sequenceserver 1.0.5 → 1.0.6

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Files changed (10) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +26 -7
  3. data/lib/sequenceserver/version.rb +1 -1
  4. data/package.json +3 -3
  5. data/public/dist/css/sequenceserver.min.css +1 -1
  6. data/public/dist/css/sequenceserver.min.css.gz +0 -0
  7. data/public/dist/js/sequenceserver.min.js +3 -3
  8. data/public/dist/js/sequenceserver.min.js.gz +0 -0
  9. data/views/search.erb +34 -33
  10. metadata +3 -2
checksums.yaml CHANGED
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+ data.tar.gz: 81586a069f9083b086217579fa3f3afdb33d1188f2088c1f62f3cb26d60fd4003287df182a091d584ad0e003c073a012320fa71ca55678da838d6ead2265f068
data/.travis.yml CHANGED
@@ -1,18 +1,37 @@
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  language: ruby
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+
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  rvm:
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  - 1.9.3
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  - 2.0.0
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- - 2.1.5
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- - 2.2.0
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+ - 2.1.7
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+ - 2.2.3
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  addons:
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+ apt:
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+ packages:
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+ - libqtwebkit-dev
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+ - xvfb
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+
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  code_climate:
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  repo_token:
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  secure: "cT2wvWS2Uk2trYGwZ38Qo9XWCeL+OOXH0lVmLfNb1Xy/tWAXycDdZsc9CN8igjhD+/cKvvh529/qdDm2PJnb1Hux1bxHSTuMuE2xQWlfJqaOR/IX0z96MbP1eITKjhGv9vccmIPdV3Rh/OQLeHkyqyHvXio9NXiARMJUZDTpRuA="
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- before_install:
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- - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz" && tar xvf ncbi-blast-2.2.30+-x64-linux.tar.gz && export PATH="./ncbi-blast-2.2.30+/bin:$PATH"
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- - sudo apt-get install libqtwebkit-dev xvfb
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- - gem install bundler
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+ branches:
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+ only:
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+ - 1.0.x # stable
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+ #- master (temporarily disabled)
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+
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+ install:
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+ - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz"
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+ - tar xvf ncbi-blast-2.2.30+-x64-linux.tar.gz
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+ - export PATH="ncbi-blast-2.2.30+/bin:$PATH"
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+ - gem install bundler && bundle
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+
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+ script: xvfb-run bundle exec rake spec
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+
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+ cache:
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+ directories:
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+ - vendor/bundle
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+ - ncbi-blast-2.2.30+
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- script: xvfb-run bundle exec rake
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+ sudo: false
data/lib/sequenceserver/version.rb CHANGED
@@ -1,4 +1,4 @@
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  # Define version number.
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  module SequenceServer
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- VERSION = '1.0.5'
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+ VERSION = '1.0.6'
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  end
data/package.json CHANGED
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  {
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  "name": "SequenceServer",
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  "description": "BLAST searching made easy!",
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- "version": "1.0.5",
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+ "version": "1.0.6",
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  "homepage": "http://www.sequenceserver.com",
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  "repository": "https://github.com/yannickwurm/sequenceserver",
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  "author": {
@@ -23,7 +23,7 @@
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  "grunt-contrib-compress": "0.13.0"
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  },
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  "scripts": {
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- "cop": "grunt cop",
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- "build": "grunt build"
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+ "cop": "grunt cop",
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+ "build": "grunt build"
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  }
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  }
data/public/dist/css/sequenceserver.min.css CHANGED
@@ -1 +1 @@
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a="sequenceTip"+this.opt.target;jQuery('<div id="'+a+'"></div>').css({position:"absolute","z-index":"999999",color:"#fff","font-size":"12px",width:"auto",display:"none"}).addClass("tooltip").appendTo("body").hide(),this.opt._tooltip=document.getElementById(a),this.opt.sequence?this._redraw():this.opt.id?this._requestSequence(this.opt.id):this.clearSequence("No sequence available","../biojs/css/images/warning_icon.png")},setSequence:function(a,b){a.match(/^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$/i)?this._requestSequence(arguments[0]):(this.opt.sequence=a,this.opt.id=b,this._highlights=[],this._highlightsCount=0,this.opt.selection={start:0,end:0},this._annotations=[],this._contentDiv.children().remove(),this._redraw())},_requestSequence:function(a){var b=this;console.log("Requesting sequence for: "+a),jQuery.ajax({url:b.opt.sequenceUrl,dataType:"xml",data:{segment:a},success:function(a){try{var c=jQuery(a).find("SEQUENCE:first");b.setSequence(c.text(),c.attr("id"),c.attr("label"))}catch(d){console.log("Error decoding response data: "+d.message),b.clearSequence("No sequence available","../biojs/css/images/warning_icon.png")}},error:function(a,c,d){console.log("Error decoding response data: "+c),b.clearSequence("Error requesting the sequence to the server "+this.url,"../biojs/css/images/warning_icon.png")}})},clearSequence:function(a,b){var c=void 0;this.opt.sequence="",this.opt.id="",this._highlights=[],this._highlightsCount=0,this.opt.selection={start:0,end:0},this._annotations=[],this._contentDiv.children().remove(),this._headerDiv.hide(),void 0!==a&&(c=jQuery("<div>"+a+"</div>").appendTo(this._contentDiv).addClass("message"),void 0!==b&&c.css({background:'transparent url("'+b+'") no-repeat center left',"padding-left":"20px"}))},setSelection:function(a,b){if(a>b){var c=b;b=a,a=c}(a!=this.opt.selection.start||b!=this.opt.selection.end)&&(this._setSelection(a,b),this.trigger(h,{start:a,end:b}))},_buildFormatSelector:function(){var a=this;this._headerDiv=jQuery("<div></div>").appendTo(this._container),this._headerDiv.append("Format: "),this._formatSelector=jQuery('<select> <option value="FASTA">FASTA</option><option value="CODATA">CODATA</option><option value="PRIDE">PRIDE</option><option value="RAW">RAW</option></select>').appendTo(a._headerDiv),this._formatSelector.change(function(b){a.opt.format=jQuery(this).val(),a._redraw()}),this._formatSelector.val(a.opt.format),this.formatSelectorVisible(this.opt.formatSelectorVisible)},addHighlight:function(a){var b="-1",c="",d="",e={};return a instanceof Object&&a.start<=a.end&&(c="string"==typeof a.color?a.color:this.opt.highlightFontColor,d="string"==typeof a.background?a.background:this.opt.highlightBackgroundColor,b="string"==typeof a.id?a.id:new Number(this._highlightsCount++).toString(),e={start:a.start,end:a.end,color:c,background:d,id:b},this._highlights.push(e),this._applyHighlight(e),this._restoreSelection(a.start,a.end)),b},_applyHighlight:function(a){for(var b=this._contentDiv.find(".sequence"),c=a.start-1;c<a.end;c++)zindex=jQuery(b[c]).css("z-index"),"auto"==zindex?(z=1,o=1):(z=0,o=.5),jQuery(b[c]).css({color:a.color,"background-color":a.background,"z-index":z,opacity:o}).addClass("highlighted")},_applyHighlights:function(a){for(var b in a)this._applyHighlight(a[b])},_restoreHighlights:function(c,d){var e=this._highlights;this._applyHighlight({start:c,end:d,color:this.opt.fontColor,background:this.opt.backgroundColor});for(var f in e)e[f].start>d||e[f].end<c||(a=e[f].start<c?c:e[f].start,b=e[f].end>d?d:e[f].end,this._applyHighlight({start:a,end:b,color:e[f].color,background:e[f].background}))},_restoreSelection:function(c,d){var e=this.opt.selection;c>e.end||d<e.start||(a=c<e.start?e.start:c,b=d>e.end?e.end:d,this._applyHighlight({start:a,end:b,color:this.opt.selectionFontColor,background:this.opt.selectionColor}))},removeHighlight:function(a){var b=this._highlights;for(i in b)if(b[i].id==a){start=b[i].start,end=b[i].end,b.splice(i,1),this._restoreHighlights(start,end),this._restoreSelection(start,end);break}},removeAllHighlights:function(){this._highlights=[],this._restoreHighlights(1,this.opt.sequence.length),this._restoreSelection(1,this.opt.sequence.length)},setFormat:function(a){this.opt.format!=a.toUpperCase()&&(this.opt.format=a.toUpperCase(),this._redraw());var b=this;this._headerDiv.find("option").each(function(){jQuery(this).val()==b.opt.format.toUpperCase()&&jQuery(this).attr("selected","selected")})},setNumCols:function(a){this.opt.columns.size=a,this._redraw()},formatSelectorVisible:function(a){a?this._headerDiv.show():this._headerDiv.hide()},showFormatSelector:function(){this._headerDiv.show()},hideFormatSelector:function(){this._headerDiv.hide()},hide:function(){this._headerDiv.hide(),this._contentDiv.hide()},show:function(){this._headerDiv.show(),this._contentDiv.show()},_setSelection:function(a,b){var c=this.opt.selection,d={};c.start==a?c.end<b?(d.start=c.end,d.end=b):this._restoreHighlights(b+1,c.end):c.end==b?c.start>a?(d.start=a,d.end=c.start):this._restoreHighlights(c.start,a-1):(this._restoreHighlights(c.start,c.end),d.start=a,d.end=b),c.start=a,c.end=b},_repaintSelection:function(){var a=this.opt.selection;this._setSelection(0,0),this._setSelection(a.start,a.end)},_redraw:function(){this._contentDiv.children().remove(),"RAW"==this.opt.format?this._drawRaw():"CODATA"==this.opt.format?this._drawCodata():"FASTA"==this.opt.format?this._drawFasta():(this.opt.format="PRIDE",this._drawPride()),this._applyHighlights(this._highlights),this._repaintSelection(),this._addSpanEvents()},_drawFasta:function(){var a=this.opt.sequence.toUpperCase().split(""),b=jQuery("<pre></pre>").appendTo(this._contentDiv),c=">"+this.opt.id+" "+a.length+" bp<br/>",d=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(d=this.opt.sequence.length);var e={numCols:d,numColsForSpace:0};c+=this._drawSequence(a,e),b.html(c),this._drawAnnotations(e)},_drawCodata:function(){var a=this.opt.sequence.toUpperCase().split("");if(void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.title&&0!=this.opt.formatOptions.title){var b=$("<pre/>").addClass("header").appendTo(this._contentDiv);b.html("ENTRY "+this.opt.id+"<br/>SEQUENCE<br/>")}var c=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(c=this.opt.sequence.length);var d={numLeft:!0,numLeftSize:7,numLeftPad:" ",numTop:!0,numTopEach:5,numCols:c,numColsForSpace:0,spaceBetweenChars:!0};if(this._drawSequence(a,d),void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.footer&&0!=this.opt.formatOptions.footer){var e=$("<pre/>").addClass("footer").appendTo(this._contentDiv);e.html("<br/>///")}this._drawAnnotations(d)},_drawAnnotations:function(a){var b=this,c=this.opt.sequence.toLowerCase().split(""),d=this._annotations,e="",f="",g="";a.numLeft&&(e+=this._formatIndex(" ",a.numLeftSize+2," "));for(var h=0;h<c.length;h+=a.numCols){f="";for(var i in d)d[i].id=this.getId()+"_"+i,g=this._getHTMLRowAnnot(h+1,d[i],a),g.length>0&&(f+="<br/>",f+=e,f+=g,f+="<br/>");var k=a.numCols,l=c.length-h;k>l&&(k=l),a.numRight?jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#numRight_"+this.getId()+"_"+(h+k)):jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#"+this.getId()+"_"+(h+k))}jQuery(this._contentDiv).find(".annotation").each(function(){b._addToolTip(this,function(){return b._getAnnotationString(jQuery(this).attr("id"))}),jQuery(this).mouseover(function(a){jQuery(".annotation."+jQuery(a.target).attr("id")).each(function(){jQuery(this).css("background-color",jQuery(this).attr("color"))})}).mouseout(function(){jQuery(".annotation").css("background-color","transparent")}).click(function(a){for(var c=void 0,d=jQuery(a.target).attr("id"),e=0;e<b._annotations.length;e++)b._annotations[e].id!=d||(c=b._annotations[e].name);b.trigger(j,{name:c})})})},_getAnnotationString:function(a){var b=this._annotations[a.substr(a.indexOf("_")+1)];return b.name+"<br/>"+(b.html?b.html:"")},_getHTMLRowAnnot:function(a,b,c){for(var d="border-left:1px solid; border-bottom:1px solid; border-color:",e="border-bottom:1px solid; border-color:",f="border-bottom:1px solid; border-right:1px solid; border-color:",g="border-left:1px solid; border-right:1px solid; border-bottom:1px solid; border-color:",h=[],i=a+c.numCols,j=c.spaceBetweenChars?" ":"",k=b.color,l=b.id,m=a;i>m;m++)for(var n in b.regions)region=b.regions[n],spaceAfter="",spaceAfter+=m%c.numColsForSpace==0?" ":"",spaceAfter+=j,color=region.color?region.color:k,data='class="annotation '+l+'" id="'+l+'" color="'+color+'" pos="'+m+'"',m==region.start&&m==region.end?(h[m]='<span style="'+g+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):m==region.start?(h[m]='<span style="'+d+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):m==region.end?(h[m]='<span style="'+f+color+' " '+data+"> ",h[m]+="</span>"):m>region.start&&m<region.end?(h[m]='<span style="'+e+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):h[m]||(h[m]=" ",h[m]+=spaceAfter);var o=h.join("");return-1==o.indexOf("span")?"":o},_drawRaw:function(){var a=this.opt.sequence.toLowerCase().split(""),b=jQuery("<pre></pre>").appendTo(this._contentDiv),c=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(c=this.opt.sequence.length);var d={numCols:c};b.html(this._drawSequence(a,d)),this._drawAnnotations(d)},_drawPride:function(){var a=this.opt.sequence.toUpperCase().split(""),b=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(b=this.opt.sequence.length),opt={numLeft:!0,numLeftSize:5,numLeftPad:" ",numRight:!1,numRightSize:5,numRightPad:"",numCols:b,numColsForSpace:this.opt.columns.spacedEach},this._drawSequence(a,opt),this._drawAnnotations(opt)},_drawSequence:function(a,b){var c="",d="",e="\n",f="";if(b.numTop){d+='<span class="numTop pos-marker">';var g=b.spaceBetweenChars?2*b.numTopEach:b.numTopEach;b.numLeft&&(d+=this._formatIndex(" ",b.numLeftSize," ")),d+=this._formatIndex(" ",g," ");for(var h=b.numTopEach;h<b.numCols;h+=b.numTopEach)d+=this._formatIndex(h,g," ",!0);d+="</span>"}b.numLeft&&(c+='<span id="numLeft_'+this.getId()+'_0"',c+='class="pos-marker">',c+=this._formatIndex(1,b.numLeftSize,b.numLeftPad),c+=" ",c+="</span>",c+="\n");for(var i=1,j=1;j<=a.length;j++)if(j%b.numCols==0){f+='<span class="sequence" id="'+this.getId()+"_"+j+'">'+a[j-1]+"</span>",b.numRight&&(e+='<span id="numRight_'+this.getId()+"_"+j+'"',e+='class="pos-marker">',e+=" ",e+=this._formatIndex(j,b.numRightSize,b.numRightPad),e+="</span>",e+="\n"),f+="<br/>";var k=a.length-j;b.numLeft&&k>0&&(c+='<span id="numLeft_'+this.getId()+"_"+j+'"',c+='class="pos-marker">',c+=this._formatIndex(j+1,b.numLeftSize,b.numLeftPad),c+=" ",c+="</span>",c+="\n"),i=1}else f+='<span class="sequence" id="'+this.getId()+"_"+j+'"',f+=i%b.numColsForSpace==0?' style="letter-spacing: 1em;"':"",f+=b.spaceBetweenChars?' style="letter-spacing: 1em;"':"",f+='">'+a[j-1],f+="</span>",i++;f+="<br/>",jQuery.browser.msie&&(f="<pre>"+f+"</pre>");return b.numTop&&$("<pre/>").html(d).addClass("indT").css({color:"#aaa"}).appendTo(this._contentDiv),b.numLeft&&$("<pre/>").html(c).addClass("indL").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),$("<pre/>").html(f).addClass("seqF").css({display:"inline-block"}).appendTo(this._contentDiv),b.numRight&&$("<pre/>").html(e).addClass("indR").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),f},_formatIndex:function(a,b,c,d){var e=a.toString(),f="",g=b-e.length;if(g>0){for(;g-->0;)f+="<span>"+c+"</span>";e=d?a+f:f+a}return e},_addSpanEvents:function(){var a,b,c=this,d=!1;c._contentDiv.find(".sequence").each(function(){jQuery(this).mousedown(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),a=b,c._setSelection(a,b),d=!0,c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end})}).mouseover(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),d&&(b>a?c._setSelection(a,b):c._setSelection(b,a),c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end}))}).mouseup(function(){d=!1,c.trigger(h,{start:c.opt.selection.start,end:c.opt.selection.end})}),c._addToolTip.call(c,this,function(){return d?"["+c.opt.selection.start+", "+c.opt.selection.end+"]":b})}).css("cursor","pointer")},_addToolTip:function(a,b){var c=this.opt._tooltip;jQuery(a).mouseover(function(d){var e=jQuery(d.target).offset();jQuery(c).is(":visible")||jQuery(c).css({"background-color":"#000",padding:"3px 10px 3px 10px",top:e.top+jQuery(d.target).height()+"px",left:e.left+jQuery(d.target).width()+"px"}).animate({opacity:"0.85"},10).html(b.call(a)).show()}).mouseout(function(){jQuery(c).hide()})},addAnnotation:function(a){this._annotations.push(a),this._redraw()},removeAnnotation:function(a){for(var b=0;b<this._annotations.length;b++)if(a!=this._annotations[b].name){this._annotations.splice(b,1),this._redraw();break}},removeAllAnnotations:function(){this._annotations=[],this._redraw()}}),c("biojs-events").mixin(Sequence.prototype),d.exports=Sequence},{"biojs-events":2,"jquery-browser-plugin":20,"js-class":22}],2:[function(a,b,c){var d=a("backbone-events-standalone");d.onAll=function(a,b){return this.on("all",a,b),this},d.oldMixin=d.mixin,d.mixin=function(a){d.oldMixin(a);for(var b=["onAll"],c=0;c<b.length;c++){var e=b[c];a[e]=this[e]}return a},b.exports=d},{"backbone-events-standalone":4}],3:[function(a,b,c){!function(){function a(){return{keys:Object.keys||function(a){if("object"!=typeof a&&"function"!=typeof a||null===a)throw new TypeError("keys() called on a non-object");var b,c=[];for(b in a)a.hasOwnProperty(b)&&(c[c.length]=b);return c},uniqueId:function(a){var b=++j+"";return a?a+b:b},has:function(a,b){return 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c,d=-1,e=a.length,f=b[0],g=b[1],h=b[2];switch(b.length){case 0:for(;++d<e;)(c=a[d]).callback.call(c.ctx);return;case 1:for(;++d<e;)(c=a[d]).callback.call(c.ctx,f);return;case 2:for(;++d<e;)(c=a[d]).callback.call(c.ctx,f,g);return;case 3:for(;++d<e;)(c=a[d]).callback.call(c.ctx,f,g,h);return;default:for(;++d<e;)(c=a[d]).callback.apply(c.ctx,b)}},o={listenTo:"on",listenToOnce:"once"};k.each(o,function(a,b){d[b]=function(b,c,d){var e=this._listeners||(this._listeners={}),f=b._listenerId||(b._listenerId=k.uniqueId("l"));return e[f]=b,"object"==typeof c&&(d=this),b[a](c,d,this),this}}),d.bind=d.on,d.unbind=d.off,d.mixin=function(a){var b=["on","once","off","trigger","stopListening","listenTo","listenToOnce","bind","unbind"];return k.each(b,function(b){a[b]=this[b]},this),a},"function"==typeof define?define(function(){return d}):"undefined"!=typeof c?("undefined"!=typeof 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c=jQuery(a).find("SEQUENCE:first");b.setSequence(c.text(),c.attr("id"),c.attr("label"))}catch(d){console.log("Error decoding response data: "+d.message),b.clearSequence("No sequence available","../biojs/css/images/warning_icon.png")}},error:function(a,c,d){console.log("Error decoding response data: "+c),b.clearSequence("Error requesting the sequence to the server "+this.url,"../biojs/css/images/warning_icon.png")}})},clearSequence:function(a,b){var c=void 0;this.opt.sequence="",this.opt.id="",this._highlights=[],this._highlightsCount=0,this.opt.selection={start:0,end:0},this._annotations=[],this._contentDiv.children().remove(),this._headerDiv.hide(),void 0!==a&&(c=jQuery("<div>"+a+"</div>").appendTo(this._contentDiv).addClass("message"),void 0!==b&&c.css({background:'transparent url("'+b+'") no-repeat center left',"padding-left":"20px"}))},setSelection:function(a,b){if(a>b){var c=b;b=a,a=c}(a!=this.opt.selection.start||b!=this.opt.selection.end)&&(this._setSelection(a,b),this.trigger(h,{start:a,end:b}))},_buildFormatSelector:function(){var a=this;this._headerDiv=jQuery("<div></div>").appendTo(this._container),this._headerDiv.append("Format: "),this._formatSelector=jQuery('<select> <option value="FASTA">FASTA</option><option value="CODATA">CODATA</option><option value="PRIDE">PRIDE</option><option value="RAW">RAW</option></select>').appendTo(a._headerDiv),this._formatSelector.change(function(b){a.opt.format=jQuery(this).val(),a._redraw()}),this._formatSelector.val(a.opt.format),this.formatSelectorVisible(this.opt.formatSelectorVisible)},addHighlight:function(a){var b="-1",c="",d="",e={};return a instanceof Object&&a.start<=a.end&&(c="string"==typeof a.color?a.color:this.opt.highlightFontColor,d="string"==typeof a.background?a.background:this.opt.highlightBackgroundColor,b="string"==typeof a.id?a.id:new Number(this._highlightsCount++).toString(),e={start:a.start,end:a.end,color:c,background:d,id:b},this._highlights.push(e),this._applyHighlight(e),this._restoreSelection(a.start,a.end)),b},_applyHighlight:function(a){for(var b=this._contentDiv.find(".sequence"),c=a.start-1;c<a.end;c++)zindex=jQuery(b[c]).css("z-index"),"auto"==zindex?(z=1,o=1):(z=0,o=.5),jQuery(b[c]).css({color:a.color,"background-color":a.background,"z-index":z,opacity:o}).addClass("highlighted")},_applyHighlights:function(a){for(var b in a)this._applyHighlight(a[b])},_restoreHighlights:function(c,d){var e=this._highlights;this._applyHighlight({start:c,end:d,color:this.opt.fontColor,background:this.opt.backgroundColor});for(var f in e)e[f].start>d||e[f].end<c||(a=e[f].start<c?c:e[f].start,b=e[f].end>d?d:e[f].end,this._applyHighlight({start:a,end:b,color:e[f].color,background:e[f].background}))},_restoreSelection:function(c,d){var e=this.opt.selection;c>e.end||d<e.start||(a=c<e.start?e.start:c,b=d>e.end?e.end:d,this._applyHighlight({start:a,end:b,color:this.opt.selectionFontColor,background:this.opt.selectionColor}))},removeHighlight:function(a){var b=this._highlights;for(i in b)if(b[i].id==a){start=b[i].start,end=b[i].end,b.splice(i,1),this._restoreHighlights(start,end),this._restoreSelection(start,end);break}},removeAllHighlights:function(){this._highlights=[],this._restoreHighlights(1,this.opt.sequence.length),this._restoreSelection(1,this.opt.sequence.length)},setFormat:function(a){this.opt.format!=a.toUpperCase()&&(this.opt.format=a.toUpperCase(),this._redraw());var b=this;this._headerDiv.find("option").each(function(){jQuery(this).val()==b.opt.format.toUpperCase()&&jQuery(this).attr("selected","selected")})},setNumCols:function(a){this.opt.columns.size=a,this._redraw()},formatSelectorVisible:function(a){a?this._headerDiv.show():this._headerDiv.hide()},showFormatSelector:function(){this._headerDiv.show()},hideFormatSelector:function(){this._headerDiv.hide()},hide:function(){this._headerDiv.hide(),this._contentDiv.hide()},show:function(){this._headerDiv.show(),this._contentDiv.show()},_setSelection:function(a,b){var c=this.opt.selection,d={};c.start==a?c.end<b?(d.start=c.end,d.end=b):this._restoreHighlights(b+1,c.end):c.end==b?c.start>a?(d.start=a,d.end=c.start):this._restoreHighlights(c.start,a-1):(this._restoreHighlights(c.start,c.end),d.start=a,d.end=b),c.start=a,c.end=b},_repaintSelection:function(){var 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border-bottom:1px solid; border-color:",e="border-bottom:1px solid; border-color:",f="border-bottom:1px solid; border-right:1px solid; border-color:",g="border-left:1px solid; border-right:1px solid; border-bottom:1px solid; border-color:",h=[],i=a+c.numCols,j=c.spaceBetweenChars?" ":"",k=b.color,l=b.id,m=a;i>m;m++)for(var n in b.regions)region=b.regions[n],spaceAfter="",spaceAfter+=m%c.numColsForSpace==0?" ":"",spaceAfter+=j,color=region.color?region.color:k,data='class="annotation '+l+'" id="'+l+'" color="'+color+'" pos="'+m+'"',m==region.start&&m==region.end?(h[m]='<span style="'+g+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):m==region.start?(h[m]='<span style="'+d+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):m==region.end?(h[m]='<span style="'+f+color+' " '+data+"> ",h[m]+="</span>"):m>region.start&&m<region.end?(h[m]='<span style="'+e+color+'" '+data+"> ",h[m]+=spaceAfter,h[m]+="</span>"):h[m]||(h[m]=" ",h[m]+=spaceAfter);var o=h.join("");return-1==o.indexOf("span")?"":o},_drawRaw:function(){var a=this.opt.sequence.toLowerCase().split(""),b=jQuery("<pre></pre>").appendTo(this._contentDiv),c=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(c=this.opt.sequence.length);var d={numCols:c};b.html(this._drawSequence(a,d)),this._drawAnnotations(d)},_drawPride:function(){var 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b.numTop&&$("<pre/>").html(d).addClass("indT").css({color:"#aaa"}).appendTo(this._contentDiv),b.numLeft&&$("<pre/>").html(c).addClass("indL").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),$("<pre/>").html(f).addClass("seqF").css({display:"inline-block"}).appendTo(this._contentDiv),b.numRight&&$("<pre/>").html(e).addClass("indR").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),f},_formatIndex:function(a,b,c,d){var e=a.toString(),f="",g=b-e.length;if(g>0){for(;g-- >0;)f+="<span>"+c+"</span>";e=d?a+f:f+a}return e},_addSpanEvents:function(){var a,b,c=this,d=!1;c._contentDiv.find(".sequence").each(function(){jQuery(this).mousedown(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),a=b,c._setSelection(a,b),d=!0,c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end})}).mouseover(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),d&&(b>a?c._setSelection(a,b):c._setSelection(b,a),c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end}))}).mouseup(function(){d=!1,c.trigger(h,{start:c.opt.selection.start,end:c.opt.selection.end})}),c._addToolTip.call(c,this,function(){return d?"["+c.opt.selection.start+", "+c.opt.selection.end+"]":b})}).css("cursor","pointer")},_addToolTip:function(a,b){var c=this.opt._tooltip;jQuery(a).mouseover(function(d){var e=jQuery(d.target).offset();jQuery(c).is(":visible")||jQuery(c).css({"background-color":"#000",padding:"3px 10px 3px 10px",top:e.top+jQuery(d.target).height()+"px",left:e.left+jQuery(d.target).width()+"px"}).animate({opacity:"0.85"},10).html(b.call(a)).show()}).mouseout(function(){jQuery(c).hide()})},addAnnotation:function(a){this._annotations.push(a),this._redraw()},removeAnnotation:function(a){for(var b=0;b<this._annotations.length;b++)if(a!=this._annotations[b].name){this._annotations.splice(b,1),this._redraw();break}},removeAllAnnotations:function(){this._annotations=[],this._redraw()}}),c("biojs-events").mixin(Sequence.prototype),d.exports=Sequence},{"biojs-events":2,"jquery-browser-plugin":20,"js-class":22}],2:[function(a,b,c){var d=a("backbone-events-standalone");d.onAll=function(a,b){return this.on("all",a,b),this},d.oldMixin=d.mixin,d.mixin=function(a){d.oldMixin(a);for(var b=["onAll"],c=0;c<b.length;c++){var e=b[c];a[e]=this[e]}return a},b.exports=d},{"backbone-events-standalone":4}],3:[function(a,b,c){!function(){function a(){return{keys:Object.keys||function(a){if("object"!=typeof a&&"function"!=typeof a||null===a)throw new TypeError("keys() called on a non-object");var b,c=[];for(b in a)a.hasOwnProperty(b)&&(c[c.length]=b);return c},uniqueId:function(a){var b=++j+"";return a?a+b:b},has:function(a,b){return 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b=[];b=a(this).data(),b.hspId=this.id,c.push(b)}),c.hitId=b.attr("id"),c.hitDef=b.data().hitDef,c.hitEvalue=b.data().hitEvalue,f.push(c)}),f},g=function(a,b,c,d){var e=a.append("g").attr("transform","translate(0,"+(d-b.margin-1.25*b.legend)+")");e.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})};a.extend({graphIt:function(h,i,j,k,l){var m={barHeight:4,barPadding:5,legend:10,margin:20},n=a.extend(m,l),o=f(h,j,k);if(o.length<1)return!1;0!==j&&i.find("svg").remove();var p=h.data().queryLen,q=h.attr("id"),r=i.width(),s=o.length*(n.barHeight+n.barPadding)+5*n.margin+3*n.legend,t=d3.select(i[0]).selectAll("svg").data([o]).enter().insert("svg",":first-child").attr("width",r).attr("height",s).append("g").attr("transform","translate("+n.margin/4+", "+n.margin/4+")"),u=d3.scale.linear().range([0,r-n.margin]);u.domain([1,p]);var v=u.ticks(11);v.pop();var w=d3.svg.axis().scale(u).orient("top").tickValues(v.concat([1,p]));t.append("g").attr("transform","translate(0, "+n.margin+")").append("g").attr("class","x axis").call(w);var x=d3.scale.ordinal().rangeBands([0,s-3*n.margin-2*n.legend],.3);x.domain(o.map(function(a){return a.hitId}));var y=d3.scale.log().domain([d3.min([1e-5,d3.min(o.map(function(a){return 0!==parseFloat(a.hitEvalue)?a.hitEvalue:void 0}))]),d3.max(o.map(function(a){return a.hitEvalue}))]).range([40,150]);t.append("g").attr("class","ghit").attr("transform","translate(0, "+(2*n.margin-n.legend)+")").selectAll(".hits").data(o).enter().append("g").attr("data-toggle","tooltip").attr("title",function(a){var b=/(\d*\.\d*)e?([+-]\d*)?/,c=b.exec(a.hitEvalue),d=parseFloat(c[1]).toFixed(3),e=a.hitDef+"<br><strong>E value:</strong> "+d;return void 0!==c[2]&&(e+=" &times; 10<sup>"+c[2]+"</sup>"),e}).each(function(a,b){var c=b+1,d=a,e=a.hitId,f=a.length;d3.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(a,b){var g=x(e)+n.barHeight/2,h=d3.rgb(y(d.hitEvalue),y(d.hitEvalue),y(d.hitEvalue));f>b+1&&(d[b].hspEnd<=d[b+1].hspStart?d3.select(this.parentNode).append("line").attr("x1",u(d[b].hspEnd)).attr("y1",g).attr("x2",u(d[b+1].hspStart)).attr("y2",g).attr("stroke",h):d[b].hspStart>d[b+1].hspEnd&&d3.select(this.parentNode).append("line").attr("x1",u(d[b+1].hspEnd)).attr("y1",g).attr("x2",u(d[b].hspStart)).attr("y2",g).attr("stroke",h)),d3.select(this).attr("xlink:href","#"+q+"_hit_"+c).append("rect").attr("x",function(a){return u(a.hspStart)}).attr("y",x(e)).attr("width",function(a){return u(a.hspEnd-a.hspStart+1)}).attr("height",n.barHeight).attr("fill",d3.rgb(h))})}),o.length>1&&g(t,n,r,s),0===j&&(e(h,i,!0),d(h,i,j,l)),b(),c(i)}})}(jQuery),SS.blast=function(){var a=function(a){if(a=a.replace(/[^A-Z]/gi,""),a=a.replace(/[NX]/gi,""),!(a.length<10)){var b,c,d;for(b=0,c=.9*a.length,d=0;d<a.length;d++)a[d].match(/[ACGTU]/i)&&(b+=1);return b>c?"nucleotide":"protein"}},b=function(){var b,c,d,e=$("#sequence").val().split(/>.*/);for(d=0;d<e.length;d++)if(c=a(e[d]))if(b){if(c!==b)return"mixed"}else b=c;return b},c=function(){return $(".databases input:checked").data("type")},d=function(){return $("#sequence").val()&&$(".databases input:checked").val()?!0:!1},e=function(){var a,c;$("#sequence").change(function(){c=b(),c&&c===a||(a=c,$(this).trigger("sequence_type_changed",a))})},f=function(){var a,b=c();$(".databases input").change(function(){a=c(),a!=b&&(b=a,$(this).trigger("database_type_changed",b))})},g=function(){var a,b;$("#blast").on("sequence_type_changed database_type_changed",function(c){b=h(),_.isEqual(b,a)||(a=b,$(this).trigger("blast_method_changed",[a.slice()]))})},h=function(){if(!d())return[];var a=c(),e=b();switch(a){case"protein":switch(e){case void 0:return["blastp","blastx"];case"protein":return["blastp"];case"nucleotide":return["blastx"]}break;case"nucleotide":switch(e){case void 0:return["tblastn","blastn","tblastx"];case"protein":return["tblastn"];case"nucleotide":return["blastn","tblastx"]}}return[]},i=function(){};return i.init=function(){e(),f(),g()},i}();
data/views/search.erb CHANGED
@@ -276,39 +276,40 @@
276
276
  <div
277
277
  class="footer" id="footer">
278
278
  <hr>
279
- <p
280
- class="text-center">
281
- <a
282
- href='http://www.sequenceserver.com'>
283
- <%=
284
- quote = [
285
- "Custom BLAST web interface by SequenceServer.",
286
- "SequenceServer: Local BLAST with bespoke html interface.",
287
- "Set up custom BLAST interface with SequenceServer.",
288
- "Easy BLASTing with SequenceServer.",
289
- "Run BLAST locally with Sequenceserver.",
290
- "BLAST against a custom, local database with SequenceServer.",
291
- "Run BLAST locally on Mac OSX with SequenceServer.",
292
- "Run BLAST locally on Ubuntu with SequenceServer.",
293
- "Run BLAST locally on Linux with SequenceServer."
294
- ][rand(9)]
295
- %>
296
- </a>
297
- <a
298
- class="twitter-share-button"
299
- href="https://twitter.com/share"
300
- data-url="http://www.sequenceserver.com" data-text="<%= quote %>" data-via="yeban" data-hashtags="bioinformatics">
301
- Tweet
302
- </a>
303
- <%#<div class="g-plusone" data-annotation="none" data-href="http://www.sequenceserver.com"></div>%>
304
-
305
- <br>
306
- Please Cite:
307
- <a href='http://www.sequenceserver.com'>
308
- Priyam, Woodcroft, Rai & Wurm, <strong>SequenceServer</strong> (<em>in prep</em>)
309
- </a>
310
- &amp; relevant data sources.
311
- </p>
279
+ <div
280
+ class="container">
281
+ <p
282
+ class="text-center">
283
+ <a
284
+ href='http://www.sequenceserver.com'>
285
+ <%=
286
+ quote = [
287
+ "Custom BLAST web interface by SequenceServer.",
288
+ "SequenceServer: Local BLAST with bespoke html interface.",
289
+ "Set up custom BLAST interface with SequenceServer.",
290
+ "Easy BLASTing with SequenceServer.",
291
+ "Run BLAST locally with Sequenceserver.",
292
+ "BLAST against a custom, local database with SequenceServer.",
293
+ "Run BLAST locally on Mac OSX with SequenceServer.",
294
+ "Run BLAST locally on Ubuntu with SequenceServer.",
295
+ "Run BLAST locally on Linux with SequenceServer."
296
+ ][rand(9)]
297
+ %>
298
+ </a>
299
+ <a
300
+ class="twitter-share-button"
301
+ href="https://twitter.com/share"
302
+ data-url="http://www.sequenceserver.com" data-text="<%= quote %>" data-via="yeban" data-hashtags="bioinformatics">
303
+ Tweet
304
+ </a>
305
+ <br>
306
+ Please cite:
307
+ <a href="http://www.biorxiv.org/content/early/2015/11/27/033142">
308
+ Priyam et al. (2015) Sequenceserver: a modern graphical user interface for custom BLAST databases
309
+ </a>
310
+ &amp; relevant data sources.
311
+ </p>
312
+ </div> <!-- /container -->
312
313
  </div>
313
314
 
314
315
  <div
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: sequenceserver
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.5
4
+ version: 1.0.6
5
5
  platform: ruby
6
6
  authors:
7
7
  - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2015-11-06 00:00:00.000000000 Z
14
+ date: 2015-12-30 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: sinatra
@@ -689,3 +689,4 @@ signing_key:
689
689
  specification_version: 4
690
690
  summary: BLAST search made easy!
691
691
  test_files: []
692
+ has_rdoc: