sequenceserver 0.7.9 → 0.8.0

data/views/_options.erb

@@ -0,0 +1,144 @@
+<%#
+
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h6>General Search Options</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup
+  table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-comp_based_stats <String>
+  Use composition-based statistics for blastp / tblastn:
+      D or d: default (equivalent to 2)
+      0 or F or f: no composition-based statistics
+      1: Composition-based statistics as in NAR 29:2994-3005, 2001
+      2 or T or t : Composition-based score adjustment as in
+      Bioinformatics 21:902-911, 2005, conditioned on sequence
+      properties
+      3: Composition-based score adjustment as in Bioinformatics
+      21:902-911, 2005, unconditionally
+  For programs other than tblastn, must either be absent or be D, F
+  or 0
+  Default = `2'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Default = `500'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = `250'| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h6>Query filtering options</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = `no'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default = `false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h6>Restrict search or results</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GI's
+    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
+  subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqId's
+    * Incompatible with:  gilist, negative_gilist, remote, subject,
+  subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the listed GIs
+    * Incompatible with:  gilist, seqidlist, remote, subject,
+      subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+    * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+    * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+    * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+    * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+    * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep| %></pre>
+  </li>
+</ul>

data/views/search.erb

@@ -8,93 +8,83 @@
   <meta name="author" content="Cedric Wurm" />
   <meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
   <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
+  <script type="text/javascript" src="<%= uri('/js/store.min.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/jquery.ui.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/jquery.scrollspy.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/jquery.index.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/bootstrap.transition.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/bootstrap.dropdown.js') %>"></script>
+  <script type="text/javascript" src="<%= uri('/js/bootstrap.modal.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/sequenceserver.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/sequenceserver.blast.js') %>"></script>
 
   <%# without a space after erb's closing tag, a / gets appended to css' path %>
   <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
+  <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.dropdown.css') %>" />
+  <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.modal.css') %>" />
+  <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.icons.css') %>" />
   <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/custom.css') %>" />
 </head>
 
 <body>
   <div class="container">
+    <noscript>
+      <div class="nojs-error">
+        <h3>SequenceServer can't work without JavaScript.</h3>
+          <ul>
+            <li>Please see if you can enable JavaScript in your browser's preferences.</li>
+            <li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
+          </ul>
+      </div>
+    </noscript>
+
     <div class="page">
-      <div class="page-header" id="banner">
+      <div id="banner">
         <h1>BLAST Sequence(s)</h1>
       </div>
 
       <form method="post" id="blast" action="<%= uri('/#result') %>">
         <div class="row">
-          <div class="span12">
-            <div class="offset-left sequence">
-              <div class="clearfix">
-                <textarea name="sequence" id="sequence" rows="11" spellcheck="false" <%= 'autofocus="true"' unless @blast %> placeholder="Paste your sequence(s) here..." ></textarea>
-              </div>
+          <div class="span16">
+            <div class="control-group">
+              <textarea name="sequence" id="sequence" spellcheck="false" autofocus="true" placeholder="Paste your sequence(s) here..." ></textarea>
             </div>
           </div>
+        </div>
 
-          <div class="span4">
-            <div class="offset-right box blastmethods">
-              <div class="clearfix">
-                <fieldset>
-                  <legend><h4>Blast methods</h4></legend>
-                    <ul class="inputs-list">
-                      <li>
-                        <label title="Protein query; protein database.">
-                          <input type="radio" name="method" value="blastp" id="blastp"/>
-                          <span>blastp</span>
-                        </label>
-                      </li>
-                      <li>
-                        <label title="Protein query; six frame translated nucleotide database.">
-                          <input type="radio" name="method" value="tblastn" id="tblastn"/>
-                          <span>tblastn</span>
-                        </label>
-                      </li>
-                      <li>
-                        <label title="Nucleotide query; nucleotide database.">
-                          <input type="radio" name="method" value="blastn" id="blastn"/>
-                          <span>blastn</span>
-                        </label>
-                      </li>
-                      <li>
-                        <label title="Translated nucleotide query; protein database">
-                          <input type="radio" name="method" value="blastx" id="blastx"/>
-                          <span>blastx</span>
-                        </label>
-                      </li>
-                      <li>
-                        <label title="Six-frame translated nucleotide query; six-frame translated nucleotide database">
-                          <input type="radio" name="method" value="tblastx" id="tblastx"/>
-                          <span>tblastx</span>
-                        </label>
-                      </li>
-                  </ul>
-                </fieldset>
-              </div>
-            </div>
+        <div class="notifications">
+          <div class="notification alert-info hide"  id="nucleotide-sequence-notification">
+            Detected: nucleotide sequence(s).
+          </div>
+
+          <div class="notification alert-info hide"  id="protein-sequence-notification">
+            Detected: protein sequence(s).
+          </div>
+
+          <div class="notification alert-error hide" id="mixed-sequence-notification">
+            Detected: mixed nucleotide and protein sequences. We can't handle that. Please try one sequence at a time.
           </div>
         </div>
 
+        <br class="large"/>
+
         <div class="row">
           <div class="span8">
             <div class="offset-left box databases nucleotide">
               <div class="clearfix">
                 <fieldset>
-                  <legend><h4>Nucleotide databases</h4></legend>
-                  <ul class="inputs-list">
-                    <% settings.databases['nucleotide'].each_with_index do |db, i| %>
-                      <li>
-                        <label>
-                          <input type="checkbox" id="ndb<%=i%>" name="db[nucleotide][]" value="<%=i%>"/>
-                          <span> <%= db.title or db.name %></span>
-                        </label>
-                      </li>
+                  <legend>Nucleotide databases</legend>
+                  <div class="controls offset-left">
+                    <% settings.databases.values.select{|database| database.type == :nucleotide}.sort.each do |database| %>
+                      <label class="checkbox">
+                        <input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
+                        <span> <%= database.title or database.name %></span>
+                      </label>
                     <% end %>
-                  </ul>
+                  </div>
                 </fieldset>
               </div>
             </div>
@@ -104,115 +94,80 @@
             <div class="offset-right box databases protein">
               <div class="clearfix">
                 <fieldset>
-                  <legend><h4>Protein databases</h4></legend>
-                  <ul class="inputs-list">
-                    <% settings.databases['protein'].each_with_index do |db, i| %>
-                      <li>
-                        <label>
-                          <input type="checkbox" id="pdb<%=i%>" name="db[protein][]" value="<%=i%>"/>
-                          <span> <%= db.title or db.name %></span>
-                        </label>
-                      </li>
+                  <legend>Protein databases</legend>
+                  <div class="controls offset-left">
+                    <% settings.databases.values.select{|database| database.type == :protein}.sort.each do |database| %>
+                      <label class="checkbox">
+                        <input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
+                        <span> <%= database.title or database.name %></span>
+                      </label>
                     <% end %>
-                  </ul>
+                  </div>
                 </fieldset>
               </div>
             </div>
           </div>
         </div>
 
+        <br class="large"/>
+
         <div class="row">
           <div class="span12">
             <div class="offset-left box advanced">
               <div class="clearfix">
-                <label class="span4" for="advanced"><h4 title="Click to show/hide advanced options.">Advanced Parameters:</h4></label>
+                <label for="advanced">Advanced Parameters:</label>
                 <input class="span8" type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
+                <span class="icon-question-sign" data-toggle="modal" href="#help"></span>
+              </div>
+
+              <div class="modal hide fade" id="help">
+                <div class="modal-header">
+                  <h3>Advanced Options</h3>
+                </div>
+                <div class="modal-body">
+                  <%= erb :_options %>
+                </div>
+                <div class="modal-footer">
+                  <button class="btn btn-primary" data-dismiss="modal">Got it!</button>
+                </div>
               </div>
-  <pre class="help">
-  <%= ERB::Util.h %q|
-  -evalue <Real>
-    Expectation value (E) threshold for saving hits
-    Default = `10'
-  -word_size <Integer, >=2>
-    Word size for wordfinder algorithm
-  -gapopen <Integer>
-    Cost to open a gap
-  -gapextend <Integer>
-    Cost to extend a gap
-  -matrix <String>
-    Scoring matrix name (normally BLOSUM62)
-  -threshold <Real, >=0>
-    Minimum word score such that the word is added to the BLAST lookup table
-  -comp_based_stats <String>
-    Use composition-based statistics for blastp / tblastn:
-        D or d: default (equivalent to 2)
-        0 or F or f: no composition-based statistics
-        1: Composition-based statistics as in NAR 29:2994-3005, 2001
-        2 or T or t : Composition-based score adjustment as in Bioinformatics
-    21:902-911,
-        2005, conditioned on sequence properties
-        3: Composition-based score adjustment as in Bioinformatics 21:902-911,
-        2005, unconditionally
-    For programs other than tblastn, must either be absent or be D, F or 0
-    Default = `2'
-  -num_descriptions <Integer, >=0>
-    Number of database sequences to show one-line descriptions for
-    Default = `500'
-  -num_alignments <Integer, >=0>
-    Number of database sequences to show alignments for
-    Default = `250'
-  *** Query filtering options
-  -seg <String>
-    Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
-    'no' to disable)
-    Default = `no'
-  -soft_masking <Boolean>
-    Apply filtering locations as soft masks
-    Default = `false'
-  -lcase_masking
-    Use lower case filtering in query and subject sequence(s)?
-  *** Restrict search or results
-  -gilist <String>
-    Restrict search of database to list of GI's
-      * Incompatible with:  negative_gilist, seqidlist, remote, subject,
-    subject_loc
-  -seqidlist <String>
-    Restrict search of database to list of SeqId's
-      * Incompatible with:  gilist, negative_gilist, remote, subject,
-    subject_loc
-  -negative_gilist <String>
-    Restrict search of database to everything except the listed GIs
-      * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
-  -entrez_query <String>
-    Restrict search with the given Entrez query
-      * Requires:  remote
-  -db_soft_mask <String>
-    Filtering algorithm ID to apply to the BLAST database as soft masking
-      * Incompatible with:  subject, subject_loc
-  -culling_limit <Integer, >=0>
-    If the query range of a hit is enveloped by that of at least this many
-    higher-scoring hits, delete the hit
-      * Incompatible with:  best_hit_overhang, best_hit_score_edge
-  -best_hit_overhang <Real, (>0 and <0.5)>
-    Best Hit algorithm overhang value (recommended value: 0.1)
-      * Incompatible with:  culling_limit
-  -best_hit_score_edge <Real, (>0 and <0.5)>
-    Best Hit algorithm score edge value (recommended value: 0.1)
-      * Incompatible with:  culling_limit
-  -max_target_seqs <Integer, >=1>
-    Maximum number of aligned sequences to keep | %>
-  </pre>
+            </div>
           </div>
-        </div>
 
           <div class="span4">
-            <input type="submit" class="btn large primary" value="BLAST!"/>
+            <div id="methods">
+              <button type="submit" class="span3 btn btn-large btn-primary" id="method" disabled="disabled">blast</button>
+              <button class="btn btn-primary btn-large dropdown-toggle hide" data-toggle="dropdown">
+                <span class="caret"></span>
+              </button>
+              <ul class="dropdown-menu"></ul>
+            </div>
           </div>
         </div>
       </form>
 
-      <div id="result" class="offset-left offset-right">
-        <%= @blast %>
+      <div class="modal hide" id="spinner" data-keyboard="false" data-backdrop="static">
+        <div class="modal-body">
+        </div>
+      </div>
+
+      <div class="results hide">
+        <div id="result">
+        </div>
+      </div>
+
+      <div class="modal hide fade" id="error">
+        <div class="modal-header">
+          <h3 id="error-short">Oops! BLAST Failed</h3>
+        </div>
+        <div class="modal-body">
+          <h4 id="error-type"></h4>
+          <br/>
+          <p id="error-message"></p>
+        </div>
+        <div class="modal-footer">
+          <button class="btn btn-danger" data-dismiss="modal">Close</button>
+        </div>
       </div>
 
       <div id="underbar">
@@ -229,5 +184,38 @@
       </div>
     </div> <!-- /page -->
   </div> <!-- /container -->
+
+  <div id="social" class="modal hide fade">
+    <div class="modal-header">
+      <h3 id="error-short">Looks like you are fond of SequenceServer :).</h3>
+    </div>
+    <div class="modal-body">
+      <p>Please consider giving us a plus-one and/or tweeting about us. Thanks!</p>
+      <br/>
+      <div class="buttons">
+        <div class="button-container well">
+          <div class="g-plusone" data-annotation="none" data-href="http://www.sequenceserver.com"></div>
+        </div>
+        <div class="button-container well">
+          <a href="https://twitter.com/share" class="twitter-share-button" data-url="http://www.sequenceserver.com" data-text="SequenceServer: BLAST search made easy." data-via="yeban" data-size="large" data-count="none" data-hashtags="bioinformatics">Tweet</a>
+        </div>
+      </div>
+    </div>
+    <div class="modal-footer">
+      <button class="btn btn-primary" data-dismiss="modal">Done</button>
+    </div>
+  </div> <!-- /social -->
+
+  <!-- google plus -->
+  <script type="text/javascript">
+    (function() {
+      var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true;
+      po.src = 'https://apis.google.com/js/plusone.js';
+      var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s);
+    })();
+  </script>
+
+  <!-- twitter -->
+  <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
 </body>
 </html>