sequenceserver 1.0.0.pre.5 → 1.0.0

data/LICENSE/d3.txt

@@ -0,0 +1,26 @@
+Copyright (c) 2010-2015, Michael Bostock
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* The name Michael Bostock may not be used to endorse or promote products
+  derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/Rakefile

@@ -0,0 +1,13 @@
+require 'rspec/core'
+require 'rspec/core/rake_task'
+require 'rubocop/rake_task'
+
+desc 'Run RuboCop to generate HTML report'
+RuboCop::RakeTask.new :rubocop
+
+desc 'Run main spec testing task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => [:spec, :rubocop]

data/bin/sequenceserver

@@ -69,7 +69,7 @@ BANNER
        'Load extension from this file',
        :argument => true
 
-    on 'h', 'host=',
+    on 'H', 'host=',
        'Host to run SequenceServer on',
        :argument => true
 
@@ -137,7 +137,8 @@ BANNER
       # error scenarios either when creating a new SequenceServer (first
       # time or later), or updating config values using -s CLI option.
 
-      rescue SequenceServer::CONFIG_FILE_ERROR => e
+      rescue SequenceServer::CONFIG_FILE_ERROR,
+             SequenceServer::BLAST_DATABASE_ERROR => e
 
         puts e
         exit!
@@ -195,6 +196,7 @@ BANNER
         exit!
 
       rescue SequenceServer::BLAST_NOT_INSTALLED,
+             SequenceServer::BLAST_NOT_EXECUTABLE,
              SequenceServer::BLAST_NOT_COMPATIBLE => e
 
         # Show original error message first.
@@ -250,8 +252,11 @@ ERR
                 end
 
           archive = File.join('/tmp', File.basename(url))
-          system "wget -c #{url} -O #{archive} && mkdir -p ~/.sequenceserver" \
-            "&& tar xvf #{archive} -C ~/.sequenceserver"
+          # -ip4 is required  to avoid this curl bug http://sourceforge.net/p/curl/bugs/1424/?limit=25
+          # see also https://github.com/yannickwurm/sequenceserver/issues/139
+          system "curl -ip4 -C - #{url} -o #{archive} && "    \
+                 'mkdir -p ~/.sequenceserver && '             \
+                 "tar xvf #{archive} -C ~/.sequenceserver"
           unless $CHILD_STATUS.success?
             puts 'Failed to install BLAST+.'
             puts '  You may need to download BLAST+ from - '
@@ -329,6 +334,24 @@ MSG
             exit! unless set?
           end
         end
+
+      rescue => e
+        # This will catch any unhandled error and some very special errors.
+        # Ideally we will never hit this block. If we do, there's a bug in
+        # SequenceServer or something really weird going on. If we hit this
+        # error block we show the stacktrace to the user requesting them to
+        # post the same to our Google Group.
+        puts <<MSG
+Something went wonky
+
+Looks like you have encountered a bug in SequenceServer. Please could you
+report this incident to our Google Group -
+https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
+
+Error:
+#{e.backtrace.unshift(e.message).join("\n")}
+MSG
+        exit
       end
 
       if interactive?

data/lib/sequenceserver.rb

@@ -51,18 +51,18 @@ module SequenceServer
     # Run SequenceServer as a self-hosted server using Thin webserver.
     def run
       check_host
-      url = "http://#{config[:host]}:#{config[:port]}"
       server = Thin::Server.new(config[:host],
                                 config[:port],
                                 :signals => false) do
-        use Rack::CommonLogger
+        use Rack::CommonLogger if SequenceServer.verbose?
         run SequenceServer
       end
       server.silent = true
       server.backend.start do
         puts '** SequenceServer is ready.'
-        puts "   Go to #{url} in your browser and start BLASTing!"
+        puts "   Go to #{server_url} in your browser and start BLASTing!"
         puts '   Press CTRL+C to quit.'
+        open_in_browser(server_url)
         [:INT, :TERM].each do |sig|
           trap sig do
             server.stop!
@@ -76,7 +76,7 @@ module SequenceServer
       end
     rescue
       puts '** Oops! There was an error.'
-      puts "   Is SequenceServer already accessible at #{url}?"
+      puts "   Is SequenceServer already accessible at #{server_url}?"
       puts '   Try running SequenceServer on another port, like so:'
       puts
       puts '       sequenceserver -p 4570.'
@@ -127,9 +127,7 @@ module SequenceServer
         fail DATABASE_DIR_NOT_FOUND, config[:database_dir]
       end
 
-      assert_blast_databases_present_in_database_dir
       logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
-
       Database.scan_databases_dir
       Database.each do |database|
         logger.debug("Found #{database.type} database '#{database.title}'" \
@@ -182,16 +180,31 @@ module SequenceServer
     def assert_blast_installed_and_compatible
       fail BLAST_NOT_INSTALLED unless command? 'blastdbcmd'
       version = `blastdbcmd -version`.split[1]
+      fail BLAST_NOT_EXECUTABLE if !$CHILD_STATUS.success? || version.empty?
       fail BLAST_NOT_COMPATIBLE, version unless version >= MINIMUM_BLAST_VERSION
     end
 
-    def assert_blast_databases_present_in_database_dir
-      cmd = "blastdbcmd -recursive -list #{config[:database_dir]}"
-      out = `#{cmd}`
-      errpat = /BLAST Database error/
-      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
-      fail BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) ||
-                                             !$CHILD_STATUS.success?
+    def server_url
+      host = config[:host]
+      host = 'localhost' if host == '127.0.0.1' || host == '0.0.0.0'
+      "http://#{host}:#{config[:port]}"
+    end
+
+    def open_in_browser(server_url)
+      return if using_ssh? || verbose?
+      if RUBY_PLATFORM =~ /linux/ && xdg?
+        `xdg-open #{server_url}`
+      elsif RUBY_PLATFORM =~ /darwin/
+        `open #{server_url}`
+      end
+    end
+
+    def using_ssh?
+      true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
+    end
+
+    def xdg?
+      true if ENV['DISPLAY'] && command?('xdg-open')
     end
 
     # Return `true` if the given command exists and is executable.

data/lib/sequenceserver/database.rb

@@ -1,4 +1,5 @@
 require 'find'
+require 'open3'
 require 'digest/md5'
 require 'forwardable'
 
@@ -96,17 +97,27 @@ module SequenceServer
 
       # Recurisvely scan `database_dir` for blast databases.
       def scan_databases_dir
-        database_dir = config[:database_dir]
-        cmd = "blastdbcmd -recursive -list #{database_dir}" \
-              ' -list_outfmt "%f	%t	%p	%n	%l	%d" 2>&1'
-        list = `#{cmd}`
-        list.each_line do |line|
-          name = line.split('	')[0]
-          next if multipart_database_name?(name)
-          self << Database.new(*line.split('	'))
+        cmd = "blastdbcmd -recursive -list #{config[:database_dir]}" \
+              ' -list_outfmt "%f	%t	%p	%n	%l	%d"'
+        Open3.popen3(cmd) do |_, out, err|
+          out = out.read
+          err = err.read
+          throw_scan_error(cmd, out, err, $CHILD_STATUS)
+          out.each_line do |line|
+            name = line.split('	')[0]
+            next if multipart_database_name?(name)
+            self << Database.new(*line.split('	'))
+          end
         end
       end
 
+      def throw_scan_error(cmd, out, err, child_status)
+        errpat = /BLAST Database error/
+        fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
+        fail BLAST_DATABASE_ERROR.new(cmd, err) if !child_status.success? ||
+                                                   err.match(errpat)
+      end
+
       # Recursively scan `database_dir` for un-formatted FASTA and format them
       # for use with BLAST+.
       def make_blast_databases

data/lib/sequenceserver/exceptions.rb

@@ -92,6 +92,14 @@ MSG
     end
   end
 
+  # Raised if SequenceServer could not successfully execute 'blastp -version'
+  # on user's system (see #141).
+  class BLAST_NOT_EXECUTABLE < StandardError
+    def to_s
+      'Error executing BLAST+ binaries.'
+    end
+  end
+
   # Raised if SequenceServer determined NCBI BLAST+ present on the user's
   # system but not meeting SequenceServer's minimum version requirement.
   class BLAST_NOT_COMPATIBLE < StandardError
@@ -132,7 +140,7 @@ MSG
   end
 
   # Raised if there was an error determining BLAST+ databases in database_dir.
-  class BLAST_DATABASE_ERROR
+  class BLAST_DATABASE_ERROR < StandardError
     def initialize(cmd, out)
       @cmd = cmd
       @out = out

data/package.json

@@ -0,0 +1,29 @@
+{
+    "name": "SequenceServer",
+    "description": "BLAST searching made easy!",
+    "version": "1.0.0-2",
+    "homepage": "http://www.sequenceserver.com",
+    "repository": "https://github.com/yannickwurm/sequenceserver",
+    "author": {
+        "name": "Anurag Priyam",
+        "email": "anurag08priyam@gmail.com"
+    },
+    "dependencies": {
+    },
+    "devDependencies": {
+        "grunt":                  "0.4.5",
+        "grunt-cli":              "0.1.13",
+        "grunt-html":             "2.0.0",
+        "grunt-bootlint":         "0.7.0",
+        "grunt-contrib-csslint":  "0.4.0",
+        "grunt-contrib-jshint":   "0.11.0",
+        "grunt-contrib-cssmin":   "0.11.0",
+        "grunt-contrib-uglify":   "0.4.0",
+        "grunt-contrib-copy":     "0.7.0",
+        "grunt-contrib-compress": "0.13.0"
+    },
+    "scripts": {
+        "cop":    "grunt cop",
+        "build":         "grunt build"
+    }
+}

data/public/css/custom.css

@@ -276,6 +276,15 @@ a.disabled:hover {
 label[for="advanced"] {
   font-family: "Roboto";
   font-size: 16px;
+  display: table-cell;
+  width: 1%;
+  white-space: nowrap;
+  vertical-align: middle;
+  padding: 5px 12px 5px 0;
+}
+input[name="advanced"] {
+  border-top-left-radius: 4px !important;
+  border-bottom-left-radius: 4px !important;
 }
 
 #methods{
@@ -368,7 +377,7 @@ svg:not(:root) {
 }
 
 .hsps {
-  margin-top: 14px;
+  padding-bottom: 14px;
 }
 .hsp-stats>thead>tr>th {
   border-bottom: none;
@@ -389,7 +398,6 @@ svg:not(:root) {
 }
 
 .hit-links {
-  padding: 14px 0;
   letter-spacing: 1px;
 }
 

data/public/dist/css/sequenceserver.min.css

@@ -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){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(g,{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(){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 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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 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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(f,{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(f,{start:c.opt.selection.start,end:c.opt.selection.end}))}).mouseup(function(){d=!1,c.trigger(g,{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){var c=a("backbone-events-standalone");c.onAll=function(a,b){return this.on("all",a,b),this},c.oldMixin=c.mixin,c.mixin=function(a){c.oldMixin(a);for(var b=["onAll"],d=0;d<b.length;d++){var e=b[d];a[e]=this[e]}return a},b.exports=c},{"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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a=$(this),b=$("#method"),c=b.text(),d=a.text();a.html(SS.decorate(c)),b.val(d).html(SS.decorate(d)),$("#methods").wiggle()}),$(".result").on("mousedown",".hitn > .page-header > h4",function(){var a=$(this);a.on("mouseup mousemove",function b(c){"mouseup"===c.type?(a.attr("data-toggle","collapse"),a.find(".fa-chevron-down").toggleClass("fa-rotate-270")):a.attr("data-toggle",""),a.off("mouseup mousemove",b)})}),$(".result").on("click",".view-sequence",function(a){a.preventDefault(),a.stopPropagation(),a.target.disabled||SS.showSequenceViewer(a.target)}),$(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=$(".sidebar");0!==b.length&&b.affix({offset:{top:b.offset().top}}).width(b.width()),location.hash=d,SS.generateGraphicalOverview(),SS.updateDownloadFastaOfAllLink(),SS.updateDownloadFastaOfSelectedLink(),SS.updateSequenceViewerLinks(),SS.setupTooltips(),SS.setupDownloadLinks(),$("body").scrollspy({target:".sidebar"}),$("#spinner").modal("hide")}).fail(function(a){SS.showErrorModal(a,function(){$("#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(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()})},e=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},f=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(g,h,i,j,k){var l={barHeight:4,barPadding:5,legend:10,margin:20},m=a.extend(l,k),n=e(g,i,j);if(n.length<1)return!1;0!==i&&h.find("svg").remove();var o=g.data().queryLen,p=g.attr("id"),q=h.width(),r=n.length*(m.barHeight+m.barPadding)+5*m.margin+3*m.legend,s=d3.select(h[0]).selectAll("svg").data([n]).enter().insert("svg",":first-child").attr("width",q).attr("height",r).append("g").attr("transform","translate("+m.margin/4+", "+m.margin/4+")"),t=d3.scale.linear().range([0,q-m.margin]);t.domain([1,o]);var u=t.ticks(11);u.pop();var v=d3.svg.axis().scale(t).orient("top").tickValues(u.concat([1,o]));s.append("g").attr("transform","translate(0, "+m.margin+")").append("g").attr("class","x axis").call(v);var w=d3.scale.ordinal().rangeBands([0,r-3*m.margin-2*m.legend],.3);w.domain(n.map(function(a){return a.hitId}));var x=d3.scale.log().domain([d3.min([1e-5,d3.min(n.map(function(a){return 0===parseFloat(a.hitEvalue)?void 0:a.hitEvalue}))]),d3.max(n.map(function(a){return a.hitEvalue}))]).range([40,150]);s.append("g").attr("class","ghit").attr("transform","translate(0, "+(2*m.margin-m.legend)+")").selectAll(".hits").data(n).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=w(e)+m.barHeight/2,h=d3.rgb(x(d.hitEvalue),x(d.hitEvalue),x(d.hitEvalue));f>b+1&&(d[b].hspEnd<=d[b+1].hspStart?d3.select(this.parentNode).append("line").attr("x1",t(d[b].hspEnd)).attr("y1",g).attr("x2",t(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",t(d[b+1].hspEnd)).attr("y1",g).attr("x2",t(d[b].hspStart)).attr("y2",g).attr("stroke",h)),d3.select(this).attr("xlink:href","#"+p+"_hit_"+c).append("rect").attr("x",function(a){return t(a.hspStart)}).attr("y",w(e)).attr("width",function(a){return t(a.hspEnd-a.hspStart+1)}).attr("height",m.barHeight).attr("fill",d3.rgb(h))})}),n.length>1&&f(s,m,q,r),0===i&&d(g,h,!0),b(),c(h)}})}(jQuery),SS.blast=function(){var a=function(a){if(a=a.replace(/[^A-Z]/gi,""),a=a.replace(/[NX]/gi,""),a.length<10)return void 0;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;$("#blast").on("sequence_type_changed database_type_changed",function(){b=h(),_.isEqual(b,a)||(a=b,$(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 void 0};return i.init=function(){e(),f(),g()},i}();

data/public/js/jquery.t.js

@@ -116,7 +116,7 @@
         hitPanels.map(function () {
             var $this = $(this);
             var _hsps = [];
-            $this.find('.hsps').each(function () {
+            $this.find('.hsp').each(function () {
                 var __hsps = [];
                 __hsps = $(this).data();
                 __hsps.hspId = this.id;
@@ -286,7 +286,7 @@
                         var p_count = d.length;
 
                         d3.select(this)
-                        .selectAll('.hsps')
+                        .selectAll('.hsp')
                         .data(d).enter()
                         .append('a')
                         .each(function (_, j) {

data/public/js/sequence.js

@@ -2,7 +2,10 @@ require=(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof requ
 // legacy!!
 $.browser = require("jquery-browser-plugin");
 
-/** 
+/**
+ * THIS FILE HAS BEEN MODIFIED FROM THE ORIGINAL
+ * (https://github.com/ljgarcia/biojs-vis-sequence/blob/master/lib/index.js).
+ *
  * Sequence component 
  * 
  * @class

data/public/js/sequenceserver.js

@@ -652,10 +652,10 @@ $(document).ready(function(){
     $('form').on('blast_method_changed', function (event, methods) {
         // reset
         $('#method')
-        .disable().val('').html('blast')
-        .removeClass('col-md-11').addClass('col-md-12');
+        .disable().val('').html('blast');
 
         $('#methods')
+        .removeClass('input-group')
         .children().not('#method').remove();
 
         // set
@@ -667,29 +667,32 @@ $(document).ready(function(){
 
             if (methods.length >=1) {
                 $('#methods')
+                .addClass('input-group')
                 .append
                 (
-                    $('<button/>')
-                    .attr('type', 'button')
-                    .addClass("btn btn-primary dropdown-toggle col-md-1")
-                    .attr('data-toggle', 'dropdown')
+                    $('<div/>')
+                    .addClass('input-group-btn')
                     .append
                     (
-                        $('<span/>')
-                        .addClass('caret')
-                    ),
-                    $('<ul/>')
-                    .addClass('dropdown-menu')
-                    .append
-                    (
-                        $.map(methods, function (method) {
-                            return $('<li/>').html(SS.decorate(method));
-                        })
+                        $('<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(methods, function (method) {
+                                return $('<li/>').html(SS.decorate(method));
+                            })
+                        )
                     )
                 );
-
-                $('#method')
-                .removeClass('col-md-12').addClass('col-md-11');
             }
 
             // jiggle
@@ -737,7 +740,7 @@ $(document).ready(function(){
             SS.showSequenceViewer(event.target);
     });
 
-    $(document).on('change', '.hit-links :checkbox', function (event) {
+    $(document).on('change', '.hitn :checkbox', function (event) {
         event.stopPropagation();
         SS.selectHit(this);
     });

data/sequenceserver.gemspec

@@ -1,12 +1,12 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '1.0.0-5'
+  s.version     = '1.0.0'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft',
                    'Vivek Rai', 'Yannick Wurm']
   s.email       = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
   s.homepage    = 'http://sequenceserver.com'
-  s.license     = 'SequenceServer (custom)'
+  s.license     = 'GNU AGPL v3'
 
   s.summary     = 'BLAST search made easy!'
   s.description = <<DESC
@@ -30,10 +30,7 @@ DESC
   s.add_development_dependency('codeclimate-test-reporter')
 
   # gem
-  s.files         = Dir['lib/**/*'] + Dir['views/**/*'] + Dir['public/**/*']
-  s.files         = s.files + ['config.ru'] + Dir['tests/**/*']
-  s.files         = s.files + ['Gemfile', 'sequenceserver.gemspec']
-  s.files         = s.files + ['LICENSE.txt', 'LICENSE.Apache.txt', 'README.md']
+  s.files         = `git ls-files`.split
   s.executables   = ['sequenceserver']
   s.require_paths = ['lib']