sequenceserver 0.8.4 → 0.8.5

data/views/search.erb

@@ -10,10 +10,10 @@
   <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
   <script type="text/javascript" src="<%= uri('/js/store.min.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
-  <script type="text/javascript" src="<%= uri('/js/jquery.ui.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/jquery-ui.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
-  <script type="text/javascript" src="<%= uri('/js/jquery.scrollspy.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/jquery-scrollspy.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.transition.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.dropdown.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.modal.js') %>"></script>
@@ -151,7 +151,7 @@
       </div>
 
       <div class="results hide">
-        <div id="result">
+        <div id="result">Waiting for BLAST to be run <!-- need bit before for UI testing so it knows when BLAST is finished -->
         </div>
       </div>
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 0.8.4
+  version: 0.8.5
   prerelease: 
 platform: ruby
 authors:
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-29 00:00:00.000000000 Z
+date: 2013-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -93,6 +93,54 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: watir-webdriver
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: headless
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
 
@@ -121,9 +169,8 @@ files:
 - public/js/bootstrap.modal.js
 - public/js/bootstrap.dropdown.js
 - public/js/bootstrap.transition.js
-- public/js/jquery.ui.js
-- public/js/Scribl.min.js
-- public/js/jquery.scrollspy.js
+- public/js/jquery-scrollspy.js
+- public/js/jquery-ui.js
 - public/js/sequenceserver.blast.js
 - public/js/store.min.js
 - public/js/sequenceserver.js~
@@ -170,7 +217,9 @@ files:
 - tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
 - tests/run
 - tests/test_sequenceserver_blast.rb
+- tests/test_ui.rb
 - tests/ui.specs.todo
+- tests/chromedriver.log
 - tests/test_sequencehelpers.rb
 - config.ru
 - example.config.yml

data/public/js/Scribl.min.js

@@ -1,53 +0,0 @@
-(function(){var a=!1,b=/xyz/.test(function(){})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(c){function d(){!a&&this.init&&this.init.apply(this,arguments)}var e=this.prototype;a=!0;var g=new this;a=!1;for(var i in c)g[i]=typeof c[i]=="function"&&typeof e[i]=="function"&&b.test(c[i])?function(a,b){return function(){var c=this._super;this._super=e[a];var d=b.apply(this,arguments);this._super=c;return d}}(i,c[i]):c[i];d.prototype=g;d.constructor=d;d.extend=arguments.callee;return d}})();var Scribl=Class.extend({init:function(a,b){this.scrolled=!1;var c=a.getContext("2d");this.width=b;this.laneSizes=50;this.laneBuffer=5;this.trackBuffer=25;this.offset=void 0;this.canvas=a;this.ctx=c;this.scale={};this.scale.pretty=!0;this.scale.max=void 0;this.scale.min=void 0;this.scale.auto=!0;this.scale.off=!1;this.scale.size=15;this.scale.font={};this.scale.font.size=15;this.scale.font.color="black";this.scale.font.buffer=10;this.glyph={};this.glyph.roundness=6;this.glyph.borderWidth=1;this.glyph.color=
-["#99CCFF","rgb(63, 128, 205)"];this.glyph.text={};this.glyph.text.color="black";this.glyph.text.size="13";this.glyph.text.font="arial";this.glyph.text.align="center";this.gene={};this.gene.text={};this.protein={};this.protein.text={};this.events={};this.events.hasClick=!1;this.events.hasMouseover=!1;this.events.clicks=[];this.events.mouseovers=[];this.events.added=!1;this.tick={};this.tick.auto=!0;this.tick.major={};this.tick.major.size=10;this.tick.major.color="black";this.tick.minor={};this.tick.minor.size=
-1;this.tick.minor.color="rgb(55,55,55)";this.tick.halfColor="rgb(10,10,10)";this.tooltips={};this.tooltips.text={};this.tooltips.text.font="arial";this.tooltips.text.size=12;this.tooltips.borderWidth=1;this.tooltips.roundness=5;this.tooltips.fade=!1;this.tooltips.style="light";this.scrollable=!1;this.scrollValues=[0,void 0];this.drawStyle="expand";this.myMouseEventHandler=new MouseEventHandler(this);this.tracks=[]},getScaleHeight:function(){return this.scale.font.size+this.scale.size},getHeight:function(){var a=
-0;this.scale.off||(a+=this.getScaleHeight());for(var b=this.tracks.length,c=0;c<b;c++)a+=this.trackBuffer,a+=this.tracks[c].getHeight();return a},addTrack:function(){var a=new Track(this.ctx);a.chart=this;if(this.tracks.length==1&&this.tracks[0]==void 0)this.tracks=[];this.tracks.push(a);return a},loadGenbank:function(a){genbank(a,this)},loadBed:function(a){bed(a,this)},loadFeatures:function(a){for(var b=0;b<a.length;b++)this.addFeature(a[b])},addGene:function(a,b,c,d){return this.addFeature(new BlockArrow("gene",
-a,b,c,d))},addProtein:function(a,b,c,d){return this.addFeature(new BlockArrow("protein",a,b,c,d))},addFeature:function(a){(this.tracks[0]||this.addTrack()).addFeature(a);return a},slice:function(a,b,c){c=c||"inclusive";for(var d=this.tracks.length,e=new Scribl(this.canvas,this.width),g=0;g<d;g++){var i=this.tracks[g],k=e.addTrack();k.drawStyle=i.drawStyle;for(var j=i.lanes.length,m=0;m<j;m++){newLane=k.addLane();for(var l=i.lanes[m].features,n=0;n<l.length;n++){var o=l[n].position+l[n].length,p=l[n].position;
-if(c=="inclusive")p>=a&&p<=b?newLane.addFeature(l[n]):o>a&&o<b?newLane.addFeature(l[n]):p<a&&o>b?newLane.addFeature(l[n]):p>a&&o<b&&newLane.addFeature(l[n]);else if(c=="strict")if(p>=a&&p<=b)if(o>a&&o<b)newLane.addFeature(l[n]);else{var q=l[n].clone();q.length=Math.abs(b-p);newLane.addFeature(q)}else if(o>a&&o<b)q=l[n].clone(),q.position=a,q.length=Math.abs(o-a),newLane.addFeature(q);else{if(p<a&&o>b)q=l[n].clone(),q.position=a,q.length=Math.abs(b-a),newLane.addFeature(q)}else c=="exclusive"&&p>=
-a&&p<=b&&o>a&&o<b&&newLane.addFeature(l[n])}}}e.laneSizes=this.laneSizes;e.drawStyle=this.drawStyle;e.loadFeatures([]);return e},draw:function(){var a=this.ctx,b=this.tracks;this.scrollable==!0&&this.initScrollable();a.save();if(this.scale.pretty){if(this.tick.auto)this.tick.major.size=this.determineMajorTick(),this.tick.minor.size=Math.round(this.tick.major.size/10);if(this.scale.auto)this.scale.min-=this.scale.min%this.tick.major.size,this.scale.max=Math.round(this.scale.max/this.tick.major.size+
-0.4)*this.tick.major.size}this.offset=this.scale.min.offset?a.measureText(this.getTickText(this.scale.min)).width/2+10:a.measureText("0").width/2+10;a.save();if(!this.scale.off){var c=a.fillStyle;this.drawScale();a.fillStyle=c}a.save();this.scale.off||a.translate(0,this.getScaleHeight()+this.laneBuffer);for(c=0;c<b.length;c++)b[c].draw();a.restore();a.restore();a.restore();this.events.added||this.registerEventListeners()},redraw:function(){this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height);
-this.tracks.length>0&&this.draw()},drawScale:function(){var a=this.ctx,b=this.scale.font.size+this.scale.size,c=this.scale.font.size+2,d=this.scale.font.size+this.scale.size*0.66,e=this.scale.font.size+this.scale.size*0.33;a.font=this.scale.font.size+"px arial";a.textBaseline="top";a.fillStyle=this.scale.font.color;for(var g=this.scale.min%this.tick.minor.size==0?this.scale.min:this.scale.min-this.scale.min%this.tick.minor.size+this.tick.minor.size;g<=this.scale.max;g+=this.tick.minor.size){a.beginPath();
-var i=this.pixelsToNts(g-this.scale.min)+this.offset;if(g%this.tick.major.size==0){var k=this.getTickText(g);a.textAlign="center";a.fillText(k,i,0);a.moveTo(i,b);a.lineTo(i,c);a.strokeStyle=this.tick.major.color}else a.moveTo(i,b),g%(this.tick.major.size/2)==0?(a.strokeStyle=this.tick.halfColor,a.lineTo(i,e)):(a.strokeStyle=this.tick.minor.color,a.lineTo(i,d));a.stroke()}},pixelsToNts:function(a){return a==void 0?this.width/(this.scale.max-this.scale.min):this.width/(this.scale.max-this.scale.min)*
-a},ntsToPixels:function(a){return a==void 0?1/this.pixelsToNts():a/this.width},initScrollable:function(){var a;if(!this.scrolled){a=document.createElement("div");var b=document.createElement("div"),c=document.createElement("div");c.id="scribl-zoom-slider";c.className="slider";c.style.cssFloat="left";c.style.height=new String(this.canvas.height*0.5)+"px";c.style.margin="30px auto auto -20px";a.style.cssText=this.canvas.style.cssText;this.canvas.style.cssText="";parentWidth=parseInt(this.canvas.width)+
-25;a.style.width=parentWidth+"px";b.style.width=this.canvas.width+"px";b.style.overflow="auto";b.id="scroll-wrapper";this.canvas.parentNode.replaceChild(a,this.canvas);a.appendChild(c);b.appendChild(this.canvas);a.appendChild(b);$(b).dragscrollable({dragSelector:"canvas:first",acceptPropagatedEvent:!1})}b=this.scale.max-this.scale.min;var d=this.scrollValues[1]||this.scale.max-b*0.35;a=this.scrollValues[0]!=void 0?this.scrollValues[0]:this.scale.max+b*0.35;var e=(d-a)/document.getElementById("scroll-wrapper").style.width.split("px")[0];
-e=b/e;this.canvas.width=e;this.width=e-30;schart=this;d=(d-a)/(this.scale.max-this.scale.min)*100;$(c).slider({orientation:"vertical",range:"min",min:1,max:100,value:d,slide:function(a,b){var c=schart.scale.max-schart.scale.min,d=b.value/100*schart.canvas.width,e=document.getElementById("scroll-wrapper");e=e.scrollLeft+parseInt(e.style.width.split("px")[0])/2;schart.scrollValues=[(e-d/2)/schart.canvas.width*c,(e+d/2)/schart.canvas.width*c];schart.ctx.clearRect(0,0,schart.canvas.width,schart.canvas.height);
-schart.draw()}});c=(a-this.scale.min)/b*this.canvas.width;document.getElementById("scroll-wrapper").scrollLeft=c;this.scrolled=!0},determineMajorTick:function(){this.ctx.font=this.scale.font.size+"px arial";var a=(this.scale.max-this.scale.min)/(this.width/(this.ctx.measureText(this.getTickTextDecimalPlaces(this.scale.max)).width+this.scale.font.buffer)),b=Math.pow(10,parseInt(a).toString().length-1);this.tick.major.size=Math.ceil(a/b)*b;a=Math.pow(10,(this.tick.major.size+"").length);b=this.tick.major.size/
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-1];if(e!=void 0&&a.position-3/this.chart.pixelsToNts()>e.position+e.length){c=!1;b=this.lanes[d];break}}c&&(b=this.addLane());b.addFeature(a);return a},getDrawStyle:function(){return this.drawStyle?this.drawStyle:this.chart.drawStyle},getHeight:function(){var a=0,b=this.lanes.length,c=this.chart.laneBuffer,d=this.getDrawStyle();if(d=="line"||d=="collapse")b=1;for(d=0;d<b;d++)a+=c,a+=this.lanes[d].getHeight();a-=c;return a},getPixelPositionY:function(){for(var a=this.chart.getScaleHeight()+this.chart.laneBuffer,
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-this.getPixelPositionY(),this.chart.width,this.getHeight())},draw:function(){var a=this.getDrawStyle(),b=this.chart.laneSizes,c=this.lanes,d=this.chart.laneBuffer,e=this.chart.trackBuffer,g=b+e,i=this.ctx;if(a==void 0||a=="expand")for(a=0;a<c.length;a++)c[a].y=g,c[a].draw(),b=c[a].getHeight(),i.translate(0,b+d),g=g+b+d;else if(a=="collapse"){b=[];for(a=0;a<c.length;a++)b=b.concat(c[a].features);b.sort(function(a,b){return a.position-b.position});for(g=0;g<b.length;g++){a=b[g].length;var k=b[g].name,
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-a.length+a.position;if(a.position<this.chart.scale.min||this.chart.scale.min==void 0)this.chart.scale.min=a.position;return a},loadFeatures:function(a){for(var b=a.length,c=0;c<b;c++)this.addFeature(a[c])},getHeight:function(){return this.height!=void 0?this.height:this.chart.laneSizes},getPixelPositionY:function(){for(var a=this.track.getPixelPositionY(),b=this.getHeight(),c=0;c<this.track.lanes.length;c++){if(this.uid==this.track.lanes[c].uid)break;a+=this.track.chart.laneBuffer;a+=b}return a},
-erase:function(){this.chart.ctx.clearRect(0,this.getPixelPositionY(),this.track.chart.width,this.getHeight())},draw:function(){for(var a=0;a<this.features.length;a++)this.features[a].draw()}});var tooltips=Class.extend({init:function(a){this.chart=a;this.ctx=a.ctx},fire:function(a){var b=this.ctx.globalAlpha;this.chart.tooltips.fade?h=1:this.draw(a,1);this.ctx.globalAlpha=b},draw:function(a,b){this.ctx.globalAlpha=b;var c=this.chart.tooltips.roundness,d=this.chart.tooltips.text.font,e=this.chart.tooltips.text.size;this.ctx.save();this.ctx.font=e+"px "+d;d=this.ctx.measureText(a.onMouseover);var g=[a.onMouseover],i=e+10,k=d.width+10,j=i-4,m,l;d=a.getPixelPositionX()+10;j=a.getPixelPositionY()-
-j;a.getPixelLength();if(k>200)g=this.ctx.measureText("s").width,g=parseInt(200/g),g=ScriblWrapLines(g,a.onMouseover),k=210,i=g[1]*e+10,g=g[0];k+d>this.chart.width&&(d=this.chart.width-k);if(this.chart.tooltips.style=="light")m=this.chart.ctx.createLinearGradient(d+k/2,j,d+k/2,j+i),m.addColorStop(0,"rgb(253, 248, 196)"),m.addColorStop(0.75,"rgb(253, 248, 196)"),m.addColorStop(1,"white"),l=this.chart.ctx.createLinearGradient(d+k/2,j,d+k/2,j+i),l.addColorStop(0,"black"),l.addColorStop(1,"rgb(64, 64, 64)"),
-this.chart.tooltips.text.color="black";else if(this.chart.tooltips.style=="dark")m=this.chart.ctx.createLinearGradient(d+k/2,j,d+k/2,j+i),m.addColorStop(0,"rgb(64, 64, 64)"),m.addColorStop(1,"rgb(121, 121, 121)"),l="white",this.chart.tooltips.text.color="white";this.chart.LastToolTip={pixels:this.ctx.getImageData(d-1,j-1,k+2,i+2),x:d-1,y:j-1};this.ctx.fillStyle=m;this.ctx.beginPath();tlc_ctrl_x=d;tlc_ctrl_y=j;tlc_lgth_x=d+c;tlc_lgth_y=j;tlc_wdth_x=d;tlc_wdth_y=j+c;blc_ctrl_x=d;blc_ctrl_y=j+i;blc_lgth_x=
-d+c;blc_lgth_y=j+i;blc_wdth_x=d;blc_wdth_y=j+i-c;brc_ctrl_x=d+k;brc_ctrl_y=j+i;brc_lgth_x=d+k-c;brc_lgth_y=j+i;brc_wdth_x=d+k;brc_wdth_y=j+i-c;trc_ctrl_x=d+k;trc_ctrl_y=j;trc_lgth_x=d+k-c;trc_lgth_y=j;trc_wdth_x=d+k;trc_wdth_y=j+c;this.ctx.moveTo(tlc_lgth_x,tlc_lgth_y);this.ctx.quadraticCurveTo(tlc_ctrl_x,tlc_ctrl_y,tlc_wdth_x,tlc_wdth_y);this.ctx.lineTo(blc_wdth_x,blc_wdth_y);this.ctx.quadraticCurveTo(blc_ctrl_x,blc_ctrl_y,blc_lgth_x,blc_lgth_y);this.ctx.lineTo(brc_lgth_x,brc_lgth_y);this.ctx.quadraticCurveTo(brc_ctrl_x,
-brc_ctrl_y,brc_wdth_x,brc_wdth_y);this.ctx.lineTo(trc_wdth_x,trc_wdth_y);this.ctx.quadraticCurveTo(trc_ctrl_x,trc_ctrl_y,trc_lgth_x,trc_lgth_y);this.ctx.lineTo(tlc_lgth_x,tlc_lgth_y);this.ctx.fill();this.ctx.lineWidth=this.chart.tooltips.borderWidth;this.ctx.strokeStyle=l;this.ctx.stroke();this.ctx.textBaseline="middle";this.ctx.fillStyle=this.chart.tooltips.text.color;for(c=0;c<g.length;c++)this.ctx.measureText(g[c]),this.ctx.fillText(g[c],d+5,j+e*(c+1));this.ctx.restore()}});var MouseEventHandler=Class.extend({init:function(a){this.chart=a;this.mouseY=this.mouseX=null;this.eventElement=void 0;this.isEventDetected=!1;this.tooltip=new tooltips(this.chart)},addEvents:function(a){var b=this.chart,c=b.ctx,d=b.myMouseEventHandler;if(a.onMouseover&&!b.events.hasMouseover)b.addMouseoverEventListener(b.myMouseEventHandler.handleMouseover),b.events.hasMouseover=!0;else if(a.parent&&a.parent.onMouseover&&!b.events.hasMouseover)b.addMouseoverEventListener(b.myMouseEventHandler.handleMouseover),
-b.events.hasMouseover=!0;if(a.onClick&&!b.events.hasClick)b.addClickEventListener(b.myMouseEventHandler.handleClick),b.addMouseoverEventListener(b.myMouseEventHandler.handleMouseStyle),b.events.hasClick=!0;else if(a.parent&&a.parent.onClick&&!b.events.hasClick)b.addClickEventListener(b.myMouseEventHandler.handleClick),b.addMouseoverEventListener(b.myMouseEventHandler.handleMouseStyle),b.events.hasClick=!0;if(!d.isEventDetected&&c.isPointInPath_mozilla(d.mouseX,d.mouseY))d.eventElement=a,d.isEventDetected=
-!0},setMousePosition:function(a){if(a!=null){var b=this.chart.canvas.getBoundingClientRect();this.mouseX=a.clientX-b.left;this.mouseY=a.clientY-b.top}},handleClick:function(a){a=a.myMouseEventHandler.eventElement;var b;if(a!=void 0&&a.onClick!=void 0)b=a.onClick;else if(a&&a.parent&&a.parent.onClick)b=a.parent.onClick;b&&(typeof b=="string"?window.open(b):typeof b=="function"&&b(a))},setMousePosition:function(a){if(a!=null){var b=this.chart.canvas.getBoundingClientRect();this.mouseX=a.clientX-b.left;
-this.mouseY=a.clientY-b.top}},handleClick:function(a){a=a.myMouseEventHandler.eventElement;var b;if(a!=void 0&&a.onClick!=void 0)b=a.onClick;else if(a&&a.parent&&a.parent.onClick)b=a.parent.onClick;b&&(typeof b=="string"?window.open(b):typeof b=="function"&&b(a))},handleMouseover:function(a){a=a.myMouseEventHandler;var b=a.eventElement;if(b!=void 0&&b.onMouseover!=void 0)a.tooltip.fire(b);else if(b&&b.parent&&b.parent.onMouseover)b.onMouseover=b.parent.onMouseover,a.tooltip.fire(b)},handleMouseStyle:function(a){var b=
-a.myMouseEventHandler.eventElement;a.ctx.canvas.style.cursor=b&&b.onClick!=void 0?"pointer":b&&b.parent&&b.parent.onClick!=void 0?"pointer":"auto"},reset:function(a){a=a.myMouseEventHandler;a.mouseX=null;a.mouseY=null;a.eventElement=void 0;a.isEventDetected=null;a.elementIndexCounter=0}});
-CanvasRenderingContext2D.prototype.isPointInPath_mozilla=function(a,b){if(navigator.userAgent.indexOf("Firefox")!=-1){this.save();this.setTransform(1,0,0,1,0,0);var c=this.isPointInPath(a,b);this.restore()}else c=this.isPointInPath(a,b);return c};function ScriblWrapLines(a,b){for(var c=[],d="",e=0,g=(""+b).split(" "),i=0;i<g.length;i++)g[i].length+d.length<=a?d+=" "+g[i]:d==""?(trunc1=g[i].slice(0,a-1),d+=" "+trunc1+"-",trunc2=g[i].slice(a,g[i].length),g.splice(i+1,0,trunc2),c.push(d),d="",e++):(i--,c.push(d),e++,d="");e++;c.push(d);return[c,e]}var idCounter=0;_uniqueId=function(a){var b=idCounter++;return a?a+b:b};var CanvasToSVG={idCounter:0,convert:function(a,b,c,d){var e=a.toDataURL(),g=document.createElementNS("http://www.w3.org/2000/svg","image");g.setAttribute("id","importedCanvas_"+this.idCounter++);g.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href",e);g.setAttribute("x",c?c:0);g.setAttribute("y",d?d:0);g.setAttribute("width",a.width);g.setAttribute("height",a.height);g.imageData=a.toDataURL();b.appendChild(g)}},toXml=function(a){return $("<p/>").text(a).html()},svgToString=function(a){for(;removeUnusedDefElems()>
-0;);pathActions.clear(!0);$.each(a.childNodes,function(b,c){b&&c.nodeType==8&&c.data.indexOf("Created with")>=0&&a.insertBefore(c,a.firstChild)});current_group&&(leaveContext(),selectOnly([current_group]));var b=[];$(a).find("g:data(gsvg)").each(function(){for(var a=this.attributes,c=a.length,g=0;g<c;g++)(a[g].nodeName=="id"||a[g].nodeName=="style")&&c--;if(c<=0)a=this.firstChild,b.push(a),$(this).replaceWith(a)});var c=svgToString(a,0);b.length&&$(b).each(function(){groupSvgElem(this)});return c};
-svgToString=function(a,b){var c=[];if(a){var d=a.attributes,e,g,i=a.childNodes;for(g=0;g<b;g++)c.push(" ");c.push("<");c.push(a.nodeName);if(a.id=="svgcontent"){g=getResolution();c.push(' width="'+g.w+'" height="'+g.h+'" xmlns="'+svgns+'"');var k={};$(a).find("*").andSelf().each(function(){$.each(this.attributes,function(a,b){var d=b.namespaceURI;d&&!k[d]&&nsMap[d]!=="xmlns"&&nsMap[d]!=="xml"&&(k[d]=!0,c.push(" xmlns:"+nsMap[d]+'="'+d+'"'))})});for(g=d.length;g--;){e=d.item(g);var j=toXml(e.nodeValue);
-if(e.nodeName.indexOf("xmlns:")!==0&&j!=""&&["width","height","xmlns","x","y","viewBox","id","overflow"].indexOf(e.localName)==-1&&(!e.namespaceURI||nsMap[e.namespaceURI]))c.push(" "),c.push(e.nodeName),c.push('="'),c.push(j),c.push('"')}}else for(g=d.length-1;g>=0;g--)e=d.item(g),j=toXml(e.nodeValue),!(["-moz-math-font-style","_moz-math-font-style"].indexOf(e.localName)>=0)&&j!=""&&j.indexOf("pointer-events")!==0&&!(e.localName==="class"&&j.indexOf("se_")===0)&&(c.push(" "),e.localName==="d"&&(j=
-pathActions.convertPath(a,!0)),c.push(e.nodeName),c.push('="'),c.push(j),c.push('"'));if(a.hasChildNodes()){c.push(">");b++;d=!1;for(g=0;g<i.length;g++)switch(e=i.item(g),e.nodeType){case 1:c.push("\n");c.push(svgToString(i.item(g),b));break;case 3:e=e.nodeValue.replace(/^\s+|\s+$/g,"");e!=""&&(d=!0,c.push(toXml(e)+""));break;case 8:c.push("\n"),c.push(Array(b+1).join(" ")),c.push("<\!--"),c.push(e.data),c.push("--\>")}b--;if(!d){c.push("\n");for(g=0;g<b;g++)c.push(" ")}c.push("</");c.push(a.nodeName);
-c.push(">")}else c.push("/>")}return c.join("")};var Glyph=Class.extend({init:function(a,b,c,d,e){this.uid=_uniqueId("feature");this.position=b;this.length=c;this.strand=d;this.type=a;this.name="";this.borderColor="none";this.borderWidth=void 0;this.text={};this.text.font=void 0;this.text.size=void 0;this.text.color=void 0;this.onMouseover=this.onClick=this.text.align=void 0;for(var g in e)this[g]=e[g]},setColorGradient:function(){if(arguments.length==1)this.color=arguments[0];else{for(var a=this.lane.ctx.createLinearGradient(this.length/2,0,this.length/
-2,this.getHeight()),b,c=0;b=arguments[c],c<arguments.length;c++)a.addColorStop(c/(arguments.length-1),b);this.color=a}},getPixelLength:function(){return this.lane.chart.pixelsToNts(this.length)||1},getPixelPositionX:function(){var a=parseInt(this.lane.track.chart.offset)||0;return this.lane.chart.pixelsToNts(this.parent?this.position+this.parent.position-this.lane.track.chart.scale.min:this.position-this.lane.track.chart.scale.min)+a},getPixelPositionY:function(){return this.lane.getPixelPositionY()},
-getEnd:function(){return this.position+this.length},clone:function(){var a=this;return a=f.orientation?eval("new"+f.glyphType+"("+f.type+","+f.position+","+f.length+","+f.orientation):eval("new"+f.glyphType+"("+f.type+","+f.position+","+f.length)},getAttr:function(a){a=a.split("-");for(var b=this,c=0;c<a.length;c++)b=b[a[c]];if(b)return b;if(this.parent){b=this.parent;for(c=0;c<a.length;c++)b=b[a[c]];if(b)return b}if(b=this.lane.chart[this.type]){for(c=0;c<a.length;c++)b=b[a[c]];if(b)return b}b=this.lane.chart.glyph;
-for(c=0;c<a.length;c++)b=b[a[c]];if(b)return b},drawText:function(a){var b=this.lane.chart.ctx,c=this.getPixelLength(),d=this.getHeight(),e=this.getAttr("text-size"),g=this.getAttr("text-style");b.font=e+"px "+g;b.textBaseline="middle";b.fillStyle=this.getAttr("text-color");var i=void 0,k=this.getAttr("text-align");k=="start"?k=this.strand=="+"?"left":"right":k=="end"&&(k=this.strand=="+"?"right":"left");b.textAlign=k;k=="left"?i=5:k=="center"?i=c/2:k=="right"&&(i=c-5);var j=b.measureText(a);if(a&&
-a!=""){for(;c-j.width<4;)if(e=/^\d+/.exec(b.font),e--,j=b.measureText(a),b.font=e+"px "+g,e<=8){a="";break}this.glyphType=="Complex"&&(c=0,e=/^\d+/.exec(b.font),k=="center"&&(c=-(b.measureText(a).width/2+2.5)),b.clearRect(i+c,d/2-e/2,b.measureText(a).width+5,e));b.fillText(a,i,d/2)}},calcRoundness:function(){return this.getHeight()*this.getAttr("roundness")/100},isContainedWithinRect:function(a,b,c,d){var e=this.getPixelPositionY(),g=this.getPixelPositionX(),i=this.getPixelPositionX()+this.getPixelLength(),
-k=e+this.getHeight();return g>=a&&i<=c&&e>=b&&k<=d},getHeight:function(){return this.lane.getHeight()},getFillStyle:function(){var a=this.getAttr("color");if(a instanceof Array){for(var b=this.lane.ctx.createLinearGradient(this.length/2,0,this.length/2,this.getHeight()),c,d=0;c=a[d],d<a.length;d++)b.addColorStop(d/(a.length-1),c);return b}else return a},getStrokeStyle:function(){var a=this.getAttr("borderColor");if(typeof a=="object"){for(var b=this.lane.ctx.createLinearGradient(this.length/2,0,this.length/
-2,this.getHeight()),c,d=0;c=a[d],d<a.length;d++)b.addColorStop(d/(a.length-1),c);return b}else return a},isSubFeature:function(){return this.parent!=void 0},erase:function(){this.ctx.save();this.ctx.setTransform(1,0,0,1,0,0);this.ctx.clearRect(this.getPixelPositionX(),this.getPixelPositionY(),this.getPixelLength(),this.getHeight());this.ctx.restore()},draw:function(){this.ctx=this.lane.chart.ctx;this.ctx.beginPath();/^\d+/.exec(this.ctx.font);var a=/\S+$/.exec(this.ctx.font);this.onClick=this.getAttr("onClick");
-this.onMouseover=this.getAttr("onMouseover");this.ctx.fillStyle=this.getFillStyle();var b=this.ctx.fillStyle,c=this.getPixelPositionX(),d=this.getHeight();d<10?this.ctx.font="10px "+a:this.ctx.font=d*0.9+"px "+a;this.ctx.translate(c,0);this.strand=="-"&&!this.isSubFeature()&&this.ctx.transform(-1,0,0,1,this.getPixelLength(),0);this._draw();if(this.borderColor!="none")this.color=="none"&&this.parent.glyphType=="Complex"&&this.erase(),a=this.ctx.strokeStyle,d=this.ctx.lineWidth,this.ctx.strokeStyle=
-this.getStrokeStyle(),this.ctx.lineWidth=this.getAttr("borderWidth"),this.ctx.stroke(),this.ctx.strokeStyle=a,this.ctx.lineWidth=d;this.color!="none"&&this.ctx.fill();this.strand=="-"&&!this.isSubFeature()&&this.ctx.transform(-1,0,0,1,this.getPixelLength(),0);this.drawText(this.getAttr("name"));this.ctx.translate(-c,0);this.ctx.fillStyle=b;this.lane.chart.myMouseEventHandler.addEvents(this)}});var BlockArrow=Glyph.extend({init:function(a,b,c,d,e){this._super(a,b,c,d,e);this.slope=1;this.glyphType="BlockArrow"},_draw:function(a,b,c,d){a=a||this.ctx;b=b||this.getPixelLength();c=c||this.getHeight();d=d+1||this.calcRoundness();d!=void 0&&(d-=1);tc_ctrl_y=tc_ctrl_x=x=y=0;tc_lgth_x=x+d;tc_lgth_y=y;tc_wdth_x=x;tc_wdth_y=y+d;bc_ctrl_x=x;bc_ctrl_y=y+c;bc_lgth_x=x+d;bc_lgth_y=y+c;bc_wdth_x=x;bc_wdth_y=y+c-d;a_b_x=x+b-d;a_t_x=x+b-d;a_max_x=x+b;t=0.5;a_ctrl_x=(a_max_x-(1-t)*(1-t)*a_b_x-t*t*a_t_x)/
-(2*(1-t)*t);a_ctrl_y=y+c/2;bs_slope=this.slope;bs_intercept=-a_ctrl_y-bs_slope*a_ctrl_x;ts_slope=-this.slope;ts_intercept=-a_ctrl_y-ts_slope*a_ctrl_x;a_b_y=-(bs_slope*a_b_x+bs_intercept);a_t_y=-(ts_slope*a_t_x+ts_intercept);bs_ctrl_y=y+c;bs_ctrl_x=(-bs_ctrl_y-bs_intercept)/this.slope;bs_ctrl_x<x?(new Rect(this.type,0,b))._draw(a,b,c,d):(bs_lgth_y=y+c,bs_lgth_x=bs_ctrl_x-d,bs_slpe_x=bs_ctrl_x+d,bs_slpe_y=-(bs_slope*bs_slpe_x+bs_intercept),ts_ctrl_y=y,ts_ctrl_x=(ts_ctrl_y+ts_intercept)/this.slope,ts_lgth_y=
-y,ts_lgth_x=ts_ctrl_x-d,ts_slpe_x=ts_ctrl_x+d,ts_slpe_y=-(ts_slope*ts_slpe_x+ts_intercept),a.beginPath(),a.moveTo(tc_lgth_x,tc_lgth_y),a.quadraticCurveTo(tc_ctrl_x,tc_ctrl_y,tc_wdth_x,tc_wdth_y),a.lineTo(bc_wdth_x,bc_wdth_y),a.quadraticCurveTo(bc_ctrl_x,bc_ctrl_y,bc_lgth_x,bc_lgth_y),a.lineTo(bs_lgth_x,bs_lgth_y),a.quadraticCurveTo(bs_ctrl_x,bs_ctrl_y,bs_slpe_x,bs_slpe_y),a.lineTo(a_b_x,a_b_y),a.quadraticCurveTo(a_ctrl_x,a_ctrl_y,a_t_x,a_t_y),a.lineTo(ts_slpe_x,ts_slpe_y),a.quadraticCurveTo(ts_ctrl_x,
-ts_ctrl_y,ts_lgth_x,ts_lgth_y),a.lineTo(tc_lgth_x,tc_lgth_y))}});var Rect=Glyph.extend({init:function(a,b,c,d){this._super(a,b,c,"+",d);this.glyphType="Rect"},_draw:function(a,b,c,d){a=a||this.ctx;b=b||this.getPixelLength();c=c||this.getHeight();d=d+1||this.calcRoundness();d!=void 0&&(d-=1);x=y=0;a.beginPath();tlc_ctrl_x=x;tlc_ctrl_y=y;tlc_lgth_x=x+d;tlc_lgth_y=y;tlc_wdth_x=x;tlc_wdth_y=y+d;blc_ctrl_x=x;blc_ctrl_y=y+c;blc_lgth_x=x+d;blc_lgth_y=y+c;blc_wdth_x=x;blc_wdth_y=y+c-d;brc_ctrl_x=x+b;brc_ctrl_y=y+c;brc_lgth_x=x+b-d;brc_lgth_y=y+c;brc_wdth_x=x+b;brc_wdth_y=
-y+c-d;trc_ctrl_x=x+b;trc_ctrl_y=y;trc_lgth_x=x+b-d;trc_lgth_y=y;trc_wdth_x=x+b;trc_wdth_y=y+d;a.moveTo(tlc_lgth_x,tlc_lgth_y);a.quadraticCurveTo(tlc_ctrl_x,tlc_ctrl_y,tlc_wdth_x,tlc_wdth_y);a.lineTo(blc_wdth_x,blc_wdth_y);a.quadraticCurveTo(blc_ctrl_x,blc_ctrl_y,blc_lgth_x,blc_lgth_y);a.lineTo(brc_lgth_x,brc_lgth_y);a.quadraticCurveTo(brc_ctrl_x,brc_ctrl_y,brc_wdth_x,brc_wdth_y);a.lineTo(trc_wdth_x,trc_wdth_y);a.quadraticCurveTo(trc_ctrl_x,trc_ctrl_y,trc_lgth_x,trc_lgth_y);a.lineTo(tlc_lgth_x,tlc_lgth_y)}});var Line=Glyph.extend({init:function(a,b,c,d){this.thickness=2;this._super(a,b,c,"+",d);this.glyphType="Line"},_draw:function(a,b,c){a=a||this.ctx;b=b||this.getPixelLength();c=c||this.getHeight();x=y=0;a.beginPath();a.moveTo(x,c/2-this.thickness/2);a.lineTo(x,c/2+this.thickness/2);a.lineTo(x+b,c/2+this.thickness/2);a.lineTo(x+b,c/2-this.thickness/2)}});var Complex=Glyph.extend({init:function(a,b,c,d,e,g){this._super(a,b,c,d,g);this.slope=1;this.glyphType="Complex";this.subFeatures=e;this.line=new Line(a,0,c);this.line.parent=this;this.line.color="black";this.line.thickness=2},addSubFeature:function(a){this.subFeatures.push(a)},_draw:function(a,b,c,d){a=a||this.ctx;b||this.getPixelLength();c||this.getHeight();d+1||this.calcRoundness();x=y=0;a.translate(-this.getPixelPositionX(),0);this.line.lane=this.lane;this.line.draw();b=this.subFeatures.length;
-for(c=0;c<b;c++)this.subFeatures[c].parent=this,this.subFeatures[c].lane=this.lane,this.subFeatures[c].draw();a.translate(this.getPixelPositionX(),0);a.beginPath()}});var Arrow=Glyph.extend({init:function(a,b,c,d){this._super(a,b,0,c,d);this.slope=1;this.glyphType="Arrow";this.thickness=4.6},getPixelThickness:function(){return this.thickness/10*(this.getHeight()/2/Math.tan(Math.atan(this.slope)))},erase:function(){var a=this.getPixelThickness();this.ctx.clearRect(-a,0,a,this.getHeight())},_draw:function(a,b,c,d){a=a||this.ctx;c=c||this.getHeight();d=d+1||this.calcRoundness();d!=void 0&&(d-=1);b=this.getPixelThickness();x=y=0;a_b_x=x-0-d;a_t_x=x-0-d;a_max_x=x-0;
-t=0.5;a_ctrl_x=(a_max_x-(1-t)*(1-t)*a_b_x-t*t*a_t_x)/(2*(1-t)*t);a_ctrl_y=y+c/2;bs_slope=this.slope;bs_intercept=-a_ctrl_y-bs_slope*a_ctrl_x;ts_slope=-this.slope;ts_intercept=-a_ctrl_y-ts_slope*a_ctrl_x;a_b_y=-(bs_slope*a_b_x+bs_intercept);a_t_y=-(ts_slope*a_t_x+ts_intercept);a.beginPath();bs_ctrl_y=y+c;bs_ctrl_x=(-bs_ctrl_y-bs_intercept)/this.slope;bs_slpe_x=bs_ctrl_x+d+d;bs_slpe_y=-(bs_slope*bs_slpe_x+bs_intercept);a.moveTo(bs_slpe_x,bs_slpe_y);a.lineTo(a_b_x,a_b_y);a.quadraticCurveTo(a_ctrl_x,
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data/public/js/jquery.scrollspy.js

@@ -1,74 +0,0 @@
-;(function ($) {
-    var defaults = {
-        approach:   0,
-        overtravel: 0
-    };
-
-    /*
-        Trigger appropriate events when the selected element is scrolled in or
-        out of view.
-
-        An element is considered to be in view if the length of document
-        scrolled is greater than or equal to the offset of the element relative
-        to the top of the document and within the vertical span of the element.
-        (its height).
-
-        Vertical span of the element can be modified by adding required
-        'approach' and 'overtravel' length.
-
-        Events:
-
-            enter.scrollspy:
-
-                When the selected element scrolls into the view.
-
-            leave.scrollspy:
-
-                When the selected element scrolls out of the view.
-
-        Options:
-
-            approach:
-
-                Extend vertical span of the element from top.  It can be
-                positive or negative.
-
-            overtravel:
-
-                Extend vertical span of the element from bottom.  It can be
-                positive or negative.
-
-            The terminology: approach and overtravel, are borrowed from
-            Machining :).
-
-        Usage:
-
-            $('.resultn').scrollspy();
-
-    */
-    $.fn.scrollspy = function (options) {
-        var elements = this;
-        var options  = $.extend({}, defaults, options);
-
-        $(window).scroll(function() {
-            var scrolled = $(this).scrollTop();
-
-            elements.each(function() {
-                var element = $(this);
-
-                //compute threshold
-                var start = element.offset().top - options.approach;
-                var end   = start + element.height() + options.overtravel;
-
-                if (scrolled >= start && scrolled <= end){
-                    element.trigger('enter.scrollspy');
-                }
-                else {
-                    element.trigger('leave.scrollspy');
-                }
-            });
-        });
-
-        return this;
-    }
-})(jQuery);

data/public/js/jquery.ui.js

@@ -1,57 +0,0 @@
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