}catch(t){console.log((0,b.default)("localStorage not available for debug namespace retrieval"))}},r.prototype.toString=function(){return"GalaxyApp("+(this.user?this.user.get("email")||"(anonymous)":"uninitialized")+")"},e.default={GalaxyApp:r}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t){t=t||{};var e=this;return 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e=this;e.options={};for(var n in i.defaultOptions)i.defaultOptions.hasOwnProperty(n)&&(e.options[n]=t.hasOwnProperty(n)?t[n]:i.defaultOptions[n]);return e.options.logLevel=e._parseLevel(e.options.logLevel),e.options.consoleLevel=e._parseLevel(e.options.consoleLevel),e._sending=!1,e._waiting=null,e._postSize=e.options.postSize,e._initCache(),e},i.prototype._initCache=function(){try{this.cache=new a({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(t){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",t]),this.options.logLevel=i.NONE}},i.prototype._parseLevel=function(t){var e=void 0===t?"undefined":r(t);if("number"===e)return t;if("string"===e){var n=t.toUpperCase();if(i.hasOwnProperty(n))return i[n]}throw new Error("Unknown log level: "+t)},i.prototype.emit=function(t,e,i){var n=this;return e=e||n.options.defaultNamespace,t&&i?(t=n._parseLevel(t),t>=n.options.logLevel&&n._addToCache(t,e,i),n.consoleLogger&&t>=n.options.consoleLevel&&n._emitToConsole(t,e,i),n):n},i.prototype._addToCache=function(t,e,i){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var n=this;try{n.cache.add(n._buildEntry(t,e,i))>=n._postSize&&n._postCache()}catch(t){n._emitToConsole("warn","MetricsLogger",["Metrics logger could not stringify logArguments:",e,i]),n._emitToConsole("error","MetricsLogger",[t])}return n},i.prototype._buildEntry=function(t,e,i){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var n={level:t,namespace:this.options.clientPrefix+e,args:i};return this.options.addTime&&(n.time=(new Date).toISOString()),n},i.prototype._postCache=function(e){if(e=e||{},this._emitToConsole("info","MetricsLogger",["_postCache",e,this._postSize]),!this.options.postUrl||this._sending)return t.when({});var i=this,n=e.count||i._postSize,a=i.cache.get(n),r=a.length,o="function"==typeof i.options.getPingData?i.options.getPingData():{};return o.metrics=JSON.stringify(a),i._sending=!0,t.post(i.options.postUrl,o).always(function(){i._sending=!1}).fail(function(t,e,n){i._postSize=i.options.maxCacheSize,i.emit("error","MetricsLogger",["_postCache error:",t.readyState,t.status,t.responseJSON||t.responseText])}).done(function(t){"function"==typeof i.options.onServerResponse&&i.options.onServerResponse(t),i.cache.remove(r),i._postSize=i.options.postSize})},i.prototype._delayPost=function(){var t=this;t._waiting=setTimeout(function(){t._waiting=null},t.options.delayPostInMs)},i.prototype._emitToConsole=function(t,e,a){var r=this,o=r.options.consoleNamespaceWhitelist;if(!r.consoleLogger)return r;if(o&&-1===o.indexOf(e))return r;var s=Array.prototype.slice.call(a,0);return s.unshift(e),r.options.consoleFlattenMessages&&(s=[s.map(n).join(" ")]),t>=i.METRIC&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.ERROR&&"function"==typeof r.consoleLogger.error?r.consoleLogger.error.apply(r.consoleLogger,s):(t>=i.WARN&&"function"==typeof r.consoleLogger.warn?r.consoleLogger.warn.apply(r.consoleLogger,s):t>=i.INFO&&"function"==typeof r.consoleLogger.info?r.consoleLogger.info.apply(r.consoleLogger,s):t>=i.DEBUG&&"function"==typeof r.consoleLogger.debug?r.consoleLogger.debug.apply(r.consoleLogger,s):"function"==typeof r.consoleLogger.log&&r.consoleLogger.log.apply(r.consoleLogger,s),r)},i.prototype.log=function(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.debug=function(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.info=function(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.warn=function(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.error=function(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},i.prototype.metric=function(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))},a.defaultOptions={maxSize:5e3},a.prototype._init=function(t){if(!this._hasStorage())throw new Error("LoggingCache needs localStorage");if(!t.key)throw new Error("LoggingCache needs key for localStorage");return this.key=t.key,this._initStorage(),this.maxSize=t.maxSize||a.defaultOptions.maxSize,this},a.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(t){return!1}},a.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},a.prototype.add=function(t){var e=this,i=e._fetchAndParse(),n=i.length+1-e.maxSize;return n>0&&i.splice(0,n),i.push(t),e._unparseAndStore(i),i.length},a.prototype._fetchAndParse=function(){var t=this;return JSON.parse(localStorage.getItem(t.key))},a.prototype._unparseAndStore=function(t){var e=this;return localStorage.setItem(e.key,JSON.stringify(t))},a.prototype.length=function(){return this._fetchAndParse().length},a.prototype.get=function(t){return this._fetchAndParse().slice(0,t)},a.prototype.remove=function(t){var e=this._fetchAndParse(),i=e.splice(0,t);return this._unparseAndStore(e),i},a.prototype.empty=function(){return 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u.default.View,Galaxy.display=this.display=function(t){t.title?(f.default.setWindowTitle(t.title),t.allow_title_display=!1):(f.default.setWindowTitle(),t.allow_title_display=!0),i.center.display(t)},Galaxy.router=this.router=e.Router&&new e.Router(i,e),this.masthead=new s.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(t){var n=t.charAt(0).toUpperCase()+t.slice(1),a=e[n];if(a){var r=new a(i,e);i[r.toString()]=r,i.panels[t]=new d.default.SidePanel({id:t,el:i.$("#"+t),view:r})}}),this.render(),this.router&&t.history.start({root:Galaxy.root,pushState:!0})},render:function(){return 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i=t.panels[e];i?i.render():(t.$("#center").css(e,0),t.$("#"+e).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var 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diff --git a/static/scripts/bundled/masthead.bundled.js b/static/scripts/bundled/masthead.bundled.js
index 33e42262574..baa76085abf 100644
--- a/static/scripts/bundled/masthead.bundled.js
+++ b/static/scripts/bundled/masthead.bundled.js
@@ -1,7 +1,7 @@
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t=this.model.attributes;this.$el.removeClass().addClass(t.cls).attr({id:t.id,href:t.href||"javascript:void(0)",title:t.title,target:t.target||"_top",disabled:t.disabled}).tooltip({placement:"bottom"}).off("click").on("click",function(){t.onclick&&!t.disabled&&t.onclick()}),this.$icon.removeClass().addClass(t.icon)}}),l=t.View.extend({initialize:function(e){this.model=e&&e.model||new t.Model({id:r.default.uid(),title:"Select/Unselect all",icons:["fa-square-o","fa-minus-square-o","fa-check-square-o"],value:0,onchange:function(){}}).set(e),this.setElement(n("<div/>").append(this.$icon=n("<span/>")).append(this.$title=n("<span/>"))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(t){var e=this,t=this.model.attributes;this.$el.addClass("ui-button-check").off("click").on("click",function(){e.model.set("value",0===e.model.get("value")&&2||0),t.onclick&&t.onclick()}),this.$title.html(t.title),this.$icon.removeClass().addClass("icon fa 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fa").addClass(t.icon),this.$title.addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right")}}),c=s.extend({$menu:null,initialize:function(e){this.model=e&&e.model||new t.Model({id:"",title:"",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(e),this.collection=new t.Collection,this.setElement(n("<div/>").append(this.$root=n("<div/>").append(this.$icon=n("<i/>")).append(this.$title=n("<span/>")))),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"change add remove reset",this.render,this),this.render()},render:function(){var t=this,e=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(e.cls).attr("id",e.id).css({display:e.visible&&this.collection.where({visible:!0}).length>0?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:e.tooltip,placement:"bottom"}).off("click").on("click",function(t){n(".tooltip").hide(),t.preventDefault(),e.onclick&&e.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.removeClass().addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=n("<ul/>").addClass("menu dropdown-menu").addClass("pull-"+t.model.get("pull")).attr("role","menu"),this.$el.append(this.$menu)),this.collection.each(function(e){var i=e.attributes;if(i.visible){var a=n("<a/>").addClass("dropdown-item").attr({href:i.href,target:i.target}).append(n("<i/>").addClass("fa").addClass(i.icon).css("display",i.icon?"inline-block":"none")).append(i.title).on("click",function(t){i.onclick&&(t.preventDefault(),i.onclick())});t.$menu.append(n("<li/>").append(a)),i.divider&&t.$menu.append(n("<li/>").addClass("divider"))}})},addMenu:function(t){this.collection.add(r.default.merge(t,{title:"",target:"",href:"",onclick:null,divider:!1,visible:!0,icon:null,cls:"button-menu btn-group"}))}});e.default={ButtonDefault:s,ButtonLink:o,ButtonIcon:d,ButtonCheck:l,ButtonMenu:c}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return 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e=this.attributes.obj_cache,i=this.attributes.key_ary,n=t.toString(),a=s.indexOf(i,function(t){return t.toString()===n});return-1!==a&&(e[n].stale?(i.splice(a,1),delete e[n]):this.move_key_to_end(t,a)),e[n]},set_elt:function(t,e){var i=this.attributes.obj_cache,n=this.attributes.key_ary,a=t.toString(),r=this.attributes.num_elements;if(!i[a]){if(n.length>=r){delete i[n.shift().toString()]}n.push(t)}return i[a]=e,e},move_key_to_end:function(t,e){this.attributes.key_ary.splice(e,1),this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=y.extend({defaults:s.extend({},y.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){y.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;s.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),i=t.Deferred(),n="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",a=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:n},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(a.go()).then(function(t){i.resolve("ok"===t||"data"===t)}),i},search_features:function(e){var i=this.get("dataset"),n={query:e,hda_ldda:i.get("hda_ldda"),data_type:"features"};return t.getJSON(i.url(),n)},load_data:function(e,i,n,a){var r=this.get("dataset"),s={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:i,resolution:n,hda_ldda:r.get("hda_ldda")};t.extend(s,a);var o=this.get("filters_manager");if(o){for(var l=[],d=o.filters,c=0;c<d.length;c++)l.push(d[c].name);s.filter_cols=JSON.stringify(l)}var u=this,h=t.getJSON(r.url(),s,function(t){t.region=e,u.set_data(e,t)});return this.set_data(e,h),h},get_data:function(t,e,i,n){var a=this.get_elt(t);if(a&&(c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)))return a;for(var r,s,o=this.get("key_ary"),l=this.get("obj_cache"),d=0;d<o.length;d++)if(r=o[d],r.contains(t)&&(s=!0,a=l[r.toString()],c.default.is_deferred(a)||this.get("data_mode_compatible")(a,e)&&this.get("can_subset")(a))){if(this.move_key_to_end(r,d),!c.default.is_deferred(a)){var u=this.subset_entry(a,t);this.set_data(t,u),a=u}return a}if(!s&&t.length()<this.attributes.min_region_size){t=t.copy();var h=this.most_recently_added();!h||t.get("start")>h.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,i,n)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,i,n,a,r){var s=this._mark_stale(e);if(!s||!this.get("data_mode_compatible")(s,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var o=e.get("start");r===this.DEEP_DATA_REQ?t.extend(a,{start_val:s.data.length+1}):r===this.BROAD_DATA_REQ&&(o=(s.max_high?s.max_high:s.data[s.data.length-1][2])+1);var l=e.copy().set("start",o),d=this,c=this.load_data(l,i,n,a),u=t.Deferred();return this.set_data(e,u),t.when(c).then(function(t){t.data&&(t.data=s.data.concat(t.data),t.max_low&&(t.max_low=s.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),d.set_data(e,t),u.resolve(t)}),u},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,i,n,a){var r=this._mark_stale(t);return r?(a||(a={}),"bigwig"===r.dataset_type&&(a.num_samples=1e3*n),this.load_data(t,e,i,a)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var i=this,n=!0,a=s.map(e.get("chroms_info").chrom_info,function(t){var e=i.get_elt(new $({chrom:t.chrom,start:0,end:t.len}));return e||(n=!1),e});if(n)return a;var r=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){i.add_data(t.data),r.resolve(t.data)}),r},subset_entry:function(t,e){var i={bigwig:function(t,e){return s.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,i){var n=i.get("start")-t.region.get("start");return t.data.slice(n,n+i.length())}},n=t.data;return!t.region.same(e)&&t.dataset_type in i&&(n=i[t.dataset_type](t.data,e)),{region:e,data:n,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new n.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,i,n){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,i,n):{data:null,region:t}}}),C=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=s.find(this.get_chroms_info(),function(e){return e.chrom===t});return new $({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return s.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),$=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),i=e[0],n=e[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new $({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),i=t.get("chrom"),n=this.get("start"),a=t.get("start"),r=this.get("end"),s=t.get("end");return e&&i&&e!==i?$.overlap_results.DIF_CHROMS:n<a?r<a?$.overlap_results.BEFORE:r<s?$.overlap_results.OVERLAP_START:$.overlap_results.CONTAINS:n>a?n>s?$.overlap_results.AFTER:r<=s?$.overlap_results.CONTAINED_BY:$.overlap_results.OVERLAP_END:r>=s?$.overlap_results.CONTAINS:$.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===$.overlap_results.CONTAINS},overlaps:function(t){return 0===s.intersection([this.compute_overlap(t)],[$.overlap_results.DIF_CHROMS,$.overlap_results.BEFORE,$.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),T=n.Collection.extend({model:$}),S=n.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new $(t.region))}}),M=n.Collection.extend({model:S}),O=n.Model.extend(g).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===s.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),A=n.Collection.extend({model:O}),E=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),z=E.extend(g).extend({defaults:s.extend({},E.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new A(t.tracks));var e=[];this.set("config",h.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs)),this.unset("tracks"),this.get("drawables").each(function(t){t.unset("preloaded_data")})},add_tracks:function(t){this.get("drawables").add(t)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(t,e){return{obj_type:"View",prefs:{name:e.get("title"),content_visible:!0},drawables:e.get("drawables")}}}}),R=n.Router.extend({initialize:function(t){this.view=t.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var e=this;e.view.on("navigate",function(t){e.navigate(t)})},change_location:function(t){this.view.go_to(t)}});e.default={BackboneTrack:O,BrowserBookmark:S,BrowserBookmarkCollection:M,Cache:y,CanvasManager:w,Genome:C,GenomeDataManager:x,GenomeRegion:$,GenomeRegionCollection:T,GenomeVisualization:z,GenomeReferenceDataManager:k,TrackBrowserRouter:R,Visualization:E,select_datasets:b}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,i){function n(t){t+="";for(var e=/(\d+)(\d{3})/;e.test(t);)t=t.replace(e,"$1,$2");return t}Object.defineProperty(e,"__esModule",{value:!0});var a=function(t){return"promise"in t},r=t.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(t){return!0}},go:function(){var t=i.Deferred(),e=this,n=e.get("ajax_settings"),a=e.get("success_fn"),r=e.get("interval");return function e(){i.ajax(n).success(function(i){a(i)?t.resolve(i):setTimeout(e,r)})}(),t}}),s=function(t){t||(t="#ffffff"),"string"==typeof t&&(t=[t]);for(var 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counts",type:"bool",default_value:!0},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0}],function(t){return t.key===e});i&&this.set(s.extend({},i,t)),void 0===this.get("value")&&void 0!==this.get("default_value")&&(this.set_value(this.get("default_value")),this.get("value")||"color"!==this.get("type")||this.set("value",l.default.get_random_color()))},set_value:function(t,e){var i=this.get("type");"float"===i?t=parseFloat(t):"int"===i&&(t=parseInt(t,10)),this.set({value:t},e)}})),u=t.Collection.extend({model:c,to_key_value_dict:function(){var t={};return this.each(function(e){t[e.get("key")]=e.get("value")}),t},get_value:function(t){var e=this.get(t);if(e)return e.get("value")},set_value:function(t,e,i){var n=this.get(t);if(n)return n.set_value(e,i)},set_default_value:function(t,e){var i=this.get(t);if(i)return i.set("default_value",e)}},{from_models_and_saved_values:function(t,e){return e&&(t=s.map(t,function(t){return s.extend({},t,{value:e[t.key]})})),new u(t)}}),h=t.View.extend({className:"config-settings-view",render:function(){var t=this.$el;return this.collection.each(function(e,i){if(!e.get("hidden")){var a="param_"+i,r=e.get("type"),o=e.get("value"),d=n("<div class='form-row' />").appendTo(t);if(d.append(n("<label />").attr("for",a).text(e.get("label")+":")),"bool"===r)d.append(n('<input type="checkbox" />').attr("id",a).attr("name",a).attr("checked",o));else if("text"===r)d.append(n('<input type="text"/>').attr("id",a).val(o).click(function(){n(this).select()}));else if("select"===r){var c=n("<select />").attr("id",a);s.each(e.get("options"),function(t){n("<option/>").text(t.label).attr("value",t.value).appendTo(c)}),c.val(o),d.append(c)}else if("color"===r){var u=n("<div/>").appendTo(d),h=n("<input 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d.append(n("<input />").attr("id",a).attr("name",a).val(o));e.help&&d.append(n("<div class='help'/>").text(e.help))}}),this},render_in_modal:function(t){var e=this,i=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc")},a=function(){Galaxy.modal.hide(),n(window).unbind("keypress.check_enter_esc"),e.update_from_form()},r=function(t){27===(t.keyCode||t.which)?i():13===(t.keyCode||t.which)&&a()};n(window).bind("keypress.check_enter_esc",r),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:t||"Configure",body:this.$el,buttons:{Cancel:i,OK:a}})},update_from_form:function(){var t=this;this.collection.each(function(e,i){if(!e.get("hidden")){var n="param_"+i,a=t.$el.find("#"+n).val();"bool"===e.get("type")&&(a=t.$el.find("#"+n).is(":checked")),e.set_value(a)}})}});e.default={ConfigSetting:c,ConfigSettingCollection:u,ConfigSettingCollectionView:h}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(12),d=r(l),c=t.View.extend({initialize:function(e){var i=this;this.data=[],this.data2=[],this.model=e&&e.model||new t.Model({id:o.default.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,readonly:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(e),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=n("<select/>")).append(this.$dropdown=n("<div/>")).append(this.$resize=n("<div/>").append(this.$resize_icon=n("<i/>"))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(e){var i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,n("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){n("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=n("<div/>")).append(this.$dropdown=n("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new d.default.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&a.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),a.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],a.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),n=a.filter(t.data2,function(i){var n=!1;return a.each(i.tags,function(i){t._match(e.term,i)&&(n=t.matched_tags[i]=!0)}),n||t._match(e.term,i.text)});e.callback({results:n.slice((e.page-1)*i,e.page*i),more:n.length>=e.page*i})},formatResult:function(e){return a.escape(e.text)+'<div class="ui-tags">'+a.reduce(e.tags,function(e,i){return t.matched_tags[i]?e+'&nbsp;<div class="label label-info">'+a.escape(i)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),a.each(this.data,function(e){t.$select.append(n("<option/>").attr("value",e.value).html(a.escape(e.label)))})),this.model.set("disabled",this.model.get("readonly")||0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var t=this._getValue();this.all_button.value(n.isArray(t)?t.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(t){return a.findWhere(this.data,{value:t})},text:function(){var t=this._getValue(),e=this.exists(n.isArray(t)?t[0]:t);return e?e.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(t,e){a.each(this.model.get("data"),function(e){e.keep&&!a.findWhere(t,{value:e.value})&&t.push(e)}),e&&t&&t.sort(e),this.model.set("data",t)},update:function(t){this.model.set("data",t)},setOnChange:function(t){this.model.set("onchange",t)},length:function(){return n.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(t){var e=this;if(null!==t&&void 0!==t||(t="__null__"),this.model.get("multiple")?t=n.isArray(t)?t:[t]:n.isArray(t)&&(t=t.length>0?t[0]:"__null__"),this.model.get("searchable")){if(n.isArray(t)){var i=[];a.each(t,function(t){var n=a.findWhere(e.data2,{id:t});n&&i.push(n)}),t=i}else{t=a.findWhere(this.data2,{id:t})}this.$select.select2("data",t)}else this.$select.val(t)},_getValue:function(){var t=null;if(this.model.get("searchable")){var e=this.$select.select2("data");e&&(n.isArray(e)?(t=[],e.sort(function(t,e){return t.order-e.order}),a.each(e,function(e){t.push(e.id)})):t=e.id)}else t=this.$select.val();return o.default.isEmpty(t)?null:t}});e.default={View:c}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(12),d=r(l),c=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({visible:!0,data:[],id:o.default.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(e),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var t=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=n("<div/>")).append(this.$menu=n("<div/>").addClass("ui-options-menu")).append(this.$options=n(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new d.default.ButtonCheck({onclick:function(){t.$("input").prop("checked",0!==t.all_button.value()),t.value(t._getValue()),t.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(t){this.model.set("data",t)},_changeData:function(){var t=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):a.each(this.model.get("data"),function(e){t.$options.append(n(t._templateOption(e)).addClass("ui-option").tooltip({title:e.tooltip,placement:"bottom"}))});var t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return t.length>0?t.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(t){var e=this;if(void 0!==t&&(this.$("input").prop("checked",!1),null!==t)){var i=n.isArray(t)?t:[t];a.each(i,function(t){e.$('input[value="'+t+'"]').first().prop("checked",!0)})}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push(n(this).val())}),o.default.isEmpty(t)?null:this.model.get("multiple")?t:t[0]},_messageShow:function(t,e){this.$message.show().removeClass().addClass("ui-message alert alert-"+e).html(t)},_template:function(){return n("<div/>").addClass("ui-options-list")}}),u=c.extend({_templateOption:function(t){var e=o.default.uid();return n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=u.extend({initialize:function(t){t.type="radio",u.prototype.initialize.call(this,t)}});var f={};f.View=u.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,u.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return t.icon&&e.append(n("<i/>").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(n("<input/>").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),e.default={Base:c,BaseIcons:u,Radio:h,RadioButton:p,Checkbox:f}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),o=i(11),l=a(o),d=i(4),c=a(d),u=t.View.extend({initialize:function(t){var e=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:t.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new "+this.name,onclick:function(){e.add({id:e.select.value(),name:e.select.text()})}}),this.setElement(this._template(t)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(t){if(void 0!==t){if(this.portlet.empty(),n.isArray(t))for(var e in t){var i=t[e],a=null,r=null;"string"!=n.type(i)?(a=i.id,r=i.name):a=r=i,null!=a&&this.add({id:a,name:r})}this._refresh()}var s=[];return this.$(".ui-list-id").each(function(){s.push({id:n(this).prop("id"),name:n(this).find(".ui-list-name").html()})}),0==s.length?null:s},add:function(t){var e=this;if(0===this.$('[id="'+t.id+'"]').length)if(s.default.isEmpty(t.id))this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else{var 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frame-shadow")}),this.$el.append(this.frame_shadow.$el),this._frameInit(this.frame_shadow,"#frame-shadow"),this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list["#frame-shadow"]=this.frame_shadow,this.visible?this.show():this.hide(),this._panelRefresh(),i(window).resize(function(){a.visible&&a._panelRefresh()})},render:function(){this.$(".frame-scroll-up")[this.top!=this.options.top_min&&"show"||"hide"](),this.$(".frame-scroll-down")[this.top!=this.top_max&&"show"||"hide"]()},add:function(t){if(this.frame_counter>=this.options.frame_max)Galaxy.modal.show({title:"Warning",body:"You have reached the maximum number of allowed frames ("+this.options.frame_max+").",buttons:{Close:function(){Galaxy.modal.hide()}}});else{var e="#frame-"+this.frame_uid++;if(0!==i(e).length)Galaxy.modal.show({title:"Error",body:"This frame already exists. This page might contain multiple frame managers.",buttons:{Close:function(){Galaxy.modal.hide()}}});else{this.top=this.options.top_min;var n=new a(t);this.$el.append(n.$el),t.width=this._toPixelCoord("width",this.options.frame.cols),t.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt(n.$el.css("z-index")),this.frame_list[e]=n,this.frame_counter++,this._frameInit(n,e),this._frameResize(n,{width:t.width,height:t.height}),this._frameInsert(n,{top:0,left:0},!0),!this.visible&&this.show(),this.trigger("add")}}},del:function(t){var e=this,i=t.$el;i.fadeOut("fast",function(){i.remove(),delete e.frame_list[t.id],e.frame_counter--,e._panelRefresh(!0),e._panelAnimationComplete(),e.trigger("remove")})},show:function(){this.visible=!0,this.$el.fadeIn("fast"),this.trigger("show")},hide:function(){this.event.type||(this.visible=!1,this.$el.fadeOut("fast",function(){i(this).hide()}),this.trigger("hide"))},length:function(){return this.frame_counter},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose"},_eventFrameMouseDown:function(t){i(".tooltip").hide(),this.event.type||((i(t.target).hasClass("f-header")||i(t.target).hasClass("f-title"))&&(this.event.type="drag"),i(t.target).hasClass("f-resize")&&(this.event.type="resize"),this.event.type&&(t.preventDefault(),this.event.target=this._frameIdentify(t.target),this.event.xy={x:t.originalEvent.pageX,y:t.originalEvent.pageY},this._frameDragStart(this.event.target)))},_eventFrameMouseMove:function(t){if(this.event.type){var e={x:t.originalEvent.pageX,y:t.originalEvent.pageY},i={x:e.x-this.event.xy.x,y:e.y-this.event.xy.y};this.event.xy=e;var n=this._frameScreen(this.event.target);if("resize"==this.event.type){n.width+=i.x,n.height+=i.y;var a=this.options.cell-this.options.margin-1;n.width=Math.max(n.width,a),n.height=Math.max(n.height,a),this._frameResize(this.event.target,n),n.width=this._toGridCoord("width",n.width)+1,n.height=this._toGridCoord("height",n.height)+1,n.width=this._toPixelCoord("width",n.width),n.height=this._toPixelCoord("height",n.height),this._frameResize(this.frame_shadow,n),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)})}else if("drag"==this.event.type){n.left+=i.x,n.top+=i.y,this._frameOffset(this.event.target,n);var r={top:this._toGridCoord("top",n.top),left:this._toGridCoord("left",n.left)};0!==r.left&&r.left++,this._frameInsert(this.frame_shadow,r)}}},_eventFrameMouseUp:function(t){this.event.type&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(t){this.event.type||(t.preventDefault(),this.del(this._frameIdentify(t.target)))},_eventHide:function(t){!this.event.type&&this.hide()},_eventPanelScroll:function(t){if(!this.event.type&&this.visible){0!==i(t.srcElement).parents(".frame").length?t.stopPropagation():(t.preventDefault(),this._panelScroll(t.originalEvent.detail?t.originalEvent.detail:t.originalEvent.wheelDelta/-3))}},_eventPanelScroll_up:function(t){this.event.type||(t.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(t){this.event.type||(t.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(t){return this.frame_list["#"+i(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),i(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),i(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var i="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+i*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var i="width"==t||"height"==t?1:-1,n=e*this.options.cell-i*this.options.margin;return"top"==t&&(n+=this.top),n},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var i=this.frame_list[e];if(null!==i.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,i.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(i(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,s=[];t&&(t.grid_location=null,s.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,s.push([t,t.grid_rank]))}),s.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(s,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var s=this.model.attributes;this.has_slider=null!==s.max&&null!==s.min&&s.max>s.min;var o=s.step;o||(o=s.precise&&this.has_slider?(s.max-s.min)/s.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:s.min,max:s.max,step:o}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),o=i(23),l=a(o),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,o){o=o||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=o.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=s.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function s(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),l=s(o),d=i(4),c=(s(d),i(11)),u=s(c),h=i(49),f=s(h),p=i(50),_=s(p),m=i(51),v=s(m),g=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new v.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],s=e.$("#"+t.id+"-section-"+a),o=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){o=!0;break}a==n&&o?s.fadeIn("fast"):s.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new g(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,s=new g(i.app,{inputs:e});r.add({id:a,$el:s.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),s=a.size(t.cache),o=0;o<Math.max(Math.max(s,t.min||0),t.default||0);o++)e(o<s?t.cache[o]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new g(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:g}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=o.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),v=r(m),g=i(57),b=r(g);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,o.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new v.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var s=this.history[i[r]+"_"+this.config[e].src];if(!s)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(s)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=o.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var s=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),s=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":s}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":s}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": 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a=i(3),r=(n(a),i(4)),s=n(r),o=i(43),l=(n(o),i(24)),d=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new u,this.options=t,this.library_select=new s.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new d.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),s=i(24),o=n(s),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new o.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),r.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),s=n(r),o=i(56),l=n(o),d=t.View.extend({initialize:function(t){var e=this;this.browse_button=new s.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new s.default.Input,this.token_textbox=new s.default.Input({type:"password"}),this.setElement(this._template(t)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(t){var e=this;l.default.openFileBrowser({successCallback:function(t){e.value(t.destination+"^"+t.token)}})},_template:function(t){return'<div class="ui-gs-select-file"><div class="ui-gs-browse-field"><span class="ui-gs-browse-button" /><span class="ui-gs-filename-textbox" /></div><div class="ui-gs-token-field"><span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span><span class="ui-gs-token-textbox" /></div></div>'},value:function(t){if(void 0===t)return this._getValue();this._setValue(t)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(t){t&&(values=t.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});e.default={View:d}}).call(e,i(1))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0}),e.default={openFileBrowser:function(t){var e=window.Galaxy.config.genomespace_ui_url,i=e+"upload/loadUrlToGenomespace.html?getLocation=true",n=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=t.successCallback,window.addEventListener("message",function(t){successCalBack(t.data)},!1),n.focus(),null!=t.errorCallback&&(n.setCallbackOnGSUploadError=config.errorCallback)}}},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return 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i._iterate(t,e)})}})),o=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},l=function t(e,i,r,s){s=n.extend(!0,{},s),a.each(e,function(t){t&&t.type&&t.name&&(s[t.name]=t)});for(var l in e){var d=e[l];d.name=d.name||l;var c=r?r+"|"+d.name:d.name;switch(d.type){case"repeat":a.each(d.cache,function(e,n){t(e,i,c+"_"+n,s)});break;case"conditional":if(d.test_param){i(d.test_param,c+"|"+d.test_param.name,s);var u=o(d,d.test_param.value);-1!=u?t(d.cases[u].inputs,i,c,s):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+c+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+c+".");break;case"section":t(d.inputs,i,c,s);break;default:i(d,c,s)}}};e.default={Manager:s,visitInputs:l}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0});var 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a=this;this.options=n.defaults(e||{},this.defaultOptions),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(i("<div/>").addClass("galaxy-frame").append(i("<div/>").addClass("frame-background")).append(i("<div/>").addClass("frame-menu frame-scroll-up fa fa-chevron-up fa-2x")).append(i("<div/>").addClass("frame-menu frame-scroll-down fa fa-chevron-down fa-2x"))),this.frame_shadow=new t.View({el:i("<div/>").addClass("corner 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t=this;i(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var i=this.top-this.options.scroll*t;if(i=Math.max(i,this.top_max),i=Math.min(i,this.options.top_min),this.top!=i){for(var n in this.frame_list){var a=this.frame_list[n];if(null!==a.grid_location){var r={top:a.screen_location.top-(this.top-i),left:a.screen_location.left};this._frameOffset(a,r,e)}}this.top=i}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,a){var r=this,s=[];t&&(t.grid_location=null,s.push([t,this._locationRank(e)])),n.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,s.push([t,t.grid_rank]))}),s.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),n.each(s,function(t){r._framePlace(t[0],a)}),this.top_max=0,n.each(this.frame_list,function(t){null!==t.grid_location&&(r.top_max=Math.max(r.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=i(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var i=this._toGrid(this._frameScreen(t)),n=!1,a=0;a<this.options.rows;a++){for(var r=0;r<Math.max(1,this.cols-i.width);r++)if(i.top=a,i.left=r,!this._isCollision(i)){n=!0;break}if(n)break}n?this._frameGrid(t,i,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,i){if(t.screen_location.left=e.left,t.screen_location.top=e.top,i){this._frameFocus(t,!0);var n=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){n._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,i){t.grid_location=e,this._frameOffset(t,this._toPixel(e),i),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:r}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({id:r.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var a=[];this.$text.on("change",function(){i.value(n(this).val())}).on("keyup",function(t){a[t.which]=!1}).on("keydown",function(t){var e=t.which;a[e]=!0,i.model.get("is_workflow")&&a[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!a[16]||e>=96&&e<=105||(190==e||110==e)&&-1==n(this).val().indexOf(".")&&i.model.get("precise")||(189==e||109==e)&&-1==n(this).val().indexOf("-")||i._isParameter(n(this).val())||a[91]||a[17]||event.preventDefault()});var s=this.model.attributes;this.has_slider=null!==s.max&&null!==s.min&&s.max>s.min;var o=s.step;o||(o=s.precise&&this.has_slider?(s.max-s.min)/s.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:s.min,max:s.max,step:o}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),o=i(23),l=a(o),d=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,a=t.isArray(e)?e:[e];n.each(a,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(a,r,o){o=o||[];for(var l in r){var d=r[l],c=d.options&&d.options.length>0,u=o.slice(0);n.header_index[d.value]=u.slice(0);var h=t("<div/>");if(c){var f=s.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:d.name,value:d.value}))),u.push(f),i(_,d.options,u),h.append(_),e(h,f)}else h.append(n._templateOption({label:d.name,value:d.value}));a.append(h)}}var n=this;this.header_index={};var a=t("<div/>");return i(a,this.model.get("data")),a},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:d}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a,r){function s(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),l=s(o),d=i(4),c=(s(d),i(11)),u=s(c),h=i(49),f=s(h),p=i(50),_=s(p),m=i(51),v=s(m),g=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new v.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),a.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=r.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var a in t.cases){var r=t.cases[a],s=e.$("#"+t.id+"-section-"+a),o=!1;for(var l in r.inputs)if(!r.inputs[l].hidden){o=!0;break}a==n&&o?s.fadeIn("fast"):s.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new g(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,s=new g(i.app,{inputs:e});r.add({id:a,$el:s.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),s=a.size(t.cache),o=0;o<Math.max(Math.max(s,t.min||0),t.default||0);o++)e(o<s?t.cache[o]:t.inputs);this.app.model.get("sustain_repeats")&&r.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:r});this._append(l.$el,t.id)},_addSection:function(t){var e=new u.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new g(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:g}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=o.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),v=r(m),g=i(57),b=r(g);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,o.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new v.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),o=r(s),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var s=this.history[i[r]+"_"+this.config[e].src];if(!s)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(s)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=o.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var s=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),s=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":s}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":s}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": "+t.name,value:t.id,tags:t.tags}),e.history[t.id+"_"+n]=t})}),a.each(this.config,function(t,n){i[t.src]&&e.fields[n].add(i[t.src],function(t,e){return e.hid-t.hid})})},_changeValue:function(){var t=this.model.get("value");if(t&&t.values&&t.values.length>0){var e=[];a.each(t.values,function(t){e.push(t.id)});for(var i=t.values[0].src,n=t.values.length>1,r=0;r<this.config.length;r++){var s=this.fields[r],o=this.config[r];if(o.src==i&&-1!==[n,!0].indexOf(o.multiple)){this.model.set("current",r),s.value(e);break}}}else a.each(this.fields,function(t){t.value(null)})},_handleDrop:function(t){try{var e=this.model.get("data"),i=this.model.get("current"),n=this.config[i],r=this.fields[i],s=JSON.parse(t.originalEvent.dataTransfer.getData("text"))[0],o=s.id,l="dataset"==s.history_content_type?"hda":"hdca",d={id:o,src:l};if(e&&a.findWhere(e[l],d)){if(n.src==l){var c=r.value();c&&n.multiple?-1==c.indexOf(o)&&c.push(o):c=o,r.value(c)}else this.model.set("value",{values:[d]}),this.model.trigger("change:value");this.trigger("change"),this._handleDropStatus("success")}else this._handleDropStatus("danger")}catch(t){this._handleDropStatus("danger")}t.preventDefault()},_handleDropStatus:function(t){var e=this;this.$el.removeClass("ui-dragover").addClass("ui-dragover-"+t),setTimeout(function(){e.$el.removeClass("ui-dragover-"+t)},this.model.get("statustimer"))},_batch:function(t){t.batch=!1;var e=this.model.get("current"),i=this.config[e];if("hdca"==i.src&&!i.multiple){var n=this.history[this.fields[e].value()+"_hdca"];n&&n.map_over_type&&(t.batch=!0)}return i.batch!=h.LINKED&&i.batch!=h.ENABLED||(t.batch=!0,i.batch==h.ENABLED&&"true"===this.button_product.value()&&(t.product=!0)),t}});e.default={View:p}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),s=n(r),o=i(43),l=(n(o),i(24)),d=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),u=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new u,this.options=t,this.library_select=new s.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new d.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),s=i(24),o=n(s),l=t.View.extend({initialize:function(t){var 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d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. 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Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var s=n("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){s.append(n("<input/>").attr({name:e,value:t}))}),s.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),o.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var s in a){i.form.highlight(s,a[s]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],s=this.form.data.match(a),o=this.form.field_list[s],l=this.form.input_list[s];if(s&&l&&o){if(!l.optional&&null==r)return this.form.highlight(s),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(s,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(s,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+d+"</b> selection(s) while a previous field contains <b>"+i+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n("<div/>").addClass("donemessagelarge").append(n("<p/>").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n("<p/>").addClass("messagerow").append(n("<b/>").text(t.hid+": "+t.name)))}),r.append(n("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var i=t.global_actions.length>=3;i&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var n in t.global_actions){var a=t.global_actions[n];e+='<li><a class="action-button use-target" target="'+a.target+'" href="'+a.url_args+'" onclick="return false;" >'+a.label+"</a></li>"}i&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='<th id="'+n.key+'-header">',n.href?e+='<a href="'+n.href+'" class="sort-link" sort_key="'+n.key+'">'+n.label+"</a>":e+=n.label,e+='<span class="sort-arrow">'+n.extra+"</span></th>")}return e+="</tr>"},body:function(e){var i="",n=0;0==e.items.length&&(i+='<tr><td colspan="100"><em>No Items</em></td></tr>',n=1);for(var a in e.items){var r=e.items[a],s=r.encode_id;i+="<tr ",e.current_item_id==r.id&&(i+='class="current"'),i+=">",e.show_item_checkboxes&&(i+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+s+'" id="'+s+'" class="grid-row-select-checkbox" /></td>');for(var o in e.columns){var l=e.columns[o];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="<td "+d+">",u?(0!=e.operations.length&&(i+='<div id="'+p+'" class="'+_+'" style="float: left;">'),i+='<a class="menubutton-label use-target" target="'+f+'" href="'+u+'" onclick="return false;">'+h+"</a>",0!=e.operations.length&&(i+="</div>")):i+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+s+'" for="'+s+'">'+(h||"")+"</label></div>",i+="</td>"}}i+="</tr>",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,s=n-r,o=0;s<=0&&(s=1,o=r-(n-s));var l,d=r+o,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(s-=l)<1&&(s=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td 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f=t.operations[h];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+n.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var s=t.columns[r];if("advanced"==s.filterable){var o=s.key,l=i[o],d=e[o];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u='<div 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class="text-filter-form" column_key="'+r+'" action="'+e.url+'" method="get" >';for(u in e.columns){var o=e.columns[u],l=n[o.key];l&&"All"!=l&&(o.is_text&&(l=JSON.stringify(l)),s+='<input type="hidden" id="'+o.key+'" name="f-'+o.key+'" value="'+l+'"/>')}s+='<span id="'+r+'-filtering-criteria">';var d=n[r];if(d){var c=t.type(d);if("string"==c&&"All"!=d&&(s+=this.filter_element(r,d)),"array"==c)for(var u in d){var h=d[u],f=d;f=f.slice(u),s+=this.filter_element(r,h)}}s+="</span>";var p="";if("standard"==i.filterable){p=i.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}s+='<span class="search-box"><input class="search-box-input" id="input-'+r+'-filter" name="f-'+r+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{s+='<span id="'+r+'-filtering-criteria">';var m=!1;for(var v in e.categorical_filters[r]){var g=e.categorical_filters[r][v],b="",w="";for(var y in g)b=y,w=g[y];m&&(s+=" | "),m=!0;var h=n[r];h&&g[r]&&h==w?s+='<span class="categorical-filter '+r+'-filter current-filter">'+v+"</span>":s+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+v+"</a></span>"}s+="</span>"}return s+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=i(146),l=a(o),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),v=i(3),g=a(v);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){g.default.cssLoadFile("static/style/jquery.rating.css"),g.default.cssLoadFile("static/style/autocomplete_tagging.css"),g.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),g.default.cssLoadFile("static/style/library.css"),g.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){s.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),s=n("<div/>").addClass("position").appendTo(r),o=(n("<a href=''/>").text(t).appendTo(s).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);o.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var o=this,d=new l.default.TracksterView(s.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,s=e.start,c=e.end,u=e.overview;n&&void 0!==s&&c?d.change_chrom(n,s,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var h=0;h<i.length;h++)d.add_drawable(l.default.object_from_template(i[h],d,d));for(var h=0;h<d.drawables.length;h++)if(d.drawables[h].config.get_value("name")===u){d.set_overview(d.drawables[h]);break}if(a)for(var f,h=0;h<a.length;h++)f=a[h],o.add_bookmark(f.position,f.annotation,r);d.has_changes=!1}),this.set_up_router({view:d}),d},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){n(document).keyup(function(e){if(!n(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){n(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){n.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){b=new x(Galaxy.root),b.createButtonMenu(),b.buttonMenu.$el.attr("style","float: right"),n("#center .unified-panel-header-inner").append(b.buttonMenu.$el),n("#right .unified-panel-title").append("Bookmarks"),n("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new m.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){n(parent.document).find("input[name=id]:checked").each(function(){t.id=n(this).val(),window.location=Galaxy.root+"visualization/trackster?"+n.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;w=b.create_visualization({container:n("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;n.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(n("#new-title").val(),n("#new-dbkey").val()),Galaxy.modal.hide()}}});var i=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&s.contains(i,galaxy_config.app.default_dbkey)&&n("#new-dbkey").val(galaxy_config.app.default_dbkey),n("#new-title").focus(),n("select[name='dbkey']").select2(),n("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function s(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var o=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(o),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),v=i(149),g=a(v),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),T=a($),S=i(151),M=a(S);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,s,o,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){s=r.position().top,o=s+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<s)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>o)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),s=a.position().top,o=s+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=s&&i.offsetY<=o)return i.offsetY-s<o-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=T.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new T.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),s=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&s++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),s>1&&s===this.drawables.length){var o,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],l[o.name]=[o];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],o.name in l&&l[o.name].push(o);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===s&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var B=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=T.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,s=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(s),n.current_height=e.clientY,n.current_x=n.offsetX;var o=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(o)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,s=i.high-i.low,o=i.viewport_container.width();i.update_location(Math.round(a/o*s)+i.low,Math.round(r/o*s)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),s=i.high-i.low,o=i.viewport_container.width(),l=i.low;i.low=Math.round(a/o*s)+l,i.high=Math.round(r/o*s)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(B.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,s=i.chrom_data.length;r<s;r++){var o=i.chrom_data[r].chrom,l=t("<option>");l.text(o),l.val(o),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var s=0,o=a.drawables.length;s<o;s++){var l=a.drawables[s];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var V=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),N=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new I({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,s=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var o=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,o,!1);o.container_div.insertBefore(r.view.content_div.children()[l]),o.add_drawable(r),r.container_div.appendTo(o.content_div),t=o}else t=r.container;var d=new r.constructor(view,t,{name:s,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),L=function(t,e){g.default.Scaler.call(this,e),this.filter=t};L.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,s,o,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=o,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),s=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?s:[r].concat(s),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new V(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new N({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),s=this.view.resolution_px_b,o=1/s;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,s=r/(view.max_high-view.max_low),o=1/s),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*o),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,s,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,s,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",s="max"===e?"max":"min",o="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(o),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(o,r(e,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,s=1/i,o=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:o.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&o.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,s,o.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,s,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return o.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),s=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return o.tile_cache.set_elt(c,void 0),void t.when(o.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=s[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,v=o.view.canvas_manager.new_canvas(),g=e.get("start"),b=e.get("end"),w=Math.ceil((b-g)*i)+o.left_offset,y=l.max(_);v.width=w,v.height=n.height||y;var x=v.getContext("2d");x.translate(o.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(s[n],x,u[n],e,i,a)}),void 0!==m&&(o.tile_cache.set_elt(c,m),o.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new g.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,s=this.view.container.width(),o=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*s);o.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(o)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var s=t[a].html_elt.find("canvas").height();s>r&&(r=s)}for(a=0;a<t.length;a++){var o=t[a];o.html_elt.find("canvas").height()!==r&&(this.draw_helper(o.region,i,{force:!0,height:r}),o.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),s=r.data,o=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=s.length;l<d;l++)e.fillStyle=this.view.get_base_color(s[l]),e.fillText(s[l],Math.floor(l*a),10);return new G(this,n,a,o,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(s(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new g.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=g.default.ArcLinkedFeaturePainter:this.painter=g.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,s=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var o={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){o[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(o,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(s.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,o)}})}if(s.filters_manager){var c,u=s.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}s.filters_available!==p&&(s.filters_available=p,s.filters_available||s.filters_manager.hide(),s.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,s){var o=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,v=t.data.length;m<v;m++){for(var g,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(g=_[y],g.update_attrs(b),!g.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new L(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return o.view.get_base_color(t)}),T=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var S=$.draw(e,l.width,l.height,a,f);T=S.feature_mapper,incomplete_features=S.incomplete_features,T.translation=-u}return s?void 0:new F(o,n,a,l,t.data,i,t.message,p,T,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=g.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),s=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&s&&s.length>1){var o;if(0===this.container_div.find(".yaxislabel.variant").length&&(o=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":o+"px",top:(this.config.get_value("summary_height")-o)/2+"px"})),this.config.get_value("show_sample_data"))){var d=s.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}o=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":o,"line-height":o}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=g.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:B,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,s){var o=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(o.model)}).appendTo(this.icons_div),s&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var s=i.display_modes[a];n[s]=function(t){return function(){i.change_mode(t)}}(s)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t,e){this.slot=t,this.feature=e},o=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(o.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var s=0,o=r.length;s<o;s++){var l=r[s];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,o=0,l=t.length;o<l;o++){e=t[o],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(o)}for(var o=0,l=a.length;o<l;o++){e=t[a[o]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new s(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:o}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},s=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},o=function(t,e,i,n,a,r){void 0===r&&(r=4);var s,o=n-e,l=a-i,d=Math.floor(Math.sqrt(o*o+l*l)/r),c=o/d,u=l/d;for(s=0;s<d;s++,e+=c,i+=u)s%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,s=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,s),t.lineTo(r,s),t.lineTo(e,i),t.lineTo(a,s),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,s=this.prefs.min_value,o=this.prefs.max_value,l=o-s,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+s/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var v,g=this.prefs.block_color||this.prefs.color,b=parseInt(g.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,$=0,T=h.length;$<T;$++)if(t.fillStyle=t.strokeStyle=g,k=C=!1,v=m[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(_=h[$][1])){if(_<s?(C=!0,_=s):_>o&&(k=!0,_=o),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,v,-_);else if("Intensity"===u){var S=(_-s)/l,M=Math.round(w+(255-w)*(1-S)),O=Math.round(y+(255-y)*(1-S)),A=Math.round(x+(255-x)*(1-S));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,v,d)}else _=Math.round(d-(_-s)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=v:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=g}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,s){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=s||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,s=this.view_start,o=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],v=m[0],g=m[1],b=m[2],w=a&&void 0!==a[v]?a[v].slot:null;("Dense"===this.mode||null!==w)&&g<o&&b>s&&(l=this.draw_element(t,this.mode,m,w,s,o,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(g<s||b>o)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,s,o,l){return[0,0]}});var _=function(t,e,i,n,a,r,s){p.call(this,t,e,i,n,a,r,s),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,s,o,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*s)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*s))),m=p,v=_,d=("Dense"===e?0:0+n)*o+this.get_top_padding(l),g=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(g=Math.floor(Math.max(0,(x-a)*s)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*s))));var T,S;if("Squish"===e?(T=1,S=3,$=!1):(T=5,S=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=S):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*s)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*s)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(S-T)/2+1,q-j,T),void 0!==g&&k>x&&!(j>b||q<g)){var D=Math.max(j,g),B=Math.min(q,b);t.fillRect(D,d+1,B-D,S),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<B&&(D+=2,B-=2),t.fillRect(D,d+1,B-D,S))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var V=this.height_scaler.gen_val(i),I=Math.ceil(S*V),N=Math.round((S-I)/2);1!==V&&(t.fillRect(p,M+1,_-p,N),t.fillRect(p,M+S-N+1,_-p,N))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,S),f&&$&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,S));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),v+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,v]}});var m=function(t,e,i,n,a,r,s,o,l){p.call(this,t,e,i,n,a,r,s),this.ref_seq=o?o.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,s=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),s=t.slice(-1);return"N"===s?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(s)&&(n[1]+=a,r+=a),[e.indexOf(s),a]});return{blocks:i,cigar:s}},draw_read:function(t,e,i,n,a,o,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,o],v=0,g=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,$=n+1,T=new x(t,C,i,e),S=[],M=[],O=this._parse_cigar(c);c=O.cigar,S=O.blocks;for(var A=0;A<S.length;A++){var E=S[A];s([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,$,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+v;if(p=f(D),_=f(D+q),s([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var B="";"X"===j?B=h.slice(g,g+q):this.ref_seq&&(B=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,o-a)));for(var V=Math.max(D,a),I=0;I<B.length;I++)if(B&&!this.prefs.show_differences||"X"===j){var N=Math.floor(Math.max(0,(V+I-a)*i));t.fillStyle=this.base_color_fn(B[I]),k&&i>w?t.fillText(B[I],N,n+9):i>.05&&t.fillRect(N-b,$,Math.max(1,Math.round(i)),C)}"X"===j&&(g+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,$+(C-1)/2,_-p,1),v+=q;break;case"D":T.draw_deletion(p,$,q),v+=q;break;case"I":var L=p-b;if(s([D,D+q],m)){var G=h.slice(g,g+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[L,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-o);break;case 1005:break;case 1002:G=G.slice(a-D,D-o)}for(var I=0,F=G.length;I<F;I++){var N=Math.floor(Math.max(0,(D+I-a)*i));t.fillText(G[I],N-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,L,n+9]})}g+=q}else v=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(v,j,q),g=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(g,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,s,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*s,(c-a-.5)*s)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*s))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var v=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,s,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):v=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,s,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):v=!1;var g=Math.ceil(Math.min(d,Math.max(-.5*s,(i[4][1]-a-.5)*s))),b=Math.floor(Math.max(-.5*s,(i[5][0]-a-.5)*s));if(v&&b>g){t.fillStyle="#ccc";var w=_+1+(m-1)/2;o(t,g,w,b,w)}}else this.draw_read(t,e,s,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,i,n,a,r,s){_.call(this,t,e,i,n,a,r,s),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var s=(i+n)/2,o=n-s;Math.PI;o>0&&(t.beginPath(),t.arc(s,r,n-s,Math.PI,0),t.stroke())}});var g=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};g.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,s=Math.max(i,n,a),o=Math.min(i,n,a),l=(s+o)/2,d=s-o;if(s===o)t=e=0;else{switch(e=l>.5?d/(2-s-o):d/(s+o),s){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,s=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,o=1-s,l=[i.rgb[0]*s+t.rgb[0]*o,i.rgb[1]*s+t.rgb[1]*o,i.rgb[2]*s+t.rgb[2]*o],d=i.alpha*n+t.alpha*(1-n);return new g(l,d)}};var b=function(t,e,i,n){this.start_color=new g(t),this.end_color=new g(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,s;if(void 0===this.prefs.min_value){var o=1/0;for(r=0,s=this.data.length;r<s;r++)o=Math.min(o,this.data[r][6]);this.prefs.min_value=o}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,s=this.data.length;r<s;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,s,o,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,g=f.length;v<g;v++)a=f[v],r=m(a[1]),s=m(a[2]),o=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,o,s-r,l-o);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,s,o,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,s=null;return"-"===e?(s="deletion",r=t.length):0===t.indexOf(e)&&i>n?(s="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(s="insertion",r=n-i,a=n),null!==s?{type:s,start:a,len:r}:{}},v=Math.max(1,Math.floor(n)),g=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===g&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],s=r[1],o=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(o,t);return a.extend(e,i)}),!(s<this.view_start||s>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(s+l[_].start,n),t.fillRect(h,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var $=c/d.length,T=Math.ceil(this.prefs.summary_height*$);t.fillRect(h,f-T,v,T),f-=T}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(s+u.start,n),"snp"===u.type){var S=u.value;t.fillStyle=this.base_color_fn(S),k.draw_details?t.fillText(S,this.get_draw_pos(s,n),f+b):t.fillRect(h,f+1,v,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(s.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var o=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){s.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,s=!1,o=t(this).parents(".slider-row");o.addClass("input"),n.slider("option","values")&&(r=2*r+1,s=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),o.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(s){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(s?"values":"value",l),o.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=o("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=o("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=s.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),s=i.filters,o=0;o<s.length;o++)"number"===s[o].type?(n=new l(s[o]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var s=[];for(var o in a)s[s.length]=[o,a[o]];!function e(i,n){var a=n[0],r=a[0],s=a[1],o="("+s.join(") and (")+")",l={cond:o,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,s)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var o=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(s.makeBwg(o)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:o}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function s(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function o(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(s(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),s=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==v)i.type="bigwig";else{if(d!=b)return d==g||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=s[2],i.numZoomLevels=s[3],i.chromTreeOffset=o(r,8),i.unzoomedDataOffset=o(r,16),i.unzoomedIndexOffset=o(r,24),i.fieldCount=s[16],i.definedFieldCount=s[17],i.asOffset=o(r,36),i.totalSummaryOffset=o(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=o(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=o(r,24*c+72),f=o(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,v=2291137574,g=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(s(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),s=(a[3],o(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=o(i,e);e+=8,c-=t.chromTreeOffset,s(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});s(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(s(a.bwg.url,this.cirTreeOffset,48)).then(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,s){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,s=4+32*a.cirBlockSize,o=0;o<t.length;++o){var u=new h(t[o],t[o]+s);i=i?f(i,u):u}for(var m=i.ranges(),v=0;v<m.length;++v){var g=m[v];p(t,g,e)}},p=function(t,e,i,o){e.max(),e.min();n.when(s(a.bwg.url,e.min(),e.max()-e.min())).then(function(s){for(var o=0;o<t.length;++o)e.contains(t[o])&&(_(s,t[o]-e.min(),i),t[o]-a.cirTreeOffset==48&&t[o]-e.min()==0&&(a.cachedCirRoot=s),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var s=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=s[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16),y=o(s,a+24);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var o=[],l=function(t,e,n,r){r||(r={});var s=new i;s._chromId=t,s.segment=a.bwg.idsToChroms[t],s.min=e,s.max=n,s.type=a.bwg.type;for(var l in r)s[l]=r[l];o.push(s)},d=function(){if(0===e.length){Date.now();return r.resolve(o)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(s(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,s=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,s.size-2);else{var o=new Uint8Array(s.size);m(new Uint8Array(t,i,s.size),0,o,0,s.size),r=o.buffer}s.data=r,i+=s.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=o[8*c],_=o[8*c+1],m=o[8*c+2],v=o[8*c+3],g=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/v,maxScore:g};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),u=o[0],y=o[1],x=(o[2],o[3]),k=o[4],C=r[20],d=s[11];if(3==C)for(var c=0;c<d;++c){var T=l[c+6],S=y+c*x+1,M=y+c*x+k;i(u,S,M)&&e(u,S,M,{score:T})}else if(2==C)for(var c=0;c<d;++c){var _=o[2*c+6]+1,m=_+k-1,T=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:T})}else if(1==C)for(var c=0;c<d;++c){var _=o[3*c+6]+1,m=o[3*c+7],T=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:T})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var T=parseInt(P[1]);isNaN(T)||(j.score=T)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];$.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var B=0|P[3],V=0|P[4],I=0|P[6],N=P[7].split(","),L=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<I;++W){var K=(0|L[W])+_,Z=K+(0|N[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(V>B){var at="+"==j.orientation?new h(B,V+3):new h(B-3,V),rt=p(tt,at);if(rt){j.type="translation";for(var st=rt.ranges(),ot=0,lt=0;st[0].min()>et[lt].max();)lt++;for(var it=0;it<st.length;++it){var dt=it;"-"==j.orientation&&(dt=st.length-it-1);var nt=st[dt];if(j.readframe=ot,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();ot=(ot+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,s=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var s=new h(t[r],t[r]+n);i=i?f(i,s):s}for(var o=i.ranges(),l=0;l<o.length;++l){var c=o[l];u(t,c,e)}}),u=function(s,o,l,c){o.max(),o.min();a.bwg.data.slice(o.min(),o.max()-o.min()).fetch(function(c){for(var u=0;u<s.length;++u)if(o.contains(s[u])&&(p(c,s[u]-o.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,s){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,s=0;s<t.length;++s){var o=t[s],l=o._chromId,d=o.min,c=o.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=o,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=o(h,d+16),C=o(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>s||y==s&&x>l)||i>0&&(b<s||b==s&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,s=i<0?y:b)),d+=32}else{for(var $=-1,T=-1,v=0;v<m;++v){var 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Uint8Array(t.buffer,t.byteOffset+e,a),i,n):o(t,e,i,n,a)}}function o(t,e,i,n,a){for(var r=0;r<a;++r)i[n+r]=t[e+r]}function l(t,e,i){e.set(t,i)}function d(e,i,n,a){e=i?n?new Uint8Array(e,i,n):new Uint8Array(e,i,e.byteLength-i):new Uint8Array(e);var r=new t;r.inflateInit(c,!0),r.next_in=e,r.next_in_index=0,r.avail_in=e.length;for(var o=[],l=0;;){var d=new Uint8Array(32e3);r.next_out=d,r.next_out_index=0,r.avail_out=d.length;var u=r.inflate(h);if(u!=f&&u!=p&&u!=_)throw r.msg;if(0!=r.avail_out){var m=new Uint8Array(d.length-r.avail_out);s(d,0,m,0,d.length-r.avail_out),d=m}if(o.push(d),l+=d.length,u==p||u==_)break}if(a&&(a[0]=(i||0)+r.next_in_index),1==o.length)return o[0].buffer;for(var v=new Uint8Array(l),g=0,b=0;b<o.length;++b){var w=o[b];s(w,0,v,g,w.length),g+=w.length}return v.buffer}var 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t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var T=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==T[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var S=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,o,l,d,c;for(o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case v:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],g=[];r(u,h,_,g,t),this.codes.init(u[0],h[0],_[0],0,g[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),s(t.next_in,o,this.window,d,i),o+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:v;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}this.blens[S[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[S[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),g=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,g,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,g[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){s(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,s){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,s,o,l,d,c=0,u=0,h=0;for(h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o;;)switch(this.mode){case 0:if(l>=258&&s>=10&&(t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=o-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);t.window[o++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,t.window[o++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,s++,h--),t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,o,l){var d,c,u,h,_,v,g,b,w,y,x,k,C,$,T,S;g=l.next_in_index,b=l.avail_in,_=o.bitb,v=o.bitk,w=o.write,y=w<o.read?o.read-w-1:o.end-w,x=m[t],k=m[e];do{for(;v<20;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if(d=_&x,c=i,u=n,S=3*(u+d),0!=(h=c[S]))for(;;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15,C=c[S+2]+(_&m[h]),_>>=h,v-=h;v<15;)b--,_|=(255&l.next_in[g++])<<v,v+=8;for(d=_&k,c=a,u=r,S=3*(u+d),h=c[S];;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15;v<h;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if($=c[S+2]+(_&m[h]),_>>=h,v-=h,y-=C,w>=$)T=w-$,o.window[w++]=o.window[T++],o.window[w++]=o.window[T++],C-=2;else{T=w-$;do{T+=o.end}while(T<0);if(h=o.end-T,C>h){if(C-=h,w-T>0&&h>w-T)do{o.window[w++]=o.window[T++]}while(0!=--h);else s(o.window,T,o.window,w,h),w+=h,T+=h,h=0;T=0}}do{o.window[w++]=o.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3;d+=c[S+2],d+=_&m[h],S=3*(u+d),h=c[S]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3);if(d+=c[S+2],d+=_&m[h],S=3*(u+d),0==(h=c[S])){_>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--;break}}else _>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,o,l,d,c,h){var p,m,v,g,b,w,y,x,k,C,$,T,S,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return o[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(v=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,S=2;0!=--b;)this.x[S]=w+=this.c[C],S++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[v],this.x[0]=b=0,C=0,g=-1,T=-x,this.u[0]=0,$=0,O=0;y<=v;y++)for(p=this.c[y];0!=p--;){for(;y>T+x;){if(g++,T+=x,O=v-T,O=O>x?x:O,(m=1<<(w=y-T))>p+1&&(m-=p+1,S=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++S]);)m-=this.c[S];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[g]=$=this.hn[0],this.hn[0]+=O,0!=g?(this.x[g]=b,this.r[0]=w,this.r[1]=x,w=b>>>T-x,this.r[2]=$-this.u[g-1]-w,s(this.r,0,d,3*(this.u[g-1]+w),3)):o[0]=$}for(this.r[1]=y-T,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-T,w=b>>>T;w<O;w+=m)s(this.r,0,d,3*($+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<T)-1;(b&k)!=this.x[g];)g--,T-=x,k=(1<<T)-1}return 0!=M&&1!=v?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,s,o,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,o,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,$,s,a,o,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;s(this.c,0,this.u,0,15),s(this.c,0,this.x,0,16)};var M=new Uint8Array(1),O="function"==typeof M.subarray;return{inflateBuffer:d,arrayCopy:s}}.apply(e,n))&&(t.exports=a)},function(t,e,i){(function(n){var a,r,s;!function(n,o){r=[i(0)],a=o,void 0!==(s="function"==typeof a?a.apply(e,r):a)&&(t.exports=s)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var i={},a=0,r={0:200,1223:204},s={},o=n.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in s)s[t]()}),i.cors=!!o&&"withCredentials"in o,i.ajax=o=!!o,t.ajaxTransport("native",function(t){var e;if(i.cors||o&&!t.crossDomain)return{send:function(i,n){var o,l=t.xhr(),d=++a,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(o in 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t=this;return n(".tooltip").remove(),this.$el.attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("dropdown-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$toggle.html(this.model.get("title")||"").removeClass().addClass("dropdown-toggle").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"dropdown-icon fa 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i.get("menu")?i.set("show_menu",!0):i.get("onclick")?i.get("onclick")():Galaxy.frame.add(i.attributes)},_formatUrl:function(t){return"string"==typeof t&&-1===t.indexOf("//")&&"/"!=t.charAt(0)?Galaxy.root+t:t},_template:function(){return'<ul class="nav navbar-nav"><li class="dropdown"><a class="dropdown-toggle"/><ul class="dropdown-menu"/><div class="dropdown-note"/></li></ul>'}});e.default={Collection:_,Tab:m}}).call(e,i(1),i(0),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(9),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.View.extend({initialize:function(){this.modal=null},makeModalIframe:function(t){var e=window.Galaxy.config.communication_server_host,i=window.Galaxy.config.communication_server_port,a=escape(window.Galaxy.user.attributes.username),o=escape(window.Galaxy.config.persistent_communication_rooms),l="?username="+a+"&persistent_communication_rooms="+o,d=e+":"+i+l,c=null,u=null,h='<iframe 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No jobs found.")},_templateError:function(t,e){return n("<div/>").addClass("errormessagelarge").append(n("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. 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g=e.categorical_filters[r][v],b="",w="";for(var y in g)b=y,w=g[y];m&&(s+=" | "),m=!0;var h=n[r];h&&g[r]&&h==w?s+='<span class="categorical-filter '+r+'-filter current-filter">'+v+"</span>":s+='<span class="categorical-filter '+r+'-filter"><a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+w+'">'+v+"</a></span>"}s+="</span>"}return s+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=r.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=i(146),l=a(o),d=i(13),c=a(d),u=i(41),h=a(u),f=i(61),p=a(f),_=i(26),m=a(_),v=i(3),g=a(v);i(170),i(169),i(171),i(157),i(174),i(159),i(172),i(173),i(25);var b=null,w=null,y=function(){this.initialize&&this.initialize.apply(this,arguments)};y.extend=t.Model.extend;var x=y.extend({initialize:function(t){g.default.cssLoadFile("static/style/jquery.rating.css"),g.default.cssLoadFile("static/style/autocomplete_tagging.css"),g.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),g.default.cssLoadFile("static/style/library.css"),g.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];n(".bookmark").each(function(){t.push({position:n(this).children(".position").text(),annotation:n(this).children(".annotation").text()})});var e=w.overview_drawable?w.overview_drawable.config.get_value("name"):null,i={view:w.to_dict(),viewport:{chrom:w.chrom,start:w.low,end:w.high,overview:e},bookmarks:t};return n.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:w.vis_id,title:w.config.get_value("name"),dbkey:w.dbkey,type:"trackster",vis_json:JSON.stringify(i)}}).success(function(t){Galaxy.modal.hide(),w.vis_id=t.vis_id,w.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=h.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:w.dbkey},function(t){s.each(t,function(t){w.add_drawable(l.default.object_from_template(t,w,w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){w.add_drawable(new l.default.DrawableGroup(w,w,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==n("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+w.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(w)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,i){var a=n("#right .unified-panel-body"),r=n("<div/>").addClass("bookmark").appendTo(a),s=n("<div/>").addClass("position").appendTo(r),o=(n("<a href=''/>").text(t).appendTo(s).click(function(){return w.go_to(t),!1}),n("<div/>").text(e).appendTo(r));if(i){var l=n("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){return r.slideUp("fast"),r.remove(),w.has_changes=!0,!1});n("<a href=''/>").addClass("icon-button delete").appendTo(l);o.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return w.has_changes=!0,r},create_visualization:function(t,e,i,a,r){var o=this,d=new l.default.TracksterView(s.extend(t,{header:!1}));return d.editor=!0,n.when(d.load_chroms_deferred).then(function(t){if(e){var n=e.chrom,s=e.start,c=e.end,u=e.overview;n&&void 0!==s&&c?d.change_chrom(n,s,c):d.change_chrom(t[0].chrom)}else d.change_chrom(t[0].chrom);if(i)for(var 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bookmark'></a>"),n("#right-border").click(function(){w.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),i={},n={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(i["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(n)},"View in new 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id="new-dbkey">',i=0;i<t.length;i++)e+='<option value="'+t[i][1]+'">'+t[i][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){n(document).trigger("convert_to_values"),w=b.create_visualization({container:n("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),w.editor=!0},init_editor:function(){n("#center .unified-panel-title").text(w.config.get_value("name")+" ("+w.dbkey+")"),galaxy_config.app.add_dataset&&n.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){w.add_drawable(l.default.object_from_template(t,w,w))}}),n("#add-bookmark-button").click(function(){var t=w.chrom+":"+w.low+"-"+w.high;return b.add_bookmark(t,"Bookmark description",!0)}),b.init_keyboard_nav(w),n(window).on("beforeunload",function(){if(w.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}function r(t,e){e||(e=0);var i=Math.pow(10,e);return Math.round(t*i)/i}function s(e){var i=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,n){i.resolve(206===n.status)}}),i}Object.defineProperty(e,"__esModule",{value:!0});var o=i(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(o),d=i(13),c=a(d),u=i(147),h=a(u),f=i(14),p=a(f),_=i(148),m=a(_),v=i(149),g=a(v),b=i(150),w=a(b),y=i(15),x=a(y),k=i(140),C=a(k),$=i(21),T=a($),S=i(151),M=a(S);i(25);var O=l.extend,A={},E=function(t,e){A[t.attr("id")]=e},z=function(e,i,n,a){n=".group",A[e.attr("id")]=a,e.bind("drag",{handle:"."+i,relative:!0},function(e,i){var a,r,s,o,l,d=(t(this),t(this).parent()),c=d.children(".track,.group"),u=A[t(this).attr("id")];if(r=t(this).parents(n),0!==r.length){s=r.position().top,o=s+r.outerHeight();var h=A[r.attr("id")];if(i.offsetY<s)return t(this).insertBefore(r),h.remove_drawable(u),void h.container.add_drawable_before(u,h);if(i.offsetY>o)return t(this).insertAfter(r),h.remove_drawable(u),void h.container.add_drawable(u)}for(r=null,l=0;l<c.length;l++)if(a=t(c.get(l)),s=a.position().top,o=s+a.outerHeight(),a.is(n)&&this!==a.get(0)&&i.offsetY>=s&&i.offsetY<=o)return i.offsetY-s<o-i.offsetY?a.find(".content-div").prepend(this):a.find(".content-div").append(this),u.container&&u.container.remove_drawable(u),void A[a.attr("id")].add_drawable(u);for(l=0;l<c.length&&(a=t(c.get(l)),!(i.offsetY<a.position().top)||a.hasClass("reference-track")||a.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(d.append(this),A[d.attr("id")].move_drawable(u,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),A[d.attr("id")].move_drawable(u,i.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",P=["Histogram","Line","Filled","Intensity"],j=function t(e,i,n){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=T.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new h.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var r=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){r.show()},function(){r.hide()})}};j.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new T.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],O(j.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,i){j.call(this,t,e,i),this.obj_type=i.obj_type,this.drawables=[]};O(q.prototype,j.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,i=0;i<t.length;i++)e=nt(t[i],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var i=this.drawables.indexOf(e);return-1!==i&&(this.drawables.splice(i,0,t),!0)},replace_drawable:function(t,e,i){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables[n]=e,i&&t.container_div.replaceWith(e.container_div),this.changed()),n},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables.splice(i,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,i=this.drawables.slice(0),n=[];0!==i.length;)e=i.shift(),e instanceof t?n.push(e):e.drawables&&(i=i.concat(e.drawables));return n}});var D=function(e,i,n){if(O(n,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,i,n),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),E(this.container_div,this),E(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new w.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new w.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};O(D.prototype,j.prototype,q.prototype,{action_icons_def:[j.prototype.action_icons_def[0],j.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},j.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof J),this.action_icons.filters_icon.hide();else{var i,n,a,r=this.drawables[0].get_type(),s=0;for(i=0;i<e;i++){if(a=this.drawables[i],a.get_type()!==r){can_composite=!1;break}a instanceof Q&&s++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),s>1&&s===this.drawables.length){var o,l={};for(a=this.drawables[0],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],l[o.name]=[o];for(i=1;i<this.drawables.length;i++)for(a=this.drawables[i],n=0;n<a.filters_manager.filters.length;n++)o=a.filters_manager.filters[n],o.name in l&&l[o.name].push(o);this.filters_manager.remove_all();var d,c;for(var u in l)d=l[u],d.length===s&&(c=new w.default.NumberFilter({name:d[0].name,index:d[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new J(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=O(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var B=n.View.extend({initialize:function(t){O(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=T.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,i=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,E(this.viewport_container,i),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:i.dbkey},function(t){l.each(t,function(t){i.add_drawable(nt(t,i,i))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var n=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&i.go_to(t(this).val()),t(this).hide(),t(this).val(""),i.location_span.show(),i.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(e,n){var a=[],r=t.map(i.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){a=a.concat(t)})});t.when.apply(t,r).done(function(){n(t.map(a,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){i.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var n=e.offsetX-this.current_x;this.current_x=e.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=i.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,n){var a=t(this),r=n.offsetX-n.current_x,s=a.scrollTop()-(e.clientY-n.current_height);a.scrollTop(s),n.current_height=e.clientY,n.current_x=n.offsetX;var o=Math.round(r/i.viewport_container.width()*(i.high-i.low));i.move_delta(o)}),this.top_labeltrack.bind("dragstart",function(e,n){return t("<div/>").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,n){t(n.proxy).css({left:Math.min(e.pageX,n.startX)-i.container.offset().left,width:Math.abs(e.pageX-n.startX)});var a=Math.min(e.pageX,n.startX)-i.container.offset().left,r=Math.max(e.pageX,n.startX)-i.container.offset().left,s=i.high-i.low,o=i.viewport_container.width();i.update_location(Math.round(a/o*s)+i.low,Math.round(r/o*s)+i.low)}).bind("dragend",function(e,n){var a=Math.min(e.pageX,n.startX),r=Math.max(e.pageX,n.startX),s=i.high-i.low,o=i.viewport_container.width(),l=i.low;i.low=Math.round(a/o*s)+l,i.high=Math.round(r/o*s)+l,t(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){i.resize_window()},500)}),t(document).bind("redraw",function(){i.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});O(B.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,i,n){if(this.timer&&clearTimeout(this.timer),n){var a=this;this.timer=setTimeout(function(){a.trigger("navigate",t+":"+e+"-"+i)},500)}else view.trigger("navigate",t+":"+e+"-"+i)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var i=this,n=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var a=new W(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=e.chrom_info,i.chrom_select.html(""),i.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var r=0,s=i.chrom_data.length;r<s;r++){var o=i.chrom_data[r].chrom,l=t("<option>");l.text(o),l.val(o),i.chrom_select.append(l)}e.prev_chroms&&i.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&i.chrom_select.append(t('<option value="next">Next 100</option>')),i.chrom_start_index=e.start_index,n.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+i.dbkey)}}),n},change_chrom:function(e,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(e,i,n)});if(e&&"None"!==e){if("previous"===e)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void a.load_chroms({low:this.chrom_start_index+100});var r=t.grep(a.chrom_data,function(t,i){return t.chrom===e})[0];if(void 0===r)return void a.load_chroms({chrom:e},function(){a.change_chrom(e,i,n)});if(e!==a.chrom){a.chrom=e,a.chrom_select.val(a.chrom),a.max_high=r.len-1,a.reset();for(var s=0,o=a.drawables.length;s<o;s++){var l=a.drawables[s];l.init&&l.init()}a.reference_track&&a.reference_track.init()}void 0===i&&void 0===n?(a.low=0,a.high=a.max_high):(a.low=void 0!==i?Math.max(i,0):0,void 0===n?(a.low=Math.max(a.low-15,0),a.high=a.low+30):a.high=Math.min(n,a.max_high)),a.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),i=e[0],n=e[1]?parseInt(e[1],10):void 0,a=e[2]?parseInt(e[2],10):void 0;this.change_chrom(i,n,a)},move_fraction:function(t){var e=this,i=e.high-e.low;this.move_delta(t*i)},move_delta:function(t){var e=this,i=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+i):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-i):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var n=e.chrom_select.val();this.trigger_navigate(n,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,i){if(q.prototype.remove_drawable.call(this,e),i){var n=this;e.container_div.hide(0,function(){t(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var i=this,n=e?[e]:i.drawables;l.each(n,function(e){var n=l.find(i.tracks_to_be_redrawn,function(t){return t[0]===e});n?n[1]=t:i.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var i=this.high-this.low;0!==this.high&&i<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var n=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,a=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:n,width:Math.max(13,a)}).show(),a<13&&this.overview_box.css("left",n-(13-a)/2),this.overview_highlight&&this.overview_highlight.css({left:n,width:a}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],i=t[1];e&&e._draw(i)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var i=this.high-this.low,n=i/2+this.low,a=i/this.zoom_factor/2;t&&(n=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(n-a),this.high=Math.round(n+a),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,i=t*this.zoom_factor/2;this.low=Math.round(e-i),this.high=Math.round(e+i),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),i=this;e.header_div.hide(),e.is_overview=!0,i.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){i.overview_highlight.show().height(i.overview_drawable.content_div.height()),i.overview_viewport.height(i.overview_drawable.content_div.height()+i.overview_box.outerHeight()),i.overview_close.show(),i.resize_window()},i.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var V=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=n.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),i=this.model;t("<div>").addClass("param-label").text(i.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(i.get("html")).appendTo(e).find(":input").val(i.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),N=n.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(n).text(i.get("name"));i.get("inputs").each(function(t){var e=new I({model:t});e.render(),n.append(e.$el)}),n.find("input").click(function(){t(this).select()});var a=t("<div>").addClass("param-row").appendTo(n),r=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(a);t("<input type='submit'>").attr("value","Run on visible region").appendTo(a).click(function(){e.run_on_region()}),r.click(function(){e.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),i=this.model,n=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),a={target_dataset_id:e.dataset.id,action:"rerun",tool_id:i.id,regions:[n.toJSON()]},r=e,s=i.get("name")+r.tool_region_and_parameters_str(n);if(r.container===view){var o=new D(view,view,{name:e.config.get_value("name")}),l=r.container.replace_drawable(r,o,!1);o.container_div.insertBefore(r.view.content_div.children()[l]),o.add_drawable(r),r.container_div.appendTo(o.content_div),t=o}else t=r.container;var d=new r.constructor(view,t,{name:s,hda_ldda:"hda"});d.init_for_tool_data(),d.change_mode(r.mode),d.set_filters_manager(r.filters_manager.copy(d)),d.update_icons(),t.add_drawable(d),d.tiles_div.text("Starting job."),this.run(a,d,function(t){d.set_dataset(new x.default.Dataset(t)),d.tiles_div.text("Running job."),d.init()})},run:function(e,i,n){e.inputs=this.model.get_inputs_dict();var a=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(a.go()).then(function(t){"no converter"===t?(i.container_div.addClass("error"),i.content_div.text(R)):t.error?(i.container_div.addClass("error"),i.content_div.text("Tool cannot be rerun: "+t.message)):n(t)})}}),L=function(t,e){g.default.Scaler.call(this,e),this.filter=t};L.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var G=function(e,i,n,a,r){this.track=e,this.region=i,this.low=i.get("start"),this.high=i.get("end"),this.w_scale=n,this.canvas=a,this.html_elt=t("<div class='track-tile'/>").append(a),this.data=r,this.stale=!1};G.prototype.predisplay_actions=function(){};var U=function(t,e,i,n,a){G.call(this,t,e,i,n,a)};U.prototype.predisplay_actions=function(){};var F=function(t,e,i,n,a,r,s,o,l,d,c){G.call(this,t,e,i,n,a),this.mode=r,this.all_slotted=o,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};O(F.prototype,G.prototype),F.prototype.predisplay_actions=function(){};var H=function(e,i,a){O(a,{drag_handle_class:"draghandle"}),j.call(this,e,i,a),this.dataset=null,a.dataset&&(this.dataset=a.dataset instanceof n.Model?a.dataset:new x.default.Dataset(a.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in a?a.data_query_wait:5e3,this.data_manager="data_manager"in a?a.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in a&&!a.resize||this.add_resize_handle())};O(H.prototype,j.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},j.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},j.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var i="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',a=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},r=function(){var i,a=t('select[name="regions"] option:selected').val(),r=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),s=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});i="cur"===a?[r]:"bookmarks"===a?s:[r].concat(s),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new n.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:a,Yes:r}})}},j.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&j.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,i=!1,n=!1,a=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=t(e.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",a),e.visible_height_px=e.max_height_px===a?0:a,e.on_resize()}).bind("dragend",function(t,r){e.tile_cache.clear(),n=!1,i||a.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof W?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof J?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=t("<div/>").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=t.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:e};return t.getJSON(this.dataset.url(),a,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(i.container_div.addClass("error"),i.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===e?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){i.init()},i.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(i.valid_chroms=e.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,t.when.apply(t,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");e.message&&(a.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(t("<span/>").text(" ")),a.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_default_value("min_value",n),e.config.set_default_value("max_value",a),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var Y=function(e,i,n){H.call(this,e,i,n);var a=this;if(z(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new w.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new V(l.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var r=new N({model:this.tool});r.render(),this.dynamic_tool_div=r.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};O(Y.prototype,j.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();O(e,{data_manager:this.data_manager});var i=new this.constructor(this.view,t,e);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var i=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),e.config.set_value("min_value",n),e.config.set_value("max_value",a)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var i=e&&e.clear_after,n=this.view.low,a=this.view.high,r=this.view.container.width(),s=this.view.resolution_px_b,o=1/s;this.is_overview&&(n=this.view.max_low,a=this.view.max_high,s=r/(view.max_high-view.max_low),o=1/s),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,u,h=Math.floor(400*o),f=Math.floor(n/h),p=[],_=[];f*h<a;)d=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*h,end:Math.min((f+1)*h,this.view.max_high)}),u=this.draw_helper(d,s,e),p.push(u),t.when(u).then(function(t){_.push(t)}),f+=1;i||this.tiles_div.children(".remove").removeClass("remove").remove();var m=this;t.when.apply(t,p).then(function(){m.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&m.postdraw_actions(_,r,s,i)})}},_add_yaxis_label:function(e,i){var n=this,a="max"===e?"top":"bottom",s="max"===e?"max":"min",o="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+a),d=r(n.config.get_value(o),1);i=i||function(){n.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(d):(l=t("<div/>").text(d).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),n.config.set_value(o,r(e,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,i,n){if(l.filter(t,function(t){return t instanceof U}).length>0){this.max_height_px=0;var a=this;l.each(t,function(t){t instanceof U||(t.html_elt.remove(),a.draw_helper(t.region,i,{force:!0,mode:"Coverage"}))}),a._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,i,n){n||(n={});var a=n.force,r=n.mode||this.mode,s=1/i,o=this,d=this._get_drawables(),c=this._gen_tile_cache_key(i,e),u=a?void 0:o.tile_cache.get_elt(c);if(u)return function(t){return t&&"track"in t}(u)&&o.show_tile(u,i),u;if(!1===n.data_fetch)return null;var h=function(){var t=l.find(P,function(t){return t===r})?"Coverage":r,i=l.map(d,function(i){return i.data_manager.get_data(e,t,s,o.data_url_extra_params)});return view.reference_track&&i.push(view.reference_track.data_manager.get_data(e,r,s,view.reference_track.data_url_extra_params)),i},f=t.Deferred();return o.tile_cache.set_elt(c,f),t.when.apply(t,h()).then(function(){var a,r=h(),s=r;if(l.find(r,function(t){return p.default.is_deferred(t)}))return o.tile_cache.set_elt(c,void 0),void t.when(o.draw_helper(e,i,n)).then(function(t){f.resolve(t)});view.reference_track&&(a=view.reference_track.data_manager.subset_entry(r.pop(),e));var u=[],_=[];l.each(d,function(t,e){var n=t.mode,a=s[e];"Auto"===n&&(n=t.get_mode(a),t.update_auto_mode(n)),u.push(n),_.push(t.get_canvas_height(a,n,i,w))});var m,v=o.view.canvas_manager.new_canvas(),g=e.get("start"),b=e.get("end"),w=Math.ceil((b-g)*i)+o.left_offset,y=l.max(_);v.width=w,v.height=n.height||y;var x=v.getContext("2d");x.translate(o.left_offset,0),d.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(d,function(t,n){m=t.draw_tile(s[n],x,u[n],e,i,a)}),void 0!==m&&(o.tile_cache.set_elt(c,m),o.show_tile(m,i)),f.resolve(m)}),f},get_canvas_height:function(t,e,i,n){return this.visible_height_px},_draw_line_track_tile:function(t,e,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var r=e.canvas;return new g.default.LinePainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new U(this,n,a,r,t.data)},draw_tile:function(t,e,i,n,a,r){},show_tile:function(t,e){var i=t.html_elt;t.predisplay_actions();var n=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};O(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),r=Math.floor(i.low/a)*a,s=this.view.container.width(),o=t("<div/>").addClass("label-container");r<i.high;){var l=Math.floor((r-i.low)/n*s);o.append(t("<div/>").addClass("pos-label").text(p.default.commatize(r)).css({left:l})),r+=a}this.content_div.children(":first").remove(),this.content_div.append(o)}});var J=function(t,e,i){if(Y.call(this,t,e,i),this.drawables=[],"drawables"in i){for(var n,a=0;a<i.drawables.length;a++)n=i.drawables[a],this.drawables[a]=nt(n,t,null),n.left_offset>this.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};O(J.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],i=0;i<this.drawables.length;i++)e.push(this.drawables[i].init());var n=this;t.when.apply(t,e).then(function(){n.enabled=!0,n.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:j.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new D(this.view,this.container,{name:this.config.get_value("name")}),i=0;i<this.drawables.length;i++)t=this.drawables[i],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(i){i.config.set_value("min_value",t),i.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,i,n){var a,r=-1;for(a=0;a<t.length;a++){var s=t[a].html_elt.find("canvas").height();s>r&&(r=s)}for(a=0;a<t.length;a++){var o=t[a];o.html_elt.find("canvas").height()!==r&&(this.draw_helper(o.region,i,{force:!0,height:r}),o.html_elt.remove())}var l=this,d=function(){l.update_all_min_max()};this._add_yaxis_label("min",d),this._add_yaxis_label("max",d)}});var W=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};O(W.prototype,j.prototype,Y.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:j.prototype.can_draw,draw_helper:function(t,e,i){var n,a=this.tiles_div.is(":visible"),r=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,r=Y.prototype.draw_helper.call(this,t,e,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),r},can_subset:function(t){return!0},draw_tile:function(t,e,i,n,a){var r=this.data_manager.subset_entry(t,n),s=r.data,o=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,d=s.length;l<d;l++)e.fillStyle=this.view.get_base_color(s[l]),e.fillText(s[l],Math.floor(l*a),10);return new G(this,n,a,o,r)}});var K=function(e,i,n){this.mode="Histogram",Y.call(this,e,i,n),this.left_offset=30;var a=this;t.when(s(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(a.data_manager=new M.default.BBIDataManager({dataset:a.dataset}))})};O(K.prototype,j.prototype,Y.prototype,{display_modes:P,build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,i,n,a){return this._draw_line_track_tile(t,e,i,n,a)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,i,n){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,i){this.mode="Heatmap",Y.call(this,t,e,i)};O(Z.prototype,j.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,i,n,a){var r=e.canvas;return new g.default.DiagonalHeatmapPainter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(e,r.width,r.height,a),new G(this,n,a,r,t.data)}});var Q=function(t,e,i){Y.call(this,t,e,i),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};O(Q.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=g.default.ArcLinkedFeaturePainter:this.painter=g.default.LinkedFeaturePainter},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r,s=this;if(0===l.filter(e,function(t){return t instanceof U}).length){var o={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){o[t[0]]=t})});var d=this;l.each(e,function(e){var i=l.omit(o,l.map(e.incomplete_features,function(t){return t[0]}));if(i=l.omit(i,l.keys(e.other_tiles_features_drawn)),0!==l.size(i)){var n={data:l.values(i)},a=d.view.canvas_manager.new_canvas(),r=a.getContext("2d");a.height=Math.max(e.canvas.height,d.get_canvas_height(n,e.mode,e.w_scale,100)),a.width=e.canvas.width,r.drawImage(e.canvas,0,0),r.translate(s.left_offset,0);var c=d.draw_tile(n,r,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=a,l.extend(e.other_tiles_features_drawn,o)}})}if(s.filters_manager){var c,u=s.filters_manager.filters;for(c=0;c<u.length;c++)u[c].update_ui_elt();var h,f,p=!1;for(r=0;r<e.length;r++)if(e[r].data.length)for(h=e[r].data[0],c=0;c<u.length;c++)if(f=u[c],f.applies_to(h)&&f.min!==f.max){p=!0;break}s.filters_available!==p&&(s.filters_available=p,s.filters_available||s.filters_manager.hide(),s.update_icons())}if(e[0]instanceof F){var _=!0;for(r=0;r<e.length;r++)if(!e[r].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,i){var n=this.view.canvas_manager.dummy_context,a=this.slotters[t];return a&&a.mode===i||(a=new m.default.FeatureSlotter(t,i,100,function(t){return n.measureText(t)}),this.slotters[t]=a),a.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,i,n){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,t.data,e),r=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,r.get_required_height(a,n))},draw_tile:function(t,e,i,n,a,r,s){var o=this,l=e.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,m=0,v=t.data.length;m<v;m++){for(var g,b=t.data[m],w=!1,y=0,x=_.length;y<x;y++)if(g=_[y],g.update_attrs(b),!g.keep(b)){w=!0;break}w||(h.push(b),b[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new L(this.filters_manager.height_filter):null,$=new this.painter(h,d,c,this.config.to_key_value_dict(),i,k,C,r,function(t){return o.view.get_base_color(t)}),T=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var S=$.draw(e,l.width,l.height,a,f);T=S.feature_mapper,incomplete_features=S.incomplete_features,T.translation=-u}return s?void 0:new F(o,n,a,l,t.data,i,t.message,p,T,incomplete_features,r)}});var tt=function(t,e,i){Y.call(this,t,e,i),this.painter=g.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};O(tt.prototype,j.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(j.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,i,n,a){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",n,a);var r=this.view;return new this.painter(t.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i,function(t){return r.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,a),new G(this,n,a,e.canvas,t.data)},get_canvas_height:function(t,e,i,n){if("bigwig"===t.dataset_type)return this.summary_draw_height;var a=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===a&&0!==t.data.length&&(a=t.data[0][7].match(/,/g),a=null===a?1:a.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(a)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,i,n,a){Y.prototype.postdraw_actions.call(this,e,i,n,a);var r=l.filter(e,function(t){return t instanceof U}),s=this.dataset.get_metadata("sample_names");if(0===r.length&&this.config.get_value("show_labels")&&s&&s.length>1){var o;if(0===this.container_div.find(".yaxislabel.variant").length&&(o=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":o+"px",top:(this.config.get_value("summary_height")-o)/2+"px"})),this.config.get_value("show_sample_data"))){var d=s.join("<br/>");this.tiles_div.prepend(t("<div/>").html(d).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}o=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":o,"line-height":o}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,i){Q.call(this,t,e,i),this.painter=g.default.ReadPainter,this.update_icons()};O(et.prototype,j.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(j.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var it={CompositeTrack:J,DrawableGroup:D,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},nt=function(t,e,i){if("copy"in t)return t.copy(i);var n=t.obj_type;return n||(n=t.track_type),new it[n](e,i,t)};e.default={TracksterView:B,DrawableGroup:D,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:J,object_from_template:nt}}).call(e,i(0),i(1))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(n("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(n("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(n("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=n("<div/>").addClass("track-icons").hide().appendTo(this.$el),r.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,i,a,r,s){var o=this;this.action_icons[t]=n("<a/>").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(function(){a(o.model)}).appendTo(this.icons_div),s&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var i=this.model,n={},a=0,r=i.display_modes.length;a<r;a++){var s=i.display_modes[a];n[s]=function(t){return function(){i.change_mode(t)}}(s)}make_popupmenu(this.action_icons.mode_icon,n)}}});e.default={TrackHeaderView:s}}).call(e,i(1),i(0))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t,e){this.slot=t,this.feature=e},o=function(t,e,i,n){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=i,this.measureText=n};r(o.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),i=Math.ceil(t[2]*this.w_scale),n=t[3];if(void 0!==n&&this.include_label){var a=this.measureText(n).width+7;e-a>=0?(e-=a,"left"):(i+=a,"right")}return[e,i]},_find_slot:function(t){for(var e=t[0],i=t[1],n=0;n<=this.max_rows;n++){var a=!1,r=this.start_end_dct[n];if(void 0!==r)for(var s=0,o=r.length;s<o;s++){var l=r[s];if(i>l[0]&&e<l[1]){a=!0;break}}if(!a)return n}return-1},slot_features:function(t){for(var e,i,n=this.start_end_dct,a=[],r=0,o=0,l=t.length;o<l;o++){e=t[o],i=e[0];var d=this.slots[i];if(d){if(e[1]<d.feature[1]||d.feature[2]<e[2])for(var c=this._get_draw_coords(d.feature),u=this._get_draw_coords(e),h=this.start_end_dct[d.slot],f=0;f<h.length;f++){var p=h[f];p[0]===c[0]&&p[1]===c[1]&&(h[f]=u)}r=Math.max(r,this.slots[i].slot)}else a.push(o)}for(var o=0,l=a.length;o<l;o++){e=t[a[o]],i=e[0];var _=this._get_draw_coords(e),m=this._find_slot(_);m>=0&&(void 0===n[m]&&(n[m]=[]),n[m].push(_),this.slots[i]=new s(m,e),r=Math.max(r,m))}return r+1}}),e.default={FeatureSlotter:o}},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=function(t,e){var i=t[0],n=t[1],a=e[0],r=e[1];return i<a?n<=a?1001:n<=r?1003:1002:i>r?1006:n<=r?1005:1004},s=function(t,e){var i=r(t,e);return 1001!==i&&1006!==i},o=function(t,e,i,n,a,r){void 0===r&&(r=4);var s,o=n-e,l=a-i,d=Math.floor(Math.sqrt(o*o+l*l)/r),c=o/d,u=l/d;for(s=0;s<d;s++,e+=c,i+=u)s%2==0&&t.fillRect(e,i,r,1)},l=function(t,e,i,n){var a=e-n/2,r=e+n/2,s=i-Math.sqrt(3*n/2);t.beginPath(),t.moveTo(a,s),t.lineTo(r,s),t.lineTo(e,i),t.lineTo(a,s),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},d=function(t){this.default_val=t||1};d.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},u=function(t,e,i,n,r){this.data=t,this.view_start=e,this.view_end=i,this.prefs=a.extend({},this.default_prefs,n),this.mode=r};u.prototype.default_prefs={},u.prototype.draw=function(t,e,i,n){},u.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},u.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},u.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},u.prototype._chrom_pos_to_draw_pos=function(t,e,i){return Math.floor(e*(Math.max(0,t-this.view_start)+i))};var h=function(t,e,i,n,a){u.call(this,t,e,i,n,a)};h.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},h.prototype.draw=function(t,e,i,n){var r=!1,s=this.prefs.min_value,o=this.prefs.max_value,l=o-s,d=i,c=this.view_start,u=this.mode,h=this.data;t.save();var f=Math.round(i+s/l*i);"Intensity"!==u&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,m;m=h.length>1?a.map(h.slice(0,-1),function(t,e){return Math.ceil((h[e+1][0]-h[e][0])*n)}):[10];for(var v,g=this.prefs.block_color||this.prefs.color,b=parseInt(g.slice(1),16),w=(16711680&b)>>16,y=(65280&b)>>8,x=255&b,k=!1,C=!1,$=0,T=h.length;$<T;$++)if(t.fillStyle=t.strokeStyle=g,k=C=!1,v=m[$],p=Math.floor((h[$][0]-c-.5)*n),null!==(_=h[$][1])){if(_<s?(C=!0,_=s):_>o&&(k=!0,_=o),"Histogram"===u)_=Math.round(_/l*d),t.fillRect(p,f,v,-_);else if("Intensity"===u){var S=(_-s)/l,M=Math.round(w+(255-w)*(1-S)),O=Math.round(y+(255-y)*(1-S)),A=Math.round(x+(255-x)*(1-S));t.fillStyle="rgb("+M+","+O+","+A+")",t.fillRect(p,0,v,d)}else _=Math.round(d-(_-s)/l*d),r?t.lineTo(p,_):(r=!0,"Filled"===u?(t.moveTo(p,d),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var E;"Histogram"===u||"Intensity"===u?E=v:(p-=2,E=4),k&&t.fillRect(p,0,E,3),C&&t.fillRect(p,d-3,E,3)}t.fillStyle=g}else r&&"Filled"===u&&t.lineTo(p,d),r=!1;"Filled"===u?(r&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,i,n){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:i,x_end:n})},f.prototype.get_feature_data=function(t,e){var i,n=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[n])return null;t+=this.translation;for(var a=0;a<this.feature_positions[n].length;a++)if(i=this.feature_positions[n][a],t>=i.x_start&&t<=i.x_end)return i.data};var p=function(t,e,i,n,a,r,s){u.call(this,t,e,i,n,a),this.alpha_scaler=r||new d,this.height_scaler=s||new d,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(p.prototype,{get_required_height:function(t,e){var i=this.get_row_height(),n=i,a=this.mode;return"no_detail"!==a&&"Squish"!==a&&"Pack"!==a||(i=t*n),i+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,i,n,a){var r=this.data,s=this.view_start,o=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,d=this.get_row_height(),u=new f(d),h=[],p=0,_=r.length;p<_;p++){var m=r[p],v=m[0],g=m[1],b=m[2],w=a&&void 0!==a[v]?a[v].slot:null;("Dense"===this.mode||null!==w)&&g<o&&b>s&&(l=this.draw_element(t,this.mode,m,w,s,o,n,d,e),u.map_feature_data(m,w,l[0],l[1]),(g<s||b>o)&&h.push(m))}return t.restore(),u.y_translation=this.get_top_padding(e),new c({incomplete_features:h,feature_mapper:u})},draw_element:function(t,e,i,n,a,r,s,o,l){return[0,0]}});var _=function(t,e,i,n,a,r,s){p.call(this,t,e,i,n,a,r,s),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,i,n,a,r,s,o,l){var d,c=(i[0],i[1]),u=i[2],h=i[3],f=i[4],p=Math.floor(Math.max(0,(c-a-.5)*s)),_=Math.ceil(Math.min(l,Math.max(0,(u-a-.5)*s))),m=p,v=_,d=("Dense"===e?0:0+n)*o+this.get_top_padding(l),g=null,b=null,w=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,y=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===e&&(n=1),"no_detail"===e)t.fillStyle=w,t.fillRect(p,d+5,_-p,1);else{var x=i[5],k=i[6],C=i[7],$=!0;x&&k&&(g=Math.floor(Math.max(0,(x-a)*s)),b=Math.ceil(Math.min(l,Math.max(0,(k-a)*s))));var T,S;if("Squish"===e?(T=1,S=3,$=!1):(T=5,S=9),C){var M,O;"Squish"===e||"Dense"===e?(M=d+Math.floor(1.5)+1,O=1):f?(M=d,O=S):(M+=2.5,O=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,M,_-p,O));for(var A=0,E=C.length;A<E;A++){var z,R,P=C[A],j=Math.floor(Math.max(0,(P[0]-a-.5)*s)),q=Math.ceil(Math.min(l,Math.max((P[1]-a-.5)*s)));if(!(j>q)){if(t.fillStyle=w,t.fillRect(j,d+(S-T)/2+1,q-j,T),void 0!==g&&k>x&&!(j>b||q<g)){var D=Math.max(j,g),B=Math.min(q,b);t.fillRect(D,d+1,B-D,S),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),D+14<B&&(D+=2,B-=2),t.fillRect(D,d+1,B-D,S))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,j,q,d),z=j,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var V=this.height_scaler.gen_val(i),I=Math.ceil(S*V),N=Math.round((S-I)/2);1!==V&&(t.fillRect(p,M+1,_-p,N),t.fillRect(p,M+S-N+1,_-p,N))}}else t.fillStyle=w,t.fillRect(p,d+1,_-p,S),f&&$&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,d+1,_-p,S));t.globalAlpha=1,h&&"Pack"===e&&c>a&&(t.fillStyle=y,0===a&&p-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,_+2,d+8,this.max_label_length),v+=t.measureText(h).width+2):(t.textAlign="right",t.fillText(h,p-2,d+8,this.max_label_length),m-=t.measureText(h).width+2))}return t.globalAlpha=1,[m,v]}});var m=function(t,e,i,n,a,r,s,o,l){p.call(this,t,e,i,n,a,r,s),this.ref_seq=o?o.data:null,this.base_color_fn=l};a.extend(m.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",i=[[0,0]],n=i[0],r=0,s=a.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var a=parseInt(t.slice(0,-1),10),s=t.slice(-1);return"N"===s?0!==n[1]&&(n=[r+a,r+a],i.push(n)):-1==="ISHP".indexOf(s)&&(n[1]+=a,r+=a),[e.indexOf(s),a]});return{blocks:i,cigar:s}},draw_read:function(t,e,i,n,a,o,d,c,u,h){var f=function(t){return Math.floor(Math.max(0,(t-a-.5)*i))};t.textAlign="center";var p,_,m=[a,o],v=0,g=0,b=Math.round(i/2),w=t.canvas.manager.char_width_px,y="+"===u?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,$=n+1,T=new x(t,C,i,e),S=[],M=[],O=this._parse_cigar(c);c=O.cigar,S=O.blocks;for(var A=0;A<S.length;A++){var E=S[A];s([d+E[0],d+E[1]],m)&&(p=f(d+E[0]),_=f(d+E[1]),p===_&&(_+=1),t.fillStyle=y,t.fillRect(p,$,_-p,C))}for(var z=0,R=c.length;z<R;z++){var P=c[z],j="MIDNSHP=X"[P[0]],q=P[1],D=d+v;if(p=f(D),_=f(D+q),s([D,D+q],m))switch(p===_&&(_+=1),j){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var B="";"X"===j?B=h.slice(g,g+q):this.ref_seq&&(B=this.ref_seq.slice(Math.max(0,D-a),Math.min(D-a+q,o-a)));for(var V=Math.max(D,a),I=0;I<B.length;I++)if(B&&!this.prefs.show_differences||"X"===j){var N=Math.floor(Math.max(0,(V+I-a)*i));t.fillStyle=this.base_color_fn(B[I]),k&&i>w?t.fillText(B[I],N,n+9):i>.05&&t.fillRect(N-b,$,Math.max(1,Math.round(i)),C)}"X"===j&&(g+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,$+(C-1)/2,_-p,1),v+=q;break;case"D":T.draw_deletion(p,$,q),v+=q;break;case"I":var L=p-b;if(s([D,D+q],m)){var G=h.slice(g,g+q);if(this.prefs.show_insertions){var U=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w){switch(t.fillStyle="yellow",t.fillRect(U-b,n-9,_-p,9),M[M.length]={type:"triangle",data:[L,n+4,5]},t.fillStyle="#ccc",r([D,D+q],m)){case 1003:G=G.slice(a-D);break;case 1004:G=G.slice(0,D-o);break;case 1005:break;case 1002:G=G.slice(a-D,D-o)}for(var I=0,F=G.length;I<F;I++){var N=Math.floor(Math.max(0,(D+I-a)*i));t.fillText(G[I],N-(_-p)/2,n)}}else t.fillStyle="yellow",t.fillRect(U,n+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==h&&i>w&&M.push({type:"text",data:[G.length,L,n+9]})}g+=q}else v=function(t,e,i){return-1!=="M=NXD".indexOf(e)&&(t+=i),t}(v,j,q),g=function(t,e,i){return-1!=="IX".indexOf(e)&&(t+=i),t}(g,j,q)}t.fillStyle="yellow";for(var H,Y,X,A=0;A<M.length;A++)H=M[A],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,i,n,a,r,s,l,d){var c=(i[0],i[1]),u=i[2],h=i[3],f=Math.floor(Math.max(-.5*s,(c-a-.5)*s)),p=Math.ceil(Math.min(d,Math.max(0,(u-a-.5)*s))),_=("Dense"===e?0:0+n)*l,m="Pack"===e?9:3;this.prefs.label_color;if(i[5]instanceof Array){var v=!0;i[4][1]>=a&&i[4][0]<=r&&i[4][2]?this.draw_read(t,e,s,_,a,r,i[4][0],i[4][2],i[4][3],i[4][4]):v=!1,i[5][1]>=a&&i[5][0]<=r&&i[5][2]?this.draw_read(t,e,s,_,a,r,i[5][0],i[5][2],i[5][3],i[5][4]):v=!1;var g=Math.ceil(Math.min(d,Math.max(-.5*s,(i[4][1]-a-.5)*s))),b=Math.floor(Math.max(-.5*s,(i[5][0]-a-.5)*s));if(v&&b>g){t.fillStyle="#ccc";var w=_+1+(m-1)/2;o(t,g,w,b,w)}}else this.draw_read(t,e,s,_,a,r,c,i[4],i[5],i[6]);return"Pack"===e&&c>=a&&"."!==h&&(t.fillStyle=this.prefs.label_color,0===a&&f-t.measureText(h).width<0?(t.textAlign="left",t.fillText(h,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,i,n,a,r,s){_.call(this,t,e,i,n,a,r,s),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,i=this.data.length;e<i;e++){var n=this.data[e],a=n[1],r=n[2];t=Math.max(t,r-a)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,i=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*i))},draw_connector:function(t,e,i,n,a,r){var s=(i+n)/2,o=n-s;Math.PI;o>0&&(t.beginPath(),t.arc(s,r,n-s,Math.PI,0),t.stroke())}});var g=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};g.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,i=this.rgb[0]/255,n=this.rgb[1]/255,a=this.rgb[2]/255,r=this.alpha,s=Math.max(i,n,a),o=Math.min(i,n,a),l=(s+o)/2,d=s-o;if(s===o)t=e=0;else{switch(e=l>.5?d/(2-s-o):d/(s+o),s){case i:t=(n-a)/d+(n<a?6:0);break;case n:t=(a-i)/d+2;break;case a:t=(i-n)/d+4}t/=6}return{h:360*t,s:e,l:l,a:r}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var i=this,n=e,a=2*n-1,r=i.toHSL().a-t.toHSL().a,s=((a*r==-1?a:(a+r)/(1+a*r))+1)/2,o=1-s,l=[i.rgb[0]*s+t.rgb[0]*o,i.rgb[1]*s+t.rgb[1]*o,i.rgb[2]*s+t.rgb[2]*o],d=i.alpha*n+t.alpha*(1-n);return new g(l,d)}};var b=function(t,e,i,n){this.start_color=new g(t),this.end_color=new g(e),this.start_value=i,this.end_value=n,this.value_range=n-i};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var w=function(t,e,i,n,a){this.positive_ramp=new b(e,i,0,a),this.negative_ramp=new b(e,t,0,-n),this.start_value=n,this.end_value=a};w.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var y=function(t,e,i,n,a){u.call(this,t,e,i,n,a);var r,s;if(void 0===this.prefs.min_value){var o=1/0;for(r=0,s=this.data.length;r<s;r++)o=Math.min(o,this.data[r][6]);this.prefs.min_value=o}if(void 0===this.prefs.max_value){var l=-1/0;for(r=0,s=this.data.length;r<s;r++)l=Math.max(l,this.data[r][6]);this.prefs.max_value=l}};y.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},y.prototype.draw=function(t,e,i,n){var a,r,s,o,l,d,c=this.prefs.min_value,u=this.prefs.max_value,h=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new w(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,u),m=function(t){return(t-h)*n};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,g=f.length;v<g;v++)a=f[v],r=m(a[1]),s=m(a[2]),o=m(a[4]),l=m(a[5]),d=a[6],t.fillStyle=_.map_value(d),t.fillRect(r,o,s-r,l-o);t.restore()};var x=function(t,e,i,n){this.ctx=t,this.row_height=e,this.px_per_base=i,this.draw_details=("Pack"===n||"Auto"===n)&&i>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(x.prototype,{draw_deletion:function(t,e,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-n),this.ctx.fillRect(t,e,i*this.px_per_base,n)}});var k=function(t,e,i,n,a,r){u.call(this,t,e,i,n,a),this.base_color_fn=r,this.divider_height=1};a.extend(k.prototype,u.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,i,n){t.save();var r,s,o,l,d,c,u,h,f,p,_,m=function(t,e){var i=t.length,n=e.length,a=0,r=1,s=null;return"-"===e?(s="deletion",r=t.length):0===t.indexOf(e)&&i>n?(s="deletion",r=i-n,a=n):0===e.indexOf(t)&&i<n&&(s="insertion",r=n-i,a=n),null!==s?{type:s,start:a,len:r}:{}},v=Math.max(1,Math.floor(n)),g=this.data.length?this.data[0][7].split(",").length:0,b="Squish"===this.mode?5:10,w=n<.1?b:"Squish"===this.mode?3:9,y=!0,k=new x(t,b,n,this.mode);1===g&&(b=w=n<t.canvas.manager.char_width_px?this.prefs.summary_height:b,k.row_height=b,y=!1),this.prefs.show_sample_data&&y&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(r=this.data[C],s=r[1],o=r[3],l=[r[4].split(",")],d=r[7].split(","),c=r.slice(8),l=a.map(a.flatten(l),function(t){var e={type:"snp",value:t,start:0},i=m(o,t);return a.extend(e,i)}),!(s<this.view_start||s>this.view_end)){if(y)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(h=this.get_start_draw_pos(s+l[_].start,n),t.fillRect(h,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var $=c/d.length,T=Math.ceil(this.prefs.summary_height*$);t.fillRect(h,f-T,v,T),f-=T}if(this.prefs.show_sample_data)for(f=y?this.prefs.summary_height+this.divider_height:0,_=0;_<d.length;_++,f+=b)if(p=d[_]?d[_].split(/\/|\|/):["0","0"],u=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(u=l[parseInt(p[0],10)-1],t.globalAlpha=1):(u="0"!==p[0]?p[0]:p[1],u=l[parseInt(u,10)-1],t.globalAlpha=.5),u)if(h=this.get_start_draw_pos(s+u.start,n),"snp"===u.type){var S=u.value;t.fillStyle=this.base_color_fn(S),k.draw_details?t.fillText(S,this.get_draw_pos(s,n),f+b):t.fillRect(h,f+1,v,w)}else"deletion"===u.type&&k.draw_deletion(h,f+1,u.len)}t.restore()}}),e.default={Scaler:d,LinePainter:h,LinkedFeaturePainter:_,ReadPainter:m,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:y,VariantPainter:k}},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(n),r=a.extend,s=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};r(s.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var o=function(e,i,n){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(i).tooltip().click(n)},l=function(e){s.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var i=this;i.parent_div=t("<div/>").addClass("filter-row slider-row");var n=t("<div/>").addClass("elt-label").appendTo(i.parent_div),a=(t("<span/>").addClass("slider-name").text(i.name+"  ").appendTo(n),t("<span/>").text(this.low+"-"+this.high)),r=t("<span/>").addClass("slider-value").appendTo(n).append("[").append(a).append("]");i.values_span=a;var l=t("<div/>").addClass("slider").appendTo(i.parent_div);i.control_element=t("<div/>").attr("id",i.name+"-filter-control").appendTo(l),i.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){i.slide(t,e)},change:function(t,e){i.control_element.slider("option","slide").call(i.control_element,t,e)}}),i.slider=i.control_element,i.slider_label=a,function(e,i,n){e.click(function(){var e=i.text(),a=parseFloat(n.slider("option","max")),r=a<=1?4:a<=1e6?a.toString().length:6,s=!1,o=t(this).parents(".slider-row");o.addClass("input"),n.slider("option","values")&&(r=2*r+1,s=!0),i.text(""),t("<input type='text'/>").attr("size",r).attr("maxlength",r).attr("value",e).appendTo(i).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),i.text(e),o.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var i=n.slider("option","min"),a=n.slider("option","max"),r=function(t){return isNaN(t)||t>a||t<i},l=t(this).val();if(s){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],r(l[0])||r(l[1]))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this)}else if(l=parseFloat(l),r(l))return alert("Parameter value must be in the range ["+i+"-"+a+"]"),t(this);n.slider(s?"values":"value",l),o.removeClass("input")}})})}(r,a,i.control_element);var d=t("<div/>").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=o("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),this.height_icon=o("Use filter for data height","arrow-resize-090",function(){i.manager.height_filter!==i?(i.manager.height_filter=i,i.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),i.height_icon.addClass("active").show()):(i.manager.height_filter=null,i.height_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(d).hide(),i.parent_div.hover(function(){i.transparency_icon.show(),i.height_icon.show()},function(){i.manager.alpha_filter!==i&&i.transparency_icon.hide(),i.manager.height_filter!==i&&i.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(i.parent_div)};r(l.prototype,{to_dict:function(){var t=s.prototype.to_dict.call(this);return r(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var i=e.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var i=!0,n=0;n<e.length;n++)if(!this._keep_val(e[n])){i=!1;break}return i}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var i=t[this.index];i instanceof Array||(i=[i]);for(var n=0;n<i.length;n++){var a=i[n];a<this.min&&(this.min=Math.floor(a),e=!0),a>this.max&&(this.max=Math.ceil(a),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var d=function(e,i){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),i&&"filters"in i){for(var n,a=("alpha_filter"in i?i.alpha_filter:null),r=("height_filter"in i?i.height_filter:null),s=i.filters,o=0;o<s.length;o++)"number"===s[o].type?(n=new l(s[o]),this.add_filter(n),n.name===a&&(this.alpha_filter=n,n.transparency_icon.addClass("active").show()),n.name===r&&(this.height_filter=n,n.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in i&&i.visible&&this.parent_div.show()}if(0!==this.filters.length){var d=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(d).click(function(){c.run_on_dataset()})}};r(d.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},i=[],n=0;n<this.filters.length;n++)t=this.filters[n],i.push(t.to_dict());return e.filters=i,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new d(t),i=0;i<this.filters.length;i++)e.add_filter(this.filters[i].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,i,n=(function(t,e,i){return e in t||(t[e]=i),t[e]}),a={},r=0;r<this.filters.length;r++)e=this.filters[r],e.tool_id&&(e.min!==e.low&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(i=n(a,e.tool_id,[]),i[i.length]=e.tool_exp_name+" <= "+e.high));var s=[];for(var o in a)s[s.length]=[o,a[o]];!function e(i,n){var a=n[0],r=a[0],s=a[1],o="("+s.join(") and (")+")",l={cond:o,input:i,target_dataset_id:i,tool_id:r};n=n.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+r,buttons:{Close:Galaxy.modal.hide()}}):0===n.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,n)})}(this.track.dataset_id,s)}}),e.default={FiltersManager:d,NumberFilter:l}}).call(e,i(0))},function(t,e,i){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var n=i(13),a=function(t){return t&&t.__esModule?t:{default:t}}(n),r=i(152),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),o=a.default.GenomeDataManager.extend({load_data:function(e,i,n,a){var r=t.Deferred();this.set_data(e,r);var o=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(s.makeBwg(o)).then(function(i,n){t.when(i.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var i=[],n={max:Number.MIN_VALUE};t.forEach(function(t){n.max!==t.min-1&&(i.push([n.max+1,0]),i.push([t.min-2,0])),i.push([t.min-1,t.score]),i.push([t.max,t.score]),n=t});var a={data:i,region:e,dataset_type:"bigwig"};l.set_data(e,a),r.resolve(a)})}),r}});e.default={BBIDataManager:o}}).call(e,i(0))},function(t,e,i){(function(n){var a,r;a=[i(153),i(154),i(155)],void 0!==(r=function(t,e){"use strict";function i(){}function a(t){t&&(this.id=t)}function r(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function s(t,e,i){Math.pow(10,6);return n.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(i-1)))},xhrFields:{responseType:"arraybuffer"}})}function o(t,e){return t[e]+t[e+1]*y+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function d(t,e,i,n){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=i,this.isSummary=n}function c(t){var e=n.Deferred(),i=new l;return i.url=t,n.when(s(i.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var a=t,r=new Uint8Array(a),s=new Int16Array(a),l=new Int32Array(a),d=r[0]+y*r[1]+x*r[2]+k*r[3];if(d==v)i.type="bigwig";else{if(d!=b)return d==g||d==w?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+d.toString(16));i.type="bigbed"}i.version=s[2],i.numZoomLevels=s[3],i.chromTreeOffset=o(r,8),i.unzoomedDataOffset=o(r,16),i.unzoomedIndexOffset=o(r,24),i.fieldCount=s[16],i.definedFieldCount=s[17],i.asOffset=o(r,36),i.totalSummaryOffset=o(r,44),i.uncompressBufSize=l[13],i.extHeaderOffset=o(r,56),i.zoomLevels=[];for(var c=0;c<i.numZoomLevels;++c){var u=l[6*c+16],h=o(r,24*c+72),f=o(r,24*c+80);i.zoomLevels.push({reduction:u,dataOffset:h,indexOffset:f})}n.when(i.readChromTree()).then(function(){i.getAutoSQL(function(t){return i.schema=t,e.resolve(i)})})}),e}function u(t,e,i,n,a){this.bbi=t,this.type=e,this.fieldCount=i,this.offset=n,this.field=a}var h=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,m=e.arrayCopy,v=2291137574,g=654086024,b=2273964779,w=3958540679,y=256,x=65536,k=16777216,C=4294967296,$=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),n.when(s(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var i=new Uint8Array(e),n=new Int16Array(e),a=new Int32Array(e),r=(a[0],a[1],a[2]),s=(a[3],o(i,16),function(e){var a=i[e],l=n[e/2+1];e+=4;for(var d=0;d<l;++d)if(0===a){e+=r;var c=o(i,e);e+=8,c-=t.chromTreeOffset,s(c)}else{for(var u="",h=0;h<r;++h){var f=i[e++];0!==f&&(u+=String.fromCharCode(f))}var p=i[e+3]<<24|i[e+2]<<16|i[e+1]<<8|i[e+0];i[e+7],i[e+6],i[e+5],i[e+4],e+=8,t.chromsToIDs[u]=p,0===u.indexOf("chr")&&(t.chromsToIDs[u.substr(3)]=p),t.idsToChroms[p]=u,t.maxID=Math.max(t.maxID,p)}});s(32)})},d.prototype.readWigData=function(t,e,i){var n=this.bwg.chromsToIDs[t];return void 0===n?[]:this.readWigDataById(n,e,i)},d.prototype.readWigDataById=function(t,e,i){var a=this,r=n.Deferred();if(!this.cirHeader)return n.when(s(a.bwg.url,this.cirTreeOffset,48)).then(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],n.when(a.readWigDataById(t,e,i)).then(function(t){r.resolve(t)})}),r;var l=[],d=0,c=(Date.now(),function(n,a,r,s){return(t<0||n==t)&&a<=i&&r>=e}),u=function(t,e){if(a.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),d+=t.length,1==t.length&&t[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,e),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}));for(var i,s=4+32*a.cirBlockSize,o=0;o<t.length;++o){var u=new h(t[o],t[o]+s);i=i?f(i,u):u}for(var m=i.ranges(),v=0;v<m.length;++v){var g=m[v];p(t,g,e)}},p=function(t,e,i,o){e.max(),e.min();n.when(s(a.bwg.url,e.min(),e.max()-e.min())).then(function(s){for(var o=0;o<t.length;++o)e.contains(t[o])&&(_(s,t[o]-e.min(),i),t[o]-a.cirTreeOffset==48&&t[o]-e.min()==0&&(a.cachedCirRoot=s),0===--d&&n.when(a.fetchFeatures(c,l)).then(function(t){r.resolve(t)}))})},_=function(n,a,r){var s=new Uint8Array(n),d=new Int16Array(n),c=new Int32Array(n),h=s[a],f=d[a/2+1];if(a+=4,0!==h)for(var p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16),y=o(s,a+24);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&l.push({offset:w,size:y}),a+=32}else{for(var x=[],p=0;p<f;++p){var _=a/4,m=c[_],v=c[_+1],g=c[_+2],b=c[_+3],w=o(s,a+16);(t<0||m<t||m==t&&v<=i)&&(t<0||g>t||g==t&&b>=e)&&x.push(w),a+=24}x.length>0&&u(x,r+1)}};return u([a.cirTreeOffset+48],1),r},d.prototype.fetchFeatures=function(t,e){var a=this,r=n.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var o=[],l=function(t,e,n,r){r||(r={});var s=new i;s._chromId=t,s.segment=a.bwg.idsToChroms[t],s.min=e,s.max=n,s.type=a.bwg.type;for(var l in r)s[l]=r[l];o.push(s)},d=function(){if(0===e.length){Date.now();return r.resolve(o)}var i=e[0];if(i.data)a.parseFeatures(i.data,l,t),e.splice(0,1),d();else{for(var c=i.offset,u=i.size,h=1;h<e.length&&e[h].offset==c+u;)u+=e[h].size,++h;n.when(s(a.bwg.url,c,u)).then(function(t){for(var i=0,n=0;i<u;){var r,s=e[n];if(a.bwg.uncompressBufSize>0)r=_(t,i+2,s.size-2);else{var o=new Uint8Array(s.size);m(new Uint8Array(t,i,s.size),0,o,0,s.size),r=o.buffer}s.data=r,i+=s.size,++n}d()})}};return d(),r},d.prototype.parseFeatures=function(t,e,i){var r=new Uint8Array(t);if(this.isSummary)for(var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),d=t.byteLength/32,c=0;c<d;++c){var u=o[8*c],_=o[8*c+1],m=o[8*c+2],v=o[8*c+3],g=(l[8*c+4],l[8*c+5]),b=l[8*c+6];l[8*c+7];if(i(u,_+1,m)){var w={type:"bigwig",score:b/v,maxScore:g};"bigbed"==this.bwg.type&&(w.type="density"),e(u,_+1,m,w)}}else if("bigwig"==this.bwg.type){var s=new Int16Array(t),o=new Int32Array(t),l=new Float32Array(t),u=o[0],y=o[1],x=(o[2],o[3]),k=o[4],C=r[20],d=s[11];if(3==C)for(var c=0;c<d;++c){var T=l[c+6],S=y+c*x+1,M=y+c*x+k;i(u,S,M)&&e(u,S,M,{score:T})}else if(2==C)for(var c=0;c<d;++c){var _=o[2*c+6]+1,m=_+k-1,T=l[2*c+7];i(u,_,m)&&e(u,_,m,{score:T})}else if(1==C)for(var c=0;c<d;++c){var _=o[3*c+6]+1,m=o[3*c+7],T=l[3*c+8];_>m&&(_=m),i(u,_,m)&&e(u,_,m,{score:T})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var O=0,A=this.bwg.definedFieldCount,E=this.bwg.schema;O<r.length;){var u=r[O+3]<<24|r[O+2]<<16|r[O+1]<<8|r[O+0],_=r[O+7]<<24|r[O+6]<<16|r[O+5]<<8|r[O+4],m=r[O+11]<<24|r[O+10]<<16|r[O+9]<<8|r[O+8];O+=12;for(var z="";;){var R=r[O++];if(0==R)break;z+=String.fromCharCode(R)}var P,j={};if(P=z.length>0?z.split("\t"):[],P.length>0&&A>3&&(j.label=P[0]),P.length>1&&A>4){var T=parseInt(P[1]);isNaN(T)||(j.score=T)}if(P.length>2&&A>5&&(j.orientation=P[2]),P.length>5&&A>8){var q=P[5];$.test(q)&&(j.itemRgb="rgb("+q+")")}if(P.length>A-3&&E)for(var D=A-3;D<P.length;++D)j[E.fields[D+3].name]=P[D];if(i(u,_+1,m,P))if(A<12)e(u,_+1,m,j);else{var B=0|P[3],V=0|P[4],I=0|P[6],N=P[7].split(","),L=P[8].split(",");if(j.exonFrames){var G=j.exonFrames.split(",");j.exonFrames=void 0}j.type="transcript";var U=new a;for(var F in j)U[F]=j[F];if(U.id=P[0],U.segment=this.bwg.idsToChroms[u],U.min=_+1,U.max=m,U.notes=[],j.groups=[U],P.length>9){var H=j.geneName||P[9],Y=H;P.length>10&&(Y=P[10]),j.geneName2&&(Y=j.geneName2);var X=n.extend({},U);X.id=H,X.label=Y,X.type="gene",j.groups.push(X)}for(var J=[],W=0;W<I;++W){var K=(0|L[W])+_,Z=K+(0|N[W]),Q=new h(K,Z);J.push(Q)}for(var tt=f(J),et=tt.ranges(),it=0;it<et.length;++it){var nt=et[it];e(u,nt.min()+1,nt.max(),j)}if(V>B){var at="+"==j.orientation?new h(B,V+3):new h(B-3,V),rt=p(tt,at);if(rt){j.type="translation";for(var st=rt.ranges(),ot=0,lt=0;st[0].min()>et[lt].max();)lt++;for(var it=0;it<st.length;++it){var dt=it;"-"==j.orientation&&(dt=st.length-it-1);var nt=st[dt];if(j.readframe=ot,G){var ct=parseInt(G[dt+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(j.readframe=ct,j.readframeExplicit=!0)}var ut=nt.max()-nt.min();ot=(ot+ut)%3,e(u,nt.min()+1,nt.max(),j)}}}}}}},d.prototype.getFirstAdjacent=function(t,e,i,n){var a=this.bwg.chromsToIDs[t];if(void 0===a)return n([]);this.getFirstAdjacentById(a,e,i,n)},d.prototype.getFirstAdjacentById=function(t,e,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(r){a.cirHeader=r;var s=new Int32Array(a.cirHeader);a.cirBlockSize=s[1],a.getFirstAdjacentById(t,e,i,n)});var r=null,s=-1,l=-1,d=0,c=(Date.now(),function(t,e){d+=t.length;for(var i,n=4+32*a.cirBlockSize,r=0;r<t.length;++r){var s=new h(t[r],t[r]+n);i=i?f(i,s):s}for(var o=i.ranges(),l=0;l<o.length;++l){var c=o[l];u(t,c,e)}}),u=function(s,o,l,c){o.max(),o.min();a.bwg.data.slice(o.min(),o.max()-o.min()).fetch(function(c){for(var u=0;u<s.length;++u)if(o.contains(s[u])&&(p(c,s[u]-o.min(),l),0==--d)){if(!r)return i>0&&(0!=t||e>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(t!=a.bwg.maxID||e<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,r,s){return i<0&&(n<t||r<e)||i>0&&(n>t||a>e)},[r],function(t){for(var e=null,a=-1,r=-1,s=0;s<t.length;++s){var o=t[s],l=o._chromId,d=o.min,c=o.max;(null==e||i<0&&(l>a||c>r)||i>0&&(l<a||d<r))&&(e=o,r=i<0?c:d,a=l)}return n(null!=e?[e]:[])})}})},p=function(n,d,u){var h=new Uint8Array(n),f=new Int16Array(n),p=new Int32Array(n),_=h[d],m=f[d/2+1];if(d+=4,0!=_)for(var v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=o(h,d+16),C=o(h,d+24);(i<0&&(b<t||b==t&&w<=e)||i>0&&(y>t||y==t&&x>=e))&&(/_random/.exec(a.bwg.idsToChroms[b])||(null==r||i<0&&(y>s||y==s&&x>l)||i>0&&(b<s||b==s&&w<l))&&(r={offset:k,size:C},l=i<0?x:w,s=i<0?y:b)),d+=32}else{for(var $=-1,T=-1,v=0;v<m;++v){var g=d/4,b=p[g],w=p[g+1],y=p[g+2],x=p[g+3],k=p[g+4]<<32|p[g+5];(i<0&&(b<t||b==t&&w<=e)&&y>=t||i>0&&(y>t||y==t&&x>=e)&&b<=t)&&($<0||x>T)&&($=k,T=i<0?x:w,i<0?y:b),d+=24}$>=0&&c([$],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,i){var n,a=i-e;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var r=0;r<this.zoomLevels.length;r++)if(a/this.zoomLevels[r].reduction<25e3){n=this.getZoomedView(r);break}return n.readWigData(t,e,i)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new d(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new d(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,i,n,a){var r=this;if(!(t>=this.zoomLevels.length-1)){var s;return s=t<0?this.getUnzoomedView():this.getZoomedView(t),s.readWigDataById(e,i,n,a)}if(this.topLevelReductionCache){for(var o=[],l=this.topLevelReductionCache,d=0;d<l.length;++d)l[d]._chromId==e&&o.push(l[d]);return a(o)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(s){return r.topLevelReductionCache=s,r._tsFetch(t,e,i,n,a)})},l.prototype.thresholdSearch=function(t,e,i,n,a){function r(){if(0==l.length)return a(null);l.sort(function(t,e){var n=t.zoom-e.zoom;return 0!=n?n:(n=t.chrOrd-e.chrOrd,0!=n?n:t.min-e.min*i)});var t=l.splice(0,1)[0];s._tsFetch(t.zoom,t.chr,t.min,t.max,function(s){var o=i>0?0:3e8;t.fromRef&&(o=e);for(var d=0;d<s.length;++d){var c,u=s[d];if(c=void 0!=u.maxScore?u.maxScore:u.score,i>0){if(c>n)if(t.zoom<0){if(u.min>o)return a(u)}else u.max>o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}else if(c>n)if(t.zoom<0){if(u.max<o)return a(u)}else u.min<o&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:u.min,max:u.max,fromRef:t.fromRef})}r()})}i=i<0?-1:1;for(var s=this,o=this.chromsToIDs[t],l=[{chrOrd:0,chr:o,zoom:s.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],d=1;d<=this.maxID+1;++d){var c=(o+i*d)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:d,chr:c,zoom:s.zoomLevels.length-1,min:0,max:3e8})}r()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);n.when(s(this.url,this.asOffset,2048)).then(function(e){for(var i=new Uint8Array(e),n="",a=0;a<i.length&&0!=i[a];++a)n+=String.fromCharCode(i[a]);var r=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,s=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,o=r.exec(n);if(o){var l={declType:o[1],name:o[2],comment:o[4],fields:[]};n=n.substring(o[0]);for(var d=s.exec(n);null!=d;d=s.exec(n))l.fields.push({type:d[1],name:d[2],comment:d[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return 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t||(t=c),i&&(i=!1),this.istate=new e,this.istate.inflateInit(this,i?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var i,n;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,i=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=p)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<<t.istate.wbits&&(a=(1<<t.istate.wbits)-1,n=i-a),t.istate.blocks.set_dictionary(e,n,a),t.istate.mode=7,f)};var T=[0,0,255,255];e.prototype.inflateSync=function(t){var e,i,n,a,r;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(i=t.next_in_index,n=t.istate.marker;0!=e&&n<4;)t.next_in[i]==T[n]?n++:n=0!=t.next_in[i]?0:4-n,i++,e--;return t.total_in+=i-t.next_in_index,t.next_in_index=i,t.avail_in=e,t.istate.marker=n,4!=n?-3:(a=t.total_in,r=t.total_out,this.inflateReset(t),t.total_in=a,t.total_out=r,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var S=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];i.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},i.prototype.proc=function(t,e){var i,n,a,o,l,d,c;for(o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d;;)switch(this.mode){case v:for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}switch(i=7&n,this.last=1&i,i>>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],g=[];r(u,h,_,g,t),this.codes.init(u[0],h[0],_[0],0,g[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if((~n>>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);if(0==c&&(d==end&&0!=read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c&&(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,d==this.end&&0!=this.read&&(d=0,c=d<this.read?this.read-d-1:this.end-d),0==c)))return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(e=f,i=this.left,i>l&&(i=l),i>c&&(i=c),s(t.next_in,o,this.window,d,i),o+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:v;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(this.table=i=16383&n,(31&i)>29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length<i)this.blens=new Int32Array(i);else for(var b=0;b<i;b++)this.blens[b]=0;n>>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}this.blens[S[this.index++]]=7&n,n>>>=3,a-=3}for(;this.index<19;)this.blens[S[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,write=d,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var b,w,y;for(i=this.bb[0];a<i;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(i=this.hufts[3*(this.tb[0]+(n&m[i]))+1],(y=this.hufts[3*(this.tb[0]+(n&m[i]))+2])<16)n>>>=i,a-=i,this.blens[this.index++]=y;else{for(b=18==y?7:y-14,w=18==y?11:3;a<i+b;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[o++])<<a,a+=8}if(n>>>=i,a-=i,w+=n&m[b],n>>>=b,a-=b,b=this.index,i=this.table,b+w>258+(31&i)+(i>>5&31)||16==y&&b<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);y=16==y?this.blens[b-1]:0;do{this.blens[b++]=y}while(0!=--w);this.index=b}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),g=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,g,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,g[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),o=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=d<this.read?this.read-d-1:this.end-d,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=d,e=this.inflate_flush(t,e),d=this.write,c=d<this.read?this.read-d-1:this.end-d,this.read!=this.write)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e);default:return e=-2,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=o-t.next_in_index,t.next_in_index=o,this.write=d,this.inflate_flush(t,e)}},i.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},i.prototype.set_dictionary=function(t,e,i){s(t,e,window,0,i),this.read=this.write=i},i.prototype.sync_point=function(){return 1==this.mode},i.prototype.inflate_flush=function(t,e){var i,n,a;return n=t.next_out_index,a=this.read,i=(a<=this.write?this.write:this.end)-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==_&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),s(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,s){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,s,o,l,d,c=0,u=0,h=0;for(h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o;;)switch(this.mode){case 0:if(l>=258&&s>=10&&(t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,s=e.avail_in,c=t.bitb,u=t.bitk,o=t.write,l=o<t.read?t.read-o-1:t.end-o,i!=f)){this.mode=i==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>>=this.tree[a+1],u-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 2:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.len+=c&m[n],c>>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}if(a=3*(this.tree_index+(c&m[n])),c>>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 4:for(n=this.get;u<n;){if(0==s)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,s--,c|=(255&e.next_in[h++])<<u,u+=8}this.dist+=c&m[n],c>>=n,u-=n,this.mode=5;case 5:for(d=o-this.dist;d<0;)d+=t.end;for(;0!=this.len;){if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);t.window[o++]=t.window[d++],l--,d==t.end&&(d=0),this.len--}this.mode=0;break;case 6:if(0==l&&(o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l&&(t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,o==t.end&&0!=t.read&&(o=0,l=o<t.read?t.read-o-1:t.end-o),0==l)))return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);i=f,t.window[o++]=this.lit,l--,this.mode=0;break;case 7:if(u>7&&(u-=8,s++,h--),t.write=o,i=t.inflate_flush(e,i),o=t.write,l=o<t.read?t.read-o-1:t.end-o,t.read!=t.write)return t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);this.mode=8;case 8:return i=p,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);case 9:return i=-3,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i);default:return i=-2,t.bitb=c,t.bitk=u,e.avail_in=s,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=o,t.inflate_flush(e,i)}},n.prototype.free=function(t){},n.prototype.inflate_fast=function(t,e,i,n,a,r,o,l){var d,c,u,h,_,v,g,b,w,y,x,k,C,$,T,S;g=l.next_in_index,b=l.avail_in,_=o.bitb,v=o.bitk,w=o.write,y=w<o.read?o.read-w-1:o.end-w,x=m[t],k=m[e];do{for(;v<20;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if(d=_&x,c=i,u=n,S=3*(u+d),0!=(h=c[S]))for(;;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15,C=c[S+2]+(_&m[h]),_>>=h,v-=h;v<15;)b--,_|=(255&l.next_in[g++])<<v,v+=8;for(d=_&k,c=a,u=r,S=3*(u+d),h=c[S];;){if(_>>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15;v<h;)b--,_|=(255&l.next_in[g++])<<v,v+=8;if($=c[S+2]+(_&m[h]),_>>=h,v-=h,y-=C,w>=$)T=w-$,o.window[w++]=o.window[T++],o.window[w++]=o.window[T++],C-=2;else{T=w-$;do{T+=o.end}while(T<0);if(h=o.end-T,C>h){if(C-=h,w-T>0&&h>w-T)do{o.window[w++]=o.window[T++]}while(0!=--h);else s(o.window,T,o.window,w,h),w+=h,T+=h,h=0;T=0}}do{o.window[w++]=o.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3;d+=c[S+2],d+=_&m[h],S=3*(u+d),h=c[S]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,p):(l.msg="invalid literal/length code",C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,-3);if(d+=c[S+2],d+=_&m[h],S=3*(u+d),0==(h=c[S])){_>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--;break}}else _>>=c[S+1],v-=c[S+1],o.window[w++]=c[S+2],y--}while(y>=258&&b>=10);return C=l.avail_in-b,C=v>>3<C?v>>3:C,b+=C,g-=C,v-=C<<3,o.bitb=_,o.bitk=v,l.avail_in=b,l.total_in+=g-l.next_in_index,l.next_in_index=g,o.write=w,f},a.prototype.huft_build=function(t,e,i,n,a,r,o,l,d,c,h){var p,m,v,g,b,w,y,x,k,C,$,T,S,M,O;C=0,b=i;do{this.c[t[e+C]]++,C++,b--}while(0!=b);if(this.c[0]==i)return o[0]=-1,l[0]=0,f;for(x=l[0],w=1;w<=15&&0==this.c[w];w++);for(y=w,x<w&&(x=w),b=15;0!=b&&0==this.c[b];b--);for(v=b,x>b&&(x=b),l[0]=x,M=1<<w;w<b;w++,M<<=1)if((M-=this.c[w])<0)return-3;if((M-=this.c[b])<0)return-3;for(this.c[b]+=M,this.x[1]=w=0,C=1,S=2;0!=--b;)this.x[S]=w+=this.c[C],S++,C++;b=0,C=0;do{0!=(w=t[e+C])&&(this.v[this.x[w]++]=b),C++}while(++b<i);for(i=this.x[v],this.x[0]=b=0,C=0,g=-1,T=-x,this.u[0]=0,$=0,O=0;y<=v;y++)for(p=this.c[y];0!=p--;){for(;y>T+x;){if(g++,T+=x,O=v-T,O=O>x?x:O,(m=1<<(w=y-T))>p+1&&(m-=p+1,S=y,w<O))for(;++w<O&&!((m<<=1)<=this.c[++S]);)m-=this.c[S];if(O=1<<w,this.hn[0]+O>u)return-3;this.u[g]=$=this.hn[0],this.hn[0]+=O,0!=g?(this.x[g]=b,this.r[0]=w,this.r[1]=x,w=b>>>T-x,this.r[2]=$-this.u[g-1]-w,s(this.r,0,d,3*(this.u[g-1]+w),3)):o[0]=$}for(this.r[1]=y-T,C>=i?this.r[0]=192:h[C]<n?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=r[this.v[C]-n]+16+64,this.r[2]=a[this.v[C++]-n]),m=1<<y-T,w=b>>>T;w<O;w+=m)s(this.r,0,d,3*($+w),3);for(w=1<<y-1;0!=(b&w);w>>>=1)b^=w;for(b^=w,k=(1<<T)-1;(b&k)!=this.x[g];)g--,T-=x,k=(1<<T)-1}return 0!=M&&1!=v?_:f},a.prototype.inflate_trees_bits=function(t,e,i,n,a){var r;return this.initWorkArea(19),this.hn[0]=0,r=this.huft_build(t,0,19,19,null,null,i,e,n,this.hn,this.v),-3==r?a.msg="oversubscribed dynamic bit lengths tree":r!=_&&0!=e[0]||(a.msg="incomplete dynamic bit lengths tree",r=-3),r},a.prototype.inflate_trees_dynamic=function(t,e,i,n,a,r,s,o,l){var d;return this.initWorkArea(288),this.hn[0]=0,(d=this.huft_build(i,0,t,257,x,k,r,n,o,this.hn,this.v))!=f||0==n[0]?(-3==d?l.msg="oversubscribed literal/length tree":-4!=d&&(l.msg="incomplete literal/length tree",d=-3),d):(this.initWorkArea(288),d=this.huft_build(i,t,e,0,C,$,s,a,o,this.hn,this.v),d!=f||0==a[0]&&t>257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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diff --git a/static/scripts/bundled/viz.bundled.js b/static/scripts/bundled/viz.bundled.js
index 0f59d328a43..f239a48d79b 100644
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dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:e.tooltip,placement:"bottom"}).off("click").on("click",function(t){i(".tooltip").hide(),t.preventDefault(),e.onclick&&e.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.removeClass().addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=i("<ul/>").addClass("menu dropdown-menu").addClass("pull-"+t.model.get("pull")).attr("role","menu"),this.$el.append(this.$menu)),this.collection.each(function(e){var n=e.attributes;if(n.visible){var r=i("<a/>").addClass("dropdown-item").attr({href:n.href,target:n.target}).append(i("<i/>").addClass("fa").addClass(n.icon).css("display",n.icon?"inline-block":"none")).append(n.title).on("click",function(t){n.onclick&&(t.preventDefault(),n.onclick())});t.$menu.append(i("<li/>").append(r)),n.divider&&t.$menu.append(i("<li/>").addClass("divider"))}})},addMenu:function(t){this.collection.add(a.default.merge(t,{title:"",target:"",href:"",onclick:null,divider:!1,visible:!0,icon:null,cls:"button-menu btn-group"}))}});e.default={ButtonDefault:o,ButtonLink:s,ButtonIcon:u,ButtonCheck:l,ButtonMenu:c}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return 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e=[];a.$("input.grid-row-select-checkbox[name=id]:checked").each(function(){window.console.log(t(this).val()),e[e.length]=t.ajax({url:Galaxy.root+"api/datasets/"+t(this).val(),dataType:"json",data:{data_type:"track_config",hda_ldda:"histories"==a.current()?"hda":"ldda"}})}),t.when.apply(t,e).then(function(){var e=arguments[0]instanceof Array?t.map(arguments,function(t){return t[0]}):[arguments[0]];n(e)}),Galaxy.modal.hide()}}})},b=function(t){this.default_font=void 0!==t?t:"9px Monaco, Lucida Console, 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e=this.attributes.obj_cache,n=this.attributes.key_ary,i=t.toString(),r=o.indexOf(n,function(t){return t.toString()===i});return-1!==r&&(e[i].stale?(n.splice(r,1),delete e[i]):this.move_key_to_end(t,r)),e[i]},set_elt:function(t,e){var n=this.attributes.obj_cache,i=this.attributes.key_ary,r=t.toString(),a=this.attributes.num_elements;if(!n[r]){if(i.length>=a){delete n[i.shift().toString()]}i.push(t)}return n[r]=e,e},move_key_to_end:function(t,e){this.attributes.key_ary.splice(e,1),this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=w.extend({defaults:o.extend({},w.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){w.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;o.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),n=t.Deferred(),i="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",r=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:i},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(r.go()).then(function(t){n.resolve("ok"===t||"data"===t)}),n},search_features:function(e){var n=this.get("dataset"),i={query:e,hda_ldda:n.get("hda_ldda"),data_type:"features"};return t.getJSON(n.url(),i)},load_data:function(e,n,i,r){var a=this.get("dataset"),o={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:n,resolution:i,hda_ldda:a.get("hda_ldda")};t.extend(o,r);var s=this.get("filters_manager");if(s){for(var l=[],u=s.filters,c=0;c<u.length;c++)l.push(u[c].name);o.filter_cols=JSON.stringify(l)}var h=this,d=t.getJSON(a.url(),o,function(t){t.region=e,h.set_data(e,t)});return this.set_data(e,d),d},get_data:function(t,e,n,i){var r=this.get_elt(t);if(r&&(c.default.is_deferred(r)||this.get("data_mode_compatible")(r,e)))return r;for(var a,o,s=this.get("key_ary"),l=this.get("obj_cache"),u=0;u<s.length;u++)if(a=s[u],a.contains(t)&&(o=!0,r=l[a.toString()],c.default.is_deferred(r)||this.get("data_mode_compatible")(r,e)&&this.get("can_subset")(r))){if(this.move_key_to_end(a,u),!c.default.is_deferred(r)){var h=this.subset_entry(r,t);this.set_data(t,h),r=h}return r}if(!o&&t.length()<this.attributes.min_region_size){t=t.copy();var d=this.most_recently_added();!d||t.get("start")>d.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,n,i)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,n,i,r,a){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,n))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");a===this.DEEP_DATA_REQ?t.extend(r,{start_val:o.data.length+1}):a===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),u=this,c=this.load_data(l,n,i,r),h=t.Deferred();return this.set_data(e,h),t.when(c).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),u.set_data(e,t),h.resolve(t)}),h},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,n,i,r){var a=this._mark_stale(t);return a?(r||(r={}),"bigwig"===a.dataset_type&&(r.num_samples=1e3*i),this.load_data(t,e,n,r)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var n=this,i=!0,r=o.map(e.get("chroms_info").chrom_info,function(t){var e=n.get_elt(new M({chrom:t.chrom,start:0,end:t.len}));return e||(i=!1),e});if(i)return r;var a=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){n.add_data(t.data),a.resolve(t.data)}),a},subset_entry:function(t,e){var n={bigwig:function(t,e){return o.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,n){var i=n.get("start")-t.region.get("start");return t.data.slice(i,i+n.length())}},i=t.data;return!t.region.same(e)&&t.dataset_type in n&&(i=n[t.dataset_type](t.data,e)),{region:e,data:i,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new i.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,n,i){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,n,i):{data:null,region:t}}}),C=i.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=o.find(this.get_chroms_info(),function(e){return e.chrom===t});return new M({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return o.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),M=i.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),n=e[0],i=e[1].split("-");this.set({chrom:n,start:parseInt(i[0],10),end:parseInt(i[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new M({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),n=t.get("chrom"),i=this.get("start"),r=t.get("start"),a=this.get("end"),o=t.get("end");return e&&n&&e!==n?M.overlap_results.DIF_CHROMS:i<r?a<r?M.overlap_results.BEFORE:a<o?M.overlap_results.OVERLAP_START:M.overlap_results.CONTAINS:i>r?i>o?M.overlap_results.AFTER:a<=o?M.overlap_results.CONTAINED_BY:M.overlap_results.OVERLAP_END:a>=o?M.overlap_results.CONTAINS:M.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===M.overlap_results.CONTAINS},overlaps:function(t){return 0===o.intersection([this.compute_overlap(t)],[M.overlap_results.DIF_CHROMS,M.overlap_results.BEFORE,M.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=i.Collection.extend({model:M}),T=i.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new M(t.region))}}),$=i.Collection.extend({model:T}),A=i.Model.extend(m).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var n=this.get("preloaded_data");n=n?n.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:n}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===o.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),E=i.Collection.extend({model:A}),O=i.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),z=O.extend(m).extend({defaults:o.extend({},O.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new E(t.tracks));var e=[];this.set("config",d.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs)),this.unset("tracks"),this.get("drawables").each(function(t){t.unset("preloaded_data")})},add_tracks:function(t){this.get("drawables").add(t)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(t,e){return{obj_type:"View",prefs:{name:e.get("title"),content_visible:!0},drawables:e.get("drawables")}}}}),R=i.Router.extend({initialize:function(t){this.view=t.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var e=this;e.view.on("navigate",function(t){e.navigate(t)})},change_location:function(t){this.view.go_to(t)}});e.default={BackboneTrack:A,BrowserBookmark:T,BrowserBookmarkCollection:$,Cache:w,CanvasManager:b,Genome:C,GenomeDataManager:x,GenomeRegion:M,GenomeRegionCollection:S,GenomeVisualization:z,GenomeReferenceDataManager:k,TrackBrowserRouter:R,Visualization:O,select_datasets:y}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,n){function i(t){t+="";for(var e=/(\d+)(\d{3})/;e.test(t);)t=t.replace(e,"$1,$2");return t}Object.defineProperty(e,"__esModule",{value:!0});var r=function(t){return"promise"in t},a=t.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(t){return!0}},go:function(){var t=n.Deferred(),e=this,i=e.get("ajax_settings"),r=e.get("success_fn"),a=e.get("interval");return function e(){n.ajax(i).success(function(n){r(n)?t.resolve(n):setTimeout(e,a)})}(),t}}),o=function(t){t||(t="#ffffff"),"string"==typeof t&&(t=[t]);for(var 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this.attributes.metadata.get(t)},urlRoot:Galaxy.root+"api/datasets"}),d=h.extend({defaults:i.extend({},h.prototype.defaults,{chunk_url:null,first_data_chunk:null,offset:0,at_eof:!1}),initialize:function(t){h.prototype.initialize.call(this),this.attributes.first_data_chunk&&(this.attributes.offset=this.attributes.first_data_chunk.offset),this.attributes.chunk_url=Galaxy.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=Galaxy.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var t=this,e=r.Deferred();return r.getJSON(this.attributes.chunk_url,{offset:t.attributes.offset}).success(function(n){var i;""!==n.ck_data?(i=n,t.attributes.offset=n.offset):(t.attributes.at_eof=!0,i=null),e.resolve(i)}),e}}),f=t.Collection.extend({model:h}),p=t.View.extend({initialize:function(t){this.row_count=0,this.loading_chunk=!1,new 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u.append(i("<input />").attr("id",r).attr("name",r).val(s));e.help&&u.append(i("<div class='help'/>").text(e.help))}}),this},render_in_modal:function(t){var e=this,n=function(){Galaxy.modal.hide(),i(window).unbind("keypress.check_enter_esc")},r=function(){Galaxy.modal.hide(),i(window).unbind("keypress.check_enter_esc"),e.update_from_form()},a=function(t){27===(t.keyCode||t.which)?n():13===(t.keyCode||t.which)&&r()};i(window).bind("keypress.check_enter_esc",a),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:t||"Configure",body:this.$el,buttons:{Cancel:n,OK:r}})},update_from_form:function(){var t=this;this.collection.each(function(e,n){if(!e.get("hidden")){var i="param_"+n,r=t.$el.find("#"+i).val();"bool"===e.get("type")&&(r=t.$el.find("#"+i).is(":checked")),e.set_value(r)}})}});e.default={ConfigSetting:c,ConfigSettingCollection:h,ConfigSettingCollectionView:d}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return 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n=e.pageY,r=t.$select.height();t.minHeight=t.minHeight||r,i("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(r+(e.pageY-n),t.minHeight))}).on("mouseup mouseleave",function(){i("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=i("<div/>")).append(this.$dropdown=i("<div/>")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,!this.model.get("multiple")||this.model.get("individual")||this.model.get("readonly")||(this.all_button=new u.default.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&r.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),r.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],r.each(this.data,function(e,n){t.data2.push({order:n,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var n=t.model.get("pagesize"),i=r.filter(t.data2,function(n){var i=!1;return r.each(n.tags,function(n){t._match(e.term,n)&&(i=t.matched_tags[n]=!0)}),i||t._match(e.term,n.text)});e.callback({results:i.slice((e.page-1)*n,e.page*n),more:i.length>=e.page*n})},formatResult:function(e){return r.escape(e.text)+'<div class="ui-tags">'+r.reduce(e.tags,function(e,n){return t.matched_tags[n]?e+'&nbsp;<div class="label label-info">'+r.escape(n)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search 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t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(i.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return 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i("<div/>").addClass("ui-option").append(i("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(i("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),d={};d.View=h.extend({initialize:function(t){t.type="radio",h.prototype.initialize.call(this,t)}});var f={};f.View=h.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,h.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=i("<label/>").addClass("btn btn-default");return t.icon&&e.append(i("<i/>").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(i("<input/>").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return i("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),e.default={Base:c,BaseIcons:h,Radio:d,RadioButton:p,Checkbox:f}}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(3),o=r(a),s=n(11),l=r(s),u=n(4),c=r(u),h=t.View.extend({initialize:function(t){var e=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:t.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new 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n=i(this._templateRow({id:t.id,name:t.name}));n.on("click",function(){n.remove(),e._refresh()}),n.on("mouseover",function(){n.addClass("portlet-highlight")}),n.on("mouseout",function(){n.removeClass("portlet-highlight")}),this.portlet.append(n),this._refresh()}else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(t){this.select.update(t)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(t){return'<div class="ui-list"><div class="ui-margin-top"><span class="ui-list-button"/><span class="ui-list-select"/></div><div class="ui-list-message"/><div class="ui-list-portlet"/></div>'},_templateRow:function(t){return'<div id="'+t.id+'" class="ui-list-id"><span class="ui-list-delete fa fa-trash"/><span 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n=t.url_data||{};a.each(t.filters,function(t,e){n["f-"+e]=t}),r.ajax({url:t.url_base+"?"+r.param(n),success:function(n){n.embedded=t.embedded,n.filters=t.filters||{},e.init_grid(n)}})}else this.init_grid(t);else this.setElement("#grid-container"),this.init_grid(t);t.use_panels&&r("#center").css({padding:"10px",overflow:"auto"})},handle_refresh:function(t){t&&r.inArray("history",t)>-1&&window.top.Galaxy&&window.top.Galaxy.currHistoryPanel&&window.top.Galaxy.currHistoryPanel.loadCurrentHistory()},init_grid:function(t){this.grid.set(t);var e=this.grid.attributes;this.allow_title_display&&e.title&&l.default.setWindowTitle(e.title),this.handle_refresh(e.refresh_frames);var 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this.frame_list["#"+n(t).closest(".frame").attr("id")]},_frameDragStart:function(t){this._frameFocus(t,!0);var e=this._frameScreen(t);this._frameResize(this.frame_shadow,e),this._frameGrid(this.frame_shadow,t.grid_location),t.grid_location=null,this.frame_shadow.$el.show(),n(".f-cover").show()},_frameDragStop:function(t){this._frameFocus(t,!1);var e=this._frameScreen(this.frame_shadow);this._frameResize(t,e),this._frameGrid(t,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,this.frame_shadow.$el.hide(),n(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(t,e){var n="width"==t||"height"==t?1:-1;return"top"==t&&(e-=this.top),parseInt((e+n*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(t,e){var n="width"==t||"height"==t?1:-1,i=e*this.options.cell-n*this.options.margin;return"top"==t&&(i+=this.top),i},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var n=this.frame_list[e];if(null!==n.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,n.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(n(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;n(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var n=this.top-this.options.scroll*t;if(n=Math.max(n,this.top_max),n=Math.min(n,this.options.top_min),this.top!=n){for(var i in this.frame_list){var r=this.frame_list[i];if(null!==r.grid_location){var a={top:r.screen_location.top-(this.top-n),left:r.screen_location.left};this._frameOffset(r,a,e)}}this.top=n}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,r){var a=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),i.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),i.each(o,function(t){a._framePlace(t[0],r)}),this.top_max=0,i.each(this.frame_list,function(t){null!==t.grid_location&&(a.top_max=Math.max(a.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=n(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var n=this._toGrid(this._frameScreen(t)),i=!1,r=0;r<this.options.rows;r++){for(var a=0;a<Math.max(1,this.cols-n.width);a++)if(n.top=r,n.left=a,!this._isCollision(n)){i=!0;break}if(i)break}i?this._frameGrid(t,n,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,n){if(t.screen_location.left=e.left,t.screen_location.top=e.top,n){this._frameFocus(t,!0);var i=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){i._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,n){t.grid_location=e,this._frameOffset(t,this._toPixel(e),n),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:a}}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=function(t){return t&&t.__esModule?t:{default:t}}(r),o=t.View.extend({initialize:function(e){var n=this;this.model=e&&e.model||new t.Model({id:a.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var r=[];this.$text.on("change",function(){n.value(i(this).val())}).on("keyup",function(t){r[t.which]=!1}).on("keydown",function(t){var e=t.which;r[e]=!0,n.model.get("is_workflow")&&r[16]&&52==e?(n.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!r[16]||e>=96&&e<=105||(190==e||110==e)&&-1==i(this).val().indexOf(".")&&n.model.get("precise")||(189==e||109==e)&&-1==i(this).val().indexOf("-")||n._isParameter(i(this).val())||r[91]||r[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){n.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(3),o=r(a),s=n(23),l=r(s),u=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var n=this,r=t.isArray(e)?e:[e];i.each(r,function(t){var e=n.header_index[t];i.each(e,function(t){n._setState(t,!0)})})}},_setState:function(t,e){var n=this.$(".button-"+t),i=this.$(".subgroup-"+t);n.data("is_expanded",e),e?(i.show(),n.removeClass("fa-plus-square").addClass("fa-minus-square")):(i.hide(),n.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var n=t.find(".button-"+e);n.on("click",function(){i._setState(e,!n.data("is_expanded"))})}function n(r,a,s){s=s||[];for(var l in a){var u=a[l],c=u.options&&u.options.length>0,h=s.slice(0);i.header_index[u.value]=h.slice(0);var d=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");d.append(t("<div/>").append(p).append(i._templateOption({label:u.name,value:u.value}))),h.push(f),n(_,u.options,h),d.append(_),e(d,f)}else d.append(i._templateOption({label:u.name,value:u.value}));r.append(d)}}var i=this;this.header_index={};var r=t("<div/>");return n(r,this.model.get("data")),r},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:u}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i,r,a){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=n(3),l=o(s),u=n(4),c=(o(u),n(11)),h=o(c),d=n(49),f=o(d),p=n(50),_=o(p),g=n(51),v=o(g),m=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new v.default,this.setElement(i("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),r.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=a.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var n=this._addRow(t.test_param);n.model&&n.model.set("onchange",function(n){var i=e.app.data.matchCase(t,n);for(var r in t.cases){var a=t.cases[r],o=e.$("#"+t.id+"-section-"+r),s=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){s=!0;break}r==i&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var i in t.cases){var r=new m(this.app,{inputs:t.cases[i].inputs});this._append(r.$el.addClass("ui-form-section"),t.id+"-section-"+i)}n.trigger("change")},_addRepeat:function(t){function e(e){var r=t.id+"-section-"+i++,o=new m(n.app,{inputs:e});a.add({id:r,$el:o.$el,ondel:function(){a.del(r),n.app.trigger("change")}})}for(var n=this,i=0,a=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),n.app.trigger("change")}}),o=r.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&a.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:a});this._append(l.$el,t.id)},_addSection:function(t){var e=new h.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new m(this.app,{inputs:t.inputs}).$el),e.append(i("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,n=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",n)};var i=this.parameters.create(t);this.app.field_list[n]=i;var r=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:i});return this.app.element_list[n]=r,this._append(r.$el,t.id),i},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:m}}).call(e,n(1),n(0),n(2),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(11),u=a(l),c=n(4),h=a(c),d=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new h.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(i("<div/>").append(this.$list=i("<div/>")).append(i("<div/>").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new h.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),n=new u.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});n.append(t.$el),n.$el.addClass("section-row").hide(),this.list[t.id]=n,this.$list.append(n.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(i("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var n=this.list[e];n.title(++t+": "+this.options.title),n[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:d}}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,n,i){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,n){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=n&&n.field||new t.View,this.model=n&&n.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(n),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var i=this.model.get("collapsible_value");this.field.collapsed=void 0!==i&&JSON.stringify(this.model.get("value"))==JSON.stringify(i),this.listenTo(this.model,"change",this.render,this),this.render();var r=this;this.$collapsible.on("click",function(){r.field.collapsed=!r.field.collapsed,e.trigger&&e.trigger("change"),r.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){r.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){n(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(i.escape(this.model.get("text_value")));var r=this.model.get("error_text");if(this.$error[r?"show":"hide"](),this.$el[r?"addClass":"removeClass"]("ui-error"),this.$error_text.html(r),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return n("<div/>").addClass("ui-form-element").append(n("<div/>").addClass("ui-form-error ui-error").append(n("<span/>").addClass("fa fa-arrow-down")).append(n("<span/>").addClass("ui-form-error-text"))).append(n("<div/>").addClass("ui-form-title").append(n("<div/>").addClass("ui-form-collapsible").append(n("<i/>").addClass("ui-form-collapsible-icon")).append(n("<span/>").addClass("ui-form-collapsible-text"))).append(n("<span/>").addClass("ui-form-title-text"))).append(n("<div/>").addClass("ui-form-field").append(n("<span/>").addClass("ui-form-info")).append(n("<div/>").addClass("ui-form-backdrop"))).append(n("<div/>").addClass("ui-form-preview"))}})}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(4),u=a(l),c=n(52),h=a(c),d=n(53),f=a(d),p=n(54),_=a(p),g=n(55),v=a(g),m=n(57),y=a(m);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],n="function"==typeof this[e]?this[e].call(this,t):null;return n||(n=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),n.value(t.value),n},_fieldData:function(t){return new h.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],i.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var n=u.default.Select;switch(t.display){case"checkboxes":n=u.default.Checkbox;break;case"radio":n=u.default.Radio;break;case"radiobutton":n=u.default.RadioButton}return new n.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new u.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(r.isArray(t.value)){var e="";for(var n in t.value){if(e+=String(t.value[n]),!t.multiple)break;e+="\n"}t.value=e}return new u.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new u.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new u.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new u.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new y.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new v.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new u.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,n(1),n(2),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(4),u=a(l),c=n(22),h=a(c),d={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:d.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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Separate jobs will be triggered for each dataset selection."));this.$batch={linked:r.clone(),enabled:r.clone().append(i("<div/>").append(i("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(i("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,n.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&n.$el.removeClass("ui-dragover")}).on("drop",function(t){n._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple 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t=this;r.each(this.fields,function(e,n){t.model.get("current")==n?(e.$el.show(),r.each(t.$batch,function(e,i){e[t.config[n].batch==i?"show":"hide"]()}),t.button_type.value(n)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var n=t.model.get("data"),i=s.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],r.each(this.config,function(e,r){t.button_data.push({value:r,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new h.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||n&&n[e.src]&&n[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(i?i+" ":"")+(a[e.src]||"content")+" 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t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:d}}).call(e,n(1))},function(t,e,n){"use strict";(function(t){function i(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=i(r),o=n(24),s=i(o),l=t.View.extend({initialize:function(t){var 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e=[];a.$("input.grid-row-select-checkbox[name=id]:checked").each(function(){window.console.log(t(this).val()),e[e.length]=t.ajax({url:Galaxy.root+"api/datasets/"+t(this).val(),dataType:"json",data:{data_type:"track_config",hda_ldda:"histories"==a.current()?"hda":"ldda"}})}),t.when.apply(t,e).then(function(){var e=arguments[0]instanceof Array?t.map(arguments,function(t){return t[0]}):[arguments[0]];n(e)}),Galaxy.modal.hide()}}})},b=function(t){this.default_font=void 0!==t?t:"9px Monaco, Lucida Console, 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e=this.attributes.obj_cache,n=this.attributes.key_ary,i=t.toString(),r=o.indexOf(n,function(t){return t.toString()===i});return-1!==r&&(e[i].stale?(n.splice(r,1),delete e[i]):this.move_key_to_end(t,r)),e[i]},set_elt:function(t,e){var n=this.attributes.obj_cache,i=this.attributes.key_ary,r=t.toString(),a=this.attributes.num_elements;if(!n[r]){if(i.length>=a){delete n[i.shift().toString()]}i.push(t)}return n[r]=e,e},move_key_to_end:function(t,e){this.attributes.key_ary.splice(e,1),this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),x=w.extend({defaults:o.extend({},w.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){w.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")<t.length&&this.set("num_elements",t.length);var e=this;o.each(t,function(t){e.set_data(t.region,t)})},data_is_ready:function(){var e=this.get("dataset"),n=t.Deferred(),i="raw_data"===this.get("data_type")?"state":"data"===this.get("data_type")?"converted_datasets_state":"error",r=new c.default.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:e.get("hda_ldda"),data_type:i},dataType:"json"},interval:5e3,success_fn:function(t){return"pending"!==t}});return t.when(r.go()).then(function(t){n.resolve("ok"===t||"data"===t)}),n},search_features:function(e){var n=this.get("dataset"),i={query:e,hda_ldda:n.get("hda_ldda"),data_type:"features"};return t.getJSON(n.url(),i)},load_data:function(e,n,i,r){var a=this.get("dataset"),o={data_type:this.get("data_type"),chrom:e.get("chrom"),low:e.get("start"),high:e.get("end"),mode:n,resolution:i,hda_ldda:a.get("hda_ldda")};t.extend(o,r);var s=this.get("filters_manager");if(s){for(var l=[],u=s.filters,c=0;c<u.length;c++)l.push(u[c].name);o.filter_cols=JSON.stringify(l)}var h=this,d=t.getJSON(a.url(),o,function(t){t.region=e,h.set_data(e,t)});return this.set_data(e,d),d},get_data:function(t,e,n,i){var r=this.get_elt(t);if(r&&(c.default.is_deferred(r)||this.get("data_mode_compatible")(r,e)))return r;for(var a,o,s=this.get("key_ary"),l=this.get("obj_cache"),u=0;u<s.length;u++)if(a=s[u],a.contains(t)&&(o=!0,r=l[a.toString()],c.default.is_deferred(r)||this.get("data_mode_compatible")(r,e)&&this.get("can_subset")(r))){if(this.move_key_to_end(a,u),!c.default.is_deferred(r)){var h=this.subset_entry(r,t);this.set_data(t,h),r=h}return r}if(!o&&t.length()<this.attributes.min_region_size){t=t.copy();var d=this.most_recently_added();!d||t.get("start")>d.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,n,i)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,n,i,r,a){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,n))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");a===this.DEEP_DATA_REQ?t.extend(r,{start_val:o.data.length+1}):a===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),u=this,c=this.load_data(l,n,i,r),h=t.Deferred();return this.set_data(e,h),t.when(c).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),u.set_data(e,t),h.resolve(t)}),h},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,n,i,r){var a=this._mark_stale(t);return a?(r||(r={}),"bigwig"===a.dataset_type&&(r.num_samples=1e3*i),this.load_data(t,e,n,r)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var n=this,i=!0,r=o.map(e.get("chroms_info").chrom_info,function(t){var e=n.get_elt(new M({chrom:t.chrom,start:0,end:t.len}));return e||(i=!1),e});if(i)return r;var a=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){n.add_data(t.data),a.resolve(t.data)}),a},subset_entry:function(t,e){var n={bigwig:function(t,e){return o.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,n){var i=n.get("start")-t.region.get("start");return t.data.slice(i,i+n.length())}},i=t.data;return!t.region.same(e)&&t.dataset_type in n&&(i=n[t.dataset_type](t.data,e)),{region:e,data:i,dataset_type:t.dataset_type}}}),k=x.extend({initialize:function(t){var e=new i.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,n,i){return t.length()<=1e5?x.prototype.load_data.call(this,t,e,n,i):{data:null,region:t}}}),C=i.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=o.find(this.get_chroms_info(),function(e){return e.chrom===t});return new M({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return o.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),M=i.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),n=e[0],i=e[1].split("-");this.set({chrom:n,start:parseInt(i[0],10),end:parseInt(i[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new M({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),n=t.get("chrom"),i=this.get("start"),r=t.get("start"),a=this.get("end"),o=t.get("end");return e&&n&&e!==n?M.overlap_results.DIF_CHROMS:i<r?a<r?M.overlap_results.BEFORE:a<o?M.overlap_results.OVERLAP_START:M.overlap_results.CONTAINS:i>r?i>o?M.overlap_results.AFTER:a<=o?M.overlap_results.CONTAINED_BY:M.overlap_results.OVERLAP_END:a>=o?M.overlap_results.CONTAINS:M.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===M.overlap_results.CONTAINS},overlaps:function(t){return 0===o.intersection([this.compute_overlap(t)],[M.overlap_results.DIF_CHROMS,M.overlap_results.BEFORE,M.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=i.Collection.extend({model:M}),T=i.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new M(t.region))}}),$=i.Collection.extend({model:T}),A=i.Model.extend(m).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new l.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var n=this.get("preloaded_data");n=n?n.data:[],this.set("data_manager",new x({dataset:this.get("dataset"),init_data:n}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===o.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),E=i.Collection.extend({model:A}),O=i.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),z=O.extend(m).extend({defaults:o.extend({},O.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new E(t.tracks));var e=[];this.set("config",d.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs)),this.unset("tracks"),this.get("drawables").each(function(t){t.unset("preloaded_data")})},add_tracks:function(t){this.get("drawables").add(t)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(t,e){return{obj_type:"View",prefs:{name:e.get("title"),content_visible:!0},drawables:e.get("drawables")}}}}),R=i.Router.extend({initialize:function(t){this.view=t.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var e=this;e.view.on("navigate",function(t){e.navigate(t)})},change_location:function(t){this.view.go_to(t)}});e.default={BackboneTrack:A,BrowserBookmark:T,BrowserBookmarkCollection:$,Cache:w,CanvasManager:b,Genome:C,GenomeDataManager:x,GenomeRegion:M,GenomeRegionCollection:S,GenomeVisualization:z,GenomeReferenceDataManager:k,TrackBrowserRouter:R,Visualization:O,select_datasets:y}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,n){function i(t){t+="";for(var e=/(\d+)(\d{3})/;e.test(t);)t=t.replace(e,"$1,$2");return t}Object.defineProperty(e,"__esModule",{value:!0});var r=function(t){return"promise"in t},a=t.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(t){return!0}},go:function(){var t=n.Deferred(),e=this,i=e.get("ajax_settings"),r=e.get("success_fn"),a=e.get("interval");return function e(){n.ajax(i).success(function(n){r(n)?t.resolve(n):setTimeout(e,a)})}(),t}}),o=function(t){t||(t="#ffffff"),"string"==typeof t&&(t=[t]);for(var 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v({model:t.model,$el:this.$el})},expand_to_container:function(){this.$el.height()<this.scroll_elt.height()&&this.attempt_to_fetch()},attempt_to_fetch:function(t){var e=this;!this.loading_chunk&&this.scrolled_to_bottom()&&(this.loading_chunk=!0,this.loading_indicator.show(),r.when(e.model.get_next_chunk()).then(function(t){t&&(e._renderChunk(t),e.loading_chunk=!1),e.loading_indicator.hide(),e.expand_to_container()}))},render:function(){this.loading_indicator=r("<div/>").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var t=r("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(t);var e=this.model.get_metadata("column_names"),n=r("<thead/>").appendTo(t),i=r("<tr/>").appendTo(n);if(e)i.append("<th>"+e.join("</th><th>")+"</th>");else for(var a=1;a<=this.model.get_metadata("columns");a++)i.append("<th>"+a+"</th>");var o=this,s=this.model.get("first_data_chunk");s?this._renderChunk(s):r.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)}),this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(t,e,n){var i=r("<td>").text(t),a=this.model.get_metadata("column_types");return void 0!==n?i.attr("colspan",n).addClass("stringalign"):a&&e<a.length&&("str"!==a[e]&&"list"!==a[e]||i.addClass("stringalign")),i},_renderRow:function(t){var e=t.split("\t"),n=r("<tr>"),a=this.model.get_metadata("columns");return 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n=t.model.get("pagesize"),i=r.filter(t.data2,function(n){var i=!1;return r.each(n.tags,function(n){t._match(e.term,n)&&(i=t.matched_tags[n]=!0)}),i||t._match(e.term,n.text)});e.callback({results:i.slice((e.page-1)*n,e.page*n),more:i.length>=e.page*n})},formatResult:function(e){return r.escape(e.text)+'<div class="ui-tags">'+r.reduce(e.tags,function(e,n){return t.matched_tags[n]?e+'&nbsp;<div class="label label-info">'+r.escape(n)+"</div>":e},"")+"</div>"}}),this.$(".select2-container .select2-search 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n="width"==t||"height"==t?1:-1,i=e*this.options.cell-n*this.options.margin;return"top"==t&&(i+=this.top),i},_toGrid:function(t){return{top:this._toGridCoord("top",t.top),left:this._toGridCoord("left",t.left),width:this._toGridCoord("width",t.width),height:this._toGridCoord("height",t.height)}},_toPixel:function(t){return{top:this._toPixelCoord("top",t.top),left:this._toPixelCoord("left",t.left),width:this._toPixelCoord("width",t.width),height:this._toPixelCoord("height",t.height)}},_isCollision:function(t){for(var e in this.frame_list){var n=this.frame_list[e];if(null!==n.grid_location&&function(t,e){return!(t.left>e.left+e.width-1||t.left+t.width-1<e.left||t.top>e.top+e.height-1||t.top+t.height-1<e.top)}(t,n.grid_location))return!0}return!1},_locationRank:function(t){return t.top*this.cols+t.left},_panelRefresh:function(t){this.cols=parseInt(n(window).width()/this.options.cell,10)+1,this._frameInsert(null,null,t)},_panelAnimationComplete:function(){var t=this;n(".frame").promise().done(function(){t._panelScroll(0,!0)})},_panelScroll:function(t,e){var n=this.top-this.options.scroll*t;if(n=Math.max(n,this.top_max),n=Math.min(n,this.options.top_min),this.top!=n){for(var i in this.frame_list){var r=this.frame_list[i];if(null!==r.grid_location){var a={top:r.screen_location.top-(this.top-n),left:r.screen_location.left};this._frameOffset(r,a,e)}}this.top=n}this.render()},_frameInit:function(t,e){t.id=e,t.screen_location={},t.grid_location={},t.grid_rank=null,t.$el.attr("id",e.substring(1))},_frameInsert:function(t,e,r){var a=this,o=[];t&&(t.grid_location=null,o.push([t,this._locationRank(e)])),i.each(this.frame_list,function(t){null!==t.grid_location&&(t.grid_location=null,o.push([t,t.grid_rank]))}),o.sort(function(t,e){return t[1]<e[1]?-1:t[1]>e[1]?1:0}),i.each(o,function(t){a._framePlace(t[0],r)}),this.top_max=0,i.each(this.frame_list,function(t){null!==t.grid_location&&(a.top_max=Math.max(a.top_max,t.grid_location.top+t.grid_location.height))}),this.top_max=n(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(t,e){t.grid_location=null;for(var n=this._toGrid(this._frameScreen(t)),i=!1,r=0;r<this.options.rows;r++){for(var a=0;a<Math.max(1,this.cols-n.width);a++)if(n.top=r,n.left=a,!this._isCollision(n)){i=!0;break}if(i)break}i?this._frameGrid(t,n,e):console.log("Grid dimensions exceeded.")},_frameFocus:function(t,e){t.$el.css("z-index",this.frame_z+(e?1:0))},_frameOffset:function(t,e,n){if(t.screen_location.left=e.left,t.screen_location.top=e.top,n){this._frameFocus(t,!0);var i=this;t.$el.animate({top:e.top,left:e.left},"fast",function(){i._frameFocus(t,!1)})}else t.$el.css({top:e.top,left:e.left})},_frameResize:function(t,e){t.$el.css({width:e.width,height:e.height}),t.screen_location.width=e.width,t.screen_location.height=e.height},_frameGrid:function(t,e,n){t.grid_location=e,this._frameOffset(t,this._toPixel(e),n),t.grid_rank=this._locationRank(e)},_frameScreen:function(t){var e=t.screen_location;return{top:e.top,left:e.left,width:e.width,height:e.height}}});e.default={View:a}}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=function(t){return t&&t.__esModule?t:{default:t}}(r),o=t.View.extend({initialize:function(e){var n=this;this.model=e&&e.model||new t.Model({id:a.default.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(e),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var r=[];this.$text.on("change",function(){n.value(i(this).val())}).on("keyup",function(t){r[t.which]=!1}).on("keydown",function(t){var e=t.which;r[e]=!0,n.model.get("is_workflow")&&r[16]&&52==e?(n.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&e<=57&&!r[16]||e>=96&&e<=105||(190==e||110==e)&&-1==i(this).val().indexOf(".")&&n.model.get("precise")||(189==e||109==e)&&-1==i(this).val().indexOf("-")||n._isParameter(i(this).val())||r[91]||r[17]||event.preventDefault()});var o=this.model.attributes;this.has_slider=null!==o.max&&null!==o.min&&o.max>o.min;var s=o.step;s||(s=o.precise&&this.has_slider?(o.max-o.min)/o.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:o.min,max:o.max,step:s}).on("slide",function(t,e){n.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(3),o=r(a),s=n(23),l=r(s),u=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var n=this,r=t.isArray(e)?e:[e];i.each(r,function(t){var e=n.header_index[t];i.each(e,function(t){n._setState(t,!0)})})}},_setState:function(t,e){var n=this.$(".button-"+t),i=this.$(".subgroup-"+t);n.data("is_expanded",e),e?(i.show(),n.removeClass("fa-plus-square").addClass("fa-minus-square")):(i.hide(),n.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var n=t.find(".button-"+e);n.on("click",function(){i._setState(e,!n.data("is_expanded"))})}function n(r,a,s){s=s||[];for(var l in a){var u=a[l],c=u.options&&u.options.length>0,h=s.slice(0);i.header_index[u.value]=h.slice(0);var d=t("<div/>");if(c){var f=o.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),_=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");d.append(t("<div/>").append(p).append(i._templateOption({label:u.name,value:u.value}))),h.push(f),n(_,u.options,h),d.append(_),e(d,f)}else d.append(i._templateOption({label:u.name,value:u.value}));r.append(d)}}var i=this;this.header_index={};var r=t("<div/>");return n(r,this.model.get("data")),r},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:u}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i,r,a){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=n(3),l=o(s),u=n(4),c=(o(u),n(11)),h=o(c),d=n(49),f=o(d),p=n(50),_=o(p),g=n(51),v=o(g),m=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new v.default,this.setElement(i("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),r.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=a.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var n=this._addRow(t.test_param);n.model&&n.model.set("onchange",function(n){var i=e.app.data.matchCase(t,n);for(var r in t.cases){var a=t.cases[r],o=e.$("#"+t.id+"-section-"+r),s=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){s=!0;break}r==i&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var i in t.cases){var r=new m(this.app,{inputs:t.cases[i].inputs});this._append(r.$el.addClass("ui-form-section"),t.id+"-section-"+i)}n.trigger("change")},_addRepeat:function(t){function e(e){var r=t.id+"-section-"+i++,o=new m(n.app,{inputs:e});a.add({id:r,$el:o.$el,ondel:function(){a.del(r),n.app.trigger("change")}})}for(var n=this,i=0,a=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),n.app.trigger("change")}}),o=r.size(t.cache),s=0;s<Math.max(Math.max(o,t.min||0),t.default||0);s++)e(s<o?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&a.hideOptions();var l=new _.default(this.app,{label:t.title||t.name,help:t.help,field:a});this._append(l.$el,t.id)},_addSection:function(t){var e=new h.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new m(this.app,{inputs:t.inputs}).$el),e.append(i("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,n=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",n)};var i=this.parameters.create(t);this.app.field_list[n]=i;var r=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:i});return this.app.element_list[n]=r,this._append(r.$el,t.id),i},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:m}}).call(e,n(1),n(0),n(2),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(11),u=a(l),c=n(4),h=a(c),d=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new h.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(i("<div/>").append(this.$list=i("<div/>")).append(i("<div/>").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new h.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),n=new u.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});n.append(t.$el),n.$el.addClass("section-row").hide(),this.list[t.id]=n,this.$list.append(n.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(i("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var n=this.list[e];n.title(++t+": "+this.options.title),n[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:d}}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,n,i){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,n){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=n&&n.field||new t.View,this.model=n&&n.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(n),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var i=this.model.get("collapsible_value");this.field.collapsed=void 0!==i&&JSON.stringify(this.model.get("value"))==JSON.stringify(i),this.listenTo(this.model,"change",this.render,this),this.render();var r=this;this.$collapsible.on("click",function(){r.field.collapsed=!r.field.collapsed,e.trigger&&e.trigger("change"),r.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){r.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){n(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(i.escape(this.model.get("text_value")));var r=this.model.get("error_text");if(this.$error[r?"show":"hide"](),this.$el[r?"addClass":"removeClass"]("ui-error"),this.$error_text.html(r),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return n("<div/>").addClass("ui-form-element").append(n("<div/>").addClass("ui-form-error ui-error").append(n("<span/>").addClass("fa fa-arrow-down")).append(n("<span/>").addClass("ui-form-error-text"))).append(n("<div/>").addClass("ui-form-title").append(n("<div/>").addClass("ui-form-collapsible").append(n("<i/>").addClass("ui-form-collapsible-icon")).append(n("<span/>").addClass("ui-form-collapsible-text"))).append(n("<span/>").addClass("ui-form-title-text"))).append(n("<div/>").addClass("ui-form-field").append(n("<span/>").addClass("ui-form-info")).append(n("<div/>").addClass("ui-form-backdrop"))).append(n("<div/>").addClass("ui-form-preview"))}})}).call(e,n(1),n(0),n(2))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(4),u=a(l),c=n(52),h=a(c),d=n(53),f=a(d),p=n(54),_=a(p),g=n(55),v=a(g),m=n(57),y=a(m);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],n="function"==typeof this[e]?this[e].call(this,t):null;return n||(n=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),n.value(t.value),n},_fieldData:function(t){return new h.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],i.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var n=u.default.Select;switch(t.display){case"checkboxes":n=u.default.Checkbox;break;case"radio":n=u.default.Radio;break;case"radiobutton":n=u.default.RadioButton}return new n.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new u.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(r.isArray(t.value)){var e="";for(var n in t.value){if(e+=String(t.value[n]),!t.multiple)break;e+="\n"}t.value=e}return new u.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new u.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new u.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new u.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new y.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new v.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new u.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,n(1),n(2),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(4),u=a(l),c=n(22),h=a(c),d={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:d.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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t=this;r.each(this.fields,function(e,n){t.model.get("current")==n?(e.$el.show(),r.each(t.$batch,function(e,i){e[t.config[n].batch==i?"show":"hide"]()}),t.button_type.value(n)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var n=t.model.get("data"),i=s.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],r.each(this.config,function(e,r){t.button_data.push({value:r,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new h.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||n&&n[e.src]&&n[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(i?i+" ":"")+(a[e.src]||"content")+" 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t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:d}}).call(e,n(1))},function(t,e,n){"use strict";(function(t){function i(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=i(r),o=n(24),s=i(o),l=t.View.extend({initialize:function(t){var 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e=this;o.each(o.keys(t),function(n){e.set_input_value(n,t[n])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(t){var e=o.extend({tool_id:this.id,inputs:this.get_inputs_dict()},t),n=i.Deferred(),r=new l.default.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return i.when(r.go()).then(function(t){n.resolve(new c.default.DatasetCollection(t))}),n}});o.extend(y.prototype,d);var b=(t.View.extend({}),t.Collection.extend({model:y})),w=t.Model.extend(d),x=t.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){o.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var e,n=!0;o.each(this.attributes.elems,function(i){i instanceof w?(e=i,e.hide()):i instanceof y&&i.apply_search_results(t)&&(n=!1,e&&e.show())}),n?this.hide():(this.show(),this.set("open",!0))}});o.extend(x.prototype,d);var k=t.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length<this.attributes.min_chars_for_search)return void this.set("results",null);var e=t;this.timer&&clearTimeout(this.timer),i("#search-clear-btn").hide(),i("#search-spinner").show();var n=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"?q="+e),i.get(n.urlRoot,{q:e},function(t){n.set("results",t),i("#search-spinner").hide(),i("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});o.extend(k.prototype,d);var C=t.Model.extend({initialize:function(e){this.attributes.tool_search=e.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=e.tools,this.attributes.layout=new t.Collection(this.parse(e.layout))},parse:function(t){var e=this,n=function t(n){var i=n.model_class;if(i.indexOf("Tool")===i.length-4)return e.attributes.tools.get(n.id);if("ToolSection"===i){var r=o.map(n.elems,t);return n.elems=r,new x(n)}return"ToolSectionLabel"===i?new w(n):void 0};return o.map(t,n)},clear_search_results:function(){this.get("layout").each(function(t){t instanceof x?t.clear_search_results():t.show()})},apply_search_results:function(){var t=this.get("tool_search").get("results");if(null===t)return void this.clear_search_results();var e=null;this.get("layout").each(function(n){n instanceof w?(e=n,e.hide()):n instanceof y?n.apply_search_results(t)&&e&&e.show():(e=null,n.apply_search_results(t))})}}),M=t.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),S=M.extend({tagName:"div",render:function(){var t=i("<div/>");t.append(z.tool_link(this.model.toJSON()));var e=this.model.get("form_style",null);if("upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("regular"===e){var n=this;t.find("a").on("click",function(t){t.preventDefault(),Galaxy.router.push("/",{tool_id:n.model.id,version:n.model.get("version")})})}return this.$el.append(t),this}}),T=M.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(i("<span/>").text(this.model.attributes.text)),this}}),$=M.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){M.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(z.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return o.each(this.model.attributes.elems,function(e){if(e instanceof y){var n=new S({model:e,className:"toolTitle"});n.render(),t.append(n.$el)}else if(e instanceof w){var i=new T({model:e});i.render(),t.append(i.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),A=t.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(z.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),i("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){if(this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which)return this.clear(),!1;this.model.set("query",this.$el.find(":input").val())}}),E=t.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new A({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof x){var n=new $({model:e});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var i=new S({model:e,className:"toolTitleNoSection"});i.render(),t.$el.append(i.$el)}else if(e instanceof w){var r=new T({model:e});r.render(),t.$el.append(r.$el)}}),t.$el.find("a.tool-link").click(function(e){var n=i(this).attr("class").split(/\s+/)[0],r=t.model.get("tools").get(n);t.trigger("tool_link_click",e,r)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?i("#search-no-results").show():i("#search-no-results").hide()}}),O=t.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(z.tool_form(this.model.toJSON()))}}),z=(t.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new E({collection:this.collection}),this.tool_form_view=new O},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,n){e.preventDefault(),t.show_tool(n)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),i("#left").width("650px")})}}),{tool_search:o.template(['<input id="tool-search-query" class="search-query parent-width" name="query" ','placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />','<a id="search-clear-btn" title="clear search (esc)"> </a>','<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>'].join("")),panel_section:o.template(['<div class="toolSectionTitle" id="title_<%- id %>">','<a href="javascript:void(0)"><span><%- name %></span></a>',"</div>",'<div id="<%- id %>" class="toolSectionBody" style="display: none;">','<div class="toolSectionBg"></div>',"<div>"].join("")),tool_link:o.template(['<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">','<span class="labels">',"<% _.each( labels, function( label ){ %>",'<span class="label label-default label-<%- label %>">',"<%- label %>","</span>","<% }); %>","</span>",'<span class="tool-old-link">',"<%- name %>","</span>"," <%- description %>","</a>"].join("")),tool_form:o.template(['<div class="toolFormTitle"><%- tool.name %> (version <%- tool.version %>)</div>','<div class="toolFormBody">',"<% _.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});e.default={ToolParameter:f,IntegerToolParameter:g,SelectToolParameter:m,Tool:y,ToolCollection:b,ToolSearch:k,ToolPanel:C,ToolPanelView:E,ToolFormView:O}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(4),u=a(l),c=n(9),h=a(c),d=n(63),f=a(d),p=n(40),_=a(p),g=t.View.extend({initialize:function(t){var e=this;this.modal=parent.Galaxy.modal||new h.default.View,this.form=new f.default(s.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(t,n){var r=n.model.attributes,a="",o={},l=r.job_id;l?a=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(a=Galaxy.root+"api/tools/"+r.id+"/build",o=i.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),r.version&&(o.tool_version=r.version),s.default.get({url:a,data:o,success:function(i){if(!i.display)return void(window.location=Galaxy.root);n.model.set(i),e._customize(n),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",i),t.resolve()},error:function(e,a){var o=e&&e.err_msg||"Uncaught error.";401==a?window.location=Galaxy.root+"user/login?"+i.param({redirect:Galaxy.root+"?tool_id="+r.id}):n.$el.is(":empty")?n.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},postchange:function(t,e){var n={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:i.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",n),s.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:n,success:function(n){e.update(n),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",n),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(t){var e=this,n=t.model.attributes,i=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+n.name+" ("+n.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){i.wait(),t.portlet.disable(),e.submit(n,function(){i.unwait(),t.portlet.enable()})}});n.buttons={execute:i},n.job_id&&n.job_remap&&n.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",n.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var n=this,a={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!n.validate(a))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=i("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return r.each(a.inputs,function(t,e){o.append(i("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",a),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:a,success:function(t){if(e&&e(),n.$el.children().hide(),n.$el.append(n._templateSuccess(t)),t.jobs&&t.jobs.length>0){n.$el.append(i("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:a.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var i=!1;if(t&&t.err_data){var r=n.form.data.matchResponse(t.err_data);for(var o in r){n.form.highlight(o,r[o]),i=!0;break}}i||n.modal.show({title:"Job submission failed",body:n._templateError(a,t&&t.err_msg),buttons:{Close:function(){n.modal.hide()}}})}})},validate:function(t){var e=t.inputs,n=-1,i=null;for(var r in e){var a=e[r],o=this.form.data.match(r),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==a)return this.form.highlight(o),!1;if(a&&a.batch){var u=a.values.length,c=u>0&&a.values[0]&&a.values[0].src;if(c)if(null===i)i=c;else if(i!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=u;else if(n!==u)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+u+"</b> selection(s) while a previous field contains <b>"+n+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,n=1==e?"1 job has":e+" jobs have",a=i("<div/>").addClass("donemessagelarge").append(i("<p/>").text(n+" been successfully added to the queue - resulting in the following datasets:"));return r.each(t.outputs,function(t){a.append(i("<p/>").addClass("messagerow").append(i("<b/>").text(t.hid+": "+t.name)))}),a.append(i("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),a}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return i("<div/>").addClass("errormessagelarge").append(i("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(i("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:g}}).call(e,n(1),n(0),n(2))},,function(t,e,n){"use strict";(function(t,n,i){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==n.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,n){if(n){var i,r=this.attributes.filters[t];if(null===r||void 0===r)i=e;else if("string"==typeof r)if("All"==r||r==e)i=e;else{var a=[];a[0]=r,a[1]=e,i=a}else i=r,-1===i.indexOf(e)&&i.push(e);this.attributes.filters[t]=i}else this.attributes.filters[t]=e},remove_filter:function(t,e){var i=this.attributes.filters[t];if(null===i||void 0===i)return!1;if("string"==typeof i)this.attributes.filters[t]="";else{var r=n.indexOf(i,e);-1!==r&&(i[r]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return n.each(n.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+i.param(this.get_url_data())+"&"+i.param(t)}})}).call(e,n(1),n(2),n(0))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=function(t){return t&&t.__esModule?t:{default:t}}(r);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var n=t.global_actions.length>=3;n&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var i in t.global_actions){var r=t.global_actions[i];e+='<li><a class="action-button use-target" target="'+r.target+'" href="'+r.url_args+'" onclick="return false;" >'+r.label+"</a></li>"}n&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var n in t.columns){var i=t.columns[n];i.visible&&(e+='<th id="'+i.key+'-header">',i.href?e+='<a href="'+i.href+'" class="sort-link" sort_key="'+i.key+'">'+i.label+"</a>":e+=i.label,e+='<span class="sort-arrow">'+i.extra+"</span></th>")}return e+="</tr>"},body:function(e){var n="",i=0;0==e.items.length&&(n+='<tr><td colspan="100"><em>No Items</em></td></tr>',i=1);for(var r in e.items){var a=e.items[r],o=a.encode_id;n+="<tr ",e.current_item_id==a.id&&(n+='class="current"'),n+=">",e.show_item_checkboxes&&(n+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var u="";l.nowrap&&(u='style="white-space:nowrap;"');var c=a.column_config[l.label],h=c.link,d=c.value,f=c.target;"string"===t.type(d)&&(d=d.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+r+"-popup",_="menubutton",""!=h&&(_+=" split"),_+=" popup"),n+="<td "+u+">",h?(0!=e.operations.length&&(n+='<div id="'+p+'" class="'+_+'" style="float: left;">'),n+='<a class="menubutton-label use-target" target="'+f+'" href="'+h+'" onclick="return false;">'+d+"</a>",0!=e.operations.length&&(n+="</div>")):n+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(d||"")+"</label></div>",n+="</td>"}}n+="</tr>",i++}return n},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var n=t.num_page_links,i=t.cur_page_num,r=t.num_pages,a=n/2,o=i-a,s=0;o<=0&&(o=1,s=a-(i-o));var l,u=a+s,c=i+u;c<=r?l=0:(c=r,l=u-(c+1-i)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(e+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var h=o;h<c+1;h++)h==t.cur_page_num?e+='<span class="page-link inactive-link" id="page-link-'+h+'">'+h+"</span>":e+='<span class="page-link" id="page-link-'+h+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+h+'">'+h+"</a></span>";c<r&&(e+='...<span class="page-link" id="page-link-'+r+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+r+'">'+r+"</a></span>"),e+="</span>",e+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(t.show_item_checkboxes){e+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var d in t.operations){var f=t.operations[d];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(d in t.operations)if(t.operations[d].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(d in t.operations){var f=t.operations[d];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+i.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,n=t.filters,i="none";t.advanced_search&&(i="block");var r=!1;for(var a in t.columns){var o=t.columns[a];if("advanced"==o.filterable){var s=o.key,l=n[s],u=e[s];l&&u&&l!=u&&(i="block"),r=!0}}var c="block";"block"==i&&(c="none");var h='<div 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m=e.categorical_filters[a][v],y="",b="";for(var w in m)y=w,b=m[w];g&&(o+=" | "),g=!0;var d=i[a];d&&m[a]&&d==b?o+='<span class="categorical-filter '+a+'-filter current-filter">'+v+"</span>":o+='<span class="categorical-filter '+a+'-filter"><a href="javascript:void(0);" filter_key="'+y+'" filter_val="'+b+'">'+v+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=a.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(146),l=r(s),u=n(13),c=r(u),h=n(41),d=r(h),f=n(61),p=r(f),_=n(26),g=r(_),v=n(3),m=r(v);n(170),n(169),n(171),n(157),n(174),n(159),n(172),n(173),n(25);var y=null,b=null,w=function(){this.initialize&&this.initialize.apply(this,arguments)};w.extend=t.Model.extend;var x=w.extend({initialize:function(t){m.default.cssLoadFile("static/style/jquery.rating.css"),m.default.cssLoadFile("static/style/autocomplete_tagging.css"),m.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),m.default.cssLoadFile("static/style/library.css"),m.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];i(".bookmark").each(function(){t.push({position:i(this).children(".position").text(),annotation:i(this).children(".annotation").text()})});var e=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,n={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:e},bookmarks:t};return i.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(t){Galaxy.modal.hide(),b.vis_id=t.vis_id,b.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=d.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(t){o.each(t,function(t){b.add_drawable(l.default.object_from_template(t,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==i("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,n){var r=i("#right .unified-panel-body"),a=i("<div/>").addClass("bookmark").appendTo(r),o=i("<div/>").addClass("position").appendTo(a),s=(i("<a href=''/>").text(t).appendTo(o).click(function(){return b.go_to(t),!1}),i("<div/>").text(e).appendTo(a));if(n){var l=i("<div/>").addClass("delete-icon-container").prependTo(a).click(function(){return a.slideUp("fast"),a.remove(),b.has_changes=!0,!1});i("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,a},create_visualization:function(t,e,n,r,a){var s=this,u=new l.default.TracksterView(o.extend(t,{header:!1}));return u.editor=!0,i.when(u.load_chroms_deferred).then(function(t){if(e){var i=e.chrom,o=e.start,c=e.end,h=e.overview;i&&void 0!==o&&c?u.change_chrom(i,o,c):u.change_chrom(t[0].chrom)}else u.change_chrom(t[0].chrom);if(n)for(var d=0;d<n.length;d++)u.add_drawable(l.default.object_from_template(n[d],u,u));for(var d=0;d<u.drawables.length;d++)if(u.drawables[d].config.get_value("name")===h){u.set_overview(u.drawables[d]);break}if(r)for(var f,d=0;d<r.length;d++)f=r[d],s.add_bookmark(f.position,f.annotation,a);u.has_changes=!1}),this.set_up_router({view:u}),u},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){i(document).keyup(function(e){if(!i(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){i(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){i.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){y=new x(Galaxy.root),y.createButtonMenu(),y.buttonMenu.$el.attr("style","float: right"),i("#center .unified-panel-header-inner").append(y.buttonMenu.$el),i("#right .unified-panel-title").append("Bookmarks"),i("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),i("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),n={},i={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(n["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(i)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new g.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){i(parent.document).find("input[name=id]:checked").each(function(){t.id=i(this).val(),window.location=Galaxy.root+"visualization/trackster?"+i.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;b=y.create_visualization({container:i("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;i.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(i("#new-title").val(),i("#new-dbkey").val()),Galaxy.modal.hide()}}});var n=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(n,galaxy_config.app.default_dbkey)&&i("#new-dbkey").val(galaxy_config.app.default_dbkey),i("#new-title").focus(),i("select[name='dbkey']").select2(),i("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',n=0;n<t.length;n++)e+='<option value="'+t[n][1]+'">'+t[n][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){i(document).trigger("convert_to_values"),b=y.create_visualization({container:i("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){i("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&i.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){b.add_drawable(l.default.object_from_template(t,b,b))}}),i("#add-bookmark-button").click(function(){var t=b.chrom+":"+b.low+"-"+b.high;return y.add_bookmark(t,"Bookmark description",!0)}),y.init_keyboard_nav(b),i(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t,e){e||(e=0);var n=Math.pow(10,e);return Math.round(t*n)/n}function o(e){var n=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,i){n.resolve(206===i.status)}}),n}Object.defineProperty(e,"__esModule",{value:!0});var s=n(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(s),u=n(13),c=r(u),h=n(147),d=r(h),f=n(14),p=r(f),_=n(148),g=r(_),v=n(149),m=r(v),y=n(150),b=r(y),w=n(15),x=r(w),k=n(140),C=r(k),M=n(21),S=r(M),T=n(151),$=r(T);n(25);var A=l.extend,E={},O=function(t,e){E[t.attr("id")]=e},z=function(e,n,i,r){i=".group",E[e.attr("id")]=r,e.bind("drag",{handle:"."+n,relative:!0},function(e,n){var r,a,o,s,l,u=(t(this),t(this).parent()),c=u.children(".track,.group"),h=E[t(this).attr("id")];if(a=t(this).parents(i),0!==a.length){o=a.position().top,s=o+a.outerHeight();var d=E[a.attr("id")];if(n.offsetY<o)return t(this).insertBefore(a),d.remove_drawable(h),void d.container.add_drawable_before(h,d);if(n.offsetY>s)return t(this).insertAfter(a),d.remove_drawable(h),void d.container.add_drawable(h)}for(a=null,l=0;l<c.length;l++)if(r=t(c.get(l)),o=r.position().top,s=o+r.outerHeight(),r.is(i)&&this!==r.get(0)&&n.offsetY>=o&&n.offsetY<=s)return n.offsetY-o<s-n.offsetY?r.find(".content-div").prepend(this):r.find(".content-div").append(this),h.container&&h.container.remove_drawable(h),void E[r.attr("id")].add_drawable(h);for(l=0;l<c.length&&(r=t(c.get(l)),!(n.offsetY<r.position().top)||r.hasClass("reference-track")||r.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(u.append(this),E[u.attr("id")].move_drawable(h,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),E[u.attr("id")].move_drawable(h,n.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",N=["Histogram","Line","Filled","Intensity"],P=function t(e,n,i){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=n,this.drag_handle_class=i.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,i.prefs),this.config.get_value("name")||this.config.set_value("name",i.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==i.header){var r=new d.default.TrackHeaderView({model:this,id:this.id});this.header_div=r.$el,this.container_div.append(this.header_div);var a=r.icons_div;this.action_icons=r.action_icons,this.container_div.hover(function(){a.show()},function(){a.hide()})}};P.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new S.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],A(P.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,n){P.call(this,t,e,n),this.obj_type=n.obj_type,this.drawables=[]};A(q.prototype,P.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,n=0;n<t.length;n++)e=it(t[n],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables.splice(n,0,t),!0)},replace_drawable:function(t,e,n){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables[i]=e,n&&t.container_div.replaceWith(e.container_div),this.changed()),i},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables.splice(n,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,n=this.drawables.slice(0),i=[];0!==n.length;)e=n.shift(),e instanceof t?i.push(e):e.drawables&&(n=n.concat(e.drawables));return i}});var j=function(e,n,i){if(A(i,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,n,i),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in i&&this.unpack_drawables(i.drawables),"filters"in i){var r=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,i.filters),r.parent_div.replaceWith(this.filters_manager.parent_div),i.filters.visible&&this.setup_multitrack_filtering()}};A(j.prototype,P.prototype,q.prototype,{action_icons_def:[P.prototype.action_icons_def[0],P.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},P.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof W),this.action_icons.filters_icon.hide();else{var n,i,r,a=this.drawables[0].get_type(),o=0;for(n=0;n<e;n++){if(r=this.drawables[n],r.get_type()!==a){can_composite=!1;break}r instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(r=this.drawables[0],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],l[s.name]=[s];for(n=1;n<this.drawables.length;n++)for(r=this.drawables[n],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var u,c;for(var h in l)u=l[h],u.length===o&&(c=new b.default.NumberFilter({name:u[0].name,index:u[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new W(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=A(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var D=i.View.extend({initialize:function(t){A(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,n=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,n),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:n.dbkey},function(t){l.each(t,function(t){n.add_drawable(it(t,n,n))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var i=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&n.go_to(t(this).val()),t(this).hide(),t(this).val(""),n.location_span.show(),n.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",i).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){n.location_span.hide(),n.chrom_select.hide(),n.nav_input.val(n.chrom+":"+n.low+"-"+n.high),n.nav_input.css("display","inline-block"),n.nav_input.select(),n.nav_input.focus(),n.nav_input.autocomplete({source:function(e,i){var r=[],a=t.map(n.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){r=r.concat(t)})});t.when.apply(t,a).done(function(){i(t.map(r,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){n.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){n.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){n.change_chrom(n.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){n.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var i=e.offsetX-this.current_x;this.current_x=e.offsetX;var r=Math.round(i/n.viewport_container.width()*(n.max_high-n.max_low));n.move_delta(-r)}),this.overview_close.click(function(){n.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>n.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=n.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,i){var r=t(this),a=i.offsetX-i.current_x,o=r.scrollTop()-(e.clientY-i.current_height);r.scrollTop(o),i.current_height=e.clientY,i.current_x=i.offsetX;var s=Math.round(a/n.viewport_container.width()*(n.high-n.low));n.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,i){return t("<div/>").addClass("zoom-area").css("height",n.browser_content_div.height()+n.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,i){t(i.proxy).css({left:Math.min(e.pageX,i.startX)-n.container.offset().left,width:Math.abs(e.pageX-i.startX)});var r=Math.min(e.pageX,i.startX)-n.container.offset().left,a=Math.max(e.pageX,i.startX)-n.container.offset().left,o=n.high-n.low,s=n.viewport_container.width();n.update_location(Math.round(r/s*o)+n.low,Math.round(a/s*o)+n.low)}).bind("dragend",function(e,i){var r=Math.min(e.pageX,i.startX),a=Math.max(e.pageX,i.startX),o=n.high-n.low,s=n.viewport_container.width(),l=n.low;n.low=Math.round(r/s*o)+l,n.high=Math.round(a/s*o)+l,t(i.proxy).remove(),n.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){n.resize_window()},500)}),t(document).bind("redraw",function(){n.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});A(D.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,n,i){if(this.timer&&clearTimeout(this.timer),i){var r=this;this.timer=setTimeout(function(){r.trigger("navigate",t+":"+e+"-"+n)},500)}else view.trigger("navigate",t+":"+e+"-"+n)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var n=this.chrom_select.val();""!==n&&this.trigger_navigate(n,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var n=this,i=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var r=new J(n);n.add_label_track(r),n.reference_track=r}n.chrom_data=e.chrom_info,n.chrom_select.html(""),n.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var a=0,o=n.chrom_data.length;a<o;a++){var s=n.chrom_data[a].chrom,l=t("<option>");l.text(s),l.val(s),n.chrom_select.append(l)}e.prev_chroms&&n.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&n.chrom_select.append(t('<option value="next">Next 100</option>')),n.chrom_start_index=e.start_index,i.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+n.dbkey)}}),i},change_chrom:function(e,n,i){var r=this;if(!r.chrom_data)return void r.load_chroms_deferred.then(function(){r.change_chrom(e,n,i)});if(e&&"None"!==e){if("previous"===e)return void r.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void r.load_chroms({low:this.chrom_start_index+100});var a=t.grep(r.chrom_data,function(t,n){return t.chrom===e})[0];if(void 0===a)return void r.load_chroms({chrom:e},function(){r.change_chrom(e,n,i)});if(e!==r.chrom){r.chrom=e,r.chrom_select.val(r.chrom),r.max_high=a.len-1,r.reset();for(var o=0,s=r.drawables.length;o<s;o++){var l=r.drawables[o];l.init&&l.init()}r.reference_track&&r.reference_track.init()}void 0===n&&void 0===i?(r.low=0,r.high=r.max_high):(r.low=void 0!==n?Math.max(n,0):0,void 0===i?(r.low=Math.max(r.low-15,0),r.high=r.low+30):r.high=Math.min(i,r.max_high)),r.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),n=e[0],i=e[1]?parseInt(e[1],10):void 0,r=e[2]?parseInt(e[2],10):void 0;this.change_chrom(n,i,r)},move_fraction:function(t){var e=this,n=e.high-e.low;this.move_delta(t*n)},move_delta:function(t){var e=this,n=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+n):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-n):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var i=e.chrom_select.val();this.trigger_navigate(i,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,n){if(q.prototype.remove_drawable.call(this,e),n){var i=this;e.container_div.hide(0,function(){t(this).remove(),i.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var n=this,i=e?[e]:n.drawables;l.each(i,function(e){var i=l.find(n.tracks_to_be_redrawn,function(t){return t[0]===e});i?i[1]=t:n.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){n._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var n=this.high-this.low;0!==this.high&&n<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var i=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,r=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:i,width:Math.max(13,r)}).show(),r<13&&this.overview_box.css("left",i-(13-r)/2),this.overview_highlight&&this.overview_highlight.css({left:i,width:r}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],n=t[1];e&&e._draw(n)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var n=this.high-this.low,i=n/2+this.low,r=n/this.zoom_factor/2;t&&(i=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(i-r),this.high=Math.round(i+r),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,n=t*this.zoom_factor/2;this.low=Math.round(e-n),this.high=Math.round(e+n),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),n=this;e.header_div.hide(),e.is_overview=!0,n.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){n.overview_highlight.show().height(n.overview_drawable.content_div.height()),n.overview_viewport.height(n.overview_drawable.content_div.height()+n.overview_box.outerHeight()),n.overview_close.show(),n.resize_window()},n.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=i.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),n=this.model;t("<div>").addClass("param-label").text(n.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(n.get("html")).appendTo(e).find(":input").val(n.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=i.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,n=this.model,i=this.$el.addClass("dynamic-tool").hide();i.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(i).text(n.get("name"));n.get("inputs").each(function(t){var e=new I({model:t});e.render(),i.append(e.$el)}),i.find("input").click(function(){t(this).select()});var r=t("<div>").addClass("param-row").appendTo(i),a=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(r);t("<input type='submit'>").attr("value","Run on visible region").appendTo(r).click(function(){e.run_on_region()}),a.click(function(){e.run_on_dataset()}),n.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),n=this.model,i=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),r={target_dataset_id:e.dataset.id,action:"rerun",tool_id:n.id,regions:[i.toJSON()]},a=e,o=n.get("name")+a.tool_region_and_parameters_str(i);if(a.container===view){var s=new j(view,view,{name:e.config.get_value("name")}),l=a.container.replace_drawable(a,s,!1);s.container_div.insertBefore(a.view.content_div.children()[l]),s.add_drawable(a),a.container_div.appendTo(s.content_div),t=s}else t=a.container;var u=new a.constructor(view,t,{name:o,hda_ldda:"hda"});u.init_for_tool_data(),u.change_mode(a.mode),u.set_filters_manager(a.filters_manager.copy(u)),u.update_icons(),t.add_drawable(u),u.tiles_div.text("Starting job."),this.run(r,u,function(t){u.set_dataset(new x.default.Dataset(t)),u.tiles_div.text("Running job."),u.init()})},run:function(e,n,i){e.inputs=this.model.get_inputs_dict();var r=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(r.go()).then(function(t){"no converter"===t?(n.container_div.addClass("error"),n.content_div.text(R)):t.error?(n.container_div.addClass("error"),n.content_div.text("Tool cannot be rerun: "+t.message)):i(t)})}}),V=function(t,e){m.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var U=function(e,n,i,r,a){this.track=e,this.region=n,this.low=n.get("start"),this.high=n.get("end"),this.w_scale=i,this.canvas=r,this.html_elt=t("<div class='track-tile'/>").append(r),this.data=a,this.stale=!1};U.prototype.predisplay_actions=function(){};var F=function(t,e,n,i,r){U.call(this,t,e,n,i,r)};F.prototype.predisplay_actions=function(){};var G=function(t,e,n,i,r,a,o,s,l,u,c){U.call(this,t,e,n,i,r),this.mode=a,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=u,this.other_tiles_features_drawn={},this.seq_data=c};A(G.prototype,U.prototype),G.prototype.predisplay_actions=function(){};var H=function(e,n,r){A(r,{drag_handle_class:"draghandle"}),P.call(this,e,n,r),this.dataset=null,r.dataset&&(this.dataset=r.dataset instanceof i.Model?r.dataset:new x.default.Dataset(r.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in r?r.data_query_wait:5e3,this.data_manager="data_manager"in r?r.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in r&&!r.resize||this.add_resize_handle())};A(H.prototype,P.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},P.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},P.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var n="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',r=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},a=function(){var n,r=t('select[name="regions"] option:selected').val(),a=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});n="cur"===r?[a]:"bookmarks"===r?o:[a].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new i.Collection(n).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:n,buttons:{No:r,Yes:a}})}},P.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&P.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,n=!1,i=!1,r=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(n=!0,r.show())},function(){n=!1,i||r.hide()}),r.hide().bind("dragstart",function(n,r){i=!0,r.original_height=t(e.content_div).height()}).bind("drag",function(n,i){var r=Math.min(Math.max(i.original_height+i.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",r),e.visible_height_px=e.max_height_px===r?0:r,e.on_resize()}).bind("dragend",function(t,a){e.tile_cache.clear(),i=!1,n||r.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof J?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof W?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var n=this;if(n.enabled=!1,n.tile_cache.clear(),n.data_manager.clear(),n.content_div.children().remove(),n.container_div.removeClass("nodata error pending"),n.tiles_div=t("<div/>").addClass("tiles").appendTo(n.content_div),n.dataset.id){var i=t.Deferred(),r={hda_ldda:n.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:n.view.chrom,retry:e};return t.getJSON(this.dataset.url(),r,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(n.container_div.addClass("error"),n.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(n.container_div.addClass("nodata"),n.show_message("No data for this chrom/contig.")):"pending"===e?(n.container_div.addClass("pending"),n.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){n.init()},n.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(n.valid_chroms=e.valid_chroms,n.update_icons()),n.tiles_div.text("Ready for display"),n.view.chrom?(n.tiles_div.text(""),n.tiles_div.css("height",n.visible_height_px+"px"),n.enabled=!0,t.when.apply(t,n.predraw_init()).done(function(){i.resolve(),n.container_div.removeClass("nodata error pending"),n.request_draw()})):i.resolve());else{n.container_div.addClass("error");var r=n.show_message("Cannot display dataset due to an error. ");e.message&&(r.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),r.append(t("<span/>").text(" ")),r.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){n.init(!0)})))}}),this.update_icons(),i}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(n&&void 0!==n.min&&void 0!==n.max){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_default_value("min_value",i),e.config.set_default_value("max_value",r),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},get_drawables:function(){return this}});var Y=function(e,n,i){H.call(this,e,n,i);var r=this;if(z(r.container_div,r.drag_handle_class,".group",r),this.filters_manager=new b.default.FiltersManager(this,"filters"in i?i.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=i.tool?new L(l.extend(i.tool,{track:this,tool_state:i.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var a=new B({model:this.tool});a.render(),this.dynamic_tool_div=a.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),i.mode&&this.change_mode(i.mode)};A(Y.prototype,P.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();A(e,{data_manager:this.data_manager});var n=new this.constructor(this.view,t,e);return n.change_mode(this.mode),n.enabled=this.enabled,n},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var n=e&&e.clear_after,i=this.view.low,r=this.view.high,a=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(i=this.view.max_low,r=this.view.max_high,o=a/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var u,h,d=Math.floor(400*s),f=Math.floor(i/d),p=[],_=[];f*d<r;)u=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*d,end:Math.min((f+1)*d,this.view.max_high)}),h=this.draw_helper(u,o,e),p.push(h),t.when(h).then(function(t){_.push(t)}),f+=1;n||this.tiles_div.children(".remove").removeClass("remove").remove();var g=this;t.when.apply(t,p).then(function(){g.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&g.postdraw_actions(_,a,o,n)})}},_add_yaxis_label:function(e,n){var i=this,r="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+r),u=a(i.config.get_value(s),1);n=n||function(){i.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(u):(l=t("<div/>").text(u).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),i.config.set_value(s,a(e,1)),n()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+r).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,n,i){if(l.filter(t,function(t){return t instanceof F}).length>0){this.max_height_px=0;var r=this;l.each(t,function(t){t instanceof F||(t.html_elt.remove(),r.draw_helper(t.region,n,{force:!0,mode:"Coverage"}))}),r._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,n,i){i||(i={});var r=i.force,a=i.mode||this.mode,o=1/n,s=this,u=this._get_drawables(),c=this._gen_tile_cache_key(n,e),h=r?void 0:s.tile_cache.get_elt(c);if(h)return function(t){return t&&"track"in t}(h)&&s.show_tile(h,n),h;if(!1===i.data_fetch)return null;var d=function(){var t=l.find(N,function(t){return t===a})?"Coverage":a,n=l.map(u,function(n){return n.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&n.push(view.reference_track.data_manager.get_data(e,a,o,view.reference_track.data_url_extra_params)),n},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,d()).then(function(){var r,a=d(),o=a;if(l.find(a,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,n,i)).then(function(t){f.resolve(t)});view.reference_track&&(r=view.reference_track.data_manager.subset_entry(a.pop(),e));var h=[],_=[];l.each(u,function(t,e){var i=t.mode,r=o[e];"Auto"===i&&(i=t.get_mode(r),t.update_auto_mode(i)),h.push(i),_.push(t.get_canvas_height(r,i,n,b))});var g,v=s.view.canvas_manager.new_canvas(),m=e.get("start"),y=e.get("end"),b=Math.ceil((y-m)*n)+s.left_offset,w=l.max(_);v.width=b,v.height=i.height||w;var x=v.getContext("2d");x.translate(s.left_offset,0),u.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(u,function(t,i){g=t.draw_tile(o[i],x,h[i],e,n,r)}),void 0!==g&&(s.tile_cache.set_elt(c,g),s.show_tile(g,n)),f.resolve(g)}),f},get_canvas_height:function(t,e,n,i){return this.visible_height_px},_draw_line_track_tile:function(t,e,n,i,r){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var a=e.canvas;return new m.default.LinePainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new F(this,i,r,a,t.data)},draw_tile:function(t,e,n,i,r,a){},show_tile:function(t,e){var n=t.html_elt;t.predisplay_actions();var i=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(i-=this.left_offset),n.css("left",i),n.hasClass("remove")?n.removeClass("remove"):this.tiles_div.append(n),n.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,n.height()-2),n.parent().children().css("height",this.max_height_px+"px");var r=this.max_height_px;0!==this.visible_height_px&&(r=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",r+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};A(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var n=this.view,i=n.high-n.low,r=Math.floor(Math.pow(10,Math.floor(Math.log(i)/Math.log(10)))),a=Math.floor(n.low/r)*r,o=this.view.container.width(),s=t("<div/>").addClass("label-container");a<n.high;){var l=Math.floor((a-n.low)/i*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(a)).css({left:l})),a+=r}this.content_div.children(":first").remove(),this.content_div.append(s)}});var W=function(t,e,n){if(Y.call(this,t,e,n),this.drawables=[],"drawables"in n){for(var i,r=0;r<n.drawables.length;r++)i=n.drawables[r],this.drawables[r]=it(i,t,null),i.left_offset>this.left_offset&&(this.left_offset=i.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};A(W.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],n=0;n<this.drawables.length;n++)e.push(this.drawables[n].init());var i=this;t.when.apply(t,e).then(function(){i.enabled=!0,i.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:P.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new j(this.view,this.container,{name:this.config.get_value("name")}),n=0;n<this.drawables.length;n++)t=this.drawables[n],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,n,i){var r,a=-1;for(r=0;r<t.length;r++){var o=t[r].html_elt.find("canvas").height();o>a&&(a=o)}for(r=0;r<t.length;r++){var s=t[r];s.html_elt.find("canvas").height()!==a&&(this.draw_helper(s.region,n,{force:!0,height:a}),s.html_elt.remove())}var l=this,u=function(){l.update_all_min_max()};this._add_yaxis_label("min",u),this._add_yaxis_label("max",u)}});var J=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};A(J.prototype,P.prototype,Y.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:P.prototype.can_draw,draw_helper:function(t,e,n){var i,r=this.tiles_div.is(":visible"),a=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),i=!0,a=Y.prototype.draw_helper.call(this,t,e,n)):(i=!1,this.tiles_div.hide()),r!==i&&this.view.resize_viewport(),a},can_subset:function(t){return!0},draw_tile:function(t,e,n,i,r){var a=this.data_manager.subset_entry(t,i),o=a.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,u=o.length;l<u;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*r),10);return new U(this,i,r,s,a)}});var K=function(e,n,i){this.mode="Histogram",Y.call(this,e,n,i),this.left_offset=30;var r=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(r.data_manager=new $.default.BBIDataManager({dataset:r.dataset}))})};A(K.prototype,P.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,n,i,r){return this._draw_line_track_tile(t,e,n,i,r)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,n,i){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,n){this.mode="Heatmap",Y.call(this,t,e,n)};A(Z.prototype,P.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,n,i,r){var a=e.canvas;return new m.default.DiagonalHeatmapPainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new U(this,i,r,a,t.data)}});var Q=function(t,e,n){Y.call(this,t,e,n),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};A(Q.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=m.default.ArcLinkedFeaturePainter:this.painter=m.default.LinkedFeaturePainter},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a,o=this;if(0===l.filter(e,function(t){return t instanceof F}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var u=this;l.each(e,function(e){var n=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(n=l.omit(n,l.keys(e.other_tiles_features_drawn)),0!==l.size(n)){var i={data:l.values(n)},r=u.view.canvas_manager.new_canvas(),a=r.getContext("2d");r.height=Math.max(e.canvas.height,u.get_canvas_height(i,e.mode,e.w_scale,100)),r.width=e.canvas.width,a.drawImage(e.canvas,0,0),a.translate(o.left_offset,0);var c=u.draw_tile(i,a,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=r,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,h=o.filters_manager.filters;for(c=0;c<h.length;c++)h[c].update_ui_elt();var d,f,p=!1;for(a=0;a<e.length;a++)if(e[a].data.length)for(d=e[a].data[0],c=0;c<h.length;c++)if(f=h[c],f.applies_to(d)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof G){var _=!0;for(a=0;a<e.length;a++)if(!e[a].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,n){var i=this.view.canvas_manager.dummy_context,r=this.slotters[t];return r&&r.mode===n||(r=new g.default.FeatureSlotter(t,n,100,function(t){return i.measureText(t)}),this.slotters[t]=r),r.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,n,i){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.incremental_slots(n,t.data,e),a=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,a.get_required_height(r,i))},draw_tile:function(t,e,n,i,r,a,o){var s=this,l=e.canvas,u=i.get("start"),c=i.get("end"),h=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,n,i,r);var d=[],f=this.slotters[r].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,g=0,v=t.data.length;g<v;g++){for(var m,y=t.data[g],b=!1,w=0,x=_.length;w<x;w++)if(m=_[w],m.update_attrs(y),!m.keep(y)){b=!0;break}b||(d.push(y),y[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,M=new this.painter(d,u,c,this.config.to_key_value_dict(),n,k,C,a,function(t){return s.view.get_base_color(t)}),S=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=M.draw(e,l.width,l.height,r,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-h}return o?void 0:new G(s,i,r,l,t.data,n,t.message,p,S,incomplete_features,a)}});var tt=function(t,e,n){Y.call(this,t,e,n),this.painter=m.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};A(tt.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,n,i,r){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",i,r);var a=this.view;return new this.painter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n,function(t){return a.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,r),new U(this,i,r,e.canvas,t.data)},get_canvas_height:function(t,e,n,i){if("bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===r&&0!==t.data.length&&(r=t.data[0][7].match(/,/g),r=null===r?1:r.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(r)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a=l.filter(e,function(t){return t instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===a.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var u=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(u).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,n){Q.call(this,t,e,n),this.painter=m.default.ReadPainter,this.update_icons()};A(et.prototype,P.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var nt={CompositeTrack:W,DrawableGroup:j,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},it=function(t,e,n){if("copy"in t)return t.copy(n);var i=t.obj_type;return i||(i=t.track_type),new nt[i](e,n,t)};e.default={TracksterView:D,DrawableGroup:j,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:W,object_from_template:it}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(r),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(i("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(i("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(i("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=i("<div/>").addClass("track-icons").hide().appendTo(this.$el),a.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,n,r,a,o){var s=this;this.action_icons[t]=i("<a/>").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(function(){r(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var n=this.model,i={},r=0,a=n.display_modes.length;r<a;r++){var o=n.display_modes[r];i[o]=function(t){return function(){n.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,i)}}});e.default={TrackHeaderView:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,n,i){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=n,this.measureText=i};a(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),n=Math.ceil(t[2]*this.w_scale),i=t[3];if(void 0!==i&&this.include_label){var r=this.measureText(i).width+7;e-r>=0?(e-=r,"left"):(n+=r,"right")}return[e,n]},_find_slot:function(t){for(var e=t[0],n=t[1],i=0;i<=this.max_rows;i++){var r=!1,a=this.start_end_dct[i];if(void 0!==a)for(var o=0,s=a.length;o<s;o++){var l=a[o];if(n>l[0]&&e<l[1]){r=!0;break}}if(!r)return i}return-1},slot_features:function(t){for(var e,n,i=this.start_end_dct,r=[],a=0,s=0,l=t.length;s<l;s++){e=t[s],n=e[0];var u=this.slots[n];if(u){if(e[1]<u.feature[1]||u.feature[2]<e[2])for(var c=this._get_draw_coords(u.feature),h=this._get_draw_coords(e),d=this.start_end_dct[u.slot],f=0;f<d.length;f++){var p=d[f];p[0]===c[0]&&p[1]===c[1]&&(d[f]=h)}a=Math.max(a,this.slots[n].slot)}else r.push(s)}for(var s=0,l=r.length;s<l;s++){e=t[r[s]],n=e[0];var _=this._get_draw_coords(e),g=this._find_slot(_);g>=0&&(void 0===i[g]&&(i[g]=[]),i[g].push(_),this.slots[n]=new o(g,e),a=Math.max(a,g))}return a+1}}),e.default={FeatureSlotter:s}},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=function(t,e){var n=t[0],i=t[1],r=e[0],a=e[1];return n<r?i<=r?1001:i<=a?1003:1002:n>a?1006:i<=a?1005:1004},o=function(t,e){var n=a(t,e);return 1001!==n&&1006!==n},s=function(t,e,n,i,r,a){void 0===a&&(a=4);var o,s=i-e,l=r-n,u=Math.floor(Math.sqrt(s*s+l*l)/a),c=s/u,h=l/u;for(o=0;o<u;o++,e+=c,n+=h)o%2==0&&t.fillRect(e,n,a,1)},l=function(t,e,n,i){var r=e-i/2,a=e+i/2,o=n-Math.sqrt(3*i/2);t.beginPath(),t.moveTo(r,o),t.lineTo(a,o),t.lineTo(e,n),t.lineTo(r,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},u=function(t){this.default_val=t||1};u.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},h=function(t,e,n,i,a){this.data=t,this.view_start=e,this.view_end=n,this.prefs=r.extend({},this.default_prefs,i),this.mode=a};h.prototype.default_prefs={},h.prototype.draw=function(t,e,n,i){},h.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},h.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},h.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},h.prototype._chrom_pos_to_draw_pos=function(t,e,n){return Math.floor(e*(Math.max(0,t-this.view_start)+n))};var d=function(t,e,n,i,r){h.call(this,t,e,n,i,r)};d.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},d.prototype.draw=function(t,e,n,i){var a=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,u=n,c=this.view_start,h=this.mode,d=this.data;t.save();var f=Math.round(n+o/l*n);"Intensity"!==h&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,g;g=d.length>1?r.map(d.slice(0,-1),function(t,e){return Math.ceil((d[e+1][0]-d[e][0])*i)}):[10];for(var v,m=this.prefs.block_color||this.prefs.color,y=parseInt(m.slice(1),16),b=(16711680&y)>>16,w=(65280&y)>>8,x=255&y,k=!1,C=!1,M=0,S=d.length;M<S;M++)if(t.fillStyle=t.strokeStyle=m,k=C=!1,v=g[M],p=Math.floor((d[M][0]-c-.5)*i),null!==(_=d[M][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===h)_=Math.round(_/l*u),t.fillRect(p,f,v,-_);else if("Intensity"===h){var T=(_-o)/l,$=Math.round(b+(255-b)*(1-T)),A=Math.round(w+(255-w)*(1-T)),E=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+$+","+A+","+E+")",t.fillRect(p,0,v,u)}else _=Math.round(u-(_-o)/l*u),a?t.lineTo(p,_):(a=!0,"Filled"===h?(t.moveTo(p,u),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===h||"Intensity"===h?O=v:(p-=2,O=4),k&&t.fillRect(p,0,O,3),C&&t.fillRect(p,u-3,O,3)}t.fillStyle=m}else a&&"Filled"===h&&t.lineTo(p,u),a=!1;"Filled"===h?(a&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,n,i){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:n,x_end:i})},f.prototype.get_feature_data=function(t,e){var n,i=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[i])return null;t+=this.translation;for(var r=0;r<this.feature_positions[i].length;r++)if(n=this.feature_positions[i][r],t>=n.x_start&&t<=n.x_end)return n.data};var p=function(t,e,n,i,r,a,o){h.call(this,t,e,n,i,r),this.alpha_scaler=a||new u,this.height_scaler=o||new u,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},r.extend(p.prototype,{get_required_height:function(t,e){var n=this.get_row_height(),i=n,r=this.mode;return"no_detail"!==r&&"Squish"!==r&&"Pack"!==r||(n=t*i),n+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,n,i,r){var a=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,u=this.get_row_height(),h=new f(u),d=[],p=0,_=a.length;p<_;p++){var g=a[p],v=g[0],m=g[1],y=g[2],b=r&&void 0!==r[v]?r[v].slot:null;("Dense"===this.mode||null!==b)&&m<s&&y>o&&(l=this.draw_element(t,this.mode,g,b,o,s,i,u,e),h.map_feature_data(g,b,l[0],l[1]),(m<o||y>s)&&d.push(g))}return t.restore(),h.y_translation=this.get_top_padding(e),new c({incomplete_features:d,feature_mapper:h})},draw_element:function(t,e,n,i,r,a,o,s,l){return[0,0]}});var _=function(t,e,n,i,r,a,o){p.call(this,t,e,n,i,r,a,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};r.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,n,i,r,a,o,s,l){var u,c=(n[0],n[1]),h=n[2],d=n[3],f=n[4],p=Math.floor(Math.max(0,(c-r-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(h-r-.5)*o))),g=p,v=_,u=("Dense"===e?0:0+i)*s+this.get_top_padding(l),m=null,y=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,w=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(n),"Dense"===e&&(i=1),"no_detail"===e)t.fillStyle=b,t.fillRect(p,u+5,_-p,1);else{var x=n[5],k=n[6],C=n[7],M=!0;x&&k&&(m=Math.floor(Math.max(0,(x-r)*o)),y=Math.ceil(Math.min(l,Math.max(0,(k-r)*o))));var S,T;if("Squish"===e?(S=1,T=3,M=!1):(S=5,T=9),C){var $,A;"Squish"===e||"Dense"===e?($=u+Math.floor(1.5)+1,A=1):f?($=u,A=T):($+=2.5,A=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,$,_-p,A));for(var E=0,O=C.length;E<O;E++){var z,R,N=C[E],P=Math.floor(Math.max(0,(N[0]-r-.5)*o)),q=Math.ceil(Math.min(l,Math.max((N[1]-r-.5)*o)));if(!(P>q)){if(t.fillStyle=b,t.fillRect(P,u+(T-S)/2+1,q-P,S),void 0!==m&&k>x&&!(P>y||q<m)){var j=Math.max(P,m),D=Math.min(q,y);t.fillRect(j,u+1,D-j,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),j+14<D&&(j+=2,D-=2),t.fillRect(j,u+1,D-j,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,P,q,u),z=P,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(n),I=Math.ceil(T*L),B=Math.round((T-I)/2);1!==L&&(t.fillRect(p,$+1,_-p,B),t.fillRect(p,$+T-B+1,_-p,B))}}else t.fillStyle=b,t.fillRect(p,u+1,_-p,T),f&&M&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,u+1,_-p,T));t.globalAlpha=1,d&&"Pack"===e&&c>r&&(t.fillStyle=w,0===r&&p-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,_+2,u+8,this.max_label_length),v+=t.measureText(d).width+2):(t.textAlign="right",t.fillText(d,p-2,u+8,this.max_label_length),g-=t.measureText(d).width+2))}return t.globalAlpha=1,[g,v]}});var g=function(t,e,n,i,r,a,o,s,l){p.call(this,t,e,n,i,r,a,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};r.extend(g.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",n=[[0,0]],i=n[0],a=0,o=r.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var r=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==i[1]&&(i=[a+r,a+r],n.push(i)):-1==="ISHP".indexOf(o)&&(i[1]+=r,a+=r),[e.indexOf(o),r]});return{blocks:n,cigar:o}},draw_read:function(t,e,n,i,r,s,u,c,h,d){var f=function(t){return Math.floor(Math.max(0,(t-r-.5)*n))};t.textAlign="center";var p,_,g=[r,s],v=0,m=0,y=Math.round(n/2),b=t.canvas.manager.char_width_px,w="+"===h?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,M=i+1,S=new x(t,C,n,e),T=[],$=[],A=this._parse_cigar(c);c=A.cigar,T=A.blocks;for(var E=0;E<T.length;E++){var O=T[E];o([u+O[0],u+O[1]],g)&&(p=f(u+O[0]),_=f(u+O[1]),p===_&&(_+=1),t.fillStyle=w,t.fillRect(p,M,_-p,C))}for(var z=0,R=c.length;z<R;z++){var N=c[z],P="MIDNSHP=X"[N[0]],q=N[1],j=u+v;if(p=f(j),_=f(j+q),o([j,j+q],g))switch(p===_&&(_+=1),P){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var D="";"X"===P?D=d.slice(m,m+q):this.ref_seq&&(D=this.ref_seq.slice(Math.max(0,j-r),Math.min(j-r+q,s-r)));for(var L=Math.max(j,r),I=0;I<D.length;I++)if(D&&!this.prefs.show_differences||"X"===P){var B=Math.floor(Math.max(0,(L+I-r)*n));t.fillStyle=this.base_color_fn(D[I]),k&&n>b?t.fillText(D[I],B,i+9):n>.05&&t.fillRect(B-y,M,Math.max(1,Math.round(n)),C)}"X"===P&&(m+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,M+(C-1)/2,_-p,1),v+=q;break;case"D":S.draw_deletion(p,M,q),v+=q;break;case"I":var V=p-y;if(o([j,j+q],g)){var U=d.slice(m,m+q);if(this.prefs.show_insertions){var F=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b){switch(t.fillStyle="yellow",t.fillRect(F-y,i-9,_-p,9),$[$.length]={type:"triangle",data:[V,i+4,5]},t.fillStyle="#ccc",a([j,j+q],g)){case 1003:U=U.slice(r-j);break;case 1004:U=U.slice(0,j-s);break;case 1005:break;case 1002:U=U.slice(r-j,j-s)}for(var I=0,G=U.length;I<G;I++){var B=Math.floor(Math.max(0,(j+I-r)*n));t.fillText(U[I],B-(_-p)/2,i)}}else t.fillStyle="yellow",t.fillRect(F,i+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b&&$.push({type:"text",data:[U.length,V,i+9]})}m+=q}else v=function(t,e,n){return-1!=="M=NXD".indexOf(e)&&(t+=n),t}(v,P,q),m=function(t,e,n){return-1!=="IX".indexOf(e)&&(t+=n),t}(m,P,q)}t.fillStyle="yellow";for(var H,Y,X,E=0;E<$.length;E++)H=$[E],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,n,i,r,a,o,l,u){var c=(n[0],n[1]),h=n[2],d=n[3],f=Math.floor(Math.max(-.5*o,(c-r-.5)*o)),p=Math.ceil(Math.min(u,Math.max(0,(h-r-.5)*o))),_=("Dense"===e?0:0+i)*l,g="Pack"===e?9:3;this.prefs.label_color;if(n[5]instanceof Array){var v=!0;n[4][1]>=r&&n[4][0]<=a&&n[4][2]?this.draw_read(t,e,o,_,r,a,n[4][0],n[4][2],n[4][3],n[4][4]):v=!1,n[5][1]>=r&&n[5][0]<=a&&n[5][2]?this.draw_read(t,e,o,_,r,a,n[5][0],n[5][2],n[5][3],n[5][4]):v=!1;var m=Math.ceil(Math.min(u,Math.max(-.5*o,(n[4][1]-r-.5)*o))),y=Math.floor(Math.max(-.5*o,(n[5][0]-r-.5)*o));if(v&&y>m){t.fillStyle="#ccc";var b=_+1+(g-1)/2;s(t,m,b,y,b)}}else this.draw_read(t,e,o,_,r,a,c,n[4],n[5],n[6]);return"Pack"===e&&c>=r&&"."!==d&&(t.fillStyle=this.prefs.label_color,0===r&&f-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(d,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,n,i,r,a,o){_.call(this,t,e,n,i,r,a,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};r.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,n=this.data.length;e<n;e++){var i=this.data[e],r=i[1],a=i[2];t=Math.max(t,a-r)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,n=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*n))},draw_connector:function(t,e,n,i,r,a){var o=(n+i)/2,s=i-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,a,i-o,Math.PI,0),t.stroke())}});var m=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};m.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,n=this.rgb[0]/255,i=this.rgb[1]/255,r=this.rgb[2]/255,a=this.alpha,o=Math.max(n,i,r),s=Math.min(n,i,r),l=(o+s)/2,u=o-s;if(o===s)t=e=0;else{switch(e=l>.5?u/(2-o-s):u/(o+s),o){case n:t=(i-r)/u+(i<r?6:0);break;case i:t=(r-n)/u+2;break;case r:t=(n-i)/u+4}t/=6}return{h:360*t,s:e,l:l,a:a}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var n=this,i=e,r=2*i-1,a=n.toHSL().a-t.toHSL().a,o=((r*a==-1?r:(r+a)/(1+r*a))+1)/2,s=1-o,l=[n.rgb[0]*o+t.rgb[0]*s,n.rgb[1]*o+t.rgb[1]*s,n.rgb[2]*o+t.rgb[2]*s],u=n.alpha*i+t.alpha*(1-i);return new m(l,u)}};var y=function(t,e,n,i){this.start_color=new m(t),this.end_color=new m(e),this.start_value=n,this.end_value=i,this.value_range=i-n};y.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var b=function(t,e,n,i,r){this.positive_ramp=new y(e,n,0,r),this.negative_ramp=new y(e,t,0,-i),this.start_value=i,this.end_value=r};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var w=function(t,e,n,i,r){h.call(this,t,e,n,i,r);var a,o;if(void 0===this.prefs.min_value){var s=1/0;for(a=0,o=this.data.length;a<o;a++)s=Math.min(s,this.data[a][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(a=0,o=this.data.length;a<o;a++)l=Math.max(l,this.data[a][6]);this.prefs.max_value=l}};w.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},w.prototype.draw=function(t,e,n,i){var r,a,o,s,l,u,c=this.prefs.min_value,h=this.prefs.max_value,d=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,h),g=function(t){return(t-d)*i};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,m=f.length;v<m;v++)r=f[v],a=g(r[1]),o=g(r[2]),s=g(r[4]),l=g(r[5]),u=r[6],t.fillStyle=_.map_value(u),t.fillRect(a,s,o-a,l-s);t.restore()};var x=function(t,e,n,i){this.ctx=t,this.row_height=e,this.px_per_base=n,this.draw_details=("Pack"===i||"Auto"===i)&&n>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};r.extend(x.prototype,{draw_deletion:function(t,e,n){this.ctx.fillStyle="black";var i=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-i),this.ctx.fillRect(t,e,n*this.px_per_base,i)}});var k=function(t,e,n,i,r,a){h.call(this,t,e,n,i,r),this.base_color_fn=a,this.divider_height=1};r.extend(k.prototype,h.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,n,i){t.save();var a,o,s,l,u,c,h,d,f,p,_,g=function(t,e){var n=t.length,i=e.length,r=0,a=1,o=null;return"-"===e?(o="deletion",a=t.length):0===t.indexOf(e)&&n>i?(o="deletion",a=n-i,r=i):0===e.indexOf(t)&&n<i&&(o="insertion",a=i-n,r=i),null!==o?{type:o,start:r,len:a}:{}},v=Math.max(1,Math.floor(i)),m=this.data.length?this.data[0][7].split(",").length:0,y="Squish"===this.mode?5:10,b=i<.1?y:"Squish"===this.mode?3:9,w=!0,k=new x(t,y,i,this.mode);1===m&&(y=b=i<t.canvas.manager.char_width_px?this.prefs.summary_height:y,k.row_height=y,w=!1),this.prefs.show_sample_data&&w&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(a=this.data[C],o=a[1],s=a[3],l=[a[4].split(",")],u=a[7].split(","),c=a.slice(8),l=r.map(r.flatten(l),function(t){var e={type:"snp",value:t,start:0},n=g(s,t);return r.extend(e,n)}),!(o<this.view_start||o>this.view_end)){if(w)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(d=this.get_start_draw_pos(o+l[_].start,i),t.fillRect(d,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var M=c/u.length,S=Math.ceil(this.prefs.summary_height*M);t.fillRect(d,f-S,v,S),f-=S}if(this.prefs.show_sample_data)for(f=w?this.prefs.summary_height+this.divider_height:0,_=0;_<u.length;_++,f+=y)if(p=u[_]?u[_].split(/\/|\|/):["0","0"],h=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(h=l[parseInt(p[0],10)-1],t.globalAlpha=1):(h="0"!==p[0]?p[0]:p[1],h=l[parseInt(h,10)-1],t.globalAlpha=.5),h)if(d=this.get_start_draw_pos(o+h.start,i),"snp"===h.type){var T=h.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,i),f+y):t.fillRect(d,f+1,v,b)}else"deletion"===h.type&&k.draw_deletion(d,f+1,h.len)}t.restore()}}),e.default={Scaler:u,LinePainter:d,LinkedFeaturePainter:_,ReadPainter:g,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:w,VariantPainter:k}},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};a(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,n,i){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(i)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var n=this;n.parent_div=t("<div/>").addClass("filter-row slider-row");var i=t("<div/>").addClass("elt-label").appendTo(n.parent_div),r=(t("<span/>").addClass("slider-name").text(n.name+"  ").appendTo(i),t("<span/>").text(this.low+"-"+this.high)),a=t("<span/>").addClass("slider-value").appendTo(i).append("[").append(r).append("]");n.values_span=r;var l=t("<div/>").addClass("slider").appendTo(n.parent_div);n.control_element=t("<div/>").attr("id",n.name+"-filter-control").appendTo(l),n.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){n.slide(t,e)},change:function(t,e){n.control_element.slider("option","slide").call(n.control_element,t,e)}}),n.slider=n.control_element,n.slider_label=r,function(e,n,i){e.click(function(){var e=n.text(),r=parseFloat(i.slider("option","max")),a=r<=1?4:r<=1e6?r.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),i.slider("option","values")&&(a=2*a+1,o=!0),n.text(""),t("<input type='text'/>").attr("size",a).attr("maxlength",a).attr("value",e).appendTo(n).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),n.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var n=i.slider("option","min"),r=i.slider("option","max"),a=function(t){return isNaN(t)||t>r||t<n},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],a(l[0])||a(l[1]))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this)}else if(l=parseFloat(l),a(l))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this);i.slider(o?"values":"value",l),s.removeClass("input")}})})}(a,r,n.control_element);var u=t("<div/>").addClass("display-controls").appendTo(n.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){n.manager.alpha_filter!==n?(n.manager.alpha_filter=n,n.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),n.transparency_icon.addClass("active").show()):(n.manager.alpha_filter=null,n.transparency_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){n.manager.height_filter!==n?(n.manager.height_filter=n,n.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),n.height_icon.addClass("active").show()):(n.manager.height_filter=null,n.height_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),n.parent_div.hover(function(){n.transparency_icon.show(),n.height_icon.show()},function(){n.manager.alpha_filter!==n&&n.transparency_icon.hide(),n.manager.height_filter!==n&&n.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(n.parent_div)};a(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return a(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var n=e.values;this.values_span.text(n[0]+"-"+n[1]),this.low=n[0],this.high=n[1];var i=this;setTimeout(function(){n[0]===i.low&&n[1]===i.high&&i.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var n=!0,i=0;i<e.length;i++)if(!this._keep_val(e[i])){n=!1;break}return n}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var n=t[this.index];n instanceof Array||(n=[n]);for(var i=0;i<n.length;i++){var r=n[i];r<this.min&&(this.min=Math.floor(r),e=!0),r>this.max&&(this.max=Math.ceil(r),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var u=function(e,n){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),n&&"filters"in n){for(var i,r=("alpha_filter"in n?n.alpha_filter:null),a=("height_filter"in n?n.height_filter:null),o=n.filters,s=0;s<o.length;s++)"number"===o[s].type?(i=new l(o[s]),this.add_filter(i),i.name===r&&(this.alpha_filter=i,i.transparency_icon.addClass("active").show()),i.name===a&&(this.height_filter=i,i.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in n&&n.visible&&this.parent_div.show()}if(0!==this.filters.length){var u=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(u).click(function(){c.run_on_dataset()})}};a(u.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},n=[],i=0;i<this.filters.length;i++)t=this.filters[i],n.push(t.to_dict());return e.filters=n,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new u(t),n=0;n<this.filters.length;n++)e.add_filter(this.filters[n].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,n,i=(function(t,e,n){return e in t||(t[e]=n),t[e]}),r={},a=0;a<this.filters.length;a++)e=this.filters[a],e.tool_id&&(e.min!==e.low&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in r)o[o.length]=[s,r[s]];!function e(n,i){var r=i[0],a=r[0],o=r[1],s="("+o.join(") and (")+")",l={cond:s,input:n,target_dataset_id:n,tool_id:a};i=i.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+a,buttons:{Close:Galaxy.modal.hide()}}):0===i.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,i)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:u,NumberFilter:l}}).call(e,n(0))},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(13),r=function(t){return t&&t.__esModule?t:{default:t}}(i),a=n(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=r.default.GenomeDataManager.extend({load_data:function(e,n,i,r){var a=t.Deferred();this.set_data(e,a);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(n,i){t.when(n.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var n=[],i={max:Number.MIN_VALUE};t.forEach(function(t){i.max!==t.min-1&&(n.push([i.max+1,0]),n.push([t.min-2,0])),n.push([t.min-1,t.score]),n.push([t.max,t.score]),i=t});var r={data:n,region:e,dataset_type:"bigwig"};l.set_data(e,r),a.resolve(r)})}),a}});e.default={BBIDataManager:s}}).call(e,n(0))},function(t,e,n){(function(i){var r,a;r=[n(153),n(154),n(155)],void 0!==(a=function(t,e){"use strict";function n(){}function r(t){t&&(this.id=t)}function a(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,n){Math.pow(10,6);return i.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(n-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*w+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function u(t,e,n,i){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=n,this.isSummary=i}function c(t){var e=i.Deferred(),n=new l;return n.url=t,i.when(o(n.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var r=t,a=new Uint8Array(r),o=new Int16Array(r),l=new Int32Array(r),u=a[0]+w*a[1]+x*a[2]+k*a[3];if(u==v)n.type="bigwig";else{if(u!=y)return u==m||u==b?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+u.toString(16));n.type="bigbed"}n.version=o[2],n.numZoomLevels=o[3],n.chromTreeOffset=s(a,8),n.unzoomedDataOffset=s(a,16),n.unzoomedIndexOffset=s(a,24),n.fieldCount=o[16],n.definedFieldCount=o[17],n.asOffset=s(a,36),n.totalSummaryOffset=s(a,44),n.uncompressBufSize=l[13],n.extHeaderOffset=s(a,56),n.zoomLevels=[];for(var c=0;c<n.numZoomLevels;++c){var h=l[6*c+16],d=s(a,24*c+72),f=s(a,24*c+80);n.zoomLevels.push({reduction:h,dataOffset:d,indexOffset:f})}i.when(n.readChromTree()).then(function(){n.getAutoSQL(function(t){return n.schema=t,e.resolve(n)})})}),e}function h(t,e,n,i,r){this.bbi=t,this.type=e,this.fieldCount=n,this.offset=i,this.field=r}var d=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,g=e.arrayCopy,v=2291137574,m=654086024,y=2273964779,b=3958540679,w=256,x=65536,k=16777216,C=4294967296,M=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),i.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var n=new Uint8Array(e),i=new Int16Array(e),r=new Int32Array(e),a=(r[0],r[1],r[2]),o=(r[3],s(n,16),function(e){var r=n[e],l=i[e/2+1];e+=4;for(var u=0;u<l;++u)if(0===r){e+=a;var c=s(n,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var h="",d=0;d<a;++d){var f=n[e++];0!==f&&(h+=String.fromCharCode(f))}var p=n[e+3]<<24|n[e+2]<<16|n[e+1]<<8|n[e+0];n[e+7],n[e+6],n[e+5],n[e+4],e+=8,t.chromsToIDs[h]=p,0===h.indexOf("chr")&&(t.chromsToIDs[h.substr(3)]=p),t.idsToChroms[p]=h,t.maxID=Math.max(t.maxID,p)}});o(32)})},u.prototype.readWigData=function(t,e,n){var i=this.bwg.chromsToIDs[t];return void 0===i?[]:this.readWigDataById(i,e,n)},u.prototype.readWigDataById=function(t,e,n){var r=this,a=i.Deferred();if(!this.cirHeader)return i.when(o(r.bwg.url,this.cirTreeOffset,48)).then(function(o){r.cirHeader=o;var s=new Int32Array(r.cirHeader);r.cirBlockSize=s[1],i.when(r.readWigDataById(t,e,n)).then(function(t){a.resolve(t)})}),a;var l=[],u=0,c=(Date.now(),function(i,r,a,o){return(t<0||i==t)&&r<=n&&a>=e}),h=function(t,e){if(r.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),u+=t.length,1==t.length&&t[0]-r.cirTreeOffset==48&&r.cachedCirRoot)return _(r.cachedCirRoot,0,e),void(0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}));for(var n,o=4+32*r.cirBlockSize,s=0;s<t.length;++s){var h=new d(t[s],t[s]+o);n=n?f(n,h):h}for(var g=n.ranges(),v=0;v<g.length;++v){var m=g[v];p(t,m,e)}},p=function(t,e,n,s){e.max(),e.min();i.when(o(r.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),n),t[s]-r.cirTreeOffset==48&&t[s]-e.min()==0&&(r.cachedCirRoot=o),0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}))})},_=function(i,r,a){var o=new Uint8Array(i),u=new Int16Array(i),c=new Int32Array(i),d=o[r],f=u[r/2+1];if(r+=4,0!==d)for(var p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16),w=s(o,r+24);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&l.push({offset:b,size:w}),r+=32}else{for(var x=[],p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&x.push(b),r+=24}x.length>0&&h(x,a+1)}};return h([r.cirTreeOffset+48],1),a},u.prototype.fetchFeatures=function(t,e){var r=this,a=i.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,i,a){a||(a={});var o=new n;o._chromId=t,o.segment=r.bwg.idsToChroms[t],o.min=e,o.max=i,o.type=r.bwg.type;for(var l in a)o[l]=a[l];s.push(o)},u=function(){if(0===e.length){Date.now();return a.resolve(s)}var n=e[0];if(n.data)r.parseFeatures(n.data,l,t),e.splice(0,1),u();else{for(var c=n.offset,h=n.size,d=1;d<e.length&&e[d].offset==c+h;)h+=e[d].size,++d;i.when(o(r.bwg.url,c,h)).then(function(t){for(var n=0,i=0;n<h;){var a,o=e[i];if(r.bwg.uncompressBufSize>0)a=_(t,n+2,o.size-2);else{var s=new Uint8Array(o.size);g(new Uint8Array(t,n,o.size),0,s,0,o.size),a=s.buffer}o.data=a,n+=o.size,++i}u()})}};return u(),a},u.prototype.parseFeatures=function(t,e,n){var a=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=t.byteLength/32,c=0;c<u;++c){var h=s[8*c],_=s[8*c+1],g=s[8*c+2],v=s[8*c+3],m=(l[8*c+4],l[8*c+5]),y=l[8*c+6];l[8*c+7];if(n(h,_+1,g)){var b={type:"bigwig",score:y/v,maxScore:m};"bigbed"==this.bwg.type&&(b.type="density"),e(h,_+1,g,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),h=s[0],w=s[1],x=(s[2],s[3]),k=s[4],C=a[20],u=o[11];if(3==C)for(var c=0;c<u;++c){var S=l[c+6],T=w+c*x+1,$=w+c*x+k;n(h,T,$)&&e(h,T,$,{score:S})}else if(2==C)for(var c=0;c<u;++c){var _=s[2*c+6]+1,g=_+k-1,S=l[2*c+7];n(h,_,g)&&e(h,_,g,{score:S})}else if(1==C)for(var c=0;c<u;++c){var _=s[3*c+6]+1,g=s[3*c+7],S=l[3*c+8];_>g&&(_=g),n(h,_,g)&&e(h,_,g,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var A=0,E=this.bwg.definedFieldCount,O=this.bwg.schema;A<a.length;){var h=a[A+3]<<24|a[A+2]<<16|a[A+1]<<8|a[A+0],_=a[A+7]<<24|a[A+6]<<16|a[A+5]<<8|a[A+4],g=a[A+11]<<24|a[A+10]<<16|a[A+9]<<8|a[A+8];A+=12;for(var z="";;){var R=a[A++];if(0==R)break;z+=String.fromCharCode(R)}var N,P={};if(N=z.length>0?z.split("\t"):[],N.length>0&&E>3&&(P.label=N[0]),N.length>1&&E>4){var S=parseInt(N[1]);isNaN(S)||(P.score=S)}if(N.length>2&&E>5&&(P.orientation=N[2]),N.length>5&&E>8){var q=N[5];M.test(q)&&(P.itemRgb="rgb("+q+")")}if(N.length>E-3&&O)for(var j=E-3;j<N.length;++j)P[O.fields[j+3].name]=N[j];if(n(h,_+1,g,N))if(E<12)e(h,_+1,g,P);else{var D=0|N[3],L=0|N[4],I=0|N[6],B=N[7].split(","),V=N[8].split(",");if(P.exonFrames){var U=P.exonFrames.split(",");P.exonFrames=void 0}P.type="transcript";var F=new r;for(var G in P)F[G]=P[G];if(F.id=N[0],F.segment=this.bwg.idsToChroms[h],F.min=_+1,F.max=g,F.notes=[],P.groups=[F],N.length>9){var H=P.geneName||N[9],Y=H;N.length>10&&(Y=N[10]),P.geneName2&&(Y=P.geneName2);var X=i.extend({},F);X.id=H,X.label=Y,X.type="gene",P.groups.push(X)}for(var W=[],J=0;J<I;++J){var K=(0|V[J])+_,Z=K+(0|B[J]),Q=new d(K,Z);W.push(Q)}for(var tt=f(W),et=tt.ranges(),nt=0;nt<et.length;++nt){var it=et[nt];e(h,it.min()+1,it.max(),P)}if(L>D){var rt="+"==P.orientation?new d(D,L+3):new d(D-3,L),at=p(tt,rt);if(at){P.type="translation";for(var ot=at.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var nt=0;nt<ot.length;++nt){var ut=nt;"-"==P.orientation&&(ut=ot.length-nt-1);var it=ot[ut];if(P.readframe=st,U){var ct=parseInt(U[ut+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(P.readframe=ct,P.readframeExplicit=!0)}var ht=it.max()-it.min();st=(st+ht)%3,e(h,it.min()+1,it.max(),P)}}}}}}},u.prototype.getFirstAdjacent=function(t,e,n,i){var r=this.bwg.chromsToIDs[t];if(void 0===r)return i([]);this.getFirstAdjacentById(r,e,n,i)},u.prototype.getFirstAdjacentById=function(t,e,n,i){var r=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(a){r.cirHeader=a;var o=new Int32Array(r.cirHeader);r.cirBlockSize=o[1],r.getFirstAdjacentById(t,e,n,i)});var a=null,o=-1,l=-1,u=0,c=(Date.now(),function(t,e){u+=t.length;for(var n,i=4+32*r.cirBlockSize,a=0;a<t.length;++a){var o=new d(t[a],t[a]+i);n=n?f(n,o):o}for(var s=n.ranges(),l=0;l<s.length;++l){var c=s[l];h(t,c,e)}}),h=function(o,s,l,c){s.max(),s.min();r.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var h=0;h<o.length;++h)if(s.contains(o[h])&&(p(c,o[h]-s.min(),l),0==--u)){if(!a)return n>0&&(0!=t||e>0)?r.getFirstAdjacentById(0,0,n,i):n<0&&(t!=r.bwg.maxID||e<1e9)?r.getFirstAdjacentById(r.bwg.maxID,1e9,n,i):i([]);r.fetchFeatures(function(i,r,a,o){return n<0&&(i<t||a<e)||n>0&&(i>t||r>e)},[a],function(t){for(var e=null,r=-1,a=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,u=s.min,c=s.max;(null==e||n<0&&(l>r||c>a)||n>0&&(l<r||u<a))&&(e=s,a=n<0?c:u,r=l)}return i(null!=e?[e]:[])})}})},p=function(i,u,h){var d=new Uint8Array(i),f=new Int16Array(i),p=new Int32Array(i),_=d[u],g=f[u/2+1];if(u+=4,0!=_)for(var v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=s(d,u+16),C=s(d,u+24);(n<0&&(y<t||y==t&&b<=e)||n>0&&(w>t||w==t&&x>=e))&&(/_random/.exec(r.bwg.idsToChroms[y])||(null==a||n<0&&(w>o||w==o&&x>l)||n>0&&(y<o||y==o&&b<l))&&(a={offset:k,size:C},l=n<0?x:b,o=n<0?w:y)),u+=32}else{for(var M=-1,S=-1,v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=p[m+4]<<32|p[m+5];(n<0&&(y<t||y==t&&b<=e)&&w>=t||n>0&&(w>t||w==t&&x>=e)&&y<=t)&&(M<0||x>S)&&(M=k,S=n<0?x:b,n<0?w:y),u+=24}M>=0&&c([M],h+1)}};c([r.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,n){var i,r=n-e;if(r<=25e3||0===this.zoomLevels.length)i=this.getUnzoomedView();else for(var a=0;a<this.zoomLevels.length;a++)if(r/this.zoomLevels[a].reduction<25e3){i=this.getZoomedView(a);break}return i.readWigData(t,e,n)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new u(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new u(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,n,i,r){var a=this;if(!(t>=this.zoomLevels.length-1)){var o;return o=t<0?this.getUnzoomedView():this.getZoomedView(t),o.readWigDataById(e,n,i,r)}if(this.topLevelReductionCache){for(var s=[],l=this.topLevelReductionCache,u=0;u<l.length;++u)l[u]._chromId==e&&s.push(l[u]);return r(s)}this.getZoomedView(this.zoomLevels.length-1).readWigDataById(-1,0,3e8,function(o){return a.topLevelReductionCache=o,a._tsFetch(t,e,n,i,r)})},l.prototype.thresholdSearch=function(t,e,n,i,r){function a(){if(0==l.length)return r(null);l.sort(function(t,e){var i=t.zoom-e.zoom;return 0!=i?i:(i=t.chrOrd-e.chrOrd,0!=i?i:t.min-e.min*n)});var t=l.splice(0,1)[0];o._tsFetch(t.zoom,t.chr,t.min,t.max,function(o){var s=n>0?0:3e8;t.fromRef&&(s=e);for(var u=0;u<o.length;++u){var c,h=o[u];if(c=void 0!=h.maxScore?h.maxScore:h.score,n>0){if(c>i)if(t.zoom<0){if(h.min>s)return r(h)}else h.max>s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:h.min,max:h.max,fromRef:t.fromRef})}else if(c>i)if(t.zoom<0){if(h.max<s)return r(h)}else h.min<s&&l.push({chr:t.chr,chrOrd:t.chrOrd,zoom:t.zoom-2,min:h.min,max:h.max,fromRef:t.fromRef})}a()})}n=n<0?-1:1;for(var o=this,s=this.chromsToIDs[t],l=[{chrOrd:0,chr:s,zoom:o.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],u=1;u<=this.maxID+1;++u){var c=(s+n*u)%(this.maxID+1);c<0&&(c+=this.maxID+1),l.push({chrOrd:u,chr:c,zoom:o.zoomLevels.length-1,min:0,max:3e8})}a()},l.prototype.getAutoSQL=function(t){if(!this.asOffset)return t(null);i.when(o(this.url,this.asOffset,2048)).then(function(e){for(var n=new Uint8Array(e),i="",r=0;r<n.length&&0!=n[r];++r)i+=String.fromCharCode(n[r]);var a=/(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/,o=/([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g,s=a.exec(i);if(s){var l={declType:s[1],name:s[2],comment:s[4],fields:[]};i=i.substring(s[0]);for(var u=o.exec(i);null!=u;u=o.exec(i))l.fields.push({type:u[1],name:u[2],comment:u[4]});return t(l)}})},l.prototype.getExtraIndices=function(t){var e=this;if(this.version<4||0==this.extHeaderOffset||"bigbed"!=this.type)return t(null);this.data.slice(this.extHeaderOffset,64).fetch(function(n){if(!n)return t(null,"Couldn't fetch extension header");var i=new Uint8Array(n),r=new Int16Array(n),a=(new Int32Array(n),r[0],r[1]),o=s(i,4);if(0==a)return t(null);e.data.slice(o,20*a).fetch(function(n){if(!n)return t(null,"Couldn't fetch index info");for(var i=new Uint8Array(n),r=new Int16Array(n),o=(new Int32Array(n),[]),l=0;l<a;++l){var u=r[10*l],c=r[10*l+1],d=s(i,20*l+4),f=r[10*l+8],p=new h(e,u,c,d,f);o.push(p)}t(o)})})},h.prototype.lookup=function(t,e){var n=this;this.bbi.data.slice(this.offset,32).fetch(function(i){function r(i){n.bbi.data.slice(i,4+u*(c+h)).fetch(function(i){var o=new Uint8Array(i),l=new Uint16Array(i),u=(new Uint32Array(i),o[0]),d=l[1],f=4;if(0!=u){for(var p=0;p<d;++p){for(var _="",g=0;g<c;++g){var v=o[f++];0!=v&&(_+=String.fromCharCode(v))}if(_==t){var m=s(o,f),y=a(o,f+8);return n.bbi.getUnzoomedView().fetchFeatures(function(e,i,r,a){if(a&&a.length>n.field-3)return a[n.field-3]==t},[{offset:m,size:y}],e)}f+=h}return e([])}for(var b=null,p=0;p<d;++p){for(var _="",g=0;g<c;++g){var v=o[f++];0!=v&&(_+=String.fromCharCode(v))}var w=s(o,f);if(f+=8,t.localeCompare(_)<0&&b)return void r(b);b=w}r(b)})}var o=new Uint8Array(i),l=(new Int16Array(i),new Int32Array(i)),u=(l[0],l[1]),c=l[2],h=l[3];s(o,16);r(n.offset+32)})},{makeBwg:c}}.apply(e,r))&&(t.exports=a)}).call(e,n(0))},function(t,e,n){var i,r;i=[],void 0!==(r=function(){"use strict";function t(t,e){if("number"!=typeof t||"number"!=typeof e)throw"Bad range "+t+","+e;this._min=t,this._max=e}function e(t){var e=t.sort(o),n=[],i=e.shift();e.forEach(function(t){t._min<=i._max?t._max>i._max&&(i._max=t._max):(n.push(i),i=t)}),n.push(i),this._ranges=n}function n(t,n){return t instanceof e||(t instanceof Array||(t=[t]),t=new e(t)),n&&t.insertRange(n),t}function i(n,i){for(var r=n.ranges(),a=i.ranges(),o=r.length,s=a.length,l=0,u=0,c=[];l<o&&u<s;){var n=r[l],i=a[u],h=Math.max(n.min(),i.min()),d=Math.min(n.max(),i.max());d>=h&&c.push(new t(h,d)),n.max()>i.max()?++u:++l}return 0==c.length?null:1==c.length?c[0]:new e(c)}function r(t){for(var e=0,n=t.ranges(),i=0;i<n.length;++i){var r=n[i];e+=r.max()-r.min()+1}return e}function a(t,e){return t.min()<e.min()?-1:t.min()>e.min()?1:t.max()<e.max()?-1:e.max()>t.max()?1:0}function o(t,e){return t._min<e._min?-1:t._min>e._min?1:t._max<e._max?-1:e._max>t._max?1:0}return t.prototype.min=function(){return this._min},t.prototype.max=function(){return this._max},t.prototype.contains=function(t){return t>=this._min&&t<=this._max},t.prototype.isContiguous=function(){return!0},t.prototype.ranges=function(){return[this]},t.prototype._pushRanges=function(t){t.push(this)},t.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},e.prototype.min=function(){return this._ranges[0].min()},e.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},e.prototype.lower_bound=function(t){var e=this.ranges();if(t>this.max())return e.length;if(t<this.min())return 0;for(var n=0,i=e.length-1;n<=i;){var r=Math.floor((n+i)/2);if(t>e[r]._max)n=r+1;else{if(!(t<e[r]._min))return r;i=r-1}}return n},e.prototype.contains=function(t){var e=this.lower_bound(t);return!!(e<this._ranges.length&&this._ranges[e].contains(t))},e.prototype.insertRange=function(t){var e=this.lower_bound(t._min);if(e===this._ranges.length)return void this._ranges.push(t);var n=this.ranges();if(t._max<n[e]._min)return void this._ranges.splice(e,0,t);n[e]._min<t._min&&(t._min=n[e]._min);for(var i=e+1;i<n.length&&n[i]._min<=t._max;)i++;i--,n[i]._max>t._max&&(t._max=n[i]._max),this._ranges.splice(e,i-e+1,t)},e.prototype.isContiguous=function(){return this._ranges.length>1},e.prototype.ranges=function(){return this._ranges},e.prototype._pushRanges=function(t){for(var e=0;e<this._ranges.length;++e)t.push(this._ranges[e])},e.prototype.toString=function(){for(var t="",e=0;e<this._ranges.length;++e)e>0&&(t+=","),t+=this._ranges[e].toString();return t},{Range:t,union:n,intersection:i,coverage:r,rangeOver:a,_rangeOrder:o}}.apply(e,i))&&(t.exports=r)},function(t,e,n){var i,r;i=[],void 0!==(r=function(){function t(){}function e(){this.was=[0]}function n(t,e,n){this.hufts=new Int32Array(3*h),this.window=new Uint8Array(n),this.end=n,this.checkfn=e,this.mode=v,this.reset(t,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new i,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new r}function i(){}function r(){}function a(t,e,n,i,r){return t[0]=m,e[0]=y,n[0]=b,i[0]=w,f}function o(t,e,n,i,r){if(0!=r){if(!t)throw"Undef src";if(!n)throw"Undef dest";0==e&&r==t.length?l(t,n,i):A?l(t.subarray(e,e+r),n,i):1==t.BYTES_PER_ELEMENT&&r>100?l(new 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c=15,h=1440,d=0,f=0,p=1,_=-5,g=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],v=0,m=9,y=5,b=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],w=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],M=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,n){return t||(t=c),n&&(n=!1),this.istate=new e,this.istate.inflateInit(this,n?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new n(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var n,i;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,n=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,i=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+i)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&i)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?n:(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(n=t.istate.blocks.proc(t,n))){t.istate.mode=13,t.istate.marker=0;break}if(n==f&&(n=e),n!=p)return n;if(n=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,n){var i=0,r=n;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,n)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),r>=1<<t.istate.wbits&&(r=(1<<t.istate.wbits)-1,i=n-r),t.istate.blocks.set_dictionary(e,i,r),t.istate.mode=7,f)};var S=[0,0,255,255];e.prototype.inflateSync=function(t){var e,n,i,r,a;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(n=t.next_in_index,i=t.istate.marker;0!=e&&i<4;)t.next_in[n]==S[i]?i++:i=0!=t.next_in[n]?0:4-i,n++,e--;return t.total_in+=n-t.next_in_index,t.next_in_index=n,t.avail_in=e,t.istate.marker=i,4!=i?-3:(r=t.total_in,a=t.total_out,this.inflateReset(t),t.total_in=r,t.total_out=a,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];n.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},n.prototype.proc=function(t,e){var n,i,r,s,l,u,c;for(s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u;;)switch(this.mode){case v:for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}switch(n=7&i,this.last=1&n,n>>>1){case 0:i>>>=3,r-=3,n=7&r,i>>>=n,r-=n,this.mode=1;break;case 1:var h=new Int32Array(1),d=new Int32Array(1),_=[],m=[];a(h,d,_,m,t),this.codes.init(h[0],d[0],_[0],0,m[0],0,t),i>>>=3,r-=3,this.mode=6;break;case 2:i>>>=3,r-=3,this.mode=3;break;case 3:return i>>>=3,r-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}break;case 1:for(;r<32;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if((~i>>>16&65535)!=(65535&i))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.left=65535&i,i=r=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);if(0==c&&(u==end&&0!=read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c&&(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,u==this.end&&0!=this.read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c)))return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(e=f,n=this.left,n>l&&(n=l),n>c&&(n=c),o(t.next_in,s,this.window,u,n),s+=n,l-=n,u+=n,c-=n,0!=(this.left-=n))break;this.mode=0!=this.last?7:v;break;case 3:for(;r<14;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(this.table=n=16383&i,(31&n)>29||(n>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(n=258+(31&n)+(n>>5&31),null==this.blens||this.blens.length<n)this.blens=new Int32Array(n);else for(var y=0;y<n;y++)this.blens[y]=0;i>>>=14,r-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}this.blens[T[this.index++]]=7&i,i>>>=3,r-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(n=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=n,-3==e&&(this.blens=null,this.mode=9),this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(n=this.table,!(this.index<258+(31&n)+(n>>5&31)))break;var y,b,w;for(n=this.bb[0];r<n;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(n=this.hufts[3*(this.tb[0]+(i&g[n]))+1],(w=this.hufts[3*(this.tb[0]+(i&g[n]))+2])<16)i>>>=n,r-=n,this.blens[this.index++]=w;else{for(y=18==w?7:w-14,b=18==w?11:3;r<n+y;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(i>>>=n,r-=n,b+=i&g[y],i>>>=y,r-=y,y=this.index,n=this.table,y+b>258+(31&n)+(n>>5&31)||16==w&&y<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);w=16==w?this.blens[y-1]:0;do{this.blens[y++]=w}while(0!=--b);this.index=y}}this.tb[0]=-1;var h=new Int32Array(1),d=new Int32Array(1),_=new Int32Array(1),m=new Int32Array(1);if(h[0]=9,d[0]=6,n=this.table,(n=this.inftree.inflate_trees_dynamic(257+(31&n),1+(n>>5&31),this.blens,h,d,_,m,this.hufts,t))!=f)return-3==n&&(this.blens=null,this.mode=13),e=n,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.codes.init(h[0],d[0],this.hufts,_[0],this.hufts,m[0],t),this.mode=6;case 6:if(this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,this.read!=this.write)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);default:return e=-2,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}},n.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},n.prototype.set_dictionary=function(t,e,n){o(t,e,window,0,n),this.read=this.write=n},n.prototype.sync_point=function(){return 1==this.mode},n.prototype.inflate_flush=function(t,e){var n,i,r;return i=t.next_out_index,r=this.read,n=(r<=this.write?this.write:this.end)-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n,r==this.end&&(r=0,this.write==this.end&&(this.write=0),n=this.write-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n),t.next_out_index=i,this.read=r,e};i.prototype.init=function(t,e,n,i,r,a,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=n,this.ltree_index=i,this.dtree=r,this.dtree_index=a,this.tree=null},i.prototype.proc=function(t,e,n){var i,r,a,o,s,l,u,c=0,h=0,d=0;for(d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,n=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,n!=f)){this.mode=n==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>>=this.tree[r+1],h-=this.tree[r+1],0==(a=this.tree[r])){this.lit=this.tree[r+2],this.mode=6;break}if(0!=(16&a)){this.get=15&a,this.len=this.tree[r+2],this.mode=2;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}if(0!=(32&a)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 2:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.len+=c&g[i],c>>=i,h-=i,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>=this.tree[r+1],h-=this.tree[r+1],0!=(16&(a=this.tree[r]))){this.get=15&a,this.dist=this.tree[r+2],this.mode=4;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}return this.mode=9,e.msg="invalid distance code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 4:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.dist+=c&g[i],c>>=i,h-=i,this.mode=5;case 5:for(u=s-this.dist;u<0;)u+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);t.window[s++]=t.window[u++],l--,u==t.end&&(u=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(h>7&&(h-=8,o++,d--),t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);this.mode=8;case 8:return n=p,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 9:return n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);default:return n=-2,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n)}},i.prototype.free=function(t){},i.prototype.inflate_fast=function(t,e,n,i,r,a,s,l){var u,c,h,d,_,v,m,y,b,w,x,k,C,M,S,T;m=l.next_in_index,y=l.avail_in,_=s.bitb,v=s.bitk,b=s.write,w=b<s.read?s.read-b-1:s.end-b,x=g[t],k=g[e];do{for(;v<20;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(u=_&x,c=n,h=i,T=3*(h+u),0!=(d=c[T]))for(;;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15,C=c[T+2]+(_&g[d]),_>>=d,v-=d;v<15;)y--,_|=(255&l.next_in[m++])<<v,v+=8;for(u=_&k,c=r,h=a,T=3*(h+u),d=c[T];;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15;v<d;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(M=c[T+2]+(_&g[d]),_>>=d,v-=d,w-=C,b>=M)S=b-M,s.window[b++]=s.window[S++],s.window[b++]=s.window[S++],C-=2;else{S=b-M;do{S+=s.end}while(S<0);if(d=s.end-S,C>d){if(C-=d,b-S>0&&d>b-S)do{s.window[b++]=s.window[S++]}while(0!=--d);else o(s.window,S,s.window,b,d),b+=d,S+=d,d=0;S=0}}do{s.window[b++]=s.window[S++]}while(0!=--C);break}if(0!=(64&d))return l.msg="invalid distance code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3;u+=c[T+2],u+=_&g[d],T=3*(h+u),d=c[T]}break}if(0!=(64&d))return 0!=(32&d)?(C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3);if(u+=c[T+2],u+=_&g[d],T=3*(h+u),0==(d=c[T])){_>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--;break}}else _>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--}while(w>=258&&y>=10);return C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,f},r.prototype.huft_build=function(t,e,n,i,r,a,s,l,u,c,d){var p,g,v,m,y,b,w,x,k,C,M,S,T,$,A;C=0,y=n;do{this.c[t[e+C]]++,C++,y--}while(0!=y);if(this.c[0]==n)return s[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(w=b,x<b&&(x=b),y=15;0!=y&&0==this.c[y];y--);for(v=y,x>y&&(x=y),l[0]=x,$=1<<b;b<y;b++,$<<=1)if(($-=this.c[b])<0)return-3;if(($-=this.c[y])<0)return-3;for(this.c[y]+=$,this.x[1]=b=0,C=1,T=2;0!=--y;)this.x[T]=b+=this.c[C],T++,C++;y=0,C=0;do{0!=(b=t[e+C])&&(this.v[this.x[b]++]=y),C++}while(++y<n);for(n=this.x[v],this.x[0]=y=0,C=0,m=-1,S=-x,this.u[0]=0,M=0,A=0;w<=v;w++)for(p=this.c[w];0!=p--;){for(;w>S+x;){if(m++,S+=x,A=v-S,A=A>x?x:A,(g=1<<(b=w-S))>p+1&&(g-=p+1,T=w,b<A))for(;++b<A&&!((g<<=1)<=this.c[++T]);)g-=this.c[T];if(A=1<<b,this.hn[0]+A>h)return-3;this.u[m]=M=this.hn[0],this.hn[0]+=A,0!=m?(this.x[m]=y,this.r[0]=b,this.r[1]=x,b=y>>>S-x,this.r[2]=M-this.u[m-1]-b,o(this.r,0,u,3*(this.u[m-1]+b),3)):s[0]=M}for(this.r[1]=w-S,C>=n?this.r[0]=192:d[C]<i?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=a[this.v[C]-i]+16+64,this.r[2]=r[this.v[C++]-i]),g=1<<w-S,b=y>>>S;b<A;b+=g)o(this.r,0,u,3*(M+b),3);for(b=1<<w-1;0!=(y&b);b>>>=1)y^=b;for(y^=b,k=(1<<S)-1;(y&k)!=this.x[m];)m--,S-=x,k=(1<<S)-1}return 0!=$&&1!=v?_:f},r.prototype.inflate_trees_bits=function(t,e,n,i,r){var a;return this.initWorkArea(19),this.hn[0]=0,a=this.huft_build(t,0,19,19,null,null,n,e,i,this.hn,this.v),-3==a?r.msg="oversubscribed dynamic bit lengths tree":a!=_&&0!=e[0]||(r.msg="incomplete dynamic bit lengths tree",a=-3),a},r.prototype.inflate_trees_dynamic=function(t,e,n,i,r,a,o,s,l){var u;return this.initWorkArea(288),this.hn[0]=0,(u=this.huft_build(n,0,t,257,x,k,a,i,s,this.hn,this.v))!=f||0==i[0]?(-3==u?l.msg="oversubscribed literal/length tree":-4!=u&&(l.msg="incomplete literal/length tree",u=-3),u):(this.initWorkArea(288),u=this.huft_build(n,t,e,0,C,M,o,r,s,this.hn,this.v),u!=f||0==r[0]&&t>257?(-3==u?l.msg="oversubscribed distance tree":u==_?(l.msg="incomplete distance tree",u=-3):-4!=u&&(l.msg="empty distance tree with lengths",u=-3),u):f)},r.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length<t&&(this.v=new Int32Array(t));for(var e=0;e<t;e++)this.v[e]=0;for(var e=0;e<16;e++)this.c[e]=0;for(var e=0;e<3;e++)this.r[e]=0;o(this.c,0,this.u,0,15),o(this.c,0,this.x,0,16)};var $=new Uint8Array(1),A="function"==typeof $.subarray;return{inflateBuffer:u,arrayCopy:o}}.apply(e,i))&&(t.exports=r)},function(t,e,n){(function(i){var r,a,o;!function(i,s){a=[n(0)],r=s,void 0!==(o="function"==typeof r?r.apply(e,a):r)&&(t.exports=o)}(0,function(t){var e=t.ajaxSettings;e.responseFields.native="responseNative",e.converters["* native"]=!0;var n={},r=0,a={0:200,1223:204},o={},s=i.ajaxSettings.xhr();window.ActiveXObject&&t(window).on("unload",function(){for(var t in o)o[t]()}),n.cors=!!s&&"withCredentials"in s,n.ajax=s=!!s,t.ajaxTransport("native",function(t){var e;if(n.cors||s&&!t.crossDomain)return{send:function(n,i){var s,l=t.xhr(),u=++r,c={};if(l.open(t.type,t.url,t.async,t.username,t.password),t.xhrFields)for(s in t.xhrFields)l[s]=t.xhrFields[s];t.mimeType&&l.overrideMimeType&&l.overrideMimeType(t.mimeType),t.crossDomain||n["X-Requested-With"]||(n["X-Requested-With"]="XMLHttpRequest");for(s in n)l.setRequestHeader(s,n[s]);e=function(t){return function(){e&&(delete o[u],e=l.onload=l.onerror=null,"abort"===t?l.abort():"error"===t?i(l.status,l.statusText):(l.response&&(c.native=l.response),i(a[l.status]||l.status,l.statusText,c,l.getAllResponseHeaders())))}},l.onload=e(),l.onerror=e("error"),e=o[u]=e("abort");try{l.send(t.hasContent&&t.data||null)}catch(t){if(e)throw t}},abort:function(){e&&e()}}}),t.getNative=function(e,n){return t.ajax({dataType:"native",url:e,xhrFields:{responseType:"arraybuffer"},success:n})}})}).call(e,n(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(t,e,n){"use strict";function i(t){return t&&t.__esModule?t:{default:t}}function r(t){new s.default.GalaxyApp(t)}function a(t){new u.default.GalaxyApp(t)}Object.defineProperty(e,"__esModule",{value:!0}),e.tracksterApp=r,e.circsterApp=a;var o=n(145),s=i(o),l=n(296),u=i(l);window.tracksterApp=r,window.circsterApp=a},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}Object.defineProperty(e,"__esModule",{value:!0});var o=n(2),s=a(o),l=n(297),u=a(l),c=n(13),h=r(c),d=n(3),f=r(d),p=n(21),_=r(p),g=n(41),v=r(g);n(159);var m=t.Model.extend({is_visible:function(t,e){var n=t.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),y={drawTicks:function(t,e,n,i,r){var a=t.append("g").selectAll("g").data(e).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"}),o=[],s=[],l=function(t){return t.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(t){return t.label})},formatNum:function(t,e){if(void 0===e&&(e=2),null===t)return null;var n=null;if(Math.abs(t)<1)n=t.toPrecision(e);else{var i=Math.round(t.toPrecision(e));t=Math.abs(t),t<1e3?n=i:t<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":t<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},b=t.Model.extend({}),w=t.View.extend({className:"circster",initialize:function(t){this.genome=t.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var e=this.model.get("config");e.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),e.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"!==t.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"===t.get("track_type")})},get_tracks_bounds:function(){var t=this.get_circular_tracks(),e=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-t.length*(e+n)+n-this.label_arc_height,a=u.range(r,i/2,e+n);return s.map(a,function(t){return[t,t+e]})},render:function(){var t=this,e=t.$el.width(),n=t.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=t.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(t.$el[0]).append("svg").attr("width",e).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var e=u.event.scale;s.attr("transform","translate("+u.event.translate+") scale("+e+")"),t.scale!==e&&(t.zoom_drag_timeout&&clearTimeout(t.zoom_drag_timeout),t.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+e/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(e,n){var i=new M({el:s.append("g")[0],track:e,radius_bounds:o[n],genome:t.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(e){var n=new S({el:s.append("g")[0],track:e,radius_bounds:o[0],genome:t.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new k({el:s.append("g")[0],track:new b,radius_bounds:c,genome:t.genome,total_gap:a}),this.label_track_view.render()},add_track:function(t){var e=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===t.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new S({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:n,genome:this.genome,total_gap:e});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();s.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])}),s.each(this.chords_views,function(t){t.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new M({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();s.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();s.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),s.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),x=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new m;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),l=o.attr("chrom"),c=n.genome.get_chrom_region(l),h=n.track.get("data_manager");h.can_get_more_detailed_data(c)&&(a=n.track.get("data_manager").get_more_detailed_data(c,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=s.find(n.chroms_layout,function(t){return t.data.chrom===l}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=s.reject(s.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds;this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=s.zip(n,i);s.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var l=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",l).style("fill",l),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return s.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),k=x.extend({initialize:function(t){x.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=s.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});s.extend(k.prototype,y);var C=x.extend({initialize:function(t){x.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return 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o=n(3),s=a(o),l=n(4),u=a(l),c=n(9),h=a(c),d=n(63),f=a(d),p=n(40),_=a(p),g=t.View.extend({initialize:function(t){var e=this;this.modal=parent.Galaxy.modal||new h.default.View,this.form=new f.default(s.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(t,n){var r=n.model.attributes,a="",o={},l=r.job_id;l?a=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(a=Galaxy.root+"api/tools/"+r.id+"/build",o=i.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),r.version&&(o.tool_version=r.version),s.default.get({url:a,data:o,success:function(i){if(!i.display)return void(window.location=Galaxy.root);n.model.set(i),e._customize(n),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",i),t.resolve()},error:function(e,a){var o=e&&e.err_msg||"Uncaught error.";401==a?window.location=Galaxy.root+"user/login?"+i.param({redirect:Galaxy.root+"?tool_id="+r.id}):n.$el.is(":empty")?n.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},postchange:function(t,e){var n={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:i.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",n),s.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:n,success:function(n){e.update(n),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",n),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement("<div/>"),this.$el.append(this.form.$el)},_customize:function(t){var e=this,n=t.model.attributes,i=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+n.name+" ("+n.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){i.wait(),t.portlet.disable(),e.submit(n,function(){i.unwait(),t.portlet.enable()})}});n.buttons={execute:i},n.job_id&&n.job_remap&&n.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",n.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var n=this,a={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!n.validate(a))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=i("<form/>").attr({action:t.action,method:t.method,enctype:t.enctype});return r.each(a.inputs,function(t,e){o.append(i("<input/>").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",a),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:a,success:function(t){if(e&&e(),n.$el.children().hide(),n.$el.append(n._templateSuccess(t)),t.jobs&&t.jobs.length>0){n.$el.append(i("<div/>",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:a.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var i=!1;if(t&&t.err_data){var r=n.form.data.matchResponse(t.err_data);for(var o in r){n.form.highlight(o,r[o]),i=!0;break}}i||n.modal.show({title:"Job submission failed",body:n._templateError(a,t&&t.err_msg),buttons:{Close:function(){n.modal.hide()}}})}})},validate:function(t){var e=t.inputs,n=-1,i=null;for(var r in e){var a=e[r],o=this.form.data.match(r),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==a)return this.form.highlight(o),!1;if(a&&a.batch){var u=a.values.length,c=u>0&&a.values[0]&&a.values[0].src;if(c)if(null===i)i=c;else if(i!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=u;else if(n!==u)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+u+"</b> selection(s) while a previous field contains <b>"+n+"</b>."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,n=1==e?"1 job has":e+" jobs have",a=i("<div/>").addClass("donemessagelarge").append(i("<p/>").text(n+" been successfully added to the queue - resulting in the following datasets:"));return r.each(t.outputs,function(t){a.append(i("<p/>").addClass("messagerow").append(i("<b/>").text(t.hid+": "+t.name)))}),a.append(i("<p/>").append("<b/>").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),a}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return i("<div/>").addClass("errormessagelarge").append(i("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(i("<pre/>").text(JSON.stringify(t,null,4)))}});e.default={View:g}}).call(e,n(1),n(0),n(2))},,function(t,e,n){"use strict";(function(t,n,i){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==n.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,n){if(n){var i,r=this.attributes.filters[t];if(null===r||void 0===r)i=e;else if("string"==typeof r)if("All"==r||r==e)i=e;else{var a=[];a[0]=r,a[1]=e,i=a}else i=r,-1===i.indexOf(e)&&i.push(e);this.attributes.filters[t]=i}else this.attributes.filters[t]=e},remove_filter:function(t,e){var i=this.attributes.filters[t];if(null===i||void 0===i)return!1;if("string"==typeof i)this.attributes.filters[t]="";else{var r=n.indexOf(i,e);-1!==r&&(i[r]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return n.each(n.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+i.param(this.get_url_data())+"&"+i.param(t)}})}).call(e,n(1),n(2),n(0))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(3),a=function(t){return t&&t.__esModule?t:{default:t}}(r);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):'<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(t)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(t),t.info_text&&(e+='<br><div class="toolParamHelp" style="clear: both;">'+t.info_text+"</div>"),e},grid_table:function(t){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(t){var e='<div class="grid-header">';if(t.embedded||(e+="<h2>"+t.title+"</h2>"),t.global_actions){e+='<ul class="manage-table-actions">';var n=t.global_actions.length>=3;n&&(e+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">');for(var i in t.global_actions){var r=t.global_actions[i];e+='<li><a class="action-button use-target" target="'+r.target+'" href="'+r.url_args+'" onclick="return false;" >'+r.label+"</a></li>"}n&&(e+="</div>"),e+="</ul>"}return t.insert&&(e+=t.insert),e+=this.grid_filters(t),e+="</div>"},header:function(t){var e="<tr>";t.show_item_checkboxes&&(e+="<th>",t.items.length>0&&(e+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'),e+="</th>");for(var n in t.columns){var i=t.columns[n];i.visible&&(e+='<th id="'+i.key+'-header">',i.href?e+='<a href="'+i.href+'" class="sort-link" sort_key="'+i.key+'">'+i.label+"</a>":e+=i.label,e+='<span class="sort-arrow">'+i.extra+"</span></th>")}return e+="</tr>"},body:function(e){var n="",i=0;0==e.items.length&&(n+='<tr><td colspan="100"><em>No Items</em></td></tr>',i=1);for(var r in e.items){var a=e.items[r],o=a.encode_id;n+="<tr ",e.current_item_id==a.id&&(n+='class="current"'),n+=">",e.show_item_checkboxes&&(n+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+o+'" id="'+o+'" class="grid-row-select-checkbox" /></td>');for(var s in e.columns){var l=e.columns[s];if(l.visible){var u="";l.nowrap&&(u='style="white-space:nowrap;"');var c=a.column_config[l.label],h=c.link,d=c.value,f=c.target;"string"===t.type(d)&&(d=d.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+r+"-popup",_="menubutton",""!=h&&(_+=" split"),_+=" popup"),n+="<td "+u+">",h?(0!=e.operations.length&&(n+='<div id="'+p+'" class="'+_+'" style="float: left;">'),n+='<a class="menubutton-label use-target" target="'+f+'" href="'+h+'" onclick="return false;">'+d+"</a>",0!=e.operations.length&&(n+="</div>")):n+='<div id="'+p+'" class="'+_+'"><label id="'+l.label_id_prefix+o+'" for="'+o+'">'+(d||"")+"</label></div>",n+="</td>"}}n+="</tr>",i++}return n},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var n=t.num_page_links,i=t.cur_page_num,r=t.num_pages,a=n/2,o=i-a,s=0;o<=0&&(o=1,s=a-(i-o));var l,u=a+s,c=i+u;c<=r?l=0:(c=r,l=u-(c+1-i)),0!=l&&(o-=l)<1&&(o=1),e+='<tr id="page-links-row">',t.show_item_checkboxes&&(e+="<td></td>"),e+='<td colspan="100"><span id="page-link-container">Page:',o>1&&(e+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...');for(var h=o;h<c+1;h++)h==t.cur_page_num?e+='<span class="page-link inactive-link" id="page-link-'+h+'">'+h+"</span>":e+='<span class="page-link" id="page-link-'+h+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+h+'">'+h+"</a></span>";c<r&&(e+='...<span class="page-link" id="page-link-'+r+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+r+'">'+r+"</a></span>"),e+="</span>",e+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(t.show_item_checkboxes){e+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected items: ';for(var d in t.operations){var f=t.operations[d];f.allow_multiple&&(e+='<input type="button" value="'+f.label+'" class="operation-button action-button">&nbsp;')}e+="</td></tr>"}var p=!1;for(d in t.operations)if(t.operations[d].global_operation){p=!0;break}if(p){e+='<tr><td colspan="100">';for(d in t.operations){var f=t.operations[d];f.global_operation&&(e+='<a class="action-button" href="'+f.global_operation+'">'+f.label+"</a>")}e+="</td></tr>"}return t.legend&&(e+='<tr><td colspan="100">'+t.legend+"</td></tr>"),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),'<p><div class="'+e+'message transient-message">'+i.escape(t.message)+'</div><div style="clear: both"></div></p>'},grid_filters:function(t){var e=t.default_filter_dict,n=t.filters,i="none";t.advanced_search&&(i="block");var r=!1;for(var a in t.columns){var o=t.columns[a];if("advanced"==o.filterable){var s=o.key,l=n[s],u=e[s];l&&u&&l!=u&&(i="block"),r=!0}}var c="block";"block"==i&&(c="none");var h='<div id="standard-search" style="display: '+c+';"><table><tr><td style="padding: 0;"><table>';for(var a in t.columns){var o=t.columns[a];"standard"==o.filterable&&(h+=this.grid_column_filter(t,o))}h+="</table></td></tr><tr><td>",r&&(h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'),h+="</td></tr></table></div>",h+='<div id="advanced-search" style="display: '+i+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var a in t.columns){var o=t.columns[a];"advanced"==o.filterable&&(h+=this.grid_column_filter(t,o))}return h+="</table></div>"},grid_column_filter:function(e,n){var i=(e.default_filter_dict,e.filters),r=n.label,a=n.key;"advanced"==n.filterable&&(r=r.toLowerCase());var o="<tr>";if("advanced"==n.filterable&&(o+='<td align="left" style="padding-left: 10px">'+r+":</td>"),o+='<td style="padding-bottom: 1px;">',n.is_text){o+='<form class="text-filter-form" column_key="'+a+'" action="'+e.url+'" method="get" >';for(h in e.columns){var s=e.columns[h],l=i[s.key];l&&"All"!=l&&(s.is_text&&(l=JSON.stringify(l)),o+='<input type="hidden" id="'+s.key+'" name="f-'+s.key+'" value="'+l+'"/>')}o+='<span id="'+a+'-filtering-criteria">';var u=i[a];if(u){var c=t.type(u);if("string"==c&&"All"!=u&&(o+=this.filter_element(a,u)),"array"==c)for(var h in u){var d=u[h],f=u;f=f.slice(h),o+=this.filter_element(a,d)}}o+="</span>";var p="";if("standard"==n.filterable){p=n.label.toLowerCase();var _=p.length;_<20&&(_=20),_+=4}o+='<span class="search-box"><input class="search-box-input" id="input-'+a+'-filter" name="f-'+a+'" type="text" placeholder="'+p+'" size="'+_+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{o+='<span id="'+a+'-filtering-criteria">';var g=!1;for(var v in e.categorical_filters[a]){var m=e.categorical_filters[a][v],y="",b="";for(var w in m)y=w,b=m[w];g&&(o+=" | "),g=!0;var d=i[a];d&&m[a]&&d==b?o+='<span class="categorical-filter '+a+'-filter current-filter">'+v+"</span>":o+='<span class="categorical-filter '+a+'-filter"><a href="javascript:void(0);" filter_key="'+y+'" filter_val="'+b+'">'+v+"</a></span>"}o+="</span>"}return o+="</td></tr>"},filter_element:function(t,e){return'<span class="text-filter-val">'+(e=a.default.sanitize(e))+'<a href="javascript:void(0);" filter_key="'+t+'" filter_val="'+e+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}).call(e,n(0),n(2))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(146),l=r(s),u=n(13),c=r(u),h=n(41),d=r(h),f=n(61),p=r(f),_=n(26),g=r(_),v=n(3),m=r(v);n(170),n(169),n(171),n(157),n(174),n(159),n(172),n(173),n(25);var y=null,b=null,w=function(){this.initialize&&this.initialize.apply(this,arguments)};w.extend=t.Model.extend;var x=w.extend({initialize:function(t){m.default.cssLoadFile("static/style/jquery.rating.css"),m.default.cssLoadFile("static/style/autocomplete_tagging.css"),m.default.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),m.default.cssLoadFile("static/style/library.css"),m.default.cssLoadFile("static/style/trackster.css"),this.baseURL=t},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var t=[];i(".bookmark").each(function(){t.push({position:i(this).children(".position").text(),annotation:i(this).children(".annotation").text()})});var e=b.overview_drawable?b.overview_drawable.config.get_value("name"):null,n={view:b.to_dict(),viewport:{chrom:b.chrom,start:b.low,end:b.high,overview:e},bookmarks:t};return i.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.vis_id,title:b.config.get_value("name"),dbkey:b.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(t){Galaxy.modal.hide(),b.vis_id=t.vis_id,b.has_changes=!1,window.history.pushState({},"",t.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var t=this,e=d.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.default.select_datasets({dbkey:b.dbkey},function(t){o.each(t,function(t){b.add_drawable(l.default.object_from_template(t,b,b))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){b.add_drawable(new l.default.DrawableGroup(b,b,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==i("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=t.baseURL+"visualization/circster?id="+b.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){t.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){t.handle_unsaved_changes(b)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=e,e},add_bookmark:function(t,e,n){var r=i("#right .unified-panel-body"),a=i("<div/>").addClass("bookmark").appendTo(r),o=i("<div/>").addClass("position").appendTo(a),s=(i("<a href=''/>").text(t).appendTo(o).click(function(){return b.go_to(t),!1}),i("<div/>").text(e).appendTo(a));if(n){var l=i("<div/>").addClass("delete-icon-container").prependTo(a).click(function(){return a.slideUp("fast"),a.remove(),b.has_changes=!0,!1});i("<a href=''/>").addClass("icon-button delete").appendTo(l);s.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return b.has_changes=!0,a},create_visualization:function(t,e,n,r,a){var s=this,u=new l.default.TracksterView(o.extend(t,{header:!1}));return u.editor=!0,i.when(u.load_chroms_deferred).then(function(t){if(e){var i=e.chrom,o=e.start,c=e.end,h=e.overview;i&&void 0!==o&&c?u.change_chrom(i,o,c):u.change_chrom(t[0].chrom)}else u.change_chrom(t[0].chrom);if(n)for(var d=0;d<n.length;d++)u.add_drawable(l.default.object_from_template(n[d],u,u));for(var d=0;d<u.drawables.length;d++)if(u.drawables[d].config.get_value("name")===h){u.set_overview(u.drawables[d]);break}if(r)for(var f,d=0;d<r.length;d++)f=r[d],s.add_bookmark(f.position,f.annotation,a);u.has_changes=!1}),this.set_up_router({view:u}),u},set_up_router:function(e){new c.default.TrackBrowserRouter(e),t.history.start()},init_keyboard_nav:function(t){i(document).keyup(function(e){if(!i(e.srcElement).is(":input"))switch(e.which){case 37:t.move_fraction(.25);break;case 38:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()-20);break;case 39:t.move_fraction(-.25);break;case 40:Math.round(t.viewport_container.height()/15);t.viewport_container.scrollTop(t.viewport_container.scrollTop()+20)}})},handle_unsaved_changes:function(t){if(t.has_changes){var e=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){i(window).off("beforeunload"),window.location=Galaxy.root+"visualization"},Save:function(){i.when(e.save_viz()).then(function(){window.location=Galaxy.root+"visualization"})}}})}else window.location=Galaxy.root+"visualization"}}),k=t.View.extend({initialize:function(){y=new x(Galaxy.root),y.createButtonMenu(),y.buttonMenu.$el.attr("style","float: right"),i("#center .unified-panel-header-inner").append(y.buttonMenu.$el),i("#right .unified-panel-title").append("Bookmarks"),i("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>"),i("#right-border").click(function(){b.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():p.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var t=this,e=p.default.get("dbkey"),n={},i={dbkey:e,dataset_id:p.default.get("dataset_id"),hda_ldda:p.default.get("hda_ldda"),gene_region:p.default.get("gene_region")};e&&(n["f-dbkey"]=e),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>"+(e||"Not available.")+"</b></li><li>or create a new session with this dataset as the only track</li></ul></p>",buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){t.view_in_saved(i)},"View in new visualization":function(){t.view_new()}}})},view_in_saved:function(t){var e=new g.default({url_base:Galaxy.root+"visualization/list_tracks",dict_format:!0,embedded:!0});Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e.$el,buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){i(parent.document).find("input[name=id]:checked").each(function(){t.id=i(this).val(),window.location=Galaxy.root+"visualization/trackster?"+i.param(t)})}}})},view_existing:function(){var t=galaxy_config.app.viz_config;b=y.create_visualization({container:i("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()},view_new:function(){var t=this;i.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:t.template_view_new(e),buttons:{Cancel:function(){window.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(i("#new-title").val(),i("#new-dbkey").val()),Galaxy.modal.hide()}}});var n=e.map(function(t){return t[1]});galaxy_config.app.default_dbkey&&o.contains(n,galaxy_config.app.default_dbkey)&&i("#new-dbkey").val(galaxy_config.app.default_dbkey),i("#new-title").focus(),i("select[name='dbkey']").select2(),i("#overlay").css("overflow","auto")}})},template_view_new:function(t){for(var e='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">',n=0;n<t.length;n++)e+='<option value="'+t[n][1]+'">'+t[n][0]+"</option>";return e+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+Galaxy.root+'custom_builds">Add a Custom Build</a></div></form>'},create_browser:function(t,e){i(document).trigger("convert_to_values"),b=y.create_visualization({container:i("#center .unified-panel-body"),name:t,dbkey:e},galaxy_config.app.gene_region),this.init_editor(),b.editor=!0},init_editor:function(){i("#center .unified-panel-title").text(b.config.get_value("name")+" ("+b.dbkey+")"),galaxy_config.app.add_dataset&&i.ajax({url:Galaxy.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(t){b.add_drawable(l.default.object_from_template(t,b,b))}}),i("#add-bookmark-button").click(function(){var t=b.chrom+":"+b.low+"-"+b.high;return y.add_bookmark(t,"Bookmark description",!0)}),y.init_keyboard_nav(b),i(window).on("beforeunload",function(){if(b.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}});e.default={TracksterUI:x,GalaxyApp:k}}).call(e,n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t,e){e||(e=0);var n=Math.pow(10,e);return Math.round(t*n)/n}function o(e){var n=t.Deferred();return t.ajax({type:"HEAD",url:e,beforeSend:function(t){t.setRequestHeader("Range","bytes=0-10")},success:function(t,e,i){n.resolve(206===i.status)}}),n}Object.defineProperty(e,"__esModule",{value:!0});var s=n(2),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(s),u=n(13),c=r(u),h=n(147),d=r(h),f=n(14),p=r(f),_=n(148),g=r(_),v=n(149),m=r(v),y=n(150),b=r(y),w=n(15),x=r(w),k=n(140),C=r(k),M=n(21),S=r(M),T=n(151),$=r(T);n(25);var A=l.extend,E={},O=function(t,e){E[t.attr("id")]=e},z=function(e,n,i,r){i=".group",E[e.attr("id")]=r,e.bind("drag",{handle:"."+n,relative:!0},function(e,n){var r,a,o,s,l,u=(t(this),t(this).parent()),c=u.children(".track,.group"),h=E[t(this).attr("id")];if(a=t(this).parents(i),0!==a.length){o=a.position().top,s=o+a.outerHeight();var d=E[a.attr("id")];if(n.offsetY<o)return t(this).insertBefore(a),d.remove_drawable(h),void d.container.add_drawable_before(h,d);if(n.offsetY>s)return t(this).insertAfter(a),d.remove_drawable(h),void d.container.add_drawable(h)}for(a=null,l=0;l<c.length;l++)if(r=t(c.get(l)),o=r.position().top,s=o+r.outerHeight(),r.is(i)&&this!==r.get(0)&&n.offsetY>=o&&n.offsetY<=s)return n.offsetY-o<s-n.offsetY?r.find(".content-div").prepend(this):r.find(".content-div").append(this),h.container&&h.container.remove_drawable(h),void E[r.attr("id")].add_drawable(h);for(l=0;l<c.length&&(r=t(c.get(l)),!(n.offsetY<r.position().top)||r.hasClass("reference-track")||r.hasClass("intro"));l++);l===c.length?this!==c.get(l-1)&&(u.append(this),E[u.attr("id")].move_drawable(h,l)):this!==c.get(l)&&(t(this).insertBefore(c.get(l)),E[u.attr("id")].move_drawable(h,n.deltaY>0?l-1:l))}).bind("dragstart",function(){t(this).addClass("dragging")}).bind("dragend",function(){t(this).removeClass("dragging")})},R="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",N=["Histogram","Line","Filled","Intensity"],P=function t(e,n,i){if(t.id_counter||(t.id_counter=0),this.id=t.id_counter++,this.view=e,this.container=n,this.drag_handle_class=i.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=S.default.ConfigSettingCollection.from_models_and_saved_values(this.config_params,i.prefs),this.config.get_value("name")||this.config.set_value("name",i.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==i.header){var r=new d.default.TrackHeaderView({model:this,id:this.id});this.header_div=r.$el,this.container_div.append(this.header_div);var a=r.icons_div;this.action_icons=r.action_icons,this.container_div.hover(function(){a.show()},function(){a.hide()})}};P.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(t){t.config.get_value("content_visible")?(t.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),t.hide_contents(),t.config.set_value("content_visible",!1)):(t.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),t.config.set_value("content_visible",!0),t.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(t){new S.default.ConfigSettingCollectionView({collection:t.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(e){t(".tooltip").remove(),e.remove()}}],A(P.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(t){},to_dict:function(){},set_name:function(t){this.old_name=this.config.get_value("name"),this.config.set_value("name",t)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var e=this.view;this.container_div.hide(0,function(){t(this).remove(),e.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var q=function(t,e,n){P.call(this,t,e,n),this.obj_type=n.obj_type,this.drawables=[]};A(q.prototype,P.prototype,{unpack_drawables:function(t){this.drawables=[];for(var e,n=0;n<t.length;n++)e=it(t[n],this.view,this),this.add_drawable(e)},init:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].init()},_draw:function(t){for(var e=0;e<this.drawables.length;e++)this.drawables[e]._draw(t)},to_dict:function(){for(var t=[],e=0;e<this.drawables.length;e++)t.push(this.drawables[e].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:t}},add_drawable:function(t){this.drawables.push(t),t.container=this,this.changed()},add_drawable_before:function(t,e){this.changed();var n=this.drawables.indexOf(e);return-1!==n&&(this.drawables.splice(n,0,t),!0)},replace_drawable:function(t,e,n){var i=this.drawables.indexOf(t);return-1!==i&&(this.drawables[i]=e,n&&t.container_div.replaceWith(e.container_div),this.changed()),i},remove_drawable:function(t){var e=this.drawables.indexOf(t);return-1!==e&&(this.drawables.splice(e,1),t.container=null,this.changed(),!0)},move_drawable:function(t,e){var n=this.drawables.indexOf(t);return-1!==n&&(this.drawables.splice(n,1),this.drawables.splice(e,0,t),this.changed(),!0)},get_drawables:function(){return this.drawables},get_tracks:function(t){for(var e,n=this.drawables.slice(0),i=[];0!==n.length;)e=n.shift(),e instanceof t?i.push(e):e.drawables&&(n=n.concat(e.drawables));return i}});var j=function(e,n,i){if(A(i,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),q.call(this,e,n,i),this.content_div=t("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),O(this.container_div,this),O(this.content_div,this),z(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new b.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(t("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in i&&this.unpack_drawables(i.drawables),"filters"in i){var r=this.filters_manager;this.filters_manager=new b.default.FiltersManager(this,i.filters),r.parent_div.replaceWith(this.filters_manager.parent_div),i.filters.visible&&this.setup_multitrack_filtering()}};A(j.prototype,P.prototype,q.prototype,{action_icons_def:[P.prototype.action_icons_def[0],P.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?(t.filters_manager.clear_filters(),t._restore_filter_managers()):(t.setup_multitrack_filtering(),t.request_draw({clear_tile_cache:!0})),t.filters_manager.toggle()}},P.prototype.action_icons_def[2]],build_container_div:function(){var e=t("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(e),e},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var e=this.drawables.length;if(0===e)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===e)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof W),this.action_icons.filters_icon.hide();else{var n,i,r,a=this.drawables[0].get_type(),o=0;for(n=0;n<e;n++){if(r=this.drawables[n],r.get_type()!==a){can_composite=!1;break}r instanceof Q&&o++}if(this.drawables[0]instanceof K?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),t(".tooltip").remove()),o>1&&o===this.drawables.length){var s,l={};for(r=this.drawables[0],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],l[s.name]=[s];for(n=1;n<this.drawables.length;n++)for(r=this.drawables[n],i=0;i<r.filters_manager.filters.length;i++)s=r.filters_manager.filters[i],s.name in l&&l[s.name].push(s);this.filters_manager.remove_all();var u,c;for(var h in l)u=l[h],u.length===o&&(c=new b.default.NumberFilter({name:u[0].name,index:u[0].index}),this.filters_manager.add_filter(c));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var t=0;t<this.drawables.length;t++)this.drawables[t].filters_manager=this.saved_filters_managers[t];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var t=0;t<this.drawables.length;t++){var e=this.drawables[t];this.saved_filters_managers.push(e.filters_manager),e.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var t=new W(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,t,!0);t.request_draw()},add_drawable:function(t){q.prototype.add_drawable.call(this,t),this.update_icons()},remove_drawable:function(t){q.prototype.remove_drawable.call(this,t),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var t=A(q.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),t},request_draw:function(t){l.each(this.drawables,function(e){e.request_draw(t)})}});var D=i.View.extend({initialize:function(t){A(t,{obj_type:"View"}),q.call(this,"View",t.container,t),this.chrom=null,this.vis_id=t.vis_id,this.dbkey=t.dbkey,this.stand_alone=void 0===t.stand_alone||t.stand_alone,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new c.default.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=S.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:t.name})},render:function(){this.requested_redraw=!1;var e=this.container,n=this;this.top_container=t("<div/>").addClass("top-container").appendTo(e),this.browser_content_div=t("<div/>").addClass("content").appendTo(e),this.bottom_container=t("<div/>").addClass("bottom-container").appendTo(e),this.top_labeltrack=t("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=t("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,O(this.viewport_container,n),this.intro_div=t("<div/>").addClass("intro").appendTo(this.viewport_container);t("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){c.default.select_datasets({dbkey:n.dbkey},function(t){l.each(t,function(t){n.add_drawable(it(t,n,n))})})});this.nav_container=t("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=t("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=t("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=t("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=t("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=t("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=t("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=t("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=t("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=t("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var i=function(e){"focusout"!==e.type&&13!==(e.keyCode||e.which)&&27!==(e.keyCode||e.which)||(27!==(e.keyCode||e.which)&&n.go_to(t(this).val()),t(this).hide(),t(this).val(""),n.location_span.show(),n.chrom_select.show()),e.stopPropagation()};this.nav_input=t("<input/>").addClass("nav-input").hide().bind("keyup focusout",i).appendTo(this.nav_controls),this.location_span=t("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){n.location_span.hide(),n.chrom_select.hide(),n.nav_input.val(n.chrom+":"+n.low+"-"+n.high),n.nav_input.css("display","inline-block"),n.nav_input.select(),n.nav_input.focus(),n.nav_input.autocomplete({source:function(e,i){var r=[],a=t.map(n.get_tracks(Q),function(t){return t.data_manager.search_features(e.term).success(function(t){r=r.concat(t)})});t.when.apply(t,a).done(function(){i(t.map(r,function(t){return{label:t[0],value:t[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=t("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=t("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){n.zoom_out()}).appendTo(this.nav_controls),this.zi_link=t("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){n.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){n.change_chrom(n.chrom_select.val())}),this.browser_content_div.click(function(e){t(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(t){n.zoom_in(t.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(t,e){this.current_x=e.offsetX}).bind("drag",function(t,e){var i=e.offsetX-this.current_x;this.current_x=e.offsetX;var r=Math.round(i/n.viewport_container.width()*(n.max_high-n.max_low));n.move_delta(-r)}),this.overview_close.click(function(){n.reset_overview()}),this.viewport_container.bind("draginit",function(t,e){if(t.clientX>n.viewport_container.width()-16)return!1}).bind("dragstart",function(t,e){e.original_low=n.low,e.current_height=t.clientY,e.current_x=e.offsetX}).bind("drag",function(e,i){var r=t(this),a=i.offsetX-i.current_x,o=r.scrollTop()-(e.clientY-i.current_height);r.scrollTop(o),i.current_height=e.clientY,i.current_x=i.offsetX;var s=Math.round(a/n.viewport_container.width()*(n.high-n.low));n.move_delta(s)}),this.top_labeltrack.bind("dragstart",function(e,i){return t("<div/>").addClass("zoom-area").css("height",n.browser_content_div.height()+n.top_labeltrack.height()+1).appendTo(t(this))}).bind("drag",function(e,i){t(i.proxy).css({left:Math.min(e.pageX,i.startX)-n.container.offset().left,width:Math.abs(e.pageX-i.startX)});var r=Math.min(e.pageX,i.startX)-n.container.offset().left,a=Math.max(e.pageX,i.startX)-n.container.offset().left,o=n.high-n.low,s=n.viewport_container.width();n.update_location(Math.round(r/s*o)+n.low,Math.round(a/s*o)+n.low)}).bind("dragend",function(e,i){var r=Math.min(e.pageX,i.startX),a=Math.max(e.pageX,i.startX),o=n.high-n.low,s=n.viewport_container.width(),l=n.low;n.low=Math.round(r/s*o)+l,n.high=Math.round(a/s*o)+l,t(i.proxy).remove(),n.request_redraw()}),this.add_label_track(new X(this,{content_div:this.top_labeltrack})),t(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){n.resize_window()},500)}),t(document).bind("redraw",function(){n.redraw()}),this.reset(),t(window).trigger("resize")},get_base_color:function(t){return this.config.get_value(t.toLowerCase()+"_color")||this.config.get_value("n_color")}});A(D.prototype,q.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(t,e,n,i){if(this.timer&&clearTimeout(this.timer),i){var r=this;this.timer=setTimeout(function(){r.trigger("navigate",t+":"+e+"-"+n)},500)}else view.trigger("navigate",t+":"+e+"-"+n)},update_location:function(t,e){this.location_span.text(p.default.commatize(t)+" - "+p.default.commatize(e)),this.nav_input.val(this.chrom+":"+p.default.commatize(t)+"-"+p.default.commatize(e));var n=this.chrom_select.val();""!==n&&this.trigger_navigate(n,this.low,this.high,!0)},load_chroms:function(e){e.num=100;var n=this,i=t.Deferred();return t.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:e,dataType:"json",success:function(e){if(0!==e.chrom_info.length){if(e.reference){var r=new J(n);n.add_label_track(r),n.reference_track=r}n.chrom_data=e.chrom_info,n.chrom_select.html(""),n.chrom_select.append(t('<option value="">Select Chrom/Contig</option>'));for(var a=0,o=n.chrom_data.length;a<o;a++){var s=n.chrom_data[a].chrom,l=t("<option>");l.text(s),l.val(s),n.chrom_select.append(l)}e.prev_chroms&&n.chrom_select.append(t('<option value="previous">Previous 100</option>')),e.next_chroms&&n.chrom_select.append(t('<option value="next">Next 100</option>')),n.chrom_start_index=e.start_index,i.resolve(e.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+n.dbkey)}}),i},change_chrom:function(e,n,i){var r=this;if(!r.chrom_data)return void r.load_chroms_deferred.then(function(){r.change_chrom(e,n,i)});if(e&&"None"!==e){if("previous"===e)return void r.load_chroms({low:this.chrom_start_index-100});if("next"===e)return void r.load_chroms({low:this.chrom_start_index+100});var a=t.grep(r.chrom_data,function(t,n){return t.chrom===e})[0];if(void 0===a)return void r.load_chroms({chrom:e},function(){r.change_chrom(e,n,i)});if(e!==r.chrom){r.chrom=e,r.chrom_select.val(r.chrom),r.max_high=a.len-1,r.reset();for(var o=0,s=r.drawables.length;o<s;o++){var l=r.drawables[o];l.init&&l.init()}r.reference_track&&r.reference_track.init()}void 0===n&&void 0===i?(r.low=0,r.high=r.max_high):(r.low=void 0!==n?Math.max(n,0):0,void 0===i?(r.low=Math.max(r.low-15,0),r.high=r.low+30):r.high=Math.min(i,r.max_high)),r.request_redraw()}},go_to:function(t){t=t.replace(/,/g,""),t=t.replace(/:|\-/g," ");var e=t.split(/\s+/),n=e[0],i=e[1]?parseInt(e[1],10):void 0,r=e[2]?parseInt(e[2],10):void 0;this.change_chrom(n,i,r)},move_fraction:function(t){var e=this,n=e.high-e.low;this.move_delta(t*n)},move_delta:function(t){var e=this,n=e.high-e.low;e.low-t<e.max_low?(e.low=e.max_low,e.high=e.max_low+n):e.high-t>e.max_high?(e.high=e.max_high,e.low=e.max_high-n):(e.high-=t,e.low-=t),e.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){e.request_redraw()},200);var i=e.chrom_select.val();this.trigger_navigate(i,e.low,e.high,!0)},add_drawable:function(t){q.prototype.add_drawable.call(this,t),t.init(),this.changed(),this.update_intro_div();var e=this;t.config.on("change",function(){e.changed()})},add_label_track:function(t){t.view=this,t.init(),this.label_tracks.push(t)},remove_drawable:function(e,n){if(q.prototype.remove_drawable.call(this,e),n){var i=this;e.container_div.hide(0,function(){t(this).remove(),i.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(t,e){var n=this,i=e?[e]:n.drawables;l.each(i,function(e){var i=l.find(n.tracks_to_be_redrawn,function(t){return t[0]===e});i?i[1]=t:n.tracks_to_be_redrawn.push([e,t])}),this.requested_redraw||(requestAnimationFrame(function(){n._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var t=this.low,e=this.high;t<this.max_low&&(t=this.max_low),e>this.max_high&&(e=this.max_high);var n=this.high-this.low;0!==this.high&&n<this.min_separation&&(e=t+this.min_separation),this.low=Math.floor(t),this.high=Math.ceil(e),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var i=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,r=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0;this.overview_box.css({left:i,width:Math.max(13,r)}).show(),r<13&&this.overview_box.css("left",i-(13-r)/2),this.overview_highlight&&this.overview_highlight.css({left:i,width:r}),l.each(this.tracks_to_be_redrawn,function(t){var e=t[0],n=t[1];e&&e._draw(n)}),this.tracks_to_be_redrawn=[],l.each(this.label_tracks,function(t){t._draw()})},zoom_in:function(t,e){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var n=this.high-this.low,i=n/2+this.low,r=n/this.zoom_factor/2;t&&(i=t/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(i-r),this.high=Math.round(i+r),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var t=this.high-this.low,e=t/2+this.low,n=t*this.zoom_factor/2;this.low=Math.round(e-n),this.high=Math.round(e+n),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(t){if(this.overview_drawable){if(this.overview_drawable.dataset.id===t.dataset.id)return;this.overview_viewport.find(".track").remove()}var e=t.copy({content_div:this.overview_viewport}),n=this;e.header_div.hide(),e.is_overview=!0,n.overview_drawable=e,this.overview_drawable.postdraw_actions=function(){n.overview_highlight.show().height(n.overview_drawable.content_div.height()),n.overview_viewport.height(n.overview_drawable.content_div.height()+n.overview_box.outerHeight()),n.overview_close.show(),n.resize_window()},n.overview_drawable.request_draw(),this.changed()},reset_overview:function(){t(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var L=C.default.Tool.extend({defaults:{track:null},initialize:function(t){C.default.Tool.prototype.initialize.call(this,t);var e=!0;void 0!==t.tool_state&&void 0!==t.tool_state.hidden&&(e=t.tool_state.hidden),this.set("hidden",e),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(t){return l.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=i.View.extend({events:{"change :input":"update_value"},render:function(){var e=this.$el.addClass("param-row"),n=this.model;t("<div>").addClass("param-label").text(n.get("label")).appendTo(e);t("<div/>").addClass("param-input").html(n.get("html")).appendTo(e).find(":input").val(n.get("value")),t("<div style='clear: both;'/>").appendTo(e)},update_value:function(e){this.model.set_value(t(e.target).val())}}),B=i.View.extend({initialize:function(t){this.model.on("change:hidden",this.set_visible,this)},render:function(){var e=this,n=this.model,i=this.$el.addClass("dynamic-tool").hide();i.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).keydown(function(t){t.stopPropagation()});t("<div class='tool-name'>").appendTo(i).text(n.get("name"));n.get("inputs").each(function(t){var e=new I({model:t});e.render(),i.append(e.$el)}),i.find("input").click(function(){t(this).select()});var r=t("<div>").addClass("param-row").appendTo(i),a=t("<input type='submit'>").attr("value","Run on complete dataset").appendTo(r);t("<input type='submit'>").attr("value","Run on visible region").appendTo(r).click(function(){e.run_on_region()}),a.click(function(){e.run_on_dataset()}),n.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var t=0;t<this.params.length;t++)this.params[t].update_value()},run_on_dataset:function(){var t=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:t.id},null,function(e){Galaxy.modal.show({title:t.get("name")+" is Running",body:t.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var t,e=this.model.get("track"),n=this.model,i=new c.default.GenomeRegion({chrom:e.view.chrom,start:e.view.low,end:e.view.high}),r={target_dataset_id:e.dataset.id,action:"rerun",tool_id:n.id,regions:[i.toJSON()]},a=e,o=n.get("name")+a.tool_region_and_parameters_str(i);if(a.container===view){var s=new j(view,view,{name:e.config.get_value("name")}),l=a.container.replace_drawable(a,s,!1);s.container_div.insertBefore(a.view.content_div.children()[l]),s.add_drawable(a),a.container_div.appendTo(s.content_div),t=s}else t=a.container;var u=new a.constructor(view,t,{name:o,hda_ldda:"hda"});u.init_for_tool_data(),u.change_mode(a.mode),u.set_filters_manager(a.filters_manager.copy(u)),u.update_icons(),t.add_drawable(u),u.tiles_div.text("Starting job."),this.run(r,u,function(t){u.set_dataset(new x.default.Dataset(t)),u.tiles_div.text("Running job."),u.init()})},run:function(e,n,i){e.inputs=this.model.get_inputs_dict();var r=new p.default.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});t.when(r.go()).then(function(t){"no converter"===t?(n.container_div.addClass("error"),n.content_div.text(R)):t.error?(n.container_div.addClass("error"),n.content_div.text("Tool cannot be rerun: "+t.message)):i(t)})}}),V=function(t,e){m.default.Scaler.call(this,e),this.filter=t};V.prototype.gen_val=function(t){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(t[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var U=function(e,n,i,r,a){this.track=e,this.region=n,this.low=n.get("start"),this.high=n.get("end"),this.w_scale=i,this.canvas=r,this.html_elt=t("<div class='track-tile'/>").append(r),this.data=a,this.stale=!1};U.prototype.predisplay_actions=function(){};var F=function(t,e,n,i,r){U.call(this,t,e,n,i,r)};F.prototype.predisplay_actions=function(){};var G=function(t,e,n,i,r,a,o,s,l,u,c){U.call(this,t,e,n,i,r),this.mode=a,this.all_slotted=s,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=u,this.other_tiles_features_drawn={},this.seq_data=c};A(G.prototype,U.prototype),G.prototype.predisplay_actions=function(){};var H=function(e,n,r){A(r,{drag_handle_class:"draghandle"}),P.call(this,e,n,r),this.dataset=null,r.dataset&&(this.dataset=r.dataset instanceof i.Model?r.dataset:new x.default.Dataset(r.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in r?r.data_query_wait:5e3,this.data_manager="data_manager"in r?r.data_manager:new c.default.GenomeDataManager({dataset:this.dataset,genome:new c.default.Genome({key:e.dbkey,chroms_info:{chrom_info:e.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=t("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in r&&!r.resize||this.add_resize_handle())};A(H.prototype,P.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},P.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(t){t.view.set_overview(t)}},P.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(t){t.filters_manager.visible()?t.filters_manager.clear_filters():t.filters_manager.init_filters(),t.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(e){e.tool.toggle(),e.tool.is_visible()?e.set_name(e.config.get_value("name")+e.tool_region_and_parameters_str()):e.revert_name(),t(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(e){var n="<strong>Tool</strong>:"+e.tool.get("name")+"<br/><strong>Dataset</strong>:"+e.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',r=function(){Galaxy.modal.hide(),t(window).unbind("keypress.check_enter_esc")},a=function(){var n,r=t('select[name="regions"] option:selected').val(),a=new c.default.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),o=l.map(t(".bookmark"),function(e){return new c.default.GenomeRegion({from_str:t(e).children(".position").text()})});n="cur"===r?[a]:"bookmarks"===r?o:[a].concat(o),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+t.param({dataset_id:e.dataset.id,hda_ldda:e.dataset.get("hda_ldda"),regions:JSON.stringify(new i.Collection(n).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:n,buttons:{No:r,Yes:a}})}},P.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&P.prototype.can_draw.call(this)},build_container_div:function(){return t("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(t){this.dataset=t,this.data_manager.set("dataset",t)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var e=this,n=!1,i=!1,r=t("<div class='track-resize'>");t(e.container_div).hover(function(){e.config.get_value("content_visible")&&(n=!0,r.show())},function(){n=!1,i||r.hide()}),r.hide().bind("dragstart",function(n,r){i=!0,r.original_height=t(e.content_div).height()}).bind("drag",function(n,i){var r=Math.min(Math.max(i.original_height+i.deltaY,e.min_height_px),e.max_height_px);t(e.tiles_div).css("height",r),e.visible_height_px=e.max_height_px===r?0:r,e.on_resize()}).bind("dragend",function(t,a){e.tile_cache.clear(),i=!1,n||r.hide(),e.config.set_value("height",e.visible_height_px),e.changed()}).appendTo(e.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof X?"LabelTrack":this instanceof J?"ReferenceTrack":this instanceof K?"LineTrack":this instanceof et?"ReadTrack":this instanceof tt?"VariantTrack":this instanceof W?"CompositeTrack":this instanceof Q?"FeatureTrack":""},show_message:function(e){return this.tiles_div.remove(),t("<span/>").addClass("message").html(e).appendTo(this.content_div)},init:function(e){var n=this;if(n.enabled=!1,n.tile_cache.clear(),n.data_manager.clear(),n.content_div.children().remove(),n.container_div.removeClass("nodata error pending"),n.tiles_div=t("<div/>").addClass("tiles").appendTo(n.content_div),n.dataset.id){var i=t.Deferred(),r={hda_ldda:n.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:n.view.chrom,retry:e};return t.getJSON(this.dataset.url(),r,function(e){if(e&&"error"!==e&&"error"!==e.kind)"no converter"===e?(n.container_div.addClass("error"),n.show_message(R)):"no data"===e||void 0!==e.data&&(null===e.data||0===e.data.length)?(n.container_div.addClass("nodata"),n.show_message("No data for this chrom/contig.")):"pending"===e?(n.container_div.addClass("pending"),n.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),setTimeout(function(){n.init()},n.data_query_wait)):"data"!==e&&"data"!==e.status||(e.valid_chroms&&(n.valid_chroms=e.valid_chroms,n.update_icons()),n.tiles_div.text("Ready for display"),n.view.chrom?(n.tiles_div.text(""),n.tiles_div.css("height",n.visible_height_px+"px"),n.enabled=!0,t.when.apply(t,n.predraw_init()).done(function(){i.resolve(),n.container_div.removeClass("nodata error pending"),n.request_draw()})):i.resolve());else{n.container_div.addClass("error");var r=n.show_message("Cannot display dataset due to an error. ");e.message&&(r.append(t("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+e.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),r.append(t("<span/>").text(" ")),r.append(t("<a href='javascript:void(0);'></a>").text("Try again").click(function(){n.init(!0)})))}}),this.update_icons(),i}},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(n&&void 0!==n.min&&void 0!==n.max){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_default_value("min_value",i),e.config.set_default_value("max_value",r),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},get_drawables:function(){return this}});var Y=function(e,n,i){H.call(this,e,n,i);var r=this;if(z(r.container_div,r.drag_handle_class,".group",r),this.filters_manager=new b.default.FiltersManager(this,"filters"in i?i.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=i.tool?new L(l.extend(i.tool,{track:this,tool_state:i.tool_state})):null,this.tile_cache=new c.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var a=new B({model:this.tool});a.render(),this.dynamic_tool_div=a.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=t("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=t("<div/>").addClass("overlay").appendTo(this.content_div),i.mode&&this.change_mode(i.mode)};A(Y.prototype,P.prototype,H.prototype,{action_icons_def:H.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(e){t(".tooltip").remove(),e.slotters[e.view.resolution_px_b].max_rows*=2,e.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(t){var e=this.to_dict();A(e,{data_manager:this.data_manager});var n=new this.constructor(this.view,t,e);return n.change_mode(this.mode),n.enabled=this.enabled,n},set_filters_manager:function(t){this.filters_manager=t,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){var n=t.data;if(isNaN(parseFloat(e.config.get_value("min_value")))||isNaN(parseFloat(e.config.get_value("max_value")))){var i=n.min,r=n.max;i=Math.floor(Math.min(0,Math.max(i,n.mean-2*n.sd))),r=Math.ceil(Math.max(0,Math.min(r,n.mean+2*n.sd))),e.config.set_value("min_value",i),e.config.set_value("max_value",r)}})},change_mode:function(t){var e=this;return e.mode=t,e.config.set_value("mode",t),"Auto"===t&&this.data_manager.clear(),e.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+e.mode+")"),e},update_icons:function(){var t=this;t.action_icons.filters_icon.toggle(t.filters_available),t.action_icons.tools_icon.toggle(null!==t.tool),t.action_icons.param_space_viz_icon.toggle(null!==t.tool)},_gen_tile_cache_key:function(t,e){return t+"_"+e},request_draw:function(t){t&&t.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(t,this)},before_draw:function(){this.max_height_px=0},_draw:function(e){if(this.can_draw()){var n=e&&e.clear_after,i=this.view.low,r=this.view.high,a=this.view.container.width(),o=this.view.resolution_px_b,s=1/o;this.is_overview&&(i=this.view.max_low,r=this.view.max_high,o=a/(view.max_high-view.max_low),s=1/o),this.before_draw(),this.tiles_div.children().addClass("remove");for(var u,h,d=Math.floor(400*s),f=Math.floor(i/d),p=[],_=[];f*d<r;)u=new c.default.GenomeRegion({chrom:this.view.chrom,start:f*d,end:Math.min((f+1)*d,this.view.max_high)}),h=this.draw_helper(u,o,e),p.push(h),t.when(h).then(function(t){_.push(t)}),f+=1;n||this.tiles_div.children(".remove").removeClass("remove").remove();var g=this;t.when.apply(t,p).then(function(){g.tiles_div.children(".remove").remove(),_=l.filter(_,function(t){return null!==t}),0!==_.length&&g.postdraw_actions(_,a,o,n)})}},_add_yaxis_label:function(e,n){var i=this,r="max"===e?"top":"bottom",o="max"===e?"max":"min",s="max"===e?"max_value":"min_value",l=this.container_div.find(".yaxislabel."+r),u=a(i.config.get_value(s),1);n=n||function(){i.request_draw({clear_tile_cache:!0})},0!==l.length?l.text(u):(l=t("<div/>").text(u).make_text_editable({num_cols:12,on_finish:function(e){t(".tooltip").remove(),i.config.set_value(s,a(e,1)),n()},help_text:"Set "+o+" value"}).addClass("yaxislabel "+r).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(t,e,n,i){if(l.filter(t,function(t){return t instanceof F}).length>0){this.max_height_px=0;var r=this;l.each(t,function(t){t instanceof F||(t.html_elt.remove(),r.draw_helper(t.region,n,{force:!0,mode:"Coverage"}))}),r._add_yaxis_label("max")}else this.container_div.find(".yaxislabel").remove(),l.find(t,function(t){return t.has_icons})&&l.each(t,function(t){t.has_icons||t.html_elt.css("padding-top",20)})},get_mode:function(t){return this.mode},update_auto_mode:function(t){},_get_drawables:function(){return[this]},draw_helper:function(e,n,i){i||(i={});var r=i.force,a=i.mode||this.mode,o=1/n,s=this,u=this._get_drawables(),c=this._gen_tile_cache_key(n,e),h=r?void 0:s.tile_cache.get_elt(c);if(h)return function(t){return t&&"track"in t}(h)&&s.show_tile(h,n),h;if(!1===i.data_fetch)return null;var d=function(){var t=l.find(N,function(t){return t===a})?"Coverage":a,n=l.map(u,function(n){return n.data_manager.get_data(e,t,o,s.data_url_extra_params)});return view.reference_track&&n.push(view.reference_track.data_manager.get_data(e,a,o,view.reference_track.data_url_extra_params)),n},f=t.Deferred();return s.tile_cache.set_elt(c,f),t.when.apply(t,d()).then(function(){var r,a=d(),o=a;if(l.find(a,function(t){return p.default.is_deferred(t)}))return s.tile_cache.set_elt(c,void 0),void t.when(s.draw_helper(e,n,i)).then(function(t){f.resolve(t)});view.reference_track&&(r=view.reference_track.data_manager.subset_entry(a.pop(),e));var h=[],_=[];l.each(u,function(t,e){var i=t.mode,r=o[e];"Auto"===i&&(i=t.get_mode(r),t.update_auto_mode(i)),h.push(i),_.push(t.get_canvas_height(r,i,n,b))});var g,v=s.view.canvas_manager.new_canvas(),m=e.get("start"),y=e.get("end"),b=Math.ceil((y-m)*n)+s.left_offset,w=l.max(_);v.width=b,v.height=i.height||w;var x=v.getContext("2d");x.translate(s.left_offset,0),u.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),l.each(u,function(t,i){g=t.draw_tile(o[i],x,h[i],e,n,r)}),void 0!==g&&(s.tile_cache.set_elt(c,g),s.show_tile(g,n)),f.resolve(g)}),f},get_canvas_height:function(t,e,n,i){return this.visible_height_px},_draw_line_track_tile:function(t,e,n,i,r){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",l.max(l.map(t.data,function(t){return t[1]}))||0);var a=e.canvas;return new m.default.LinePainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new F(this,i,r,a,t.data)},draw_tile:function(t,e,n,i,r,a){},show_tile:function(t,e){var n=t.html_elt;t.predisplay_actions();var i=Math.round((t.low-(this.is_overview?this.view.max_low:this.view.low))*e);this.left_offset&&(i-=this.left_offset),n.css("left",i),n.hasClass("remove")?n.removeClass("remove"):this.tiles_div.append(n),n.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,n.height()-2),n.parent().children().css("height",this.max_height_px+"px");var r=this.max_height_px;0!==this.visible_height_px&&(r=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",r+"px")},tool_region_and_parameters_str:function(t){var e=this;return" - region=["+(void 0!==t?t.toString():"all")+"], parameters=["+l.values(e.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(t,e){return"Auto"===e||("Coverage"===e?"bigwig"===t.dataset_type:"bigwig"!==t.dataset_type&&"no_detail"!==t.extra_info)},can_subset:function(t){return!t.message&&"no_detail"!==t.extra_info&&("bigwig"!==t.dataset_type||t.data[1][0]-t.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var X=function(t,e){H.call(this,t,e,{resize:!1,header:!1}),this.container_div.addClass("label-track")};A(X.prototype,H.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(e){for(var n=this.view,i=n.high-n.low,r=Math.floor(Math.pow(10,Math.floor(Math.log(i)/Math.log(10)))),a=Math.floor(n.low/r)*r,o=this.view.container.width(),s=t("<div/>").addClass("label-container");a<n.high;){var l=Math.floor((a-n.low)/i*o);s.append(t("<div/>").addClass("pos-label").text(p.default.commatize(a)).css({left:l})),a+=r}this.content_div.children(":first").remove(),this.content_div.append(s)}});var W=function(t,e,n){if(Y.call(this,t,e,n),this.drawables=[],"drawables"in n){for(var i,r=0;r<n.drawables.length;r++)i=n.drawables[r],this.drawables[r]=it(i,t,null),i.left_offset>this.left_offset&&(this.left_offset=i.left_offset);this.enabled=!0}l.each(this.drawables,function(t){(t instanceof Q||t instanceof et)&&t.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};A(W.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(e){t(".tooltip").remove(),e.show_group()}}].concat(Y.prototype.action_icons_def),to_dict:q.prototype.to_dict,add_drawable:q.prototype.add_drawable,unpack_drawables:q.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var t=this.visible_height_px;l.each(this.drawables,function(e){e.visible_height_px=t}),H.prototype.on_resize.call(this)},change_mode:function(t){Y.prototype.change_mode.call(this,t);for(var e=0;e<this.drawables.length;e++)this.drawables[e].change_mode(t)},init:function(){for(var e=[],n=0;n<this.drawables.length;n++)e.push(this.drawables[n].init());var i=this;t.when.apply(t,e).then(function(){i.enabled=!0,i.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:P.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var t,e=new j(this.view,this.container,{name:this.config.get_value("name")}),n=0;n<this.drawables.length;n++)t=this.drawables[n],t.update_icons(),e.add_drawable(t),t.container=e,e.content_div.append(t.container_div);this.container.replace_drawable(this,e,!0);e.request_draw({clear_tile_cache:!0})},before_draw:function(){var t=l.min(l.map(this.drawables,function(t){return t.config.get_value("min_value")})),e=l.max(l.map(this.drawables,function(t){return t.config.get_value("max_value")}));this.config.set_value("min_value",t),this.config.set_value("max_value",e),l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)})},update_all_min_max:function(){var t=this.config.get_value("min_value"),e=this.config.get_value("max_value");l.each(this.drawables,function(n){n.config.set_value("min_value",t),n.config.set_value("max_value",e)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(t,e,n,i){var r,a=-1;for(r=0;r<t.length;r++){var o=t[r].html_elt.find("canvas").height();o>a&&(a=o)}for(r=0;r<t.length;r++){var s=t[r];s.html_elt.find("canvas").height()!==a&&(this.draw_helper(s.region,n,{force:!0,height:a}),s.html_elt.remove())}var l=this,u=function(){l.update_all_min_max()};this._add_yaxis_label("min",u),this._add_yaxis_label("max",u)}});var J=function(t){Y.call(this,t,{content_div:t.top_labeltrack},{resize:!1,header:!1}),this.left_offset=t.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new c.default.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};A(J.prototype,P.prototype,Y.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}])},init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:P.prototype.can_draw,draw_helper:function(t,e,n){var i,r=this.tiles_div.is(":visible"),a=null;return e>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),i=!0,a=Y.prototype.draw_helper.call(this,t,e,n)):(i=!1,this.tiles_div.hide()),r!==i&&this.view.resize_viewport(),a},can_subset:function(t){return!0},draw_tile:function(t,e,n,i,r){var a=this.data_manager.subset_entry(t,i),o=a.data,s=e.canvas;e.font=e.canvas.manager.default_font,e.textAlign="center";for(var l=0,u=o.length;l<u;l++)e.fillStyle=this.view.get_base_color(o[l]),e.fillText(o[l],Math.floor(l*r),10);return new U(this,i,r,s,a)}});var K=function(e,n,i){this.mode="Histogram",Y.call(this,e,n,i),this.left_offset=30;var r=this;t.when(o(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(t){t&&(r.data_manager=new $.default.BBIDataManager({dataset:r.dataset}))})};A(K.prototype,P.prototype,Y.prototype,{display_modes:N,build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(t,e,n,i,r){return this._draw_line_track_tile(t,e,n,i,r)},can_subset:function(t){return t.data[1][0]-t.data[0][0]==1},postdraw_actions:function(t,e,n,i){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var Z=function(t,e,n){this.mode="Heatmap",Y.call(this,t,e,n)};A(Z.prototype,P.prototype,Y.prototype,{display_modes:["Heatmap"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var e=this;return t.getJSON(e.dataset.url(),{data_type:"data",stats:!0,chrom:e.view.chrom,low:0,high:e.view.max_high,hda_ldda:e.dataset.get("hda_ldda")},function(t){t.data})},draw_tile:function(t,e,n,i,r){var a=e.canvas;return new m.default.DiagonalHeatmapPainter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n).draw(e,a.width,a.height,r),new U(this,i,r,a,t.data)}});var Q=function(t,e,n){Y.call(this,t,e,n),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};A(Q.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){"arcs"===this.config.get_value("connector_style")?this.painter=m.default.ArcLinkedFeaturePainter:this.painter=m.default.LinkedFeaturePainter},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a,o=this;if(0===l.filter(e,function(t){return t instanceof F}).length){var s={};l.each(l.pluck(e,"incomplete_features"),function(t){l.each(t,function(t){s[t[0]]=t})});var u=this;l.each(e,function(e){var n=l.omit(s,l.map(e.incomplete_features,function(t){return t[0]}));if(n=l.omit(n,l.keys(e.other_tiles_features_drawn)),0!==l.size(n)){var i={data:l.values(n)},r=u.view.canvas_manager.new_canvas(),a=r.getContext("2d");r.height=Math.max(e.canvas.height,u.get_canvas_height(i,e.mode,e.w_scale,100)),r.width=e.canvas.width,a.drawImage(e.canvas,0,0),a.translate(o.left_offset,0);var c=u.draw_tile(i,a,e.mode,e.region,e.w_scale,e.seq_data);t(e.canvas).replaceWith(t(c.canvas)),e.canvas=r,l.extend(e.other_tiles_features_drawn,s)}})}if(o.filters_manager){var c,h=o.filters_manager.filters;for(c=0;c<h.length;c++)h[c].update_ui_elt();var d,f,p=!1;for(a=0;a<e.length;a++)if(e[a].data.length)for(d=e[a].data[0],c=0;c<h.length;c++)if(f=h[c],f.applies_to(d)&&f.min!==f.max){p=!0;break}o.filters_available!==p&&(o.filters_available=p,o.filters_available||o.filters_manager.hide(),o.update_icons())}if(e[0]instanceof G){var _=!0;for(a=0;a<e.length;a++)if(!e[a].all_slotted){_=!1;break}this.action_icons.show_more_rows_icon.toggle(!_)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(t){"Auto"===this.mode&&("no_detail"===t&&(t="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+t+")"))},incremental_slots:function(t,e,n){var i=this.view.canvas_manager.dummy_context,r=this.slotters[t];return r&&r.mode===n||(r=new g.default.FeatureSlotter(t,n,100,function(t){return i.measureText(t)}),this.slotters[t]=r),r.slot_features(e)},get_mode:function(t){return"no_detail"===t.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>12e3?"Squish":"Pack"},get_canvas_height:function(t,e,n,i){if("Coverage"===e||"bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.incremental_slots(n,t.data,e),a=new this.painter(null,null,null,this.config.to_key_value_dict(),e);return Math.max(this.min_height_px,a.get_required_height(r,i))},draw_tile:function(t,e,n,i,r,a,o){var s=this,l=e.canvas,u=i.get("start"),c=i.get("end"),h=this.left_offset;if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,n,i,r);var d=[],f=this.slotters[r].slots,p=!0;if(t.data)for(var _=this.filters_manager.filters,g=0,v=t.data.length;g<v;g++){for(var m,y=t.data[g],b=!1,w=0,x=_.length;w<x;w++)if(m=_[w],m.update_attrs(y),!m.keep(y)){b=!0;break}b||(d.push(y),y[0]in f||(p=!1))}var k=this.filters_manager.alpha_filter?new V(this.filters_manager.alpha_filter):null,C=this.filters_manager.height_filter?new V(this.filters_manager.height_filter):null,M=new this.painter(d,u,c,this.config.to_key_value_dict(),n,k,C,a,function(t){return s.view.get_base_color(t)}),S=null;if(e.fillStyle=this.config.get_value("block_color"),e.font=e.canvas.manager.default_font,e.textAlign="right",t.data){var T=M.draw(e,l.width,l.height,r,f);S=T.feature_mapper,incomplete_features=T.incomplete_features,S.translation=-h}return o?void 0:new G(s,i,r,l,t.data,n,t.message,p,S,incomplete_features,a)}});var tt=function(t,e,n){Y.call(this,t,e,n),this.painter=m.default.VariantPainter,this.summary_draw_height=30,this.left_offset=30};A(tt.prototype,P.prototype,Y.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],build_config_params:function(){return l.union(P.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(t,e,n,i,r){if("bigwig"===t.dataset_type)return this._draw_line_track_tile(t,e,"Histogram",i,r);var a=this.view;return new this.painter(t.data,i.get("start"),i.get("end"),this.config.to_key_value_dict(),n,function(t){return a.get_base_color(t)}).draw(e,e.canvas.width,e.canvas.height,r),new U(this,i,r,e.canvas,t.data)},get_canvas_height:function(t,e,n,i){if("bigwig"===t.dataset_type)return this.summary_draw_height;var r=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;return 0===r&&0!==t.data.length&&(r=t.data[0][7].match(/,/g),r=null===r?1:r.length+1),new this.painter(null,null,null,this.config.to_key_value_dict(),e).get_required_height(r)},predraw_init:function(){var t=[H.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||t.push(this.dataset.fetch()),t},postdraw_actions:function(e,n,i,r){Y.prototype.postdraw_actions.call(this,e,n,i,r);var a=l.filter(e,function(t){return t instanceof F}),o=this.dataset.get_metadata("sample_names");if(0===a.length&&this.config.get_value("show_labels")&&o&&o.length>1){var s;if(0===this.container_div.find(".yaxislabel.variant").length&&(s=this.config.get_value("summary_height")/2,this.tiles_div.prepend(t("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":s+"px",top:(this.config.get_value("summary_height")-s)/2+"px"})),this.config.get_value("show_sample_data"))){var u=o.join("<br/>");this.tiles_div.prepend(t("<div/>").html(u).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}s=("Squish"===this.mode?5:10)+"px",t(this.tiles_div).find(".sample").css({"font-size":s,"line-height":s}),t(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var et=function(t,e,n){Q.call(this,t,e,n),this.painter=m.default.ReadPainter,this.update_icons()};A(et.prototype,P.prototype,Y.prototype,Q.prototype,{build_config_params:function(){return l.union(P.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var nt={CompositeTrack:W,DrawableGroup:j,DiagonalHeatmapTrack:Z,FeatureTrack:Q,LineTrack:K,ReadTrack:et,VariantTrack:tt,VcfTrack:tt},it=function(t,e,n){if("copy"in t)return t.copy(n);var i=t.obj_type;return i||(i=t.track_type),new nt[i](e,n,t)};e.default={TracksterView:D,DrawableGroup:j,LineTrack:K,FeatureTrack:Q,DiagonalHeatmapTrack:Z,ReadTrack:et,VariantTrack:tt,CompositeTrack:W,object_from_template:it}}).call(e,n(0),n(1))},function(t,e,n){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0});var r=n(2),a=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(r),o=t.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this),this.render()},render:function(){this.$el.append(i("<div/>").addClass(this.model.drag_handle_class)),this.$el.append(i("<div/>").addClass("track-name").text(this.model.config.get_value("name"))),this.action_icons={},this.render_action_icons(),this.$el.dblclick(function(t){t.stopPropagation()}),this.$el.append(i("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var t=this;this.icons_div=i("<div/>").addClass("track-icons").hide().appendTo(this.$el),a.each(this.model.action_icons_def,function(e){t.add_action_icon(e.name,e.title,e.css_class,e.on_click_fn,e.prepend,e.hide)}),this.set_display_modes(this.model.display_modes)},add_action_icon:function(t,e,n,r,a,o){var s=this;this.action_icons[t]=i("<a/>").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(function(){r(s.model)}).appendTo(this.icons_div),o&&this.action_icons[t].hide()},set_display_modes:function(t,e){if(t){this.model.display_modes=t,this.model.mode=e||this.model.config.get_value("mode")||this.model.display_modes[0],this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");for(var n=this.model,i={},r=0,a=n.display_modes.length;r<a;r++){var o=n.display_modes[r];i[o]=function(t){return function(){n.change_mode(t)}}(o)}make_popupmenu(this.action_icons.mode_icon,i)}}});e.default={TrackHeaderView:o}}).call(e,n(1),n(0))},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t,e){this.slot=t,this.feature=e},s=function(t,e,n,i){this.slots={},this.start_end_dct={},this.w_scale=t,this.mode=e,this.include_label="Pack"===e,this.max_rows=n,this.measureText=i};a(s.prototype,{_get_draw_coords:function(t){var e=Math.floor(t[1]*this.w_scale),n=Math.ceil(t[2]*this.w_scale),i=t[3];if(void 0!==i&&this.include_label){var r=this.measureText(i).width+7;e-r>=0?(e-=r,"left"):(n+=r,"right")}return[e,n]},_find_slot:function(t){for(var e=t[0],n=t[1],i=0;i<=this.max_rows;i++){var r=!1,a=this.start_end_dct[i];if(void 0!==a)for(var o=0,s=a.length;o<s;o++){var l=a[o];if(n>l[0]&&e<l[1]){r=!0;break}}if(!r)return i}return-1},slot_features:function(t){for(var e,n,i=this.start_end_dct,r=[],a=0,s=0,l=t.length;s<l;s++){e=t[s],n=e[0];var u=this.slots[n];if(u){if(e[1]<u.feature[1]||u.feature[2]<e[2])for(var c=this._get_draw_coords(u.feature),h=this._get_draw_coords(e),d=this.start_end_dct[u.slot],f=0;f<d.length;f++){var p=d[f];p[0]===c[0]&&p[1]===c[1]&&(d[f]=h)}a=Math.max(a,this.slots[n].slot)}else r.push(s)}for(var s=0,l=r.length;s<l;s++){e=t[r[s]],n=e[0];var _=this._get_draw_coords(e),g=this._find_slot(_);g>=0&&(void 0===i[g]&&(i[g]=[]),i[g].push(_),this.slots[n]=new o(g,e),a=Math.max(a,g))}return a+1}}),e.default={FeatureSlotter:s}},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=function(t,e){var n=t[0],i=t[1],r=e[0],a=e[1];return n<r?i<=r?1001:i<=a?1003:1002:n>a?1006:i<=a?1005:1004},o=function(t,e){var n=a(t,e);return 1001!==n&&1006!==n},s=function(t,e,n,i,r,a){void 0===a&&(a=4);var o,s=i-e,l=r-n,u=Math.floor(Math.sqrt(s*s+l*l)/a),c=s/u,h=l/u;for(o=0;o<u;o++,e+=c,n+=h)o%2==0&&t.fillRect(e,n,a,1)},l=function(t,e,n,i){var r=e-i/2,a=e+i/2,o=n-Math.sqrt(3*i/2);t.beginPath(),t.moveTo(r,o),t.lineTo(a,o),t.lineTo(e,n),t.lineTo(r,o),t.strokeStyle=this.fillStyle,t.fill(),t.stroke(),t.closePath()},u=function(t){this.default_val=t||1};u.prototype.gen_val=function(t){return this.default_val};var c=function(t){this.incomplete_features=t.incomplete_features,this.feature_mapper=t.feature_mapper},h=function(t,e,n,i,a){this.data=t,this.view_start=e,this.view_end=n,this.prefs=r.extend({},this.default_prefs,i),this.mode=a};h.prototype.default_prefs={},h.prototype.draw=function(t,e,n,i){},h.prototype.get_start_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,-.5)},h.prototype.get_end_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,.5)},h.prototype.get_draw_pos=function(t,e){return this._chrom_pos_to_draw_pos(t,e,0)},h.prototype._chrom_pos_to_draw_pos=function(t,e,n){return Math.floor(e*(Math.max(0,t-this.view_start)+n))};var d=function(t,e,n,i,r){h.call(this,t,e,n,i,r)};d.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},d.prototype.draw=function(t,e,n,i){var a=!1,o=this.prefs.min_value,s=this.prefs.max_value,l=s-o,u=n,c=this.view_start,h=this.mode,d=this.data;t.save();var f=Math.round(n+o/l*n);"Intensity"!==h&&(t.fillStyle="#aaa",t.fillRect(0,f,e,1)),t.beginPath();var p,_,g;g=d.length>1?r.map(d.slice(0,-1),function(t,e){return Math.ceil((d[e+1][0]-d[e][0])*i)}):[10];for(var v,m=this.prefs.block_color||this.prefs.color,y=parseInt(m.slice(1),16),b=(16711680&y)>>16,w=(65280&y)>>8,x=255&y,k=!1,C=!1,M=0,S=d.length;M<S;M++)if(t.fillStyle=t.strokeStyle=m,k=C=!1,v=g[M],p=Math.floor((d[M][0]-c-.5)*i),null!==(_=d[M][1])){if(_<o?(C=!0,_=o):_>s&&(k=!0,_=s),"Histogram"===h)_=Math.round(_/l*u),t.fillRect(p,f,v,-_);else if("Intensity"===h){var T=(_-o)/l,$=Math.round(b+(255-b)*(1-T)),A=Math.round(w+(255-w)*(1-T)),E=Math.round(x+(255-x)*(1-T));t.fillStyle="rgb("+$+","+A+","+E+")",t.fillRect(p,0,v,u)}else _=Math.round(u-(_-o)/l*u),a?t.lineTo(p,_):(a=!0,"Filled"===h?(t.moveTo(p,u),t.lineTo(p,_)):t.moveTo(p,_));if(t.fillStyle=this.prefs.overflow_color,k||C){var O;"Histogram"===h||"Intensity"===h?O=v:(p-=2,O=4),k&&t.fillRect(p,0,O,3),C&&t.fillRect(p,u-3,O,3)}t.fillStyle=m}else a&&"Filled"===h&&t.lineTo(p,u),a=!1;"Filled"===h?(a&&(t.lineTo(p,f),t.lineTo(0,f)),t.fill()):t.stroke(),t.restore()};var f=function(t){this.feature_positions={},this.slot_height=t,this.translation=0,this.y_translation=0};f.prototype.map_feature_data=function(t,e,n,i){this.feature_positions[e]||(this.feature_positions[e]=[]),this.feature_positions[e].push({data:t,x_start:n,x_end:i})},f.prototype.get_feature_data=function(t,e){var n,i=Math.floor((e-this.y_translation)/this.slot_height);if(!this.feature_positions[i])return null;t+=this.translation;for(var r=0;r<this.feature_positions[i].length;r++)if(n=this.feature_positions[i][r],t>=n.x_start&&t<=n.x_end)return n.data};var p=function(t,e,n,i,r,a,o){h.call(this,t,e,n,i,r),this.alpha_scaler=a||new u,this.height_scaler=o||new u,this.max_label_length=200};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},r.extend(p.prototype,{get_required_height:function(t,e){var n=this.get_row_height(),i=n,r=this.mode;return"no_detail"!==r&&"Squish"!==r&&"Pack"!==r||(n=t*i),n+this.get_top_padding(e)},get_top_padding:function(t){return 0},draw:function(t,e,n,i,r){var a=this.data,o=this.view_start,s=this.view_end;t.save(),t.fillStyle=this.prefs.block_color,t.textAlign="right";for(var l,u=this.get_row_height(),h=new f(u),d=[],p=0,_=a.length;p<_;p++){var g=a[p],v=g[0],m=g[1],y=g[2],b=r&&void 0!==r[v]?r[v].slot:null;("Dense"===this.mode||null!==b)&&m<s&&y>o&&(l=this.draw_element(t,this.mode,g,b,o,s,i,u,e),h.map_feature_data(g,b,l[0],l[1]),(m<o||y>s)&&d.push(g))}return t.restore(),h.y_translation=this.get_top_padding(e),new c({incomplete_features:d,feature_mapper:h})},draw_element:function(t,e,n,i,r,a,o,s,l){return[0,0]}});var _=function(t,e,n,i,r,a,o){p.call(this,t,e,n,i,r,a,o),this.draw_background_connector=!0,this.draw_individual_connectors=!1};r.extend(_.prototype,p.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"no_detail"===t?3:"Squish"===t?5:10},draw_element:function(t,e,n,i,r,a,o,s,l){var u,c=(n[0],n[1]),h=n[2],d=n[3],f=n[4],p=Math.floor(Math.max(0,(c-r-.5)*o)),_=Math.ceil(Math.min(l,Math.max(0,(h-r-.5)*o))),g=p,v=_,u=("Dense"===e?0:0+i)*s+this.get_top_padding(l),m=null,y=null,b=f&&"+"!==f&&"."!==f?this.prefs.reverse_strand_color:this.prefs.block_color,w=this.prefs.label_color;if(t.globalAlpha=this.alpha_scaler.gen_val(n),"Dense"===e&&(i=1),"no_detail"===e)t.fillStyle=b,t.fillRect(p,u+5,_-p,1);else{var x=n[5],k=n[6],C=n[7],M=!0;x&&k&&(m=Math.floor(Math.max(0,(x-r)*o)),y=Math.ceil(Math.min(l,Math.max(0,(k-r)*o))));var S,T;if("Squish"===e?(S=1,T=3,M=!1):(S=5,T=9),C){var $,A;"Squish"===e||"Dense"===e?($=u+Math.floor(1.5)+1,A=1):f?($=u,A=T):($+=2.5,A=1),this.draw_background_connector&&("Squish"===e||"Dense"===e?t.fillStyle="#ccc":f?"+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand")):t.fillStyle="#ccc",t.fillRect(p,$,_-p,A));for(var E=0,O=C.length;E<O;E++){var z,R,N=C[E],P=Math.floor(Math.max(0,(N[0]-r-.5)*o)),q=Math.ceil(Math.min(l,Math.max((N[1]-r-.5)*o)));if(!(P>q)){if(t.fillStyle=b,t.fillRect(P,u+(T-S)/2+1,q-P,S),void 0!==m&&k>x&&!(P>y||q<m)){var j=Math.max(P,m),D=Math.min(q,y);t.fillRect(j,u+1,D-j,T),1===C.length&&"Pack"===e&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),j+14<D&&(j+=2,D-=2),t.fillRect(j,u+1,D-j,T))}this.draw_individual_connectors&&z&&this.draw_connector(t,z,R,P,q,u),z=P,R=q}}if("Pack"===e){t.globalAlpha=1,t.fillStyle="white";var L=this.height_scaler.gen_val(n),I=Math.ceil(T*L),B=Math.round((T-I)/2);1!==L&&(t.fillRect(p,$+1,_-p,B),t.fillRect(p,$+T-B+1,_-p,B))}}else t.fillStyle=b,t.fillRect(p,u+1,_-p,T),f&&M&&("+"===f?t.fillStyle=t.canvas.manager.get_pattern("right_strand_inv"):"-"===f&&(t.fillStyle=t.canvas.manager.get_pattern("left_strand_inv")),t.fillRect(p,u+1,_-p,T));t.globalAlpha=1,d&&"Pack"===e&&c>r&&(t.fillStyle=w,0===r&&p-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,_+2,u+8,this.max_label_length),v+=t.measureText(d).width+2):(t.textAlign="right",t.fillText(d,p-2,u+8,this.max_label_length),g-=t.measureText(d).width+2))}return t.globalAlpha=1,[g,v]}});var g=function(t,e,n,i,r,a,o,s,l){p.call(this,t,e,n,i,r,a,o),this.ref_seq=s?s.data:null,this.base_color_fn=l};r.extend(g.prototype,p.prototype,{get_row_height:function(){var t,e=this.mode;return"Dense"===e?t=10:"Squish"===e?t=5:(t=10,this.prefs.show_insertions&&(t*=2)),t},_parse_cigar:function(t){var e="MIDNSHP=X",n=[[0,0]],i=n[0],a=0,o=r.map(t.match(/[0-9]+[MIDNSHP=X]/g),function(t){var r=parseInt(t.slice(0,-1),10),o=t.slice(-1);return"N"===o?0!==i[1]&&(i=[a+r,a+r],n.push(i)):-1==="ISHP".indexOf(o)&&(i[1]+=r,a+=r),[e.indexOf(o),r]});return{blocks:n,cigar:o}},draw_read:function(t,e,n,i,r,s,u,c,h,d){var f=function(t){return Math.floor(Math.max(0,(t-r-.5)*n))};t.textAlign="center";var p,_,g=[r,s],v=0,m=0,y=Math.round(n/2),b=t.canvas.manager.char_width_px,w="+"===h?this.prefs.detail_block_color:this.prefs.reverse_strand_color,k="Pack"===e,C=k?9:3,M=i+1,S=new x(t,C,n,e),T=[],$=[],A=this._parse_cigar(c);c=A.cigar,T=A.blocks;for(var E=0;E<T.length;E++){var O=T[E];o([u+O[0],u+O[1]],g)&&(p=f(u+O[0]),_=f(u+O[1]),p===_&&(_+=1),t.fillStyle=w,t.fillRect(p,M,_-p,C))}for(var z=0,R=c.length;z<R;z++){var N=c[z],P="MIDNSHP=X"[N[0]],q=N[1],j=u+v;if(p=f(j),_=f(j+q),o([j,j+q],g))switch(p===_&&(_+=1),P){case"H":case"S":case"P":break;case"M":v+=q;break;case"=":case"X":var D="";"X"===P?D=d.slice(m,m+q):this.ref_seq&&(D=this.ref_seq.slice(Math.max(0,j-r),Math.min(j-r+q,s-r)));for(var L=Math.max(j,r),I=0;I<D.length;I++)if(D&&!this.prefs.show_differences||"X"===P){var B=Math.floor(Math.max(0,(L+I-r)*n));t.fillStyle=this.base_color_fn(D[I]),k&&n>b?t.fillText(D[I],B,i+9):n>.05&&t.fillRect(B-y,M,Math.max(1,Math.round(n)),C)}"X"===P&&(m+=q),v+=q;break;case"N":t.fillStyle="#ccc",t.fillRect(p,M+(C-1)/2,_-p,1),v+=q;break;case"D":S.draw_deletion(p,M,q),v+=q;break;case"I":var V=p-y;if(o([j,j+q],g)){var U=d.slice(m,m+q);if(this.prefs.show_insertions){var F=p-(_-p)/2;if(("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b){switch(t.fillStyle="yellow",t.fillRect(F-y,i-9,_-p,9),$[$.length]={type:"triangle",data:[V,i+4,5]},t.fillStyle="#ccc",a([j,j+q],g)){case 1003:U=U.slice(r-j);break;case 1004:U=U.slice(0,j-s);break;case 1005:break;case 1002:U=U.slice(r-j,j-s)}for(var I=0,G=U.length;I<G;I++){var B=Math.floor(Math.max(0,(j+I-r)*n));t.fillText(U[I],B-(_-p)/2,i)}}else t.fillStyle="yellow",t.fillRect(F,i+("Dense"!==this.mode?2:5),_-p,"Dense"!==e?3:9)}else("Pack"===e||"Auto"===this.mode)&&void 0!==d&&n>b&&$.push({type:"text",data:[U.length,V,i+9]})}m+=q}else v=function(t,e,n){return-1!=="M=NXD".indexOf(e)&&(t+=n),t}(v,P,q),m=function(t,e,n){return-1!=="IX".indexOf(e)&&(t+=n),t}(m,P,q)}t.fillStyle="yellow";for(var H,Y,X,E=0;E<$.length;E++)H=$[E],Y=H.type,X=H.data,"text"===Y?(t.save(),t.font="bold "+t.font,t.fillText(X[0],X[1],X[2]),t.restore()):"triangle"===Y&&l(t,X[0],X[1],X[2])},draw_element:function(t,e,n,i,r,a,o,l,u){var c=(n[0],n[1]),h=n[2],d=n[3],f=Math.floor(Math.max(-.5*o,(c-r-.5)*o)),p=Math.ceil(Math.min(u,Math.max(0,(h-r-.5)*o))),_=("Dense"===e?0:0+i)*l,g="Pack"===e?9:3;this.prefs.label_color;if(n[5]instanceof Array){var v=!0;n[4][1]>=r&&n[4][0]<=a&&n[4][2]?this.draw_read(t,e,o,_,r,a,n[4][0],n[4][2],n[4][3],n[4][4]):v=!1,n[5][1]>=r&&n[5][0]<=a&&n[5][2]?this.draw_read(t,e,o,_,r,a,n[5][0],n[5][2],n[5][3],n[5][4]):v=!1;var m=Math.ceil(Math.min(u,Math.max(-.5*o,(n[4][1]-r-.5)*o))),y=Math.floor(Math.max(-.5*o,(n[5][0]-r-.5)*o));if(v&&y>m){t.fillStyle="#ccc";var b=_+1+(g-1)/2;s(t,m,b,y,b)}}else this.draw_read(t,e,o,_,r,a,c,n[4],n[5],n[6]);return"Pack"===e&&c>=r&&"."!==d&&(t.fillStyle=this.prefs.label_color,0===r&&f-t.measureText(d).width<0?(t.textAlign="left",t.fillText(d,p+2,_+9,this.max_label_length)):(t.textAlign="right",t.fillText(d,f-2,_+9,this.max_label_length))),[0,0]}});var v=function(t,e,n,i,r,a,o){_.call(this,t,e,n,i,r,a,o),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};r.extend(v.prototype,p.prototype,_.prototype,{calculate_longest_feature_length:function(){for(var t=0,e=0,n=this.data.length;e<n;e++){var i=this.data[e],r=i[1],a=i[2];t=Math.max(t,a-r)}return t},get_top_padding:function(t){var e=this.view_end-this.view_start,n=t/e;return Math.min(128,Math.ceil(this.longest_feature_length/2*n))},draw_connector:function(t,e,n,i,r,a){var o=(n+i)/2,s=i-o;Math.PI;s>0&&(t.beginPath(),t.arc(o,a,i-o,Math.PI,0),t.stroke())}});var m=function(t,e){Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(t){return parseInt(t,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(t){return parseInt(t,16)}):this.rgb=t.split("").map(function(t){return parseInt(t+t,16)}),this.alpha="number"==typeof e?e:1};m.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(t){return Math.round(t)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},toHSL:function(){var t,e,n=this.rgb[0]/255,i=this.rgb[1]/255,r=this.rgb[2]/255,a=this.alpha,o=Math.max(n,i,r),s=Math.min(n,i,r),l=(o+s)/2,u=o-s;if(o===s)t=e=0;else{switch(e=l>.5?u/(2-o-s):u/(o+s),o){case n:t=(i-r)/u+(i<r?6:0);break;case i:t=(r-n)/u+2;break;case r:t=(n-i)/u+4}t/=6}return{h:360*t,s:e,l:l,a:a}},toARGB:function(){return"#"+[Math.round(255*this.alpha)].concat(this.rgb).map(function(t){return t=Math.round(t),t=(t>255?255:t<0?0:t).toString(16),1===t.length?"0"+t:t}).join("")},mix:function(t,e){var n=this,i=e,r=2*i-1,a=n.toHSL().a-t.toHSL().a,o=((r*a==-1?r:(r+a)/(1+r*a))+1)/2,s=1-o,l=[n.rgb[0]*o+t.rgb[0]*s,n.rgb[1]*o+t.rgb[1]*s,n.rgb[2]*o+t.rgb[2]*s],u=n.alpha*i+t.alpha*(1-i);return new m(l,u)}};var y=function(t,e,n,i){this.start_color=new m(t),this.end_color=new m(e),this.start_value=n,this.end_value=i,this.value_range=i-n};y.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t=(t-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-t).toCSS()};var b=function(t,e,n,i,r){this.positive_ramp=new y(e,n,0,r),this.negative_ramp=new y(e,t,0,-i),this.start_value=i,this.end_value=r};b.prototype.map_value=function(t){return t=Math.max(t,this.start_value),t=Math.min(t,this.end_value),t>=0?this.positive_ramp.map_value(t):this.negative_ramp.map_value(-t)};var w=function(t,e,n,i,r){h.call(this,t,e,n,i,r);var a,o;if(void 0===this.prefs.min_value){var s=1/0;for(a=0,o=this.data.length;a<o;a++)s=Math.min(s,this.data[a][6]);this.prefs.min_value=s}if(void 0===this.prefs.max_value){var l=-1/0;for(a=0,o=this.data.length;a<o;a++)l=Math.max(l,this.data[a][6]);this.prefs.max_value=l}};w.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},w.prototype.draw=function(t,e,n,i){var r,a,o,s,l,u,c=this.prefs.min_value,h=this.prefs.max_value,d=this.view_start,f=(this.mode,this.data),p=1/Math.sqrt(2),_=new b(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,c,h),g=function(t){return(t-d)*i};t.save(),t.rotate(-45*Math.PI/180),t.scale(p,p);for(var v=0,m=f.length;v<m;v++)r=f[v],a=g(r[1]),o=g(r[2]),s=g(r[4]),l=g(r[5]),u=r[6],t.fillStyle=_.map_value(u),t.fillRect(a,s,o-a,l-s);t.restore()};var x=function(t,e,n,i){this.ctx=t,this.row_height=e,this.px_per_base=n,this.draw_details=("Pack"===i||"Auto"===i)&&n>=t.canvas.manager.char_width_px,this.delete_details_thickness=.2};r.extend(x.prototype,{draw_deletion:function(t,e,n){this.ctx.fillStyle="black";var i=(this.draw_details?this.delete_details_thickness:1)*this.row_height;e+=.5*(this.row_height-i),this.ctx.fillRect(t,e,n*this.px_per_base,i)}});var k=function(t,e,n,i,r,a){h.call(this,t,e,n,i,r),this.base_color_fn=a,this.divider_height=1};r.extend(k.prototype,h.prototype,{get_row_height:function(){var t=this.mode;return"Dense"===t?10:"Squish"===t?5:10},get_required_height:function(t){var e=this.prefs.summary_height;return t>1&&this.prefs.show_sample_data&&(e+=this.divider_height+t*this.get_row_height()),e},draw:function(t,e,n,i){t.save();var a,o,s,l,u,c,h,d,f,p,_,g=function(t,e){var n=t.length,i=e.length,r=0,a=1,o=null;return"-"===e?(o="deletion",a=t.length):0===t.indexOf(e)&&n>i?(o="deletion",a=n-i,r=i):0===e.indexOf(t)&&n<i&&(o="insertion",a=i-n,r=i),null!==o?{type:o,start:r,len:a}:{}},v=Math.max(1,Math.floor(i)),m=this.data.length?this.data[0][7].split(",").length:0,y="Squish"===this.mode?5:10,b=i<.1?y:"Squish"===this.mode?3:9,w=!0,k=new x(t,y,i,this.mode);1===m&&(y=b=i<t.canvas.manager.char_width_px?this.prefs.summary_height:y,k.row_height=y,w=!1),this.prefs.show_sample_data&&w&&(t.fillStyle="#F3F3F3",t.globalAlpha=1,t.fillRect(0,this.prefs.summary_height-this.divider_height,e,this.divider_height)),t.textAlign="center";for(var C=0;C<this.data.length;C++)if(a=this.data[C],o=a[1],s=a[3],l=[a[4].split(",")],u=a[7].split(","),c=a.slice(8),l=r.map(r.flatten(l),function(t){var e={type:"snp",value:t,start:0},n=g(s,t);return r.extend(e,n)}),!(o<this.view_start||o>this.view_end)){if(w)for(t.fillStyle="#999999",t.globalAlpha=1,_=0;_<l.length;_++)for(d=this.get_start_draw_pos(o+l[_].start,i),t.fillRect(d,0,v,this.prefs.summary_height),f=this.prefs.summary_height,_=0;_<l.length;_++){t.fillStyle="deletion"===l[_].type?"black":this.base_color_fn(l[_].value);var M=c/u.length,S=Math.ceil(this.prefs.summary_height*M);t.fillRect(d,f-S,v,S),f-=S}if(this.prefs.show_sample_data)for(f=w?this.prefs.summary_height+this.divider_height:0,_=0;_<u.length;_++,f+=y)if(p=u[_]?u[_].split(/\/|\|/):["0","0"],h=null,p[0]===p[1]?"."===p[0]||"0"!==p[0]&&(h=l[parseInt(p[0],10)-1],t.globalAlpha=1):(h="0"!==p[0]?p[0]:p[1],h=l[parseInt(h,10)-1],t.globalAlpha=.5),h)if(d=this.get_start_draw_pos(o+h.start,i),"snp"===h.type){var T=h.value;t.fillStyle=this.base_color_fn(T),k.draw_details?t.fillText(T,this.get_draw_pos(o,i),f+y):t.fillRect(d,f+1,v,b)}else"deletion"===h.type&&k.draw_deletion(d,f+1,h.len)}t.restore()}}),e.default={Scaler:u,LinePainter:d,LinkedFeaturePainter:_,ReadPainter:g,ArcLinkedFeaturePainter:v,DiagonalHeatmapPainter:w,VariantPainter:k}},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(i),a=r.extend,o=function(t){this.manager=null,this.name=t.name,this.index=t.index,this.tool_id=t.tool_id,this.tool_exp_name=t.tool_exp_name};a(o.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var s=function(e,n,i){return t("<a/>").attr("href","javascript:void(0);").attr("title",e).addClass("icon-button").addClass(n).tooltip().click(i)},l=function(e){o.call(this,e),this.low="low"in e?e.low:-Number.MAX_VALUE,this.high="high"in e?e.high:Number.MAX_VALUE,this.min="min"in e?e.min:Number.MAX_VALUE,this.max="max"in e?e.max:-Number.MAX_VALUE,this.container=null,this.slider=null,this.slider_label=null;var n=this;n.parent_div=t("<div/>").addClass("filter-row slider-row");var i=t("<div/>").addClass("elt-label").appendTo(n.parent_div),r=(t("<span/>").addClass("slider-name").text(n.name+"  ").appendTo(i),t("<span/>").text(this.low+"-"+this.high)),a=t("<span/>").addClass("slider-value").appendTo(i).append("[").append(r).append("]");n.values_span=r;var l=t("<div/>").addClass("slider").appendTo(n.parent_div);n.control_element=t("<div/>").attr("id",n.name+"-filter-control").appendTo(l),n.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(t,e){n.slide(t,e)},change:function(t,e){n.control_element.slider("option","slide").call(n.control_element,t,e)}}),n.slider=n.control_element,n.slider_label=r,function(e,n,i){e.click(function(){var e=n.text(),r=parseFloat(i.slider("option","max")),a=r<=1?4:r<=1e6?r.toString().length:6,o=!1,s=t(this).parents(".slider-row");s.addClass("input"),i.slider("option","values")&&(a=2*a+1,o=!0),n.text(""),t("<input type='text'/>").attr("size",a).attr("maxlength",a).attr("value",e).appendTo(n).focus().select().click(function(t){t.stopPropagation()}).blur(function(){t(this).remove(),n.text(e),s.removeClass("input")}).keyup(function(e){if(27===e.keyCode)t(this).trigger("blur");else if(13===e.keyCode){var n=i.slider("option","min"),r=i.slider("option","max"),a=function(t){return isNaN(t)||t>r||t<n},l=t(this).val();if(o){if(l=l.split("-"),l=[parseFloat(l[0]),parseFloat(l[1])],a(l[0])||a(l[1]))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this)}else if(l=parseFloat(l),a(l))return alert("Parameter value must be in the range ["+n+"-"+r+"]"),t(this);i.slider(o?"values":"value",l),s.removeClass("input")}})})}(a,r,n.control_element);var u=t("<div/>").addClass("display-controls").appendTo(n.parent_div);this.transparency_icon=s("Use filter for data transparency","layer-transparent",function(){n.manager.alpha_filter!==n?(n.manager.alpha_filter=n,n.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),n.transparency_icon.addClass("active").show()):(n.manager.alpha_filter=null,n.transparency_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),this.height_icon=s("Use filter for data height","arrow-resize-090",function(){n.manager.height_filter!==n?(n.manager.height_filter=n,n.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),n.height_icon.addClass("active").show()):(n.manager.height_filter=null,n.height_icon.removeClass("active")),n.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(u).hide(),n.parent_div.hover(function(){n.transparency_icon.show(),n.height_icon.show()},function(){n.manager.alpha_filter!==n&&n.transparency_icon.hide(),n.manager.height_filter!==n&&n.height_icon.hide()}),t("<div style='clear: both;'/>").appendTo(n.parent_div)};a(l.prototype,{to_dict:function(){var t=o.prototype.to_dict.call(this);return a(t,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new l({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(t,e){return e-t<=2?.01:1},slide:function(t,e){var n=e.values;this.values_span.text(n[0]+"-"+n[1]),this.low=n[0],this.high=n[1];var i=this;setTimeout(function(){n[0]===i.low&&n[1]===i.high&&i.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(t){return t.length>this.index},_keep_val:function(t){return isNaN(t)||t>=this.low&&t<=this.high},keep:function(t){if(!this.applies_to(t))return!0;var e=t[this.index];if(e instanceof Array){for(var n=!0,i=0;i<e.length;i++)if(!this._keep_val(e[i])){n=!1;break}return n}return this._keep_val(t[this.index])},update_attrs:function(t){var e=!1;if(!this.applies_to(t))return e;var n=t[this.index];n instanceof Array||(n=[n]);for(var i=0;i<n.length;i++){var r=n[i];r<this.min&&(this.min=Math.floor(r),e=!0),r>this.max&&(this.max=Math.ceil(r),e=!0)}return e},update_ui_elt:function(){this.min<this.max?this.parent_div.show():this.parent_div.hide();var t=this.slider.slider("option","min"),e=this.slider.slider("option","max");(this.min<t||this.max>e)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var u=function(e,n){if(this.track=e,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=t("<div/>").addClass("filters").hide(),this.parent_div.bind("drag",function(t){t.stopPropagation()}).click(function(t){t.stopPropagation()}).bind("dblclick",function(t){t.stopPropagation()}).bind("keydown",function(t){t.stopPropagation()}),n&&"filters"in n){for(var i,r=("alpha_filter"in n?n.alpha_filter:null),a=("height_filter"in n?n.height_filter:null),o=n.filters,s=0;s<o.length;s++)"number"===o[s].type?(i=new l(o[s]),this.add_filter(i),i.name===r&&(this.alpha_filter=i,i.transparency_icon.addClass("active").show()),i.name===a&&(this.height_filter=i,i.height_icon.addClass("active").show())):console.log("ERROR: unsupported filter: ",name,type);"visible"in n&&n.visible&&this.parent_div.show()}if(0!==this.filters.length){var u=t("<div/>").addClass("param-row").appendTo(this.parent_div),c=this;t("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(u).click(function(){c.run_on_dataset()})}};a(u.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var t,e={},n=[],i=0;i<this.filters.length;i++)t=this.filters[i],n.push(t.to_dict());return e.filters=n,e.alpha_filter=this.alpha_filter?this.alpha_filter.name:null,e.height_filter=this.height_filter?this.height_filter.name:null,e.visible=this.parent_div.is(":visible"),e},copy:function(t){for(var e=new u(t),n=0;n<this.filters.length;n++)e.add_filter(this.filters[n].copy());return e},add_filter:function(t){t.manager=this,this.parent_div.append(t.parent_div),this.filters.push(t)},remove_all:function(){this.filters=[],this.parent_div.children().remove()},init_filters:function(){for(var t=0;t<this.filters.length;t++){this.filters[t].update_ui_elt()}},clear_filters:function(){for(var t=0;t<this.filters.length;t++){var e=this.filters[t];e.slider.slider("option","values",[e.min,e.max])}this.alpha_filter=null,this.height_filter=null,this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){for(var e,n,i=(function(t,e,n){return e in t||(t[e]=n),t[e]}),r={},a=0;a<this.filters.length;a++)e=this.filters[a],e.tool_id&&(e.min!==e.low&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" >= "+e.low),e.max!==e.high&&(n=i(r,e.tool_id,[]),n[n.length]=e.tool_exp_name+" <= "+e.high));var o=[];for(var s in r)o[o.length]=[s,r[s]];!function e(n,i){var r=i[0],a=r[0],o=r[1],s="("+o.join(") and (")+")",l={cond:s,input:n,target_dataset_id:n,tool_id:a};i=i.slice(1),t.getJSON(run_tool_url,l,function(t){t.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+a,buttons:{Close:Galaxy.modal.hide()}}):0===i.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):e(t.dataset_id,i)})}(this.track.dataset_id,o)}}),e.default={FiltersManager:u,NumberFilter:l}}).call(e,n(0))},function(t,e,n){"use strict";(function(t){Object.defineProperty(e,"__esModule",{value:!0});var i=n(13),r=function(t){return t&&t.__esModule?t:{default:t}}(i),a=n(152),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=r.default.GenomeDataManager.extend({load_data:function(e,n,i,r){var a=t.Deferred();this.set_data(e,a);var s=Galaxy.root+"datasets/"+this.get("dataset").id+"/display",l=this;new t.Deferred;return t.when(o.makeBwg(s)).then(function(n,i){t.when(n.readWigData(e.get("chrom"),e.get("start"),e.get("end"))).then(function(t){var n=[],i={max:Number.MIN_VALUE};t.forEach(function(t){i.max!==t.min-1&&(n.push([i.max+1,0]),n.push([t.min-2,0])),n.push([t.min-1,t.score]),n.push([t.max,t.score]),i=t});var r={data:n,region:e,dataset_type:"bigwig"};l.set_data(e,r),a.resolve(r)})}),a}});e.default={BBIDataManager:s}}).call(e,n(0))},function(t,e,n){(function(i){var r,a;r=[n(153),n(154),n(155)],void 0!==(a=function(t,e){"use strict";function n(){}function r(t){t&&(this.id=t)}function a(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function o(t,e,n){Math.pow(10,6);return i.ajax({type:"GET",dataType:"native",url:t,timeout:5e3,beforeSend:function(t){t.setRequestHeader("Range","bytes="+e+"-"+(e+(n-1)))},xhrFields:{responseType:"arraybuffer"}})}function s(t,e){return t[e]+t[e+1]*w+t[e+2]*x+t[e+3]*k+t[e+4]*C}function l(){}function u(t,e,n,i){this.bwg=t,this.cirTreeOffset=e,this.cirTreeLength=n,this.isSummary=i}function c(t){var e=i.Deferred(),n=new l;return n.url=t,i.when(o(n.url,0,512)).then(function(t){if(!t)return e.resolve(null,"Couldn't fetch file");var r=t,a=new Uint8Array(r),o=new Int16Array(r),l=new Int32Array(r),u=a[0]+w*a[1]+x*a[2]+k*a[3];if(u==v)n.type="bigwig";else{if(u!=y)return u==m||u==b?e.resolve(null,"Currently don't support big-endian BBI files"):e.resolve(null,"Not a supported format, magic=0x"+u.toString(16));n.type="bigbed"}n.version=o[2],n.numZoomLevels=o[3],n.chromTreeOffset=s(a,8),n.unzoomedDataOffset=s(a,16),n.unzoomedIndexOffset=s(a,24),n.fieldCount=o[16],n.definedFieldCount=o[17],n.asOffset=s(a,36),n.totalSummaryOffset=s(a,44),n.uncompressBufSize=l[13],n.extHeaderOffset=s(a,56),n.zoomLevels=[];for(var c=0;c<n.numZoomLevels;++c){var h=l[6*c+16],d=s(a,24*c+72),f=s(a,24*c+80);n.zoomLevels.push({reduction:h,dataOffset:d,indexOffset:f})}i.when(n.readChromTree()).then(function(){n.getAutoSQL(function(t){return n.schema=t,e.resolve(n)})})}),e}function h(t,e,n,i,r){this.bbi=t,this.type=e,this.fieldCount=n,this.offset=i,this.field=r}var d=t.Range,f=t.union,p=t.intersection,_=e.inflateBuffer,g=e.arrayCopy,v=2291137574,m=654086024,y=2273964779,b=3958540679,w=256,x=65536,k=16777216,C=4294967296,M=new RegExp("^[0-9]+,[0-9]+,[0-9]+");return l.prototype.readChromTree=function(){var t=this;this.chromsToIDs={},this.idsToChroms={},this.maxID=0;var e=this.unzoomedDataOffset;return e=e+4-(e-this.chromTreeOffset&3),i.when(o(this.url,this.chromTreeOffset,e-this.chromTreeOffset)).then(function(e){var n=new Uint8Array(e),i=new Int16Array(e),r=new Int32Array(e),a=(r[0],r[1],r[2]),o=(r[3],s(n,16),function(e){var r=n[e],l=i[e/2+1];e+=4;for(var u=0;u<l;++u)if(0===r){e+=a;var c=s(n,e);e+=8,c-=t.chromTreeOffset,o(c)}else{for(var h="",d=0;d<a;++d){var f=n[e++];0!==f&&(h+=String.fromCharCode(f))}var p=n[e+3]<<24|n[e+2]<<16|n[e+1]<<8|n[e+0];n[e+7],n[e+6],n[e+5],n[e+4],e+=8,t.chromsToIDs[h]=p,0===h.indexOf("chr")&&(t.chromsToIDs[h.substr(3)]=p),t.idsToChroms[p]=h,t.maxID=Math.max(t.maxID,p)}});o(32)})},u.prototype.readWigData=function(t,e,n){var i=this.bwg.chromsToIDs[t];return void 0===i?[]:this.readWigDataById(i,e,n)},u.prototype.readWigDataById=function(t,e,n){var r=this,a=i.Deferred();if(!this.cirHeader)return i.when(o(r.bwg.url,this.cirTreeOffset,48)).then(function(o){r.cirHeader=o;var s=new Int32Array(r.cirHeader);r.cirBlockSize=s[1],i.when(r.readWigDataById(t,e,n)).then(function(t){a.resolve(t)})}),a;var l=[],u=0,c=(Date.now(),function(i,r,a,o){return(t<0||i==t)&&r<=n&&a>=e}),h=function(t,e){if(r.bwg.instrument&&console.log("level="+e+"; offset="+t+"; time="+(0|Date.now())),u+=t.length,1==t.length&&t[0]-r.cirTreeOffset==48&&r.cachedCirRoot)return _(r.cachedCirRoot,0,e),void(0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}));for(var n,o=4+32*r.cirBlockSize,s=0;s<t.length;++s){var h=new d(t[s],t[s]+o);n=n?f(n,h):h}for(var g=n.ranges(),v=0;v<g.length;++v){var m=g[v];p(t,m,e)}},p=function(t,e,n,s){e.max(),e.min();i.when(o(r.bwg.url,e.min(),e.max()-e.min())).then(function(o){for(var s=0;s<t.length;++s)e.contains(t[s])&&(_(o,t[s]-e.min(),n),t[s]-r.cirTreeOffset==48&&t[s]-e.min()==0&&(r.cachedCirRoot=o),0===--u&&i.when(r.fetchFeatures(c,l)).then(function(t){a.resolve(t)}))})},_=function(i,r,a){var o=new Uint8Array(i),u=new Int16Array(i),c=new Int32Array(i),d=o[r],f=u[r/2+1];if(r+=4,0!==d)for(var p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16),w=s(o,r+24);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&l.push({offset:b,size:w}),r+=32}else{for(var x=[],p=0;p<f;++p){var _=r/4,g=c[_],v=c[_+1],m=c[_+2],y=c[_+3],b=s(o,r+16);(t<0||g<t||g==t&&v<=n)&&(t<0||m>t||m==t&&y>=e)&&x.push(b),r+=24}x.length>0&&h(x,a+1)}};return h([r.cirTreeOffset+48],1),a},u.prototype.fetchFeatures=function(t,e){var r=this,a=i.Deferred();if(e.sort(function(t,e){return(0|t.offset)-(0|e.offset)}),0===e.length)return[];var s=[],l=function(t,e,i,a){a||(a={});var o=new n;o._chromId=t,o.segment=r.bwg.idsToChroms[t],o.min=e,o.max=i,o.type=r.bwg.type;for(var l in a)o[l]=a[l];s.push(o)},u=function(){if(0===e.length){Date.now();return a.resolve(s)}var n=e[0];if(n.data)r.parseFeatures(n.data,l,t),e.splice(0,1),u();else{for(var c=n.offset,h=n.size,d=1;d<e.length&&e[d].offset==c+h;)h+=e[d].size,++d;i.when(o(r.bwg.url,c,h)).then(function(t){for(var n=0,i=0;n<h;){var a,o=e[i];if(r.bwg.uncompressBufSize>0)a=_(t,n+2,o.size-2);else{var s=new Uint8Array(o.size);g(new Uint8Array(t,n,o.size),0,s,0,o.size),a=s.buffer}o.data=a,n+=o.size,++i}u()})}};return u(),a},u.prototype.parseFeatures=function(t,e,n){var a=new Uint8Array(t);if(this.isSummary)for(var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),u=t.byteLength/32,c=0;c<u;++c){var h=s[8*c],_=s[8*c+1],g=s[8*c+2],v=s[8*c+3],m=(l[8*c+4],l[8*c+5]),y=l[8*c+6];l[8*c+7];if(n(h,_+1,g)){var b={type:"bigwig",score:y/v,maxScore:m};"bigbed"==this.bwg.type&&(b.type="density"),e(h,_+1,g,b)}}else if("bigwig"==this.bwg.type){var o=new Int16Array(t),s=new Int32Array(t),l=new Float32Array(t),h=s[0],w=s[1],x=(s[2],s[3]),k=s[4],C=a[20],u=o[11];if(3==C)for(var c=0;c<u;++c){var S=l[c+6],T=w+c*x+1,$=w+c*x+k;n(h,T,$)&&e(h,T,$,{score:S})}else if(2==C)for(var c=0;c<u;++c){var _=s[2*c+6]+1,g=_+k-1,S=l[2*c+7];n(h,_,g)&&e(h,_,g,{score:S})}else if(1==C)for(var c=0;c<u;++c){var _=s[3*c+6]+1,g=s[3*c+7],S=l[3*c+8];_>g&&(_=g),n(h,_,g)&&e(h,_,g,{score:S})}else console.log("Currently not handling bwgType="+C)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var A=0,E=this.bwg.definedFieldCount,O=this.bwg.schema;A<a.length;){var h=a[A+3]<<24|a[A+2]<<16|a[A+1]<<8|a[A+0],_=a[A+7]<<24|a[A+6]<<16|a[A+5]<<8|a[A+4],g=a[A+11]<<24|a[A+10]<<16|a[A+9]<<8|a[A+8];A+=12;for(var z="";;){var R=a[A++];if(0==R)break;z+=String.fromCharCode(R)}var N,P={};if(N=z.length>0?z.split("\t"):[],N.length>0&&E>3&&(P.label=N[0]),N.length>1&&E>4){var S=parseInt(N[1]);isNaN(S)||(P.score=S)}if(N.length>2&&E>5&&(P.orientation=N[2]),N.length>5&&E>8){var q=N[5];M.test(q)&&(P.itemRgb="rgb("+q+")")}if(N.length>E-3&&O)for(var j=E-3;j<N.length;++j)P[O.fields[j+3].name]=N[j];if(n(h,_+1,g,N))if(E<12)e(h,_+1,g,P);else{var D=0|N[3],L=0|N[4],I=0|N[6],B=N[7].split(","),V=N[8].split(",");if(P.exonFrames){var U=P.exonFrames.split(",");P.exonFrames=void 0}P.type="transcript";var F=new r;for(var G in P)F[G]=P[G];if(F.id=N[0],F.segment=this.bwg.idsToChroms[h],F.min=_+1,F.max=g,F.notes=[],P.groups=[F],N.length>9){var H=P.geneName||N[9],Y=H;N.length>10&&(Y=N[10]),P.geneName2&&(Y=P.geneName2);var X=i.extend({},F);X.id=H,X.label=Y,X.type="gene",P.groups.push(X)}for(var W=[],J=0;J<I;++J){var K=(0|V[J])+_,Z=K+(0|B[J]),Q=new d(K,Z);W.push(Q)}for(var tt=f(W),et=tt.ranges(),nt=0;nt<et.length;++nt){var it=et[nt];e(h,it.min()+1,it.max(),P)}if(L>D){var rt="+"==P.orientation?new d(D,L+3):new d(D-3,L),at=p(tt,rt);if(at){P.type="translation";for(var ot=at.ranges(),st=0,lt=0;ot[0].min()>et[lt].max();)lt++;for(var nt=0;nt<ot.length;++nt){var ut=nt;"-"==P.orientation&&(ut=ot.length-nt-1);var it=ot[ut];if(P.readframe=st,U){var ct=parseInt(U[ut+lt]);"number"==typeof ct&&ct>=0&&ct<=2&&(P.readframe=ct,P.readframeExplicit=!0)}var ht=it.max()-it.min();st=(st+ht)%3,e(h,it.min()+1,it.max(),P)}}}}}}},u.prototype.getFirstAdjacent=function(t,e,n,i){var r=this.bwg.chromsToIDs[t];if(void 0===r)return i([]);this.getFirstAdjacentById(r,e,n,i)},u.prototype.getFirstAdjacentById=function(t,e,n,i){var r=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(a){r.cirHeader=a;var o=new Int32Array(r.cirHeader);r.cirBlockSize=o[1],r.getFirstAdjacentById(t,e,n,i)});var a=null,o=-1,l=-1,u=0,c=(Date.now(),function(t,e){u+=t.length;for(var n,i=4+32*r.cirBlockSize,a=0;a<t.length;++a){var o=new d(t[a],t[a]+i);n=n?f(n,o):o}for(var s=n.ranges(),l=0;l<s.length;++l){var c=s[l];h(t,c,e)}}),h=function(o,s,l,c){s.max(),s.min();r.bwg.data.slice(s.min(),s.max()-s.min()).fetch(function(c){for(var h=0;h<o.length;++h)if(s.contains(o[h])&&(p(c,o[h]-s.min(),l),0==--u)){if(!a)return n>0&&(0!=t||e>0)?r.getFirstAdjacentById(0,0,n,i):n<0&&(t!=r.bwg.maxID||e<1e9)?r.getFirstAdjacentById(r.bwg.maxID,1e9,n,i):i([]);r.fetchFeatures(function(i,r,a,o){return n<0&&(i<t||a<e)||n>0&&(i>t||r>e)},[a],function(t){for(var e=null,r=-1,a=-1,o=0;o<t.length;++o){var s=t[o],l=s._chromId,u=s.min,c=s.max;(null==e||n<0&&(l>r||c>a)||n>0&&(l<r||u<a))&&(e=s,a=n<0?c:u,r=l)}return i(null!=e?[e]:[])})}})},p=function(i,u,h){var d=new Uint8Array(i),f=new Int16Array(i),p=new Int32Array(i),_=d[u],g=f[u/2+1];if(u+=4,0!=_)for(var v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=s(d,u+16),C=s(d,u+24);(n<0&&(y<t||y==t&&b<=e)||n>0&&(w>t||w==t&&x>=e))&&(/_random/.exec(r.bwg.idsToChroms[y])||(null==a||n<0&&(w>o||w==o&&x>l)||n>0&&(y<o||y==o&&b<l))&&(a={offset:k,size:C},l=n<0?x:b,o=n<0?w:y)),u+=32}else{for(var M=-1,S=-1,v=0;v<g;++v){var m=u/4,y=p[m],b=p[m+1],w=p[m+2],x=p[m+3],k=p[m+4]<<32|p[m+5];(n<0&&(y<t||y==t&&b<=e)&&w>=t||n>0&&(w>t||w==t&&x>=e)&&y<=t)&&(M<0||x>S)&&(M=k,S=n<0?x:b,n<0?w:y),u+=24}M>=0&&c([M],h+1)}};c([r.cirTreeOffset+48],1)},l.prototype.readWigData=function(t,e,n){var i,r=n-e;if(r<=25e3||0===this.zoomLevels.length)i=this.getUnzoomedView();else for(var a=0;a<this.zoomLevels.length;a++)if(r/this.zoomLevels[a].reduction<25e3){i=this.getZoomedView(a);break}return i.readWigData(t,e,n)},l.prototype.getUnzoomedView=function(){if(!this.unzoomedView){var t=4e3;this.zoomLevels[0]&&(t=this.zoomLevels[0].dataOffset-this.unzoomedIndexOffset),this.unzoomedView=new u(this,this.unzoomedIndexOffset,t,!1)}return this.unzoomedView},l.prototype.getZoomedView=function(t){var e=this.zoomLevels[t];return e.view||(e.view=new u(this,e.indexOffset,4e3,!0)),e.view},l.prototype._tsFetch=function(t,e,n,i,r){var a=this;if(!(t>=this.zoomLevels.length-1)){var o;return 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c=15,h=1440,d=0,f=0,p=1,_=-5,g=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],v=0,m=9,y=5,b=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],w=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],x=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],k=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],C=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],M=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13];t.prototype.inflateInit=function(t,n){return t||(t=c),n&&(n=!1),this.istate=new e,this.istate.inflateInit(this,n?-t:t)},t.prototype.inflate=function(t){return null==this.istate?-2:this.istate.inflate(this,t)},t.prototype.inflateEnd=function(){if(null==this.istate)return-2;var t=istate.inflateEnd(this);return this.istate=null,t},t.prototype.inflateSync=function(){return istate.inflateSync(this)},t.prototype.inflateSetDictionary=function(t,e){return istate.inflateSetDictionary(this,t,e)},e.prototype.inflateReset=function(t){return null==t||null==t.istate?-2:(t.total_in=t.total_out=0,t.msg=null,t.istate.mode=0!=t.istate.nowrap?7:0,t.istate.blocks.reset(t,null),f)},e.prototype.inflateEnd=function(t){return null!=this.blocks&&this.blocks.free(t),this.blocks=null,f},e.prototype.inflateInit=function(t,e){return t.msg=null,this.blocks=null,nowrap=0,e<0&&(e=-e,nowrap=1),e<8||e>15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new n(t,0!=t.istate.nowrap?null:this,1<<e),this.inflateReset(t),f)},e.prototype.inflate=function(t,e){var n,i;if(null==t||null==t.istate||null==t.next_in)return-2;for(e=4==e?_:f,n=_;;)switch(t.istate.mode){case 0:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,8!=(15&(t.istate.method=t.next_in[t.next_in_index++]))){t.istate.mode=13,t.msg="unknown compression method",t.istate.marker=5;break}if(8+(t.istate.method>>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,i=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+i)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&i)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?n:(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(n=t.istate.blocks.proc(t,n))){t.istate.mode=13,t.istate.marker=0;break}if(n==f&&(n=e),n!=p)return n;if(n=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return n;n=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return n;if(n=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,n){var i=0,r=n;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,n)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),r>=1<<t.istate.wbits&&(r=(1<<t.istate.wbits)-1,i=n-r),t.istate.blocks.set_dictionary(e,i,r),t.istate.mode=7,f)};var S=[0,0,255,255];e.prototype.inflateSync=function(t){var e,n,i,r,a;if(null==t||null==t.istate)return-2;if(13!=t.istate.mode&&(t.istate.mode=13,t.istate.marker=0),0==(e=t.avail_in))return _;for(n=t.next_in_index,i=t.istate.marker;0!=e&&i<4;)t.next_in[n]==S[i]?i++:i=0!=t.next_in[n]?0:4-i,n++,e--;return t.total_in+=n-t.next_in_index,t.next_in_index=n,t.avail_in=e,t.istate.marker=i,4!=i?-3:(r=t.total_in,a=t.total_out,this.inflateReset(t),t.total_in=r,t.total_out=a,t.istate.mode=7,f)},e.prototype.inflateSyncPoint=function(t){return null==t||null==t.istate||null==t.istate.blocks?-2:t.istate.blocks.sync_point()};var T=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];n.prototype.reset=function(t,e){e&&(e[0]=this.check),6==this.mode&&this.codes.free(t),this.mode=v,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(t.adler=this.check=t._adler.adler32(0,null,0,0))},n.prototype.proc=function(t,e){var n,i,r,s,l,u,c;for(s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u;;)switch(this.mode){case v:for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}switch(n=7&i,this.last=1&n,n>>>1){case 0:i>>>=3,r-=3,n=7&r,i>>>=n,r-=n,this.mode=1;break;case 1:var h=new Int32Array(1),d=new Int32Array(1),_=[],m=[];a(h,d,_,m,t),this.codes.init(h[0],d[0],_[0],0,m[0],0,t),i>>>=3,r-=3,this.mode=6;break;case 2:i>>>=3,r-=3,this.mode=3;break;case 3:return i>>>=3,r-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}break;case 1:for(;r<32;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if((~i>>>16&65535)!=(65535&i))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.left=65535&i,i=r=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);if(0==c&&(u==end&&0!=read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c&&(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,u==this.end&&0!=this.read&&(u=0,c=u<this.read?this.read-u-1:this.end-u),0==c)))return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(e=f,n=this.left,n>l&&(n=l),n>c&&(n=c),o(t.next_in,s,this.window,u,n),s+=n,l-=n,u+=n,c-=n,0!=(this.left-=n))break;this.mode=0!=this.last?7:v;break;case 3:for(;r<14;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(this.table=n=16383&i,(31&n)>29||(n>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(n=258+(31&n)+(n>>5&31),null==this.blens||this.blens.length<n)this.blens=new Int32Array(n);else for(var y=0;y<n;y++)this.blens[y]=0;i>>>=14,r-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;r<3;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}this.blens[T[this.index++]]=7&i,i>>>=3,r-=3}for(;this.index<19;)this.blens[T[this.index++]]=0;if(this.bb[0]=7,(n=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=n,-3==e&&(this.blens=null,this.mode=9),this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(n=this.table,!(this.index<258+(31&n)+(n>>5&31)))break;var y,b,w;for(n=this.bb[0];r<n;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(n=this.hufts[3*(this.tb[0]+(i&g[n]))+1],(w=this.hufts[3*(this.tb[0]+(i&g[n]))+2])<16)i>>>=n,r-=n,this.blens[this.index++]=w;else{for(y=18==w?7:w-14,b=18==w?11:3;r<n+y;){if(0==l)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,i|=(255&t.next_in[s++])<<r,r+=8}if(i>>>=n,r-=n,b+=i&g[y],i>>>=y,r-=y,y=this.index,n=this.table,y+b>258+(31&n)+(n>>5&31)||16==w&&y<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);w=16==w?this.blens[y-1]:0;do{this.blens[y++]=w}while(0!=--b);this.index=y}}this.tb[0]=-1;var h=new Int32Array(1),d=new Int32Array(1),_=new Int32Array(1),m=new Int32Array(1);if(h[0]=9,d[0]=6,n=this.table,(n=this.inftree.inflate_trees_dynamic(257+(31&n),1+(n>>5&31),this.blens,h,d,_,m,this.hufts,t))!=f)return-3==n&&(this.blens=null,this.mode=13),e=n,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.codes.init(h[0],d[0],this.hufts,_[0],this.hufts,m[0],t),this.mode=6;case 6:if(this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,(e=this.codes.proc(this,t,e))!=p)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,i=this.bitb,r=this.bitk,u=this.write,c=u<this.read?this.read-u-1:this.end-u,0==this.last){this.mode=v;break}this.mode=7;case 7:if(this.write=u,e=this.inflate_flush(t,e),u=this.write,c=u<this.read?this.read-u-1:this.end-u,this.read!=this.write)return this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);mode=12;case 8:return e=p,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);case 9:return e=-3,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);default:return e=-2,this.bitb=i,this.bitk=r,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}},n.prototype.free=function(t){this.reset(t,null),this.window=null,this.hufts=null},n.prototype.set_dictionary=function(t,e,n){o(t,e,window,0,n),this.read=this.write=n},n.prototype.sync_point=function(){return 1==this.mode},n.prototype.inflate_flush=function(t,e){var n,i,r;return i=t.next_out_index,r=this.read,n=(r<=this.write?this.write:this.end)-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n,r==this.end&&(r=0,this.write==this.end&&(this.write=0),n=this.write-r,n>t.avail_out&&(n=t.avail_out),0!=n&&e==_&&(e=f),t.avail_out-=n,t.total_out+=n,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,r,n)),o(this.window,r,t.next_out,i,n),i+=n,r+=n),t.next_out_index=i,this.read=r,e};i.prototype.init=function(t,e,n,i,r,a,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=n,this.ltree_index=i,this.dtree=r,this.dtree_index=a,this.tree=null},i.prototype.proc=function(t,e,n){var i,r,a,o,s,l,u,c=0,h=0,d=0;for(d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s;;)switch(this.mode){case 0:if(l>=258&&o>=10&&(t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,n=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),d=e.next_in_index,o=e.avail_in,c=t.bitb,h=t.bitk,s=t.write,l=s<t.read?t.read-s-1:t.end-s,n!=f)){this.mode=n==p?7:9;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=1;case 1:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>>=this.tree[r+1],h-=this.tree[r+1],0==(a=this.tree[r])){this.lit=this.tree[r+2],this.mode=6;break}if(0!=(16&a)){this.get=15&a,this.len=this.tree[r+2],this.mode=2;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}if(0!=(32&a)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 2:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.len+=c&g[i],c>>=i,h-=i,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(i=this.need;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}if(r=3*(this.tree_index+(c&g[i])),c>>=this.tree[r+1],h-=this.tree[r+1],0!=(16&(a=this.tree[r]))){this.get=15&a,this.dist=this.tree[r+2],this.mode=4;break}if(0==(64&a)){this.need=a,this.tree_index=r/3+this.tree[r+2];break}return this.mode=9,e.msg="invalid distance code",n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 4:for(i=this.get;h<i;){if(0==o)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,o--,c|=(255&e.next_in[d++])<<h,h+=8}this.dist+=c&g[i],c>>=i,h-=i,this.mode=5;case 5:for(u=s-this.dist;u<0;)u+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);t.window[s++]=t.window[u++],l--,u==t.end&&(u=0),this.len--}this.mode=0;break;case 6:if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l&&(t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,s==t.end&&0!=t.read&&(s=0,l=s<t.read?t.read-s-1:t.end-s),0==l)))return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);n=f,t.window[s++]=this.lit,l--,this.mode=0;break;case 7:if(h>7&&(h-=8,o++,d--),t.write=s,n=t.inflate_flush(e,n),s=t.write,l=s<t.read?t.read-s-1:t.end-s,t.read!=t.write)return t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);this.mode=8;case 8:return n=p,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);case 9:return n=-3,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n);default:return n=-2,t.bitb=c,t.bitk=h,e.avail_in=o,e.total_in+=d-e.next_in_index,e.next_in_index=d,t.write=s,t.inflate_flush(e,n)}},i.prototype.free=function(t){},i.prototype.inflate_fast=function(t,e,n,i,r,a,s,l){var u,c,h,d,_,v,m,y,b,w,x,k,C,M,S,T;m=l.next_in_index,y=l.avail_in,_=s.bitb,v=s.bitk,b=s.write,w=b<s.read?s.read-b-1:s.end-b,x=g[t],k=g[e];do{for(;v<20;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(u=_&x,c=n,h=i,T=3*(h+u),0!=(d=c[T]))for(;;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15,C=c[T+2]+(_&g[d]),_>>=d,v-=d;v<15;)y--,_|=(255&l.next_in[m++])<<v,v+=8;for(u=_&k,c=r,h=a,T=3*(h+u),d=c[T];;){if(_>>=c[T+1],v-=c[T+1],0!=(16&d)){for(d&=15;v<d;)y--,_|=(255&l.next_in[m++])<<v,v+=8;if(M=c[T+2]+(_&g[d]),_>>=d,v-=d,w-=C,b>=M)S=b-M,s.window[b++]=s.window[S++],s.window[b++]=s.window[S++],C-=2;else{S=b-M;do{S+=s.end}while(S<0);if(d=s.end-S,C>d){if(C-=d,b-S>0&&d>b-S)do{s.window[b++]=s.window[S++]}while(0!=--d);else o(s.window,S,s.window,b,d),b+=d,S+=d,d=0;S=0}}do{s.window[b++]=s.window[S++]}while(0!=--C);break}if(0!=(64&d))return l.msg="invalid distance code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3;u+=c[T+2],u+=_&g[d],T=3*(h+u),d=c[T]}break}if(0!=(64&d))return 0!=(32&d)?(C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,p):(l.msg="invalid literal/length code",C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,-3);if(u+=c[T+2],u+=_&g[d],T=3*(h+u),0==(d=c[T])){_>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--;break}}else _>>=c[T+1],v-=c[T+1],s.window[b++]=c[T+2],w--}while(w>=258&&y>=10);return C=l.avail_in-y,C=v>>3<C?v>>3:C,y+=C,m-=C,v-=C<<3,s.bitb=_,s.bitk=v,l.avail_in=y,l.total_in+=m-l.next_in_index,l.next_in_index=m,s.write=b,f},r.prototype.huft_build=function(t,e,n,i,r,a,s,l,u,c,d){var p,g,v,m,y,b,w,x,k,C,M,S,T,$,A;C=0,y=n;do{this.c[t[e+C]]++,C++,y--}while(0!=y);if(this.c[0]==n)return s[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(w=b,x<b&&(x=b),y=15;0!=y&&0==this.c[y];y--);for(v=y,x>y&&(x=y),l[0]=x,$=1<<b;b<y;b++,$<<=1)if(($-=this.c[b])<0)return-3;if(($-=this.c[y])<0)return-3;for(this.c[y]+=$,this.x[1]=b=0,C=1,T=2;0!=--y;)this.x[T]=b+=this.c[C],T++,C++;y=0,C=0;do{0!=(b=t[e+C])&&(this.v[this.x[b]++]=y),C++}while(++y<n);for(n=this.x[v],this.x[0]=y=0,C=0,m=-1,S=-x,this.u[0]=0,M=0,A=0;w<=v;w++)for(p=this.c[w];0!=p--;){for(;w>S+x;){if(m++,S+=x,A=v-S,A=A>x?x:A,(g=1<<(b=w-S))>p+1&&(g-=p+1,T=w,b<A))for(;++b<A&&!((g<<=1)<=this.c[++T]);)g-=this.c[T];if(A=1<<b,this.hn[0]+A>h)return-3;this.u[m]=M=this.hn[0],this.hn[0]+=A,0!=m?(this.x[m]=y,this.r[0]=b,this.r[1]=x,b=y>>>S-x,this.r[2]=M-this.u[m-1]-b,o(this.r,0,u,3*(this.u[m-1]+b),3)):s[0]=M}for(this.r[1]=w-S,C>=n?this.r[0]=192:d[C]<i?(this.r[0]=this.v[C]<256?0:96,this.r[2]=this.v[C++]):(this.r[0]=a[this.v[C]-i]+16+64,this.r[2]=r[this.v[C++]-i]),g=1<<w-S,b=y>>>S;b<A;b+=g)o(this.r,0,u,3*(M+b),3);for(b=1<<w-1;0!=(y&b);b>>>=1)y^=b;for(y^=b,k=(1<<S)-1;(y&k)!=this.x[m];)m--,S-=x,k=(1<<S)-1}return 0!=$&&1!=v?_:f},r.prototype.inflate_trees_bits=function(t,e,n,i,r){var a;return this.initWorkArea(19),this.hn[0]=0,a=this.huft_build(t,0,19,19,null,null,n,e,i,this.hn,this.v),-3==a?r.msg="oversubscribed dynamic bit lengths tree":a!=_&&0!=e[0]||(r.msg="incomplete dynamic bit lengths tree",a=-3),a},r.prototype.inflate_trees_dynamic=function(t,e,n,i,r,a,o,s,l){var u;return this.initWorkArea(288),this.hn[0]=0,(u=this.huft_build(n,0,t,257,x,k,a,i,s,this.hn,this.v))!=f||0==i[0]?(-3==u?l.msg="oversubscribed literal/length tree":-4!=u&&(l.msg="incomplete literal/length tree",u=-3),u):(this.initWorkArea(288),u=this.huft_build(n,t,e,0,C,M,o,r,s,this.hn,this.v),u!=f||0==r[0]&&t>257?(-3==u?l.msg="oversubscribed distance tree":u==_?(l.msg="incomplete distance tree",u=-3):-4!=u&&(l.msg="empty distance tree with lengths",u=-3),u):f)},r.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new 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t=this.get_circular_tracks(),e=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-t.length*(e+n)+n-this.label_arc_height,a=u.range(r,i/2,e+n);return s.map(a,function(t){return[t,t+e]})},render:function(){var t=this,e=t.$el.width(),n=t.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=t.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(t.$el[0]).append("svg").attr("width",e).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var e=u.event.scale;s.attr("transform","translate("+u.event.translate+") scale("+e+")"),t.scale!==e&&(t.zoom_drag_timeout&&clearTimeout(t.zoom_drag_timeout),t.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+e/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(e,n){var i=new M({el:s.append("g")[0],track:e,radius_bounds:o[n],genome:t.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(e){var n=new S({el:s.append("g")[0],track:e,radius_bounds:o[0],genome:t.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new k({el:s.append("g")[0],track:new b,radius_bounds:c,genome:t.genome,total_gap:a}),this.label_track_view.render()},add_track:function(t){var e=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===t.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new S({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:n,genome:this.genome,total_gap:e});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();s.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])}),s.each(this.chords_views,function(t){t.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new M({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();s.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();s.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),s.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),x=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new m;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),l=o.attr("chrom"),c=n.genome.get_chrom_region(l),h=n.track.get("data_manager");h.can_get_more_detailed_data(c)&&(a=n.track.get("data_manager").get_more_detailed_data(c,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=s.find(n.chroms_layout,function(t){return t.data.chrom===l}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=s.reject(s.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds;this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=s.zip(n,i);s.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var l=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",l).style("fill",l),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return s.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),k=x.extend({initialize:function(t){x.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=s.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});s.extend(k.prototype,y);var C=x.extend({initialize:function(t){x.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return i?t.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",e.data.chrom).attr("d",i):null},_get_path_function:function(t,e){if("string"==typeof e||!e.data||0===e.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,e.data.length]).range([t.startAngle,t.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(t){return n(t[1])}).angle(function(t,e){return i(e)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var t=this,e=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),e,!0).classed("min_max",!0);s.each(n,function(e){i(e).click(function(){new _.default.ConfigSettingCollectionView({collection:t.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var t=this,e=s.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>.08}),n=s.filter(e,function(t,e){return e%3==0}),i=s.flatten(s.map(n,function(e){return t._data_bounds_ticks_fn()(e)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"})}},_data_bounds_ticks_fn:function(){var t=this;return visibleChroms=0,function(e){return[{radius:t.radius_bounds[0],angle:e.startAngle,label:t.formatNum(t.data_bounds[0])},{radius:t.radius_bounds[1],angle:e.startAngle,label:t.formatNum(t.data_bounds[1])}]}},get_data_bounds:function(t){}});s.extend(C.prototype,y);var M=C.extend({get_data_bounds:function(t){var e=s.flatten(s.map(t,function(t){return t?s.map(t.data,function(t){return parseInt(t[1],10)||0}):0}));return[s.min(e),this._quantile(e,.98)||s.max(e)]}}),S=x.extend({render:function(){var t=this;i.when(t.track.get("data_manager").data_is_ready()).then(function(){i.when(t.track.get("data_manager").get_genome_wide_data(t.genome)).then(function(e){var n=[],i=t.genome.get_chroms_info();s.each(e,function(e,r){var a=i[r].chrom,o=s.map(e.data,function(e){var n=t._get_region_angle(a,e[1]),i=t._get_region_angle(e[3],e[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),t.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",t.get_fill_color()).attr("d",u.svg.chord().radius(t.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(t){this.radius_bounds=t,this.parent_elt.selectAll("path").transition().attr("d",u.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(t,e){var n=s.find(this.chroms_layout,function(e){return e.data.chrom===t});return 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s=r.step;s||(s=r.precise&&this.has_slider?(r.max-r.min)/r.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:r.min,max:r.max,step:s}).on("slide",function(t,e){i.value(e.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.get("value");this.has_slider&&this.$slider.slider("value",t),t!==this.$text.val()&&this.$text.val(t)},value:function(t){var e=this.model.attributes;return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),!e.precise&&(t=Math.round(t)),null!==e.max&&(t=Math.min(t,e.max)),null!==e.min&&(t=Math.max(t,e.min))),this.model.set("value",t),this.model.trigger("change"),e.onchange(t)),this.model.get("value")},_isParameter:function(t){return this.model.get("is_workflow")&&"$"===String(t).substring(0,1)},_template:function(){return'<div class="ui-form-slider"><input class="ui-form-slider-text" type="text"/><div class="ui-form-slider-element"/></div>'}});e.default={View:r}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=o(a),s=i(23),l=o(s),u=l.default.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.type,l.default.BaseIcons.prototype.initialize.call(this,t)},_setValue:function(e){if(l.default.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,o=t.isArray(e)?e:[e];n.each(o,function(t){var e=i.header_index[t];n.each(e,function(t){i._setState(t,!0)})})}},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function e(t,e){var i=t.find(".button-"+e);i.on("click",function(){n._setState(e,!i.data("is_expanded"))})}function i(o,a,s){s=s||[];for(var l in a){var u=a[l],c=u.options&&u.options.length>0,d=s.slice(0);n.header_index[u.value]=d.slice(0);var h=t("<div/>");if(c){var f=r.default.uid(),p=t("<span/>").addClass("button-"+f).addClass("ui-drilldown-button fa fa-plus-square"),m=t("<div/>").addClass("subgroup-"+f).addClass("ui-drilldown-subgroup");h.append(t("<div/>").append(p).append(n._templateOption({label:u.name,value:u.value}))),d.push(f),i(m,u.options,d),h.append(m),e(h,f)}else h.append(n._templateOption({label:u.name,value:u.value}));o.append(h)}}var n=this;this.header_index={};var o=t("<div/>");return i(o,this.model.get("data")),o},_template:function(){return t("<div/>").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});e.default={View:u}}).call(e,i(0),i(2))},function(t,e,i){"use strict";(function(t,n,o,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var s=i(3),l=r(s),u=i(4),c=(r(u),i(11)),d=r(c),h=i(49),f=r(h),p=i(50),m=r(p),v=i(51),g=r(v),_=t.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new g.default,this.setElement(n("<div/>")),this.render()},render:function(){var t=this;this.$el.empty(),o.each(this.inputs,function(e){t.add(e)})},add:function(t){var e=a.extend(!0,{},t);switch(e.id=t.id=l.default.uid(),this.app.input_list[e.id]=e,e.type){case"conditional":this._addConditional(e);break;case"repeat":this._addRepeat(e);break;case"section":this._addSection(e);break;default:this._addRow(e)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var o in t.cases){var a=t.cases[o],r=e.$("#"+t.id+"-section-"+o),s=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){s=!0;break}o==n&&s?r.fadeIn("fast"):r.hide()}e.app.trigger("change")});for(var n in t.cases){var o=new _(this.app,{inputs:t.cases[n].inputs});this._append(o.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var o=t.id+"-section-"+n++,r=new _(i.app,{inputs:e});a.add({id:o,$el:r.$el,ondel:function(){a.del(o),i.app.trigger("change")}})}for(var i=this,n=0,a=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),r=o.size(t.cache),s=0;s<Math.max(Math.max(r,t.min||0),t.default||0);s++)e(s<r?t.cache[s]:t.inputs);this.app.model.get("sustain_repeats")&&a.hideOptions();var l=new m.default(this.app,{label:t.title||t.name,help:t.help,field:a});this._append(l.$el,t.id)},_addSection:function(t){var e=new d.default.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!t.expanded});e.append(new _(this.app,{inputs:t.inputs}).$el),e.append(n("<div/>").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var o=new m.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=o,this._append(o.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:_}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),l=i(11),u=a(l),c=i(4),d=a(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new d.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("<div/>").append(this.$list=n("<div/>")).append(n("<div/>").append(this.button_new.$el)))},size:function(){return o.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new d.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new u.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),o.each(this.list,function(t){t.hideOperation("button_delete")}),o.isEmpty(this.list)&&this.$el.append(n("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var o=this;this.$collapsible.on("click",function(){o.field.collapsed=!o.field.collapsed,e.trigger&&e.trigger("change"),o.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){o.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var o=this.model.get("error_text");if(this.$error[o?"show":"hide"](),this.$el[o?"addClass":"removeClass"]("ui-error"),this.$error_text.html(o),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),l=i(4),u=a(l),c=i(52),d=a(c),h=i(53),f=a(h),p=i(54),m=a(p),v=i(55),g=a(v),_=i(57),w=a(_);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new d.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=u.default.Select;switch(t.display){case"checkboxes":i=u.default.Checkbox;break;case"radio":i=u.default.Radio;break;case"radiobutton":i=u.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new u.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(o.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new u.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new u.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new u.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new u.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new w.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new m.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new u.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),l=i(4),u=a(l),c=i(22),d=a(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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t=this;o.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),o.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],o.each(this.config,function(e,o){t.button_data.push({value:o,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new d.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(a[e.src]||"content")+" 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t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),a=n(o),r=i(24),s=n(r),l=t.View.extend({initialize:function(t){var 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t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(n.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return 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n("<div/>").addClass("ui-option").append(n("<input/>").attr({id:e,type:this.model.get("type"),name:this.model.id,value:t.value})).append(n("<label/>").addClass("ui-options-label").attr("for",e).html(t.label))}}),h={};h.View=d.extend({initialize:function(t){t.type="radio",d.prototype.initialize.call(this,t)}});var f={};f.View=d.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,d.prototype.initialize.call(this,t)}});var p={};p.View=c.extend({initialize:function(t){c.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=n("<label/>").addClass("btn btn-default");return t.icon&&e.append(n("<i/>").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(n("<input/>").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return n("<div/>").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),e.default={Base:c,BaseIcons:d,Radio:h,RadioButton:p,Checkbox:f}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=o(a),s=i(11),l=o(s),u=i(4),c=o(u),d=t.View.extend({initialize:function(t){var e=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new c.default.Message,this.portlet=new l.default.View({cls:"ui-portlet-section"}),this.select=new c.default.Select.View({optional:t.optional}),this.button=new c.default.ButtonIcon({icon:"fa fa-sign-in",tooltip:"Insert new 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o=this.model.get("error_text");if(this.$error[o?"show":"hide"](),this.$el[o?"addClass":"removeClass"]("ui-error"),this.$error_text.html(o),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return i("<div/>").addClass("ui-form-element").append(i("<div/>").addClass("ui-form-error ui-error").append(i("<span/>").addClass("fa fa-arrow-down")).append(i("<span/>").addClass("ui-form-error-text"))).append(i("<div/>").addClass("ui-form-title").append(i("<div/>").addClass("ui-form-collapsible").append(i("<i/>").addClass("ui-form-collapsible-icon")).append(i("<span/>").addClass("ui-form-collapsible-text"))).append(i("<span/>").addClass("ui-form-title-text"))).append(i("<div/>").addClass("ui-form-field").append(i("<span/>").addClass("ui-form-info")).append(i("<div/>").addClass("ui-form-backdrop"))).append(i("<div/>").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),l=i(4),u=a(l),c=i(52),d=a(c),h=i(53),f=a(h),p=i(54),m=a(p),v=i(55),g=a(v),_=i(57),w=a(_);e.default=t.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new d.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=u.default.Select;switch(t.display){case"checkboxes":i=u.default.Checkbox;break;case"radio":i=u.default.Radio;break;case"radiobutton":i=u.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new u.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(o.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new u.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new u.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new u.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new u.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new w.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new m.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new u.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),s=a(r),l=i(4),u=a(l),c=i(22),d=a(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple 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datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("<div/>").addClass("ui-select-content")),this.button_product=new u.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var o=n("<div/>").addClass("ui-form-info").append(n("<i/>").addClass("fa fa-sitemap")).append(n("<span/>").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:o.clone(),enabled:o.clone().append(n("<div/>").append(n("<div/>").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("<div/>").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var o=this._batch({values:[]});for(var a in i){var r=this.history[i[a]+"_"+this.config[e].src];if(!r)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[a]+"'."),null;o.values.push(r)}return o.values.sort(function(t,e){return t.hid-e.hid}),o}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;o.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),o.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),a=this.model.get("src_labels");this.fields=[],this.button_data=[],o.each(this.config,function(e,o){t.button_data.push({value:o,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new d.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(a[e.src]||"content")+" 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o=i(3),a=(n(o),i(4)),r=n(a),s=i(43),l=(n(s),i(24)),u=n(l),c=t.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),d=t.Collection.extend({initialize:function(){var e=this;this.config=new t.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),h=t.View.extend({initialize:function(t){var e=this;this.libraries=new c,this.datasets=new d,this.options=t,this.library_select=new r.default.Select.View({onchange:function(t){e.datasets.config.set("library_id",t)}}),this.dataset_list=new u.default.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var t=[];e.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),e.library_select.update(t)}),this.datasets.on("reset",function(){var t=[];null!==e.library_select.text()&&e.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),e.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),a=n(o),r=i(24),s=n(r),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new s.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),a.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),a=(n(o),i(4)),r=n(a),s=i(56),l=n(s),u=t.View.extend({initialize:function(t){var e=this;this.browse_button=new r.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new r.default.Input,this.token_textbox=new r.default.Input({type:"password"}),this.setElement(this._template(t)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(t){var e=this;l.default.openFileBrowser({successCallback:function(t){e.value(t.destination+"^"+t.token)}})},_template:function(t){return'<div class="ui-gs-select-file"><div class="ui-gs-browse-field"><span class="ui-gs-browse-button" /><span class="ui-gs-filename-textbox" /></div><div class="ui-gs-token-field"><span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span><span class="ui-gs-token-textbox" /></div></div>'},value:function(t){if(void 0===t)return this._getValue();this._setValue(t)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(t){t&&(values=t.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});e.default={View:u}}).call(e,i(1))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0}),e.default={openFileBrowser:function(t){var e=window.Galaxy.config.genomespace_ui_url,i=e+"upload/loadUrlToGenomespace.html?getLocation=true",n=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=t.successCallback,window.addEventListener("message",function(t){successCalBack(t.data)},!1),n.focus(),null!=t.errorCallback&&(n.setCallbackOnGSUploadError=config.errorCallback)}}},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),a=function(t){return t&&t.__esModule?t:{default:t}}(o);e.default=t.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},initialize:function(t){this.options=a.default.merge(t,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var e=this;this.$boxes.on("click",function(){e.value(n(this).css("background-color")),e.$header.trigger("click")}),this.$header.on("click",function(){e.visible=!e.visible,e.visible?e.$view.fadeIn("fast"):e.$view.fadeOut("fast")})},value:function(t){return void 0!==t&&null!==t&&(this.$value.css("background-color",t),this.$(".ui-color-picker-box").empty(),this.$(this._getValue()).html(this._templateCheck()),this.options.onchange&&this.options.onchange(t)),this._getValue()},_getValue:function(){var t=this.$value.css("background-color");if(t=t.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/)){var e=function(t){return("0"+parseInt(t).toString(16)).slice(-2)};return"#"+e(t[1])+e(t[2])+e(t[3])}return null},_build:function(){this._content({colors:this.colors.base});for(var t in this.colors.theme){var e={};0==t?e.bottom=!0:t!=this.colors.theme.length-1?(e.top=!0,e.bottom=!0):e.top=!0,e.colors=this.colors.theme[t],this._content(e)}this._content({colors:this.colors.standard})},_content:function(t){var 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t(".tag-area").click(),!1}),(0,C.default)("workflow-annotation","workflow-annotation",l.urls.annotate_async,"new_annotation",25,!0,4)},_buildToolPanelWorkflows:function(){var e=this,i=t('<div class="toolSectionWrapper"><div class="toolSectionTitle"><a href="#"><span>Workflows</span></a></div><div class="toolSectionBody"><div class="toolSectionBg"/></div></div>');return o.each(this.options.workflows,function(n){if(n.id!==e.options.id){var o=new y.default.ButtonIcon({icon:"fa fa-copy",cls:"ui-button-icon-plain",tooltip:"Copy and insert individual steps",onclick:function(){n.step_count<2?e.copy_into_workflow(n.id,n.name):Galaxy.modal.show({title:"Warning",body:"This will copy "+n.step_count+" new steps into your workflow.",buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){Galaxy.modal.hide(),e.copy_into_workflow(n.id,n.name)}}})}}),a=t("<a/>").attr("href","#").html(n.name).on("click",function(){e.add_node_for_subworkflow(n.latest_id,n.name)});i.find(".toolSectionBg").append(t("<div/>").addClass("toolTitle").append(a).append(o.$el))}}),i},copy_into_workflow:function(e){var i=this;this._workflowLoadAjax(e,{success:function(e){i.workflow.from_simple(e,!1);var n="";t.each(e.upgrade_messages,function(e,o){n+="<li>Step "+(parseInt(e,10)+1)+": "+i.workflow.nodes[e].name+"<ul>",t.each(o,function(t,e){n+="<li>"+e+"</li>"}),n+="</ul></li>"}),n?window.show_modal("Subworkflow embedded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+n+"</ul>",{Continue:hide_modal}):hide_modal()},beforeSubmit:function(t){show_message("Importing workflow","progress")}})},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=window.workflow_globals.workflow=new d.default(this,t("#canvas-container"))},scroll_to_nodes:function(){var e,i,n=t("#canvas-viewport"),o=t("#canvas-container");i=o.width()<n.width()?(n.width()-o.width())/2:0,e=o.height()<n.height()?(n.height()-o.height())/2:0,o.css({left:i,top:e})},_workflowLoadAjax:function(e,i){t.ajax(u.default.merge(i,{url:this.urls.load_workflow,data:{id:e,_:"true"},dataType:"json",cache:!1}))},_moduleInitAjax:function(t,e){var i=this;u.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:e,success:function(e){t.init_field_data(e),t.update_field_data(e),i.workflow.activate_node(t)}})},add_node_for_tool:function(t,e){var i=this.workflow.create_node("tool",e,t);this._moduleInitAjax(i,{type:"tool",tool_id:t,_:"true"})},add_node_for_subworkflow:function(t,e){var i=this.workflow.create_node("subworkflow",e,t);this._moduleInitAjax(i,{type:"subworkflow",content_id:t,_:"true"})},add_node_for_module:function(t,e){var i=this.workflow.create_node(t,e);this._moduleInitAjax(i,{type:t,_:"true"})},display_file_list:function(t){var e="<select id='node_data_list' name='node_data_list'>";for(var i in t.output_terminals)e+="<option value='"+i+"'>"+i+"</option>";return e+="</select>"},showWorkflowParameters:function(){var e=/\$\{.+?\}/g,i=[],n=t("#workflow-parameters-container"),o=t("#workflow-parameters-box"),a="",r=[];t.each(this.workflow.nodes,function(n,o){o.config_form&&o.config_form.inputs&&u.default.deepeach(o.config_form.inputs,function(t){if("string"==typeof t.value){var i=t.value.match(e);i&&(r=r.concat(i))}}),o.post_job_actions&&t.each(o.post_job_actions,function(i,n){n.action_arguments&&t.each(n.action_arguments,function(t,i){var n=i.match(e);n&&(r=r.concat(n))})}),r&&t.each(r,function(e,n){-1===t.inArray(n,i)&&i.push(n)})}),i&&0!==i.length?(t.each(i,function(t,e){a+="<div>"+e.substring(2,e.length-1)+"</div>"}),n.html(a),o.show()):(n.html(a),o.hide())},showAttributes:function(){t(".right-content").hide(),t("#edit-attributes").show()},showForm:function(e,i){var n="right-content",o=n+"-"+i.id,a=t("#"+n);if(e&&0==a.find("#"+o).length){var r=t('<div id="'+o+'" class="'+n+'"/>');if(e.node=i,e.workflow=this.workflow,e.datatypes=this.datatypes,e.icon=g.default[i.type],e.cls="ui-portlet-narrow",i){var s="tool"==i.type?"Tool":"Default";r.append(new w.default[s](e).form.$el),a.append(r)}else Galaxy.emit.debug("workflow-view::initialize()","Node not found in workflow.")}t("."+n).hide(),a.find("#"+o).show(),a.show(),a.scrollTop()},isSubType:function(t,e){return t=this.ext_to_type[t],e=this.ext_to_type[e],this.type_to_type[t]&&e in this.type_to_type[t]},prebuildNode:function(e,i,n){var o=this,a=t("<div class='toolForm toolFormInCanvas'/>"),r=t("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+i+"</div></div>");s(r.find(".nodeTitle"),e),a.append(r),a.css("left",t(window).scrollLeft()+20),a.css("top",t(window).scrollTop()+20),a.append(t("<div class='toolFormBody'></div>"));var l=new m.default(this,{element:a});l.type=e,l.content_id=n;var u="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";a.find(".toolFormBody").append(u);var c=t("<div class='buttons' style='float: right;'></div>");c.append(t("<div/>").addClass("fa-icon-button fa fa-times").click(function(t){l.destroy()})),a.appendTo("#canvas-container");var d=t("#canvas-container").position(),h=t("#canvas-container").parent(),f=a.width(),p=a.height();return a.css({left:-d.left+h.width()/2-f/2,top:-d.top+h.height()/2-p/2}),c.prependTo(a.find(".toolFormTitle")),f+=c.width()+10,a.css("width",f),a.bind("dragstart",function(){o.workflow.activate_node(l)}).bind("dragend",function(){o.workflow.node_changed(this),o.workflow.fit_canvas_to_nodes(),o.canvas_manager.draw_overview()}).bind("dragclickonly",function(){o.workflow.activate_node(l)}).bind("drag",function(e,i){var n=t(this).offsetParent().offset(),o=i.offsetX-n.left,a=i.offsetY-n.top;t(this).css({left:o,top:a}),t(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t){function n(t,e){this.app=t,this.canvas_container=e,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(224),a=function(t){return t&&t.__esModule?t:{default:t}}(o),r=i(42),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r);t.extend(n.prototype,{canLabelOutputWith:function(t){return!t||!(t in this.workflowOutputLabels)},registerOutputLabel:function(t){t&&(this.workflowOutputLabels[t]=!0)},unregisterOutputLabel:function(t){t&&delete this.workflowOutputLabels[t]},updateOutputLabel:function(t,e){t&&this.unregisterOutputLabel(t),this.canLabelOutputWith(e)||s.warning("Workflow contains duplicate workflow output labels "+e+". This must be fixed before it can be saved."),e&&this.registerOutputLabel(e)},attemptUpdateOutputLabel:function(t,e,i){return!!this.canLabelOutputWith(i)&&(t.labelWorkflowOutput(e,i),t.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(t,e,i){var n=this.app.prebuildNode(t,e,i);return this.add_node(n),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(n),n},add_node:function(t){t.id=this.id_counter,t.element.attr("id","wf-node-step-"+t.id),this.id_counter++,this.nodes[t.id]=t,this.has_changes=!0,t.workflow=this},remove_node:function(t){this.active_node==t&&this.clear_active_node(),delete this.nodes[t.id],this.has_changes=!0},remove_all:function(){var e=this;t.each(this.nodes,function(t,i){i.destroy(),e.remove_node(i)})},rectify_workflow_outputs:function(){var e=!1,i=!1;if(t.each(this.nodes,function(n,o){o.workflow_outputs&&o.workflow_outputs.length>0&&(e=!0),t.each(o.post_job_actions,function(t,e){"HideDatasetAction"===e.action_type&&(i=!0)})}),!1!==e||!1!==i){var n=this;t.each(this.nodes,function(i,o){if("tool"===o.type){var a=!1;null===o.post_job_actions&&(o.post_job_actions={},a=!0);var r=[];t.each(o.post_job_actions,function(t,e){"HideDatasetAction"==e.action_type&&r.push(t)}),r.length>0&&t.each(r,function(t,e){a=!0,delete o.post_job_actions[e]}),e&&t.each(o.output_terminals,function(t,e){if(!0==!o.isWorkflowOutput(e.name)){a=!0;var i={action_type:"HideDatasetAction",output_name:e.name,action_arguments:{}};o.post_job_actions["HideDatasetAction"+e.name]=null,o.post_job_actions["HideDatasetAction"+e.name]=i}}),n.active_node==o&&!0===a&&n.reload_active_node()}})}},to_simple:function(){var e={};return t.each(this.nodes,function(i,n){var o={};t.each(n.input_terminals,function(e,i){o[i.name]=null;var n=[];t.each(i.connectors,function(t,e){if(e.handle1){var a={id:e.handle1.node.id,output_name:e.handle1.name},r=i.attributes.input.input_subworkflow_step_id;void 0!==r&&(a.input_subworkflow_step_id=r),n[t]=a,o[i.name]=n}})});var a={};n.post_job_actions&&t.each(n.post_job_actions,function(t,e){var i={action_type:e.action_type,output_name:e.output_name,action_arguments:e.action_arguments};a[e.action_type+e.output_name]=null,a[e.action_type+e.output_name]=i}),n.workflow_outputs||(n.workflow_outputs=[]);var r={id:n.id,type:n.type,content_id:n.content_id,tool_version:n.config_form.version,tool_state:n.tool_state,errors:n.errors,input_connections:o,position:t(n.element).position(),annotation:n.annotation,post_job_actions:n.post_job_actions,uuid:n.uuid,label:n.label,workflow_outputs:n.workflow_outputs};e[n.id]=r}),{steps:e}},from_simple:function(e,i){var n=void 0===i||i,o=this,r=0;n?o.name=e.name:r=Object.keys(o.nodes).length;var s=r,l=!1;t.each(e.steps,function(e,i){var a=o.app.prebuildNode(i.type,i.name,i.content_id);n||(i.uuid=null,t.each(i.workflow_outputs,function(t,e){e.uuid=null})),a.init_field_data(i),i.position&&a.element.css({top:i.position.top,left:i.position.left}),a.id=parseInt(i.id)+r,o.nodes[a.id]=a,s=Math.max(s,parseInt(e)+r),l||(a.workflow_outputs.length>0?l=!0:t.each(a.post_job_actions||[],function(t,e){"HideDatasetAction"===e.action_type&&(l=!0)}))}),o.id_counter=s+1,t.each(e.steps,function(e,i){var n=o.nodes[parseInt(e)+r];t.each(i.input_connections,function(e,i){i&&(t.isArray(i)||(i=[i]),t.each(i,function(t,i){var s=o.nodes[parseInt(i.id)+r],l=new a.default;l.connect(s.output_terminals[i.output_name],n.input_terminals[e]),l.redraw()}))}),l&&t.each(n.output_terminals,function(e,i){if(void 0===n.post_job_actions["HideDatasetAction"+i.name]){n.addWorkflowOutput(i.name);t(n.element).find(".callout."+i.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),o.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,t("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var t=this.active_node;this.clear_active_node(),this.activate_node(t)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showAttributes()},activate_node:function(t){this.active_node!=t&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(t.config_form,t),t.make_active(),this.active_node=t)},node_changed:function(t,e){this.has_changes=!0,this.active_node==t&&e&&(this.check_changes_in_active_form(),this.app.showForm(t.config_form,t)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var e={},i={};t.each(this.nodes,function(t,n){void 0===e[t]&&(e[t]=0),void 0===i[t]&&(i[t]=[])}),t.each(this.nodes,function(n,o){t.each(o.input_terminals,function(n,a){t.each(a.connectors,function(t,n){var a=n.handle1.node;e[o.id]+=1,i[a.id].push(o.id)})})});for(var n=[];;){var o=[];for(var a in e)0===e[a]&&o.push(a);if(0===o.length)break;n.push(o);for(var r in o){var s=o[r];delete e[s];for(var l in i[s])e[i[s][l]]-=1}}if(!e.length){var u=this.nodes,c=80;t.each(n,function(e,i){i.sort(function(e,i){return t(u[e].element).position().top-t(u[i].element).position().top});var n=0,o=30;t.each(i,function(e,i){var a=u[i],r=t(a.element);t(r).css({top:o,left:c}),n=Math.max(n,t(r).width()),o+=t(r).height()+30}),c+=n+80}),t.each(u,function(t,e){e.redraw()})}},bounds_for_all_nodes:function(){var e,i=1/0,n=-1/0,o=1/0,a=-1/0;return t.each(this.nodes,function(r,s){var l=t(s.element);e=l.position(),i=Math.min(i,e.left),n=Math.max(n,e.left+l.width()),o=Math.min(o,e.top),a=Math.max(a,e.top+l.width())}),{xmin:i,xmax:n,ymin:o,ymax:a}},fit_canvas_to_nodes:function(){function e(t,e){return Math.ceil(t/e)*e}function i(t,e){if(t<e||t>3*e){return-(t-(Math.ceil(t%e/e)+1)*e)}return 0}var n=this.bounds_for_all_nodes(),o=this.canvas_container.position(),a=this.canvas_container.parent(),r=i(n.xmin,100),s=i(n.ymin,100);r=Math.max(r,o.left),s=Math.max(s,o.top);var l=o.left-r,u=o.top-s,c=e(n.xmax+100,100)+r,d=e(n.ymax+100,100)+s;c=Math.max(c,-l+a.width()),d=Math.max(d,-u+a.height()),this.canvas_container.css({left:l,top:u,width:c,height:d}),this.canvas_container.children().each(function(){var e=t(this).position();t(this).css("left",e.left+r),t(this).css("top",e.top+s)})}}),e.default=n}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t,e,i){this.app=t,this.cv=e,this.cc=this.cv.find("#canvas-container"),this.overview=i,this.oc=i.find("#overview-canvas"),this.ov=i.find("#overview-viewport"),this.init_drag()}function n(t){this.panel=t}Object.defineProperty(e,"__esModule",{value:!0}),t.extend(i.prototype,{init_drag:function(){var e=this,i=function(t,i){t=Math.min(t,e.cv.width()/2),t=Math.max(t,-e.cc.width()+e.cv.width()/2),i=Math.min(i,e.cv.height()/2),i=Math.max(i,-e.cc.height()+e.cv.height()/2),e.cc.css({left:t,top:i}),e.cv.css({"background-position-x":t,"background-position-y":i}),e.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new n(this)});var o,a;this.cv.bind("dragstart",function(){var i=t(this).offset(),n=e.cc.position();a=n.top-i.top,o=n.left-i.left}).bind("drag",function(t,e){i(e.offsetX+o,e.offsetY+a)}).bind("dragend",function(){e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),this.overview.click(function(t){if(e.overview.hasClass("blockaclick"))e.overview.removeClass("blockaclick");else{var n=e.cc.width(),o=e.cc.height(),a=e.oc.width(),r=e.oc.height(),s=t.pageX-e.oc.offset().left-e.ov.width()/2,l=t.pageY-e.oc.offset().top-e.ov.height()/2;i(-s/a*n,-l/r*o),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}}),this.ov.bind("drag",function(t,n){var o=e.cc.width(),a=e.cc.height(),r=e.oc.width(),s=e.oc.height(),l=n.offsetX-e.overview.offset().left,u=n.offsetY-e.overview.offset().top;i(-l/r*o,-u/s*a)}).bind("dragend",function(){e.overview.addClass("blockaclick"),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),t("#overview-border").bind("drag",function(i,n){var o=t(this).offsetParent(),a=o.offset(),r=Math.max(o.width()-(n.offsetX-a.left),o.height()-(n.offsetY-a.top));t(this).css({width:r,height:r}),e.draw_overview()}),t("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,i=this.oc,n=this.ov,o=t.width(),a=t.height(),r=i.width(),s=i.height(),l=t.position();n.css({left:-l.left/o*r,top:-l.top/a*s,width:e.width()/o*r-2,height:e.height()/a*s-2})},draw_overview:function(){var e,i,n,o,a=t("#overview-canvas"),r=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=t("#canvas-container").width(),u=t("#canvas-container").height(),c=this.cv.width(),d=this.cv.height();l<c&&u<d?(n=l/c*r,o=(r-n)/2,e=u/d*r,i=(r-e)/2):l<u?(i=0,e=r,n=Math.ceil(e*l/u),o=(r-n)/2):(n=r,o=0,e=Math.ceil(n*u/l),i=(r-e)/2),a.parent().css({left:o,top:i,width:n,height:e}),a.attr("width",n),a.attr("height",e),t.each(this.app.workflow.nodes,function(i,o){s.fillStyle="#D2C099",s.strokeStyle="#D8B365",s.lineWidth=1;var a=t(o.element),r=a.position(),c=r.left/l*n,d=r.top/u*e,h=a.width()/l*n,f=a.height()/u*e;o.errors?(s.fillStyle="#FFCCCC",s.strokeStyle="#AA6666"):void 0!==o.workflow_outputs&&o.workflow_outputs.length>0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(c,d,h,f),s.strokeRect(c,d,h,f)}),this.update_viewport_overlay()}}),t.extend(n.prototype,{test:function(e,i){clearTimeout(this.timeout);var n=e.pageX,o=e.pageY,a=t(this.panel),r=a.position(),s=a.width(),l=a.height(),u=a.parent(),c=u.width(),d=u.height(),h=u.offset(),f=h.left,p=h.top,m=f+u.width(),v=p+u.height(),g=-(s-c/2),_=-(l-d/2),w=c/2,b=d/2,y=!1;if(n-5<f){if(r.left<w){var x=Math.min(23,w-r.left);a.css("left",r.left+x),y=!0}}else if(n+5>m){if(r.left>g){var x=Math.min(23,r.left-g);a.css("left",r.left-x),y=!0}}else if(o-5<p){if(r.top<b){var x=Math.min(23,b-r.top);a.css("top",r.top+x),y=!0}}else if(o+5>v&&r.top>_){var x=Math.min(23,r.top-g);a.css("top",r.top-x+"px"),y=!0}if(y){i();var a=this;this.timeout=setTimeout(function(){a.test(e,i)},50)}},stop:function(t,e){clearTimeout(this.timeout)}}),e.default=i}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,o){Object.defineProperty(e,"__esModule",{value:!0});var a=i(289),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return n.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var i={output_name:t};return e&&(i.label=e),this.workflow_outputs.push(i),!0}return!1},labelWorkflowOutput:function(t,e){var i=!1,n=null;if(this.isWorkflowOutput(t)){var o=this.getWorkflowOutput(t);n=o.label,o.label=e,i=n!=e}else i=this.addWorkflowOutput(t,e);return i&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),i},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.connectors.length>0&&e.push(i)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var i=t[e];if(i.connectors.length>0&&i.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&i.connectors.length>0&&e.push(i)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&e.push(i)}),e},hasMappedOverInputTerminals:function(){var t=!1;return n.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){o.each(this.input_terminals,function(t,e){e.redraw()}),o.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){o.each(this.input_terminals,function(t,e){e.destroy()}),o.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),o(this.element).remove()},make_active:function(){o(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),o(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,i=new r.default({el:this.element[0],node:e});e.nodeView=i,o.each(t.data_inputs,function(t,e){i.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&i.addRule(),o.each(t.data_outputs,function(t,e){i.addDataOutput(e)}),i.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,i=e.nodeView,a=[];if(o.each(i.outputViews,function(e,i){var o=i.output.name,r=t.data_outputs,s=!1;n.each(r,function(t){t.name==o&&(s=!0)}),!1===s&&a.push(o)}),n.each(a,function(t){n.each(i.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),i.outputViews[t].remove(),delete i.outputViews[t],delete e.output_terminals[t]}),o.each(e.workflow_outputs,function(t,i){i&&!e.output_terminals[i.output_name]&&e.workflow_outputs.splice(t,1)}),o.each(t.data_outputs,function(t,n){i.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):i.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var r=t.post_job_actions;this.post_job_actions=r||{}}e.nodeView.renderToolErrors();var s=i.$("div.inputs"),l=i.newInputsDiv(),u={};n.each(t.data_inputs,function(t){var i=e.nodeView.addDataInput(t,l);u[t.name]=i}),n.each(n.difference(n.values(i.terminalViews),n.values(u)),function(t){t.el.terminal.destroy()}),i.terminalViews=u,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&i.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=o(this.element).find(".toolFormBody");e.find("div").remove();var i="<div style='color: red; text-style: italic;'>"+t+"</div>";this.config_form=i,e.html(i),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=s}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=i(290),l=o(s),u=i(292),c=o(u);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return n("<div/>").addClass("inputs")},updateMaxWidth:function(t){this.output_width=Math.max(this.output_width,t)},addRule:function(){this.tool_body.append(n("<div/>").addClass("rule"))},addDataInput:function(t,e){var i=!0;e||(e=this.$(".inputs"),i=!1);var n=this.terminalViews[t.name],o="dataset_collection"==t.input_type?l.default.InputCollectionTerminalView:l.default.InputTerminalView;if(!n||n instanceof o||(n.el.terminal.destroy(),n=null),n){var a=n.el.terminal;a.update(t),a.destroyInvalidConnections()}else n=new o({node:this.node,input:t});this.terminalViews[t.name]=n;var r=n.el,s=new c.default.DataInputView({terminalElement:r,input:t,nodeView:this,skipResize:i}),u=s.$el;return e.append(u.prepend(n.terminalElements())),n},addDataOutput:function(t){var e=t.collection?l.default.OutputCollectionTerminalView:l.default.OutputTerminalView,i=new e({node:this.node,output:t}),n=new c.default.DataOutputView({output:t,terminalElement:i.el,nodeView:this});this.outputViews[t.name]=n,this.tool_body.append(n.$el.append(i.terminalElements()))},redrawWorkflowOutputs:function(){r.each(this.outputViews,function(t){t.redrawWorkflowOutput()})},updateDataOutput:function(t){this.node.output_terminals[t.name].update(t)}})}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(291),s=a(r),l=i(224),u=a(l);window.workflow_globals=window.workflow_globals||{};var c=t.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(t){this.$el.tooltip({delay:500,title:"Run tool in parallel over collection"}),this.model.bind("change",n.bind(this.render,this))},render:function(){this.model.mapOver.isCollection?this.$el.show():this.$el.hide()}}),d=c.extend({events:{click:"onClick",mouseenter:"onMouseEnter",mouseleave:"onMouseLeave"},onMouseEnter:function(t){var e=this.model;!e.terminal.connected()&&e.mapOver.isCollection&&this.$el.css("color","red")},onMouseLeave:function(t){this.$el.css("color","black")},onClick:function(t){var e=this.model;!e.terminal.connected()&&e.mapOver.isCollection&&e.terminal.resetMapping()}}),h=t.View.extend({setupMappingView:function(t){var e=new this.terminalMappingClass({terminal:t}),i=new this.terminalMappingViewClass({model:e});i.render(),t.terminalMappingView=i,this.terminalMappingView=i},terminalElements:function(){return this.terminalMappingView?[this.terminalMappingView.el,this.el]:[this.el]}}),f=h.extend({className:"terminal input-terminal",initialize:function(t){var e=t.node,i=t.input,n=i.name,o=this.terminalForInput(i);o.multiple||this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.input_terminals[n]=o},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(t,e){var i=this.el.terminal;return o(e.drag).hasClass("output-terminal")&&i.canAccept(e.drag.terminal)},onDropStart:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(t,e){var i=this.el.terminal;new u.default(e.drag.terminal,i).redraw()},onHover:function(){var t=this.el,e=t.terminal;if(e.connectors.length>0){var i=o("<div class='callout'></div>").css({display:"none"}).appendTo("body").append(o("<div class='button'></div>").append(o("<div/>").addClass("fa-icon-button fa fa-times").click(function(){o.each(e.connectors,function(t,e){e&&e.destroy()}),i.remove()}))).bind("mouseleave",function(){o(this).remove()});i.css({top:o(t).offset().top-2,left:o(t).offset().left-i.width(),"padding-right":o(t).width()}).show()}}}),p=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForInput:function(t){return new s.default.InputTerminal({element:this.el,input:t})}}),m=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForInput:function(t){return new s.default.InputCollectionTerminal({element:this.el,input:t})}}),v=h.extend({className:"terminal output-terminal",initialize:function(t){var e=t.node,i=t.output,n=i.name,o=this.terminalForOutput(i);this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.output_terminals[n]=o},events:{drag:"onDrag",dragstart:"onDragStart",dragend:"onDragEnd"},onDrag:function(t,e){var i=function(){var t=o(e.proxy).offsetParent().offset(),i=e.offsetX-t.left,n=e.offsetY-t.top;o(e.proxy).css({left:i,top:n}),e.proxy.terminal.redraw(),window.workflow_globals.canvas_manager.update_viewport_overlay()};i(),o("#canvas-container").get(0).scroll_panel.test(t,i)},onDragStart:function(t,e){o(e.available).addClass("input-terminal-active"),window.workflow_globals.workflow.check_changes_in_active_form();var i=o('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new s.default.OutputTerminal({element:i});var n=new u.default;return n.dragging=!0,n.connect(this.el.terminal,i.terminal),i},onDragEnd:function(t,e){var i=e.proxy.terminal.connectors[0];i&&i.destroy(),o(e.proxy).remove(),o(e.available).removeClass("input-terminal-active"),o("#canvas-container").get(0).scroll_panel.stop()}}),g=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.extensions;return new s.default.OutputTerminal({element:this.el,datatypes:e})}}),_=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.collection_type,i=t.collection_type_source;return new s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:i,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:g,InputCollectionTerminalView:m,OutputCollectionTerminalView:_}}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,i,n){function o(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(t){return!1},canMapOver:function(t){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},r={isCollection:!0,canMatch:function(t){return a!==t},canMapOver:function(t){return!1},toString:function(){return"AnyCollectionType[]"},append:function(t){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(t){return t===this}};t.extend(o.prototype,{append:function(t){return t===a?this:t===r?otherCollectionType:new o(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==a&&(t===r||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===a)return!1;if(t===r)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new o(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var s=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||a,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),l=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){n.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),n.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),u=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||n.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),n.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||n.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var t;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:t=!1:t=!0:t=!1,t},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(n.first(n.values(this.node.output_terminals)).mapOver()):n.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var i=this.datatypes[e];if("input"==i)return!0;var n=new Array;if(n=n.concat(t.datatypes),t.node.post_job_actions)for(var o in t.node.post_job_actions){var a=t.node.post_job_actions[o];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=t.name||!a.action_arguments||n.push(a.action_arguments.newtype)}for(var r in n){var s=n[r];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(n[r],i))return!0}}return!1},_otherCollectionType:function(t){var e=a;t.isCollection&&(e=t.collectionType);var i=t.mapOver();return i.isCollection&&(e=i.append(e)),e}}),d=c.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._otherCollectionType(e);i.isCollection&&this.setMapOver(i)}},attachable:function(t){var e=this._otherCollectionType(t),i=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(i.isCollection&&i.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(n.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!i.isCollection&&this._producesAcceptableDatatype(t)}}),h=c.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?n.each(t.collection_types,function(t){e.push(new o(t))}):e.push(r),this.collectionTypes=e},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._effectiveMapOver(e);this.setMapOver(i)}},_effectiveMapOver:function(t){var e=this.collectionTypes,i=this._otherCollectionType(t);if(!n.some(e,function(t){return t.canMatch(i)}))for(var o in e){var r=e[o];if(i.canMapOver(r)){var s=i.effectiveMapOver(r);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var t=this.mapOver();return n.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var i=this._effectiveCollectionTypes(),o=this.mapOver();if(n.some(i,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(o.isCollection)return!1;if(n.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),f=l.extend({initialize:function(t){if(l.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=r}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=r}e.collectionType!=this.collectionType.collectionType&&n.each(this.connectors,function(t){t.destroy()}),this.collectionType=e}});e.default={InputTerminal:d,OutputTerminal:u,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:o,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:r}}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var n=t.View.extend({className:"form-row dataRow 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a({label:n,output:e,node:o});this.calloutView=r,this.$el.append(r.el),this.$el.hover(function(){r.hoverImage()},function(){r.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,n=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(i("<div class='buttons'></div>").append(i("<img/>").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var 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a.css({left:-d.left+h.width()/2-f/2,top:-d.top+h.height()/2-p/2}),c.prependTo(a.find(".toolFormTitle")),f+=c.width()+10,a.css("width",f),a.bind("dragstart",function(){o.workflow.activate_node(l)}).bind("dragend",function(){o.workflow.node_changed(this),o.workflow.fit_canvas_to_nodes(),o.canvas_manager.draw_overview()}).bind("dragclickonly",function(){o.workflow.activate_node(l)}).bind("drag",function(e,i){var n=t(this).offsetParent().offset(),o=i.offsetX-n.left,a=i.offsetY-n.top;t(this).css({left:o,top:a}),t(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t){function n(t,e){this.app=t,this.canvas_container=e,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(224),a=function(t){return t&&t.__esModule?t:{default:t}}(o),r=i(42),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r);t.extend(n.prototype,{canLabelOutputWith:function(t){return!t||!(t in this.workflowOutputLabels)},registerOutputLabel:function(t){t&&(this.workflowOutputLabels[t]=!0)},unregisterOutputLabel:function(t){t&&delete this.workflowOutputLabels[t]},updateOutputLabel:function(t,e){t&&this.unregisterOutputLabel(t),this.canLabelOutputWith(e)||s.warning("Workflow contains duplicate workflow output labels "+e+". This must be fixed before it can be saved."),e&&this.registerOutputLabel(e)},attemptUpdateOutputLabel:function(t,e,i){return!!this.canLabelOutputWith(i)&&(t.labelWorkflowOutput(e,i),t.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(t,e,i){var n=this.app.prebuildNode(t,e,i);return this.add_node(n),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(n),n},add_node:function(t){t.id=this.id_counter,t.element.attr("id","wf-node-step-"+t.id),this.id_counter++,this.nodes[t.id]=t,this.has_changes=!0,t.workflow=this},remove_node:function(t){this.active_node==t&&this.clear_active_node(),delete this.nodes[t.id],this.has_changes=!0},remove_all:function(){var e=this;t.each(this.nodes,function(t,i){i.destroy(),e.remove_node(i)})},rectify_workflow_outputs:function(){var e=!1,i=!1;if(t.each(this.nodes,function(n,o){o.workflow_outputs&&o.workflow_outputs.length>0&&(e=!0),t.each(o.post_job_actions,function(t,e){"HideDatasetAction"===e.action_type&&(i=!0)})}),!1!==e||!1!==i){var n=this;t.each(this.nodes,function(i,o){if("tool"===o.type){var a=!1;null===o.post_job_actions&&(o.post_job_actions={},a=!0);var r=[];t.each(o.post_job_actions,function(t,e){"HideDatasetAction"==e.action_type&&r.push(t)}),r.length>0&&t.each(r,function(t,e){a=!0,delete o.post_job_actions[e]}),e&&t.each(o.output_terminals,function(t,e){if(!0==!o.isWorkflowOutput(e.name)){a=!0;var i={action_type:"HideDatasetAction",output_name:e.name,action_arguments:{}};o.post_job_actions["HideDatasetAction"+e.name]=null,o.post_job_actions["HideDatasetAction"+e.name]=i}}),n.active_node==o&&!0===a&&n.reload_active_node()}})}},to_simple:function(){var e={};return t.each(this.nodes,function(i,n){var o={};t.each(n.input_terminals,function(e,i){o[i.name]=null;var n=[];t.each(i.connectors,function(t,e){if(e.handle1){var a={id:e.handle1.node.id,output_name:e.handle1.name},r=i.attributes.input.input_subworkflow_step_id;void 0!==r&&(a.input_subworkflow_step_id=r),n[t]=a,o[i.name]=n}})});var a={};n.post_job_actions&&t.each(n.post_job_actions,function(t,e){var i={action_type:e.action_type,output_name:e.output_name,action_arguments:e.action_arguments};a[e.action_type+e.output_name]=null,a[e.action_type+e.output_name]=i}),n.workflow_outputs||(n.workflow_outputs=[]);var r={id:n.id,type:n.type,content_id:n.content_id,tool_version:n.config_form.version,tool_state:n.tool_state,errors:n.errors,input_connections:o,position:t(n.element).position(),annotation:n.annotation,post_job_actions:n.post_job_actions,uuid:n.uuid,label:n.label,workflow_outputs:n.workflow_outputs};e[n.id]=r}),{steps:e}},from_simple:function(e,i){var n=void 0===i||i,o=this,r=0;n?o.name=e.name:r=Object.keys(o.nodes).length;var s=r,l=!1;t.each(e.steps,function(e,i){var a=o.app.prebuildNode(i.type,i.name,i.content_id);n||(i.uuid=null,t.each(i.workflow_outputs,function(t,e){e.uuid=null})),a.init_field_data(i),i.position&&a.element.css({top:i.position.top,left:i.position.left}),a.id=parseInt(i.id)+r,o.nodes[a.id]=a,s=Math.max(s,parseInt(e)+r),l||(a.workflow_outputs.length>0?l=!0:t.each(a.post_job_actions||[],function(t,e){"HideDatasetAction"===e.action_type&&(l=!0)}))}),o.id_counter=s+1,t.each(e.steps,function(e,i){var n=o.nodes[parseInt(e)+r];t.each(i.input_connections,function(e,i){i&&(t.isArray(i)||(i=[i]),t.each(i,function(t,i){var s=o.nodes[parseInt(i.id)+r],l=new a.default;l.connect(s.output_terminals[i.output_name],n.input_terminals[e]),l.redraw()}))}),l&&t.each(n.output_terminals,function(e,i){if(void 0===n.post_job_actions["HideDatasetAction"+i.name]){n.addWorkflowOutput(i.name);t(n.element).find(".callout."+i.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),o.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,t("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var t=this.active_node;this.clear_active_node(),this.activate_node(t)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showAttributes()},activate_node:function(t){this.active_node!=t&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(t.config_form,t),t.make_active(),this.active_node=t)},node_changed:function(t,e){this.has_changes=!0,this.active_node==t&&e&&(this.check_changes_in_active_form(),this.app.showForm(t.config_form,t)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var e={},i={};t.each(this.nodes,function(t,n){void 0===e[t]&&(e[t]=0),void 0===i[t]&&(i[t]=[])}),t.each(this.nodes,function(n,o){t.each(o.input_terminals,function(n,a){t.each(a.connectors,function(t,n){var a=n.handle1.node;e[o.id]+=1,i[a.id].push(o.id)})})});for(var n=[];;){var o=[];for(var a in e)0===e[a]&&o.push(a);if(0===o.length)break;n.push(o);for(var r in o){var s=o[r];delete e[s];for(var l in i[s])e[i[s][l]]-=1}}if(!e.length){var u=this.nodes,c=80;t.each(n,function(e,i){i.sort(function(e,i){return t(u[e].element).position().top-t(u[i].element).position().top});var n=0,o=30;t.each(i,function(e,i){var a=u[i],r=t(a.element);t(r).css({top:o,left:c}),n=Math.max(n,t(r).width()),o+=t(r).height()+30}),c+=n+80}),t.each(u,function(t,e){e.redraw()})}},bounds_for_all_nodes:function(){var e,i=1/0,n=-1/0,o=1/0,a=-1/0;return t.each(this.nodes,function(r,s){var l=t(s.element);e=l.position(),i=Math.min(i,e.left),n=Math.max(n,e.left+l.width()),o=Math.min(o,e.top),a=Math.max(a,e.top+l.width())}),{xmin:i,xmax:n,ymin:o,ymax:a}},fit_canvas_to_nodes:function(){function e(t,e){return Math.ceil(t/e)*e}function i(t,e){if(t<e||t>3*e){return-(t-(Math.ceil(t%e/e)+1)*e)}return 0}var n=this.bounds_for_all_nodes(),o=this.canvas_container.position(),a=this.canvas_container.parent(),r=i(n.xmin,100),s=i(n.ymin,100);r=Math.max(r,o.left),s=Math.max(s,o.top);var l=o.left-r,u=o.top-s,c=e(n.xmax+100,100)+r,d=e(n.ymax+100,100)+s;c=Math.max(c,-l+a.width()),d=Math.max(d,-u+a.height()),this.canvas_container.css({left:l,top:u,width:c,height:d}),this.canvas_container.children().each(function(){var e=t(this).position();t(this).css("left",e.left+r),t(this).css("top",e.top+s)})}}),e.default=n}).call(e,i(0))},function(t,e,i){"use strict";(function(t){function i(t,e,i){this.app=t,this.cv=e,this.cc=this.cv.find("#canvas-container"),this.overview=i,this.oc=i.find("#overview-canvas"),this.ov=i.find("#overview-viewport"),this.init_drag()}function n(t){this.panel=t}Object.defineProperty(e,"__esModule",{value:!0}),t.extend(i.prototype,{init_drag:function(){var e=this,i=function(t,i){t=Math.min(t,e.cv.width()/2),t=Math.max(t,-e.cc.width()+e.cv.width()/2),i=Math.min(i,e.cv.height()/2),i=Math.max(i,-e.cc.height()+e.cv.height()/2),e.cc.css({left:t,top:i}),e.cv.css({"background-position-x":t,"background-position-y":i}),e.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new n(this)});var o,a;this.cv.bind("dragstart",function(){var i=t(this).offset(),n=e.cc.position();a=n.top-i.top,o=n.left-i.left}).bind("drag",function(t,e){i(e.offsetX+o,e.offsetY+a)}).bind("dragend",function(){e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),this.overview.click(function(t){if(e.overview.hasClass("blockaclick"))e.overview.removeClass("blockaclick");else{var n=e.cc.width(),o=e.cc.height(),a=e.oc.width(),r=e.oc.height(),s=t.pageX-e.oc.offset().left-e.ov.width()/2,l=t.pageY-e.oc.offset().top-e.ov.height()/2;i(-s/a*n,-l/r*o),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}}),this.ov.bind("drag",function(t,n){var o=e.cc.width(),a=e.cc.height(),r=e.oc.width(),s=e.oc.height(),l=n.offsetX-e.overview.offset().left,u=n.offsetY-e.overview.offset().top;i(-l/r*o,-u/s*a)}).bind("dragend",function(){e.overview.addClass("blockaclick"),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),t("#overview-border").bind("drag",function(i,n){var o=t(this).offsetParent(),a=o.offset(),r=Math.max(o.width()-(n.offsetX-a.left),o.height()-(n.offsetY-a.top));t(this).css({width:r,height:r}),e.draw_overview()}),t("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,i=this.oc,n=this.ov,o=t.width(),a=t.height(),r=i.width(),s=i.height(),l=t.position();n.css({left:-l.left/o*r,top:-l.top/a*s,width:e.width()/o*r-2,height:e.height()/a*s-2})},draw_overview:function(){var e,i,n,o,a=t("#overview-canvas"),r=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=t("#canvas-container").width(),u=t("#canvas-container").height(),c=this.cv.width(),d=this.cv.height();l<c&&u<d?(n=l/c*r,o=(r-n)/2,e=u/d*r,i=(r-e)/2):l<u?(i=0,e=r,n=Math.ceil(e*l/u),o=(r-n)/2):(n=r,o=0,e=Math.ceil(n*u/l),i=(r-e)/2),a.parent().css({left:o,top:i,width:n,height:e}),a.attr("width",n),a.attr("height",e),t.each(this.app.workflow.nodes,function(i,o){s.fillStyle="#D2C099",s.strokeStyle="#D8B365",s.lineWidth=1;var a=t(o.element),r=a.position(),c=r.left/l*n,d=r.top/u*e,h=a.width()/l*n,f=a.height()/u*e;o.errors?(s.fillStyle="#FFCCCC",s.strokeStyle="#AA6666"):void 0!==o.workflow_outputs&&o.workflow_outputs.length>0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(c,d,h,f),s.strokeRect(c,d,h,f)}),this.update_viewport_overlay()}}),t.extend(n.prototype,{test:function(e,i){clearTimeout(this.timeout);var n=e.pageX,o=e.pageY,a=t(this.panel),r=a.position(),s=a.width(),l=a.height(),u=a.parent(),c=u.width(),d=u.height(),h=u.offset(),f=h.left,p=h.top,m=f+u.width(),v=p+u.height(),g=-(s-c/2),_=-(l-d/2),w=c/2,b=d/2,y=!1;if(n-5<f){if(r.left<w){var x=Math.min(23,w-r.left);a.css("left",r.left+x),y=!0}}else if(n+5>m){if(r.left>g){var x=Math.min(23,r.left-g);a.css("left",r.left-x),y=!0}}else if(o-5<p){if(r.top<b){var x=Math.min(23,b-r.top);a.css("top",r.top+x),y=!0}}else if(o+5>v&&r.top>_){var x=Math.min(23,r.top-g);a.css("top",r.top-x+"px"),y=!0}if(y){i();var a=this;this.timeout=setTimeout(function(){a.test(e,i)},50)}},stop:function(t,e){clearTimeout(this.timeout)}}),e.default=i}).call(e,i(0))},function(t,e,i){"use strict";(function(t,n,o){Object.defineProperty(e,"__esModule",{value:!0});var a=i(289),r=function(t){return t&&t.__esModule?t:{default:t}}(a),s=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return n.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var i={output_name:t};return e&&(i.label=e),this.workflow_outputs.push(i),!0}return!1},labelWorkflowOutput:function(t,e){var i=!1,n=null;if(this.isWorkflowOutput(t)){var o=this.getWorkflowOutput(t);n=o.label,o.label=e,i=n!=e}else i=this.addWorkflowOutput(t,e);return i&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),i},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.connectors.length>0&&e.push(i)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var i=t[e];if(i.connectors.length>0&&i.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&i.connectors.length>0&&e.push(i)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return o.each(t,function(t,i){i.mapOver().isCollection&&e.push(i)}),e},hasMappedOverInputTerminals:function(){var t=!1;return n.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){o.each(this.input_terminals,function(t,e){e.redraw()}),o.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){o.each(this.input_terminals,function(t,e){e.destroy()}),o.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),o(this.element).remove()},make_active:function(){o(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),o(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,i=new r.default({el:this.element[0],node:e});e.nodeView=i,o.each(t.data_inputs,function(t,e){i.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&i.addRule(),o.each(t.data_outputs,function(t,e){i.addDataOutput(e)}),i.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,i=e.nodeView,a=[];if(o.each(i.outputViews,function(e,i){var o=i.output.name,r=t.data_outputs,s=!1;n.each(r,function(t){t.name==o&&(s=!0)}),!1===s&&a.push(o)}),n.each(a,function(t){n.each(i.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),i.outputViews[t].remove(),delete i.outputViews[t],delete e.output_terminals[t]}),o.each(e.workflow_outputs,function(t,i){i&&!e.output_terminals[i.output_name]&&e.workflow_outputs.splice(t,1)}),o.each(t.data_outputs,function(t,n){i.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):i.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var r=t.post_job_actions;this.post_job_actions=r||{}}e.nodeView.renderToolErrors();var s=i.$("div.inputs"),l=i.newInputsDiv(),u={};n.each(t.data_inputs,function(t){var i=e.nodeView.addDataInput(t,l);u[t.name]=i}),n.each(n.difference(n.values(i.terminalViews),n.values(u)),function(t){t.el.terminal.destroy()}),i.terminalViews=u,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&i.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=o(this.element).find(".toolFormBody");e.find("div").remove();var i="<div style='color: red; text-style: italic;'>"+t+"</div>";this.config_form=i,e.html(i),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=s}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(2),r=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(a),s=i(290),l=o(s),u=i(292),c=o(u);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return n("<div/>").addClass("inputs")},updateMaxWidth:function(t){this.output_width=Math.max(this.output_width,t)},addRule:function(){this.tool_body.append(n("<div/>").addClass("rule"))},addDataInput:function(t,e){var i=!0;e||(e=this.$(".inputs"),i=!1);var n=this.terminalViews[t.name],o="dataset_collection"==t.input_type?l.default.InputCollectionTerminalView:l.default.InputTerminalView;if(!n||n instanceof o||(n.el.terminal.destroy(),n=null),n){var a=n.el.terminal;a.update(t),a.destroyInvalidConnections()}else n=new o({node:this.node,input:t});this.terminalViews[t.name]=n;var r=n.el,s=new c.default.DataInputView({terminalElement:r,input:t,nodeView:this,skipResize:i}),u=s.$el;return e.append(u.prepend(n.terminalElements())),n},addDataOutput:function(t){var e=t.collection?l.default.OutputCollectionTerminalView:l.default.OutputTerminalView,i=new e({node:this.node,output:t}),n=new c.default.DataOutputView({output:t,terminalElement:i.el,nodeView:this});this.outputViews[t.name]=n,this.tool_body.append(n.$el.append(i.terminalElements()))},redrawWorkflowOutputs:function(){r.each(this.outputViews,function(t){t.redrawWorkflowOutput()})},updateDataOutput:function(t){this.node.output_terminals[t.name].update(t)}})}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n,o){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(291),s=a(r),l=i(224),u=a(l);window.workflow_globals=window.workflow_globals||{};var c=t.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(t){this.$el.tooltip({delay:500,title:"Run tool in parallel over 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e=t.node,i=t.input,n=i.name,o=this.terminalForInput(i);o.multiple||this.setupMappingView(o),this.el.terminal=o,o.node=e,o.name=n,e.input_terminals[n]=o},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(t,e){var i=this.el.terminal;return o(e.drag).hasClass("output-terminal")&&i.canAccept(e.drag.terminal)},onDropStart:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(t,e){e.proxy.terminal&&(e.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(t,e){var i=this.el.terminal;new u.default(e.drag.terminal,i).redraw()},onHover:function(){var t=this.el,e=t.terminal;if(e.connectors.length>0){var i=o("<div class='callout'></div>").css({display:"none"}).appendTo("body").append(o("<div class='button'></div>").append(o("<div/>").addClass("fa-icon-button fa 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t=o(e.proxy).offsetParent().offset(),i=e.offsetX-t.left,n=e.offsetY-t.top;o(e.proxy).css({left:i,top:n}),e.proxy.terminal.redraw(),window.workflow_globals.canvas_manager.update_viewport_overlay()};i(),o("#canvas-container").get(0).scroll_panel.test(t,i)},onDragStart:function(t,e){o(e.available).addClass("input-terminal-active"),window.workflow_globals.workflow.check_changes_in_active_form();var i=o('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new s.default.OutputTerminal({element:i});var n=new u.default;return n.dragging=!0,n.connect(this.el.terminal,i.terminal),i},onDragEnd:function(t,e){var i=e.proxy.terminal.connectors[0];i&&i.destroy(),o(e.proxy).remove(),o(e.available).removeClass("input-terminal-active"),o("#canvas-container").get(0).scroll_panel.stop()}}),g=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.extensions;return new s.default.OutputTerminal({element:this.el,datatypes:e})}}),_=v.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:c,terminalForOutput:function(t){var e=t.collection_type,i=t.collection_type_source;return new s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:i,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:g,InputCollectionTerminalView:m,OutputCollectionTerminalView:_}}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,i,n){function o(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(t){return!1},canMapOver:function(t){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},r={isCollection:!0,canMatch:function(t){return a!==t},canMapOver:function(t){return!1},toString:function(){return"AnyCollectionType[]"},append:function(t){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(t){return t===this}};t.extend(o.prototype,{append:function(t){return t===a?this:t===r?otherCollectionType:new o(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==a&&(t===r||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===a)return!1;if(t===r)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new o(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var s=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||a,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),l=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){n.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),n.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),u=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||n.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),n.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||n.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var t;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:t=!1:t=!0:t=!1,t},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(n.first(n.values(this.node.output_terminals)).mapOver()):n.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var i=this.datatypes[e];if("input"==i)return!0;var n=new Array;if(n=n.concat(t.datatypes),t.node.post_job_actions)for(var o in t.node.post_job_actions){var a=t.node.post_job_actions[o];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=t.name||!a.action_arguments||n.push(a.action_arguments.newtype)}for(var r in n){var s=n[r];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(n[r],i))return!0}}return!1},_otherCollectionType:function(t){var e=a;t.isCollection&&(e=t.collectionType);var i=t.mapOver();return i.isCollection&&(e=i.append(e)),e}}),d=c.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._otherCollectionType(e);i.isCollection&&this.setMapOver(i)}},attachable:function(t){var e=this._otherCollectionType(t),i=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(i.isCollection&&i.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(n.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!i.isCollection&&this._producesAcceptableDatatype(t)}}),h=c.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?n.each(t.collection_types,function(t){e.push(new o(t))}):e.push(r),this.collectionTypes=e},connect:function(t){c.prototype.connect.call(this,t);var e=t.handle1;if(e){var i=this._effectiveMapOver(e);this.setMapOver(i)}},_effectiveMapOver:function(t){var e=this.collectionTypes,i=this._otherCollectionType(t);if(!n.some(e,function(t){return t.canMatch(i)}))for(var o in e){var r=e[o];if(i.canMapOver(r)){var s=i.effectiveMapOver(r);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var t=this.mapOver();return n.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var i=this._effectiveCollectionTypes(),o=this.mapOver();if(n.some(i,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(o.isCollection)return!1;if(n.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),f=l.extend({initialize:function(t){if(l.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=r}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new o(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=r}e.collectionType!=this.collectionType.collectionType&&n.each(this.connectors,function(t){t.destroy()}),this.collectionType=e}});e.default={InputTerminal:d,OutputTerminal:u,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:o,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:r}}).call(e,i(0),i(1),i(2))},function(t,e,i){"use strict";(function(t,i){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var n=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),o=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,n=e.name,o=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(n=n+" ("+e.extensions.join(", ")+")"),this.$el.html(n),this.calloutView=null,["tool","subworkflow"].indexOf(o.type)>=0){var r=new a({label:n,output:e,node:o});this.calloutView=r,this.$el.append(r.el),this.$el.hover(function(){r.hoverImage()},function(){r.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),i("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,n=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(i("<div class='buttons'></div>").append(i("<img/>").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;n.isWorkflowOutput(t)?(n.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(n.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});e.default={DataInputView:n,DataOutputView:o}}).call(e,i(1),i(0))},function(t,e,i){"use strict";(function(t,n){function o(t){return t&&t.__esModule?t:{default:t}}function a(t){var e=t.model.attributes,i=e.workflow,n=e.node;e.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:n.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),e.inputs.unshift({type:"text",name:"__label",label:"Label",value:n.label,help:"Add a step label.",fixed:!0,onchange:function(e){var o=!1;for(var a in i.nodes){var r=i.nodes[a];if(r.label&&r.label==e&&r.id!=n.id){o=!0;break}}var s=t.data.match("__label");t.element_list[s].model.set("error_text",o&&"Duplicate label. Please fix this before saving the workflow."),t.trigger("change")}})}function r(t,e,i,n){var o=n.node.post_job_actions;e=e||[],e.push(t);for(var a in t.inputs){var s=t.inputs[a];if(s.action){if(s.name="pja__"+i+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var u=o[s.action+i];if(u){for(var c in e)e[c].expanded=!0;s.pja_arg?s.value=u.action_arguments&&u.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&r(s,e.slice(0),i,n)}}function s(t,e){var i=[],n=[],o=e.datatypes,a=e.node,s=e.workflow;for(var l in o)i.push({0:o[l],1:o[l]});for(l in a.input_terminals)n.push(a.input_terminals[l].name);i.sort(function(t,e){return t.label>e.label?1:t.label<e.label?-1:0}),i.unshift({0:"Sequences",1:"Sequences"}),i.unshift({0:"Roadmaps",1:"Roadmaps"}),i.unshift({0:"Leave unchanged",1:"__empty__"});var u,c={title:"Configure Output: '"+t+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(u=a.getWorkflowOutput(t))&&u.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(e){s.attemptUpdateOutputLabel(a,t,e)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>'+n.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:i,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return r(c,[],t,e),c}function l(t){var e=t.model.attributes,i=e.inputs,n=e.node,o=n.post_job_actions,a=n.output_terminals&&Object.keys(n.output_terminals)[0];if(a){i.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(o["EmailAction"+a])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),i.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(o["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var r in n.output_terminals)i.push(s(r,e))}}Object.defineProperty(e,"__esModule",{value:!0});var u=i(3),c=o(u),d=i(20),h=o(d),f=i(63),p=o(f),m=t.View.extend({initialize:function(t){var e=this,i=t.node;this.form=new h.default(c.default.merge(t,{onchange:function(){c.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:i.id,type:i.type,content_id:i.content_id,inputs:e.form.data.create()},success:function(t){i.update_field_data(t)}})}})),a(this.form),this.form.render()}}),v=t.View.extend({initialize:function(t){var e=this,i=t.node;this.form=new p.default(c.default.merge(t,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(t,i){e._customize(i),t.resolve()},buildmodel:function(t,e){e.model.get("postchange")(t,e)},postchange:function(t,o){var a=o.model.attributes,r={tool_id:a.id,tool_version:a.version,type:"tool",inputs:n.extend(!0,{},o.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",r),c.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:r,success:function(n){o.model.set(n.config_form),e._customize(o),o.update(n.config_form),o.errors(n.config_form),i.update_field_data(n),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",n),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",e),t.reject()}})}}))},_customize:function(t){var e=t.model.attributes;c.default.deepeach(e.inputs,function(t){t.type&&(-1!=["data","data_collection"].indexOf(t.type)?(t.type="hidden",t.info="Data input '"+t.name+"' ("+c.default.textify(t.extensions)+")",t.value={__class__:"RuntimeValue"}):t.fixed||(t.collapsible_value={__class__:"RuntimeValue"},t.is_workflow=t.options&&0===t.options.length||-1!=["integer","float"].indexOf(t.type)))}),c.default.deepeach(e.inputs,function(t){"conditional"===t.type&&(t.test_param.collapsible_value=void 0)}),l(t),a(t)}});e.default={Default:m,Tool:v}}).call(e,i(1),i(0))}],[284]);
\ No newline at end of file
diff --git a/test/functional/tools/bibtex.xml b/test/functional/tools/bibtex.xml
index 031dbb017d0..5564c015fbf 100644
--- a/test/functional/tools/bibtex.xml
+++ b/test/functional/tools/bibtex.xml
@@ -1,19 +1,12 @@
-<tool id="bibtex" name="Concatenate datasets (with a bunch of citations)">
-    <command>
-      cat $input1
-      #for $q in $queries
-            ${q.input2}
-      #end for
-      &gt; $out_file1;
-    </command>
+<tool id="bibtex" name="bibtex" version="0.1.0">
+    <command><![CDATA[
+      echo "$input1" > "$out_file1"
+   ]]></command>
     <inputs>
-        <param name="input1" type="data" label="Concatenate Dataset" />
-        <repeat name="queries" title="Dataset">
-            <param name="input2" type="data" label="Select" />
-        </repeat>
+        <param name="input1" type="integer" help="integer" value="8" />
     </inputs>
     <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
+        <data name="out_file1" format="txt" />
     </outputs>
     <help>
 
@@ -24,6 +17,7 @@
     </help>
     <citations>
       <citation type="doi">10.1101/gr.4086505</citation>
+      <citation type="doi">10.6084/m9.figshare.979190</citation>
       <citation type="bibtex">
 @misc{Garrison2015,
   author = {Garrison, Erik},
@@ -32,6 +26,16 @@
   publisher = {GitHub},
   journal = {GitHub repository},
   url = {https://github.com/ekg/vcflib},
+}
+      </citation>
+      <citation type="bibtex">
+@online{lh32017,
+  author = {Heng Li},
+  year = {2017},
+  title = {bwa},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/lh3/bwa},
 }
       </citation>
       <!-- BibTeX examples taken from:
@@ -317,6 +321,5 @@
    note = "Talk at Fanstord University (this is a full UNPUBLISHED entry)",
 }
       </citation>
-      <citation type="doi">10.1101/gr.4086505</citation>
     </citations>
 </tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index a469930b9c3..aac89a43dd5 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -12,6 +12,7 @@
   <tool file="disambiguate_cond.xml" />
   <tool file="multi_repeats.xml"/>
   <tool file="library_data.xml"/>
+  <tool file="bibtex.xml"/>
   <tool file="multi_select.xml" />
   <tool file="multi_output.xml" />
   <tool file="multi_output_configured.xml" />
diff --git a/test/galaxy_selenium/navigation.yml b/test/galaxy_selenium/navigation.yml
index 19416c72fdb..2f8f67c0fe8 100644
--- a/test/galaxy_selenium/navigation.yml
+++ b/test/galaxy_selenium/navigation.yml
@@ -196,6 +196,10 @@ tool_form:
   selectors:
     options: '#options .dropdown-toggle'
     execute: 'button#execute'
+    citations: '.citations-formatted'
+    reference: '.citations-formatted .formatted-reference'
+    show_bibtex: 'button.citations-to-bibtex'
+    bibtex_area: '.citations-bibtex textarea'
 
   labels:
     generate_tour: 'Generate Tour'
@@ -253,3 +257,8 @@ libraries:
 published_grids:
   selectors:
     search: '#input-free-text-search-filter'
+
+charts:
+  selectors:
+    visualize_button: '.ui-portlet .button i.fa-line-chart'  # without icon - it waits on other buttons that aren't visible, need more specific class
+    viewport_canvas: 'svg.charts-viewport-canvas'
diff --git a/test/selenium_tests/test_tool_form.py b/test/selenium_tests/test_tool_form.py
index 0a0277bd4e7..e46aa582809 100644
--- a/test/selenium_tests/test_tool_form.py
+++ b/test/selenium_tests/test_tool_form.py
@@ -1,6 +1,7 @@
 from galaxy_selenium.navigates_galaxy import retry_call_during_transitions
 
 from .framework import (
+    retry_assertion_during_transitions,
     selenium_test,
     SeleniumTestCase,
     UsesHistoryItemAssertions,
@@ -105,6 +106,33 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         assert latest_hda["hid"] == 3
         assert latest_hda["name"] == "Select first on data 1"
 
+    @selenium_test
+    def test_bibtex_rendering(self):
+        self.home()
+        # prefetch citations so they will be available quickly when rendering tool form.
+        citations_api = self.api_get("tools/bibtex/citations")
+        assert len(citations_api) == 29, len(citations_api)
+        self.tool_open("bibtex")
+        self.components.tool_form.citations.wait_for_visible()
+
+        @retry_assertion_during_transitions
+        def assert_citations_visible():
+            references = self.components.tool_form.reference.all()
+            # This should be 29, but bugs I guess?
+            assert len(references) > 0, len(references)
+            return references
+
+        references = assert_citations_visible()
+
+        doi_resolved_citation = references[0]
+        assert "Galaxy: A platform for interactive" in doi_resolved_citation.text
+        self.screenshot("tool_form_citations_formatted")
+
+        self.components.tool_form.show_bibtex.wait_for_and_click()
+        textarea = self.components.tool_form.bibtex_area.wait_for_visible()
+        assert "Galaxy: A platform for interactive" in textarea.get_attribute("value")
+        self.screenshot("tool_form_citations_bibtex")
+
     def _check_dataset_details_for_inttest_value(self, hid, expected_value="42"):
         self.hda_click_primary_action_button(hid, "info")