sequenceserver 1.0.7 → 1.0.8

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Files changed (13) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequenceserver.rb +2 -2
  3. data/lib/sequenceserver/version.rb +1 -1
  4. data/package.json +1 -1
  5. data/public/css/custom.css +14 -0
  6. data/public/dist/css/sequenceserver.min.css +1 -1
  7. data/public/dist/css/sequenceserver.min.css.gz +0 -0
  8. data/public/dist/js/sequenceserver.min.js +1 -1
  9. data/public/dist/js/sequenceserver.min.js.gz +0 -0
  10. data/public/js/sequenceserver.js +12 -8
  11. data/sequenceserver.gemspec +1 -1
  12. metadata +2 -3
  13. data/Gemfile +0 -3
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  ---
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  SHA1:
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- metadata.gz: c21df6999089afe99472221336d91a389b567515
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- data.tar.gz: eafe129ee7fbd7226c36139be759b82469e64a89
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+ metadata.gz: df39d51ed4e4f8e552a1ea11da47e6e25eb8a212
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+ data.tar.gz: 2f03f99e59871472ca053b5eb146af275736efb7
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  SHA512:
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- metadata.gz: 309d5c31f845ca60b46daa2b43bebaa5e210be94ef035dc9767a8ac7f7c649398280c97cfb3aedba258ad8e36a63de3e05f5dfd1295db610d3580486f3f6c6d4
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- data.tar.gz: f71215c34b4b3c9ac5801af562a696a3258070784e5265f9e14546ff64fcd19bf02d60409043f41fbf69c6fd1e07a413ea579c1934996b9bcb79033c2c13a012
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+ metadata.gz: 89b7d44e5ff6574b58d993079e98499f438690b45c0c6eff6db39c515d565cf9a11953a09ad72cfedd62eb5a395b2a92a4970f83233b8667724421818cc62f4b
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+ data.tar.gz: 6dba5e3a22b1dba4f7366695896084b620bcec57f2baa3270d9367c0aab4a55f8625ef885143d1c78643ce2ed3c232d6887805455c306548d703b63a2b8e8c74
data/lib/sequenceserver.rb CHANGED
@@ -194,9 +194,9 @@ module SequenceServer
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  def open_in_browser(server_url)
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  return if using_ssh? || verbose?
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  if RUBY_PLATFORM =~ /linux/ && xdg?
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- `xdg-open #{server_url}`
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+ system "xdg-open #{server_url}"
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  elsif RUBY_PLATFORM =~ /darwin/
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- `open #{server_url}`
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+ system "open #{server_url}"
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  end
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  end
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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 = '1.0.7'
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+ VERSION = '1.0.8'
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  end
data/package.json CHANGED
@@ -1,7 +1,7 @@
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  {
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  "name": "SequenceServer",
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  "description": "BLAST search made easy!",
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- "version": "1.0.7",
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+ "version": "1.0.8",
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  "homepage": "http://www.sequenceserver.com",
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  "repository": "https://github.com/yannickwurm/sequenceserver",
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  "author": {
data/public/css/custom.css CHANGED
@@ -487,3 +487,17 @@ svg:not(:root) {
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  border-radius: 0;
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  background-color: inherit;
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  }
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+
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+ /* Medium devices (desktops, 992px and up) */
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+ @media (min-width: 992px) {
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+ .sidebar.affix {
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+ width: 243.5px;
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+ }
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+ }
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+
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+ /* Large devices (large desktops, 1200px and up) */
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+ @media (min-width: 1200px) {
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+ .sidebar.affix {
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+ width: 292.5px;
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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; 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":"",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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12
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.checkbox").addClass("disabled");break;default:$(".databases input:checkbox").enable(),$(".databases .checkbox").removeClass("disabled")}}),$("form").on("blast_method_changed",function(a,b){if($("#method").disable().val("").html("blast"),$("#methods").removeClass("input-group").children().not("#method").remove(),b.length>0){var c=b.shift();$("#method").enable().val(c).html(SS.decorate(c)),b.length>=1&&$("#methods").addClass("input-group").append($("<div/>").addClass("input-group-btn").append($("<button/>").attr("type","button").addClass("btn btn-primary dropdown-toggle").attr("data-toggle","dropdown").append($("<span/>").addClass("caret")),$("<ul/>").addClass("dropdown-menu dropdown-menu-right").append($.map(b,function(a){return $("<li/>").html(SS.decorate(a))})))),$("#methods").wiggle()}}),$(document).on("click","#methods .dropdown-menu li",function(a){var b=$(this),c=$("#method"),d=c.text(),e=b.text();b.html(SS.decorate(d)),c.val(e).html(SS.decorate(e)),$("#methods").wiggle()}),$(".result").on("mousedown",".hitn > .page-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function c(a){"mouseup"===a.type?(b.attr("data-toggle","collapse"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")):b.attr("data-toggle",""),b.off("mouseup mousemove",c)})}),$(".result").on("click",".view-sequence",function(a){a.preventDefault(),a.stopPropagation(),a.target.disabled||SS.showSequenceViewer(a.target)}),$(document).on("change",".hitn :checkbox",function(a){a.stopPropagation(),SS.selectHit(this)}),$("#blast").submit(function(){var a=$(this).attr("action"),b=a.indexOf("#"),c=a.slice(0,b),d=a.slice(b,a.length);location.hash="",$("#spinner").modal();var e=$(this).serialize()+"&method="+$("#method").val();return $.post(c,e).done(function(a){$(".result").html(a).show();var b=$(".sidebar"),c=!1,e=function(){b.is(":visible")&&!c&&(b.affix({offset:{top:b.offset().top}}),c=!0)};e(),$(window).resize(_.debounce(e,125)),location.hash=d,SS.generateGraphicalOverview(),SS.updateDownloadFastaOfAllLink(),SS.updateDownloadFastaOfSelectedLink(),SS.updateSequenceViewerLinks(),SS.setupTooltips(),SS.setupDownloadLinks(),$("body").scrollspy({target:".sidebar"}),$("#spinner").modal("hide")}).fail(function(a,b,c){SS.showErrorModal(a,function(){$("#spinner").modal("hide")})}),!1}),SS.$sequence.poll()}),function(a){var b=function(){a('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true","white-space":"nowrap"})},c=function(b){a("a",b).click(function(b){b.preventDefault(),b.stopPropagation(),window.location.hash=a(this).attr("href")})},d=function(b,c,d,e){var f=a(window).width(),g=_.debounce(function(){if(f!==a(window).width()){var g=b.find(".ghit > g").length;a.graphIt(b,c,g,d,e),f=a(window).width()}},125);a(window).resize(g)},e=function(c,d,e){var f,g,h,i,j=20,k=function(){f=c.data().hitCount,g=c.find(".ghit > g").length},l=function(b,c){c.append(a("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",b.attr("id")).html("View More&nbsp;").append(a("<i/>").addClass("fa fa-angle-double-down")),a("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",b.attr("id")).html("View Less&nbsp;").append(a("<i/>").addClass("fa fa-angle-double-up"))),h=a(".less",c),i=a(".more",c)},m=function(){k(),f===j||j>g?(h.hide(),i.hide()):g===f?(i.hide(),h.show()):g===j?(h.hide(),i.show()):(h.show(),i.show())};e===!0&&(l(c,d),m()),i.on("click",function(e){k(),a.graphIt(c,d,g,j),m(),b(),e.stopPropagation()}),h.on("click",function(e){k();var f=g-j;f>=j?(a.graphIt(c,d,g,-j),m()):0!==f&&(a.graphIt(c,d,g,j-g),m()),b(),e.stopPropagation()})},f=function(b,c,d){var e,f=[];return e=b.find(".hitn").slice(0,c+d),e.map(function(){var b=a(this),c=[];b.find(".hsp").each(function(){var 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/public/js/sequenceserver.js CHANGED
@@ -768,15 +768,19 @@ $(document).ready(function(){
768
768
  $('.result').html(data).show();
769
769
 
770
770
  // affix sidebar
771
- var $sidebar = $('.sidebar');
772
- if ($sidebar.length !== 0) {
773
- $sidebar.affix({
774
- offset: {
775
- top: $sidebar.offset().top
776
- }
777
- })
778
- .width($sidebar.width());
771
+ var $sidebar = $('.sidebar'), affixed = false;
772
+ var affixSidebar = function () {
773
+ if ($sidebar.is(':visible') && !affixed) {
774
+ $sidebar.affix({
775
+ offset: {
776
+ top: $sidebar.offset().top
777
+ }
778
+ });
779
+ affixed = true;
780
+ }
779
781
  }
782
+ affixSidebar();
783
+ $(window).resize(_.debounce(affixSidebar, 125));
780
784
 
781
785
  //jump to the results
782
786
  location.hash = hash;
data/sequenceserver.gemspec CHANGED
@@ -32,7 +32,7 @@ DESC
32
32
  '~> 0.4', '>= 0.4.7')
33
33
 
34
34
  # gem
35
- s.files = `git ls-files`.split
35
+ s.files = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']
36
36
  s.executables = ['sequenceserver']
37
37
  s.require_paths = ['lib']
38
38
 
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: 1.0.7
4
+ version: 1.0.8
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: 2016-02-05 00:00:00.000000000 Z
14
+ date: 2016-03-18 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: sinatra
@@ -252,7 +252,6 @@ files:
252
252
  - ".rubocop.yml"
253
253
  - ".travis.yml"
254
254
  - COPYRIGHT.txt
255
- - Gemfile
256
255
  - Gruntfile.js
257
256
  - LICENSE.txt
258
257
  - LICENSE/Apache.txt
data/Gemfile DELETED
@@ -1,3 +0,0 @@
1
- source 'http://rubygems.org'
2
-
3
- gemspec