From 7800c6fe1cbdb494a1de22dce6dbee070dfd442e Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Sun, 23 Oct 2011 16:32:04 -0400 Subject: [PATCH] Trackster: make overview its own track, add icons for showing/hiding overview, and make track header optional. --- .../images/fugue/application-dock-270-bw.png | Bin 0 -> 1288 bytes static/images/fugue/application-dock-270.png | Bin 0 -> 516 bytes static/june_2007_style/blue/trackster.css | 6 +- static/june_2007_style/trackster.css.tmpl | 11 +- static/scripts/packed/trackster.js | 2 +- static/scripts/packed/trackster_ui.js | 2 +- static/scripts/trackster.js | 198 ++++++++---------- static/scripts/trackster_ui.js | 2 +- templates/tracks/browser.mako | 3 +- 9 files changed, 100 insertions(+), 124 deletions(-) create mode 100644 static/images/fugue/application-dock-270-bw.png create mode 100755 static/images/fugue/application-dock-270.png diff --git a/static/images/fugue/application-dock-270-bw.png b/static/images/fugue/application-dock-270-bw.png new file mode 100644 index 0000000000000000000000000000000000000000..1d0ad1bb6ce468022d7d7cf0314144905cccf5a9 GIT binary patch literal 1288 zcmV+j1^4=iP)4Tx0C)j~RL^S@K@|QrZmG~B2wH0nvUrdpNm;9CMbtL^5n^i$+aIn^?(HA4aZWV5ov6ELTdbo0FI&wK{O>*+w4vx20?>!`FrQsdJlnHR>OPy zcd~b_n$otK2Za4V;76L-DzNVtaSB-y0*E}{p()372;bw_^6ZZ}PI-92wGS&j#91PI zKs7DSe@(bk%_Y-7gGe}(^>I=@oY#w#*Bu9GZf3^F5WP>3rn}7Ut74&?PWBFvy`A)a zPP5)V!Xd&78LdA?xQ(9mjMYElVd13a#D+Z_7&Y|xU=_C-srWU*6kiZcC!$nw*)9$7 zn6CX+@=AhmkT}X@VSsa5NKe;HZuq)~1$`#h6R+ZTR#D-3j}vF!)ZOnz+5)dI4jl{{ z44Mr{P!L4~VVJN`K!!XTF*LGrKO?IK8z<8w`3e3jI8lUGNUta*C8 zn(P`s>{pjD=7Kek#B;Fw@hxAK%$F&Q6vg9J^Xf~4by_hu-=A!MJ3Znq&n~srbFGPs zH&&aMXZ>nO`|hf|ljc?VPhR!${AbO?W8x_>CU%PFA&Hm8F7cAsOREdwU~R_;ot1_u z(ruCYB-LPGn!NQdT|ZlRy+(fw^-+`=%+gee_kY4FWHg<*4sZI8+sFJD270UUORdLHO0nA4V) z%{fwsET5CQ>B?eK%uw4yQc~9?*JVo2}ze(;aRcp*ceL#HUJSllrgm5wQKR zQu+C;QrUh^8rFfA`ftFz{YAidi-`aL010qNS#tmY3ljhU3ljkVnw%H_00F>BL_t(I z5tULsYXU(Kom)33mygCErV$C)SqcdXrtue8izx(ufN4w_A;u=QcIJ18Rlp{_pj8k{ z6+|Q!dV80Bqbpt!F>@?)^XARlnY*!ax!kSmx_3f|OFGdsf2sLj-EQ|=Dy8n9wMB2D zN#!WoY&Lw>>oqx!L&{ZT=?A8ZNJ>f5>9pT!wca%JEj`b>S}vE##bQCO=MqG;C?5#u z+gK1DxT7?t++?rUyMU++1Oi?@pU1n;CX)%-=Qgc=RuqXud^rT2PKVpV2$t@GZ$D%W z1_O%4Vl*C)DSRD1Op&kzx?ur<7qrH$qy63K_xpq{;0?C-+Yz@N=sCr1F5fM~;gAxE z1i|B59GVCSU;-FM5KuOxMx#Na(TMr@1GCwTN~IFT<8i81tBgxeVgwez2m;0C_oY%P zn$PD{d@M2<9x-sk0e>%mR&bL^rqgLE6be*-t+N0;V&H}YKI%Y_8srg>G?vX~nOu9R zQMp_u6PrAi33Z6AOeW)*#DBeBCQAl`L8?4e$l3V6^f57cCaL+}WQw$Hn-@cGs@Xh$*QYuD23`S*!^>wpmf!i>vIBUj*07eUVJR<8>e!h9SD2im((5K;4)`>bSrKDAS(mE{FIu$FD#O z*MS@H`5+E9XRwpLMS45J_uf8T!4(i@SFRoWF`jN#1zAyoI8`GsJSY4VK3T@zd5N!O zzkeKpAV6le1`XoV92ZcOvBKF^EB;&iG{?p0xBO3h3NQdF`Bu**MA5ha0000c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetYam){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq=aw&&av.offsetY<=am){if(av.offsetY-aw0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("
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").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("
").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("
").addClass("param-row").appendTo(this.parent_div);var am=$("").attr("value","Run on complete dataset").appendTo(ax);var ah=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.minah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("
").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("
").addClass("filter-row slider-row").appendTo(ax);var aG=$("
").addClass("elt-label").appendTo(aH.container);var aE=$("").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("");var aJ=$("").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("
").addClass("slider").appendTo(aH.container);aH.control_element=$("
").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("
").appendTo(aH.container)});if(this.filters.length!==0){var am=$("
").addClass("param-row").appendTo(ax);var ao=$("").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("
").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("
").addClass("filter-row").appendTo(ar),an=$("").addClass("elt-label").text(aE+":").appendTo(au),aq=$("').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("").attr("id",aj).attr("name",aj).val(ao);var ap=$("
").hide();var al=$("
").appendTo(ap);var aq=$("
").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("
").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("
").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("").appendTo(az);$("
").appendTo(aA).text(ax);$("").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ar,al,at,aj,ai){r.call(this,ak,ar,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("
").addClass("track").attr("id","track_"+this.id).css("position","relative");if(!this.hidden){this.header_div=$("
").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("
").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("
").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",am.config.build_form(),{Cancel:aw,OK:au})});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("
").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ao=0,aq=am.display_modes.length;ao").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("
").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" ").text("View error").click(function(){show_modal("Trackster Error","
"+ai.message+"
",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){},});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},set_is_overview:function(ah){this.is_overview=ah;this.update_track_icons()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("
");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("
"),ap=$("
").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("").addClass("icon more-down").appendTo(ap),ah=$("").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("
");while(ah"+commatize(ah)+"
").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("
").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("
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q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;OD){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var 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I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;OE)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var 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ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case 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U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;ec){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida 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n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetYam){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq=aw&&av.offsetY<=am){if(av.offsetY-aw0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("
").addClass("track-header").appendTo(this.container_div);this.header_div.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("
").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;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=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("
").addClass("top-container").appendTo(aj);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("
").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("
").addClass("intro");var ak=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("nav-container").prependTo(this.top_container);this.nav=$("
").addClass("nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("
").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='';for(var an=0,ak=ah.chrom_data.length;an'+am+""}if(al.prev_chroms){ao+='"}if(al.next_chroms){ao+='"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;alah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;amthis.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("
").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("
").addClass("param-row").appendTo(ao.parent_div);var ay=$("
").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("
").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("
").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("
").addClass("param-row").appendTo(this.parent_div);var am=$("").attr("value","Run on complete dataset").appendTo(ax);var ah=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.minah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("
").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("
").addClass("filter-row slider-row").appendTo(ax);var aG=$("
").addClass("elt-label").appendTo(aH.container);var aE=$("").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("");var aJ=$("").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("
").addClass("slider").appendTo(aH.container);aH.control_element=$("
").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("
").appendTo(aH.container)});if(this.filters.length!==0){var am=$("
").addClass("param-row").appendTo(ax);var ao=$("").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("
").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("
").addClass("filter-row").appendTo(ar),an=$("").addClass("elt-label").text(aE+":").appendTo(au),aq=$("').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("").attr("id",aj).attr("name",aj).val(ao);var ap=$("
").hide();var al=$("
").appendTo(ap);var aq=$("
").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("
").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("
").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("").appendTo(az);$("
").appendTo(aA).text(ax);$("").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("
").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("
").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("
").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("
").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("
").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("
").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" ").text("View error").click(function(){show_modal("Trackster Error","
"+ai.message+"
",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("
");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("
"),ao=$("
").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("").addClass("icon more-down").appendTo(ao),ah=$("").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("
");while(ah"+commatize(ah)+"
").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("
").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("
").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;alaq){aq=av}}for(var al=0;alaj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(avak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("
").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aEB[0]&&G=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;OD){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;OE)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;aiX){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||XP){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var 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ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case 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U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js index 67fef91ff89..0915be0fc30 100644 --- a/static/scripts/packed/trackster_ui.js +++ b/static/scripts/packed/trackster_ui.js @@ -1 +1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("
").addClass("bookmark").appendTo(g),c=$("
").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("").addClass("icon-button delete").appendTo(c),f=$("
").addClass("position").appendTo(d),h=$("").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d").addClass("bookmark").appendTo(g),c=$("
").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("").addClass("icon-button delete").appendTo(c),f=$("
").addClass("position").appendTo(d),h=$("").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("
").addClass("overview-viewport").appendTo(this.overview); - this.overview_close = $("Close Overview").addClass("overview-close").hide().appendTo(this.overview_viewport); + this.overview_close = $("").attr("href", "javascript:void(0);").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport); this.overview_highlight = $("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport); this.overview_box_background = $("
").addClass("overview-boxback").appendTo(this.overview_viewport); this.overview_box = $("
").addClass("overview-box").appendTo(this.overview_viewport); @@ -1195,13 +1196,14 @@ extend( View.prototype, DrawableCollection.prototype, { /** * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. */ + // FIXME: change method call so that track is first and additional parameters are optional. request_redraw: function(nodraw, force, clear_after, track) { var view = this, - // Either redrawing a single track or all view's tracks. + // Either redrawing a single drawable or all view's drawables. track_list = (track ? [track] : view.drawables), track_index; - + // Add/update tracks in track list to redraw list. var track; for (var i = 0; i < track_list.length; i++) { @@ -1318,42 +1320,44 @@ extend( View.prototype, DrawableCollection.prototype, { this.nav_container.width( this.container.width() ); this.request_redraw(); }, - /** Show a track in the overview. */ - set_overview: function(track) { - // Get data and draw tile. - $.when(track.get_overview_tile()).then(function(tile) { - // Update UI. - view.overview_viewport.find(".track-tile").remove(); - view.overview_close.show(); - view.overview_viewport.append(tile.canvas); - view.overview_highlight.show().height(tile.canvas.height()); - view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight()); - view.resize_window(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); + /** Show a Drawable in the overview. */ + set_overview: function(drawable) { + if (this.overview_drawable) { + // If drawable to be set as overview is already in overview, do nothing. + // Otherwise, remove overview. + if (this.overview_drawable.dataset_id === drawable.dataset_id) { + return; } - view.overview_track = track; - track.set_is_overview(true); - }); + this.overview_viewport.find(".track").remove(); + } + + // Set new overview. + var + overview_drawable = drawable.copy( { content_div: this.overview_viewport } ), + view = this; + overview_drawable.header_div.hide(); + overview_drawable.is_overview = true; + view.overview_drawable = overview_drawable; + this.overview_drawable.postdraw_actions = function() { + view.overview_highlight.show().height(view.overview_drawable.content_div.height()); + view.overview_viewport.height(view.overview_drawable.content_div.height() + view.overview_box.outerHeight()); + view.overview_close.show(); + view.resize_window(); + }; + this.overview_drawable.init(); view.has_changes = true; }, /** Close and reset overview. */ reset_overview: function() { // Update UI. + $(".tipsy").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(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); - } - view.overview_track = null; + view.overview_drawable = null; } }); @@ -2243,7 +2247,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() { * -------> ToolDataFeatureTrack * -------> VcfTrack */ -var Track = function(name, view, container, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2263,8 +2267,8 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) { // this.container_div = $("
").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); - // Create and initialize track header and icons. Only non-hidden tracks have headers. - if (!this.hidden) { + // Create and initialize track header and icons. + if (show_header) { this.header_div = $("
").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("
").addClass(this.drag_handle_class).appendTo(this.header_div); } this.name_div = $("
").addClass("track-name").appendTo(this.header_div).text(this.name) @@ -2275,6 +2279,9 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) { this.settings_icon = $("").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); + this.overview_icon = $("").attr("href", "javascript:void(0);").attr("title", "Set as overview") + .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); this.filters_icon = $("").attr("href", "javascript:void(0);").attr("title", "Filters") .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div).hide(); @@ -2312,18 +2319,10 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) { }); }); - // FIXME: old code for overview. - /* - track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { - if (track.is_overview) { - track.view.reset_overview(); - } - else { - track.view.set_overview(track); - } - }; - */ - + this.overview_icon.click( function() { + track.view.set_overview(track); + }); + this.filters_icon.click( function() { // TODO: update tipsy text. track.filters_div.toggle(); @@ -2488,7 +2487,7 @@ extend(Track.prototype, Drawable.prototype, { /** * Additional initialization required before drawing track for the first time. */ - predraw_init: function() {}, + predraw_init: function() {} }); var TiledTrack = function(filters_list, tool_dict) { @@ -2504,27 +2503,32 @@ var TiledTrack = function(filters_list, tool_dict) { this.filters_available = false; this.filters_visible = false; this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); - this.is_overview = false; - if (track.hidden) { return; } + if (this.header_div) { + // + // Create filters div. + // + if (this.filters_manager) { + this.filters_div = this.filters_manager.parent_div + this.header_div.after(this.filters_div); + } - // - // Create filters div. - // - if (this.filters_manager) { - this.filters_div = this.filters_manager.parent_div - this.header_div.after(this.filters_div); - } - - // - // Create dynamic tool div. - // - if (this.tool) { - this.dynamic_tool_div = this.tool.parent_div; - this.header_div.after(this.dynamic_tool_div); + // + // Create dynamic tool div. + // + if (this.tool) { + this.dynamic_tool_div = this.tool.parent_div; + this.header_div.after(this.dynamic_tool_div); + } } }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { + /** + * Returns a copy of the track. + */ + copy: function(container) { + return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool); + }, /** * Convert track to JSON object. */ @@ -2588,52 +2592,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { } */ }, - /** - * Set track's overview status. - */ - set_is_overview: function(is_overview) { - this.is_overview = is_overview; - this.update_track_icons(); - }, - /** - * Returns a jQuery Deferred object that resolves to a Tile with track's overview. - * TODO: this should be the approach used when drawing any tile so that tile drawing is not blocking. - */ - get_overview_tile: function() { - var - track = this; - view = track.view, - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )), - view_width = view.container.width(), - // w_scale units are pixels per base. - w_scale = view_width / (view.max_high - view.max_low), - overview_tile = $.Deferred(); - $.when(track.data_manager.get_data(view.max_low, view.max_high, "Auto", resolution, track.data_url_extra_params)).then(function(overview_data) { - var - key = track._gen_tile_cache_key(view_width, w_scale, 0), - tile = track.tile_cache.get(key); - - // Draw tile if necessary. - if (!tile) { - tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale); - track.tile_cache.set(key, tile); - } - - // Always copy tile because it may need to be used in viz. - var - src_canvas = $(tile.canvas.find("canvas")), - new_canvas = src_canvas.clone(), - src_ctx = src_canvas.get(0).getContext("2d"), - tgt_ctx = new_canvas.get(0).getContext("2d"), - data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - // Need to undo offsets when placing image data. - tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0)); - new_tile = new Tile(track, -1, resolution, new_canvas); - overview_tile.resolve(new_tile); - }); - - return overview_tile; - }, /** * Generate a key for the tile cache. * TODO: create a TileCache object (like DataCache) and generate key internally. @@ -2667,6 +2625,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { w_scale = width / range, resolution = this.view.resolution, parent_element = $("
"); + + // For overview, adjust high, low, resolution, and w_scale. + if (this.is_overview) { + low = this.view.max_low; + high = this.view.max_high; + resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )); + w_scale = width / (view.max_high - view.max_low); + } if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); @@ -2777,7 +2743,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { // Can't draw now, so trigger another redraw when the data is ready $.when( tile_data, seq_data ).then( function() { - view.request_redraw(); + view.request_redraw(false, false, false, track); }); // Indicate to caller that this tile could not be drawn @@ -2837,8 +2803,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { tile.predisplay_actions(); // Position tile element, recalculate left position at display time - var range = this.view.high - this.view.low, - left = (tile.low - this.view.low) * w_scale; + var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale; if (this.left_offset) { left -= this.left_offset; } @@ -2875,8 +2840,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { }); var LabelTrack = function (view, container) { - this.hidden = true; - Track.call(this, "label", view, container, {} ); + Track.call(this, "label", view, container, false, {} ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -2906,8 +2870,7 @@ extend(LabelTrack.prototype, Track.prototype, { }); var ReferenceTrack = function (view) { - this.hidden = true; - Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); + Track.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); TiledTrack.call(this); view.reference_track = this; @@ -3109,7 +3072,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, // // FIXME: cleaner init needed; should just be able to call TiledTrack() - Track.call(this, name, view, container, prefs); + Track.call(this, name, view, container, true, prefs); TiledTrack.call(this, filters, tool); // Define and restore track configuration. @@ -3371,9 +3334,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { if (mode === "Auto") { if (result.dataset_type === "summary_tree") { mode = result.dataset_type; - } else if (result.extra_info === "no_detail") { + } + // HACK: use no_detail mode track is in overview to prevent overview from being too large. + else if (result.extra_info === "no_detail" || track.is_overview) { mode = "no_detail"; - } else { + } + else { // Choose b/t Squish and Pack. // Proxy measures for using Squish: // (a) error message re: limiting number of features shown; diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js index 900dfc6a929..87b0f68e2b7 100644 --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -114,7 +114,7 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi // Set overview. var overview_track; for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].name == overview_track_name) { + if (view.drawables[i].name === overview_track_name) { view.set_overview(view.drawables[i]); break; } diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako index 565aa4743d2..86d860a2289 100644 --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -195,7 +195,8 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e }; }); - var overview_track_name = (view.overview_track ? view.overview_track.name : null); + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null); var payload = { 'view': view.to_json(), 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },