From 7d9dde723527b444cd340733b16a95414f574b04 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Thu, 17 Dec 2009 14:32:44 -0500
Subject: [PATCH] Packed scripts

---
 static/scripts/packed/autocomplete_tagging.js | 2 +-
 static/scripts/packed/galaxy.base.js          | 2 +-
 static/scripts/packed/trackster.js            | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/static/scripts/packed/autocomplete_tagging.js b/static/scripts/packed/autocomplete_tagging.js
index 3cb132ee29b..60072d30cd2 100644
--- a/static/scripts/packed/autocomplete_tagging.js
+++ b/static/scripts/packed/autocomplete_tagging.js
@@ -1 +1 @@
-jQuery.fn.autocomplete_tagging=function(f,d){var g={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var q=jQuery.extend(g,d);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var e=$("#"+f);var m=$(this).attr("id").split("-");var a=m[m.length-1];var l=e.find("#tag-area-"+a);var s=e.find("#toggle-link-"+a);var n=e.find("#tag-input");var h=e.find(".add-tag-button");s.click(function(){var x=$(this).attr("id").split("-")[2];var v=$("#tag-area-"+x);var u=(v.css("display")=="none");var w;if(u){w=function(){var y=$(this).find(".tag-button").length;if(y==0){v.click()}}}else{w=function(){v.blur()}}v.slideToggle("fast",w);return $(this)});if(q.editable){n.hide()}n.keyup(function(z){if(z.keyCode==27){$(this).trigger("blur")}else{if((z.keyCode==13)||(z.keyCode==188)||(z.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((z.keyCode==188)||(z.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var w=j(new_value);var v=l.children(".tag-button");if(v.length!=0){var A=v.slice(v.length-1);A.after(w)}else{l.prepend(w)}var u=new_value.split(":");q.tags[u[0]]=u[1];var x=q.get_toggle_link_text_fn(q.tags);s.text(x);var y=$(this);$.ajax({url:q.ajax_add_tag_url,data:{new_tag:new_value},error:function(){w.remove();delete q.tags[u[0]];var B=q.get_toggle_link_text_fn(q.tags);s.text(B);alert("Add tag failed")},success:function(){y.flushCache()}});return false}}});var c=function(w,v,u,y,x){tag_name_and_value=y.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var k={selectFirst:false,formatItem:c,autoFill:false,highlight:false};n.autocomplete(q.ajax_autocomplete_tag_url,k);e.find(".delete-tag-img").each(function(){p($(this))});e.find(".tag-name").each(function(){$(this).click(function(){var v=$(this).text();var u=v.split(":");q.tag_click_fn(u[0],u[1]);return true})});h.click(function(){$(this).hide();l.click();return false});if(q.editable){l.blur(function(u){r=o(q.tags);if(r!=0){h.show();n.hide();l.removeClass("active-tag-area")}else{}});l.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");h.hide();n.show();n.focus();var u=function(y){var x=l.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){l.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(q.use_toggle_link){l.hide()}else{var r=o(q.tags);if(r==0){h.hide();n.show()}}function b(v,u){return v+((u!=""&&u)?":"+u:"")}function p(u){$(u).mouseenter(function(){$(this).attr("src",q.delete_tag_img_rollover)});$(u).mouseleave(function(){$(this).attr("src",q.delete_tag_img)});$(u).click(function(){var A=$(this).parent();var z=A.find(".tag-name").eq(0);var y=z.text();var w=i(y);var C=w[0];var v=w[1];var B=A.prev();A.remove();delete q.tags[C];var x=q.get_toggle_link_text_fn(q.tags);s.text(x);$.ajax({url:q.ajax_delete_tag_url,data:{tag_name:C},error:function(){q.tags[C]=v;if(B.hasClass("tag-button")){B.after(A)}else{l.prepend(A)}var D=q.get_toggle_link_text_fn(q.tags);alert("Remove tag failed");s.text(D);u.mouseenter(function(){$(this).attr("src",q.delete_tag_img_rollover)});u.mouseleave(function(){$(this).attr("src",q.delete_tag_img)})},success:function(){}});return true})}function t(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"}function i(u){return u.split(":")}function j(u){var v=$("<img src='"+q.delete_tag_img+"'/>").addClass("delete-tag-img");p(v);var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");q.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(q.editable){x.append(v)}return x}};
\ No newline at end of file
+function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" Tags":" Tag")}else{t="Add tags"}return t},tag_click_fn:function(r,s){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var e=jQuery.extend(g,q);var o=function(r){if(r.length){return r.length}var s=0;for(element in r){s++}return s};var h=$(this);var c=h.find(".tag-area");var f=h.find(".toggle-link");var b=h.find(".tag-input");var n=h.find(".add-tag-button");f.click(function(){var r=(c.css("display")=="none");var s;if(r){s=function(){var t=$(this).find(".tag-button").length;if(t==0){c.click()}}}else{s=function(){c.blur()}}c.slideToggle("fast",s);return $(this)});if(e.editable){b.hide()}b.keyup(function(w){if(w.keyCode==27){$(this).trigger("blur")}else{if((w.keyCode==13)||(w.keyCode==188)||(w.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((w.keyCode==188)||(w.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var t=k(new_value);var s=c.children(".tag-button");if(s.length!=0){var x=s.slice(s.length-1);x.after(t)}else{c.prepend(t)}var r=new_value.split(":");e.tags[r[0]]=r[1];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);var v=$(this);$.ajax({url:e.ajax_add_tag_url,data:{new_tag:new_value},error:function(){t.remove();delete e.tags[r[0]];var y=e.get_toggle_link_text_fn(e.tags);f.text(y);alert("Add tag failed")},success:function(){v.flushCache()}});return false}}});var j=function(t,s,r,v,u){tag_name_and_value=v.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var i={selectFirst:false,formatItem:j,autoFill:false,highlight:false};b.autocomplete(e.ajax_autocomplete_tag_url,i);h.find(".delete-tag-img").each(function(){d($(this))});init_tag_click_function($(this),e.tag_click_fn);n.click(function(){$(this).hide();c.click();return false});if(e.editable){c.blur(function(r){p=o(e.tags);if(p!=0){n.show();b.hide();c.removeClass("active-tag-area")}else{}});c.click(function(t){var s=$(this).hasClass("active-tag-area");if($(t.target).hasClass("delete-tag-img")&&!s){return false}if($(t.target).hasClass("tag-name")&&!s){return false}$(this).addClass("active-tag-area");n.hide();b.show();b.focus();var r=function(v){var u=c.attr("id");if(($(v.target).attr("id")!=u)&&($(v.target).parents().filter(u).length==0)){c.blur();$(document).unbind("click",r)}};$(window).click(r);return false})}if(e.use_toggle_link){c.hide()}else{var p=o(e.tags);if(p==0){n.hide();b.show()}}function l(s,r){return s+((r!=""&&r)?":"+r:"")}function d(r){$(r).mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});$(r).mouseleave(function(){$(this).attr("src",e.delete_tag_img)});$(r).click(function(){var x=$(this).parent();var w=x.find(".tag-name").eq(0);var v=w.text();var t=m(v);var z=t[0];var s=t[1];var y=x.prev();x.remove();delete e.tags[z];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);$.ajax({url:e.ajax_delete_tag_url,data:{tag_name:z},error:function(){e.tags[z]=s;if(y.hasClass("tag-button")){y.after(x)}else{c.prepend(x)}var A=e.get_toggle_link_text_fn(e.tags);alert("Remove tag failed");f.text(A);r.mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});r.mouseleave(function(){$(this).attr("src",e.delete_tag_img)})},success:function(){}});return true})}function a(r){var s=new Array();for(key in r){s[s.length]=key+"-->"+r[key]}return"{"+s.join(",")+"}"}function m(r){return r.split(":")}function k(r){var s=$("<img src='"+e.delete_tag_img+"'/>").addClass("delete-tag-img");d(s);var t=$("<span>").text(r).addClass("tag-name");t.click(function(){tag_name_and_value=r.split(":");e.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var u=$("<span></span>").addClass("tag-button");u.append(t);if(e.editable){u.append(s)}return u}};
\ No newline at end of file
diff --git a/static/scripts/packed/galaxy.base.js b/static/scripts/packed/galaxy.base.js
index 76f7b902190..15d6fc19a66 100644
--- a/static/scripts/packed/galaxy.base.js
+++ b/static/scripts/packed/galaxy.base.js
@@ -1 +1 @@
-$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.attr("value","?")}}}})}};
\ No newline at end of file
+$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.attr("value","?")}}}})}};
\ No newline at end of file
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 3c31d271dd6..cf65781807f 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c)}else{h=this.draw_tile(d,a,k,l);if(h){this.tile_cache.set(j,h)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});
\ No newline at end of file
+var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});
\ No newline at end of file