sequenceserver 0.7.8 → 0.7.9

data/lib/sequenceserver.rb

@@ -229,12 +229,6 @@ module SequenceServer
       # evaluate empty sequence as nil, otherwise as fasta
       sequence = sequence.empty? ? nil : to_fasta(sequence)
 
-      # TODO: detect sequence type in the browser itself (no AJAX)
-      if request.xhr?
-        # if the AJAX request didn't specify a blast method, it must be interested in sequence type only
-        return (sequence && type_of_sequences(sequence)).to_s unless method
-      end
-
       # Raise ArgumentError if there is no database selected
       if db_type_param.nil?
         raise ArgumentError, "No BLAST database selected"

data/public/css/custom.css

@@ -1,4 +1,8 @@
 /* generic */
+html, body{
+  height: 100%;
+}
+
 .offset-left {
   margin-left: 20px;
 }

data/public/js/sequenceserver.blast.js

@@ -26,6 +26,57 @@
 SS.blast = (function () {
     /* private methods */
 
+    // TODO: embedding magic numbers in the code is bad
+    // TODO: magic numbers in JS and Ruby should be in sync
+    var guess_sequence_type = function (sequence) {
+        var putative_NA_count, threshold, i;
+
+        putative_NA_count = 0;
+
+        // remove 'noisy' characters
+        sequence = sequence.replace(/[^A-Z]/gi, '') // non-letter characters
+        sequence = sequence.replace(/[NX]/gi,   '') // ambiguous  characters
+
+        // guessing the type of a small sequence is unsafe
+        if (sequence.length < 10) {
+            return undefined
+        }
+
+        // count the number of putative NA
+        for (i = 0; i < sequence.length; i++) {
+            if (sequence[i].match(/[ACGTU]/i)) {
+                putative_NA_count += 1;
+            }
+        }
+
+        threshold = 0.9 * sequence.length
+
+        return putative_NA_count > threshold ? 'nucleotide' : 'protein'
+    }
+
+    var type_of_sequences = function () {
+        var sequences = $('#sequence').val().split(/>.*/)
+        var type, tmp, i;
+
+        for (i = 0; i < sequences.length; i++) {
+            tmp = guess_sequence_type(sequences[i]);
+
+            // could not guess the sequence type; try the next sequence
+            if (!tmp) { continue }
+
+            if (!type) {
+              // successfully guessed the type of atleast one sequence
+              type = tmp
+            }
+            else if (tmp !== type) {
+              // user has mixed different type of sequences
+              return undefined
+            }
+        }
+
+        return type;
+    }
+
     /*
         check if blast is valid (sufficient input to blast or not)
     */
@@ -64,36 +115,22 @@ SS.blast = (function () {
     }
 
     /*
-        determine input sequence type, store it, and trigger
-        'sequence_type_changed' event if the input sequence has changed
-        (TODO: the method is doing too much; split it)
+        determine input sequence type, and trigger 'sequence_type_changed'
+        event if the input sequence type has changed
     */
     var signal_sequence_type_changed = function () {
-        var prev_seq = prev_seq_type = '';
-
-        (function poll () {
-            setTimeout(function (){
-                var seq, seq_type;
-                seq = $('#sequence').val();
-
-                //act only if user input has changed
-                if (seq != prev_seq){
-                    prev_seq = seq;
-                    $('#sequence').change();
-
-                    //get input sequence type from the server
-                    $.post('', {sequence: seq}, function(seq_type){
-                        if (seq_type != prev_seq_type){
-                            prev_seq_type = seq_type;
-
-                            //store sequence type and notify listeners
-                            $('#sequence').data('sequence_type', seq_type).trigger('sequence_type_changed');
-                        }
-                    });
-                }
-                poll();
-              }, 100)
-        }());
+        var type, tmp;
+
+        $('#sequence').change(function () {
+            tmp = type_of_sequences();
+
+            if (tmp != type){
+              type = tmp;
+
+              //notify listeners
+              $(this).trigger('sequence_type_changed', type);
+            }
+        });
     };
 
 

data/public/js/sequenceserver.js

@@ -52,6 +52,27 @@
     };
 })( jQuery );
 
+(function ($) {
+    $.fn.poll = function () {
+        var that, val, tmp;
+
+        that = this;
+
+        (function ping () {
+            tmp = that.val();
+
+            if (tmp != val){
+                val = tmp;
+                that.change();
+            }
+
+            setTimeout(ping, 100);
+        }());
+
+        return this;
+    };
+}(jQuery));
+
 /*
     SS - SequenceServer's JavaScript module
 
@@ -80,6 +101,9 @@ if (!SS) {
 }()); //end SS module
 
 $(document).ready(function(){
+    // poll the sequence textbox for a change in user input
+    $('#sequence').poll();
+
     // start SequenceServer's event loop
     SS.main();
     $('input:submit').disable();
@@ -92,17 +116,16 @@ $(document).ready(function(){
         $('input:submit').disable();
     });
 
-    $('#sequence').bind('sequence_type_changed', function(){
-        var seq_type = $(this).data('sequence_type');
-        if (seq_type == "nucleotide"){
+    $('#sequence').bind('sequence_type_changed', function(event, type){
+        if (type == "nucleotide"){
             $("#blastn, #tblastx, #blastx").enable();
             $("#blastp, #tblastn").uncheck().disable().first().change();
         }
-        else if (seq_type == "protein"){
+        else if (type == "protein"){
             $("#blastp, #tblastn").enable();
             $("#blastn, #tblastx, #blastx").uncheck().disable().first().change();
         }
-        else if (seq_type == ""){
+        else if (type == undefined){
             //reset blast methods
             $('.blastmethods input[type=radio]').enable().first().change();
         }
@@ -148,7 +171,13 @@ $(document).ready(function(){
     });
 
     $('#blast').submit(function(){
-        var button = $(this);
+        //parse AJAX URL
+        var action = $(this).attr('action');
+        var index  = action.indexOf('#');
+        var url    = action.slice(0, index);
+        var hash   = action.slice(index, action.length);
+
+        var button = $(this).find('input:submit');
 
         //prevent submitting another query while this one is being processed
         button.disable();
@@ -173,13 +202,13 @@ $(document).ready(function(){
         });
 
         // BLAST now
-        $.post('', $('form').serialize()).
+        $.post(url, $('form').serialize()).
           done(function (data) {
             // BLASTed successfully
 
             // display the result
             $('#result').html(data);
-            location.hash = '#result';
+            location.hash = hash;
         }).
           fail(function (jqXHR, status, error) {
             // BLAST failed

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.7.8'
+  s.version     = '0.7.9'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

data/views/search.erb

@@ -216,7 +216,16 @@
       </div>
 
       <div id="underbar">
-        <p>&copy; <a href='http://www.sequenceserver.com'>SequenceServer: BLAST search made easy!</a></p>
+        <p><strong><a href='http://www.sequenceserver.com'>
+            <%=  [ "&copy; SequenceServer: BLAST search made easy!",
+                   "Custom BLAST web interface by SequenceServer.",
+                   "SequenceServer: Local BLAST with bespoke html interface.",
+                   "Set up custom BLAST interface with SequenceServer.",
+                   "Please cite: Priyam A, Woodcroft BJ, Wurm Y (<em>in prep</em>). " +
+                   "Sequenceserver: BLAST searching made easy."
+            ][rand(5)]
+          %>
+        </a></strong></p>
       </div>
     </div> <!-- /page -->
   </div> <!-- /container -->

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 0.7.8
+  version: 0.7.9
   prerelease: 
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-21 00:00:00.000000000Z
+date: 2012-04-11 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &21083000 !ruby/object:Gem::Requirement
+  requirement: &22947800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -23,10 +23,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *21083000
+  version_requirements: *22947800
 - !ruby/object:Gem::Dependency
   name: sinatra
-  requirement: &21082380 !ruby/object:Gem::Requirement
+  requirement: &22947280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -34,10 +34,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *21082380
+  version_requirements: *22947280
 - !ruby/object:Gem::Dependency
   name: ptools
-  requirement: &21081860 !ruby/object:Gem::Requirement
+  requirement: &22946860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -45,7 +45,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *21081860
+  version_requirements: *22946860
 description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
 
@@ -67,7 +67,6 @@ files:
 - views/search.erb
 - views/500.erb
 - public/favicon.ico
-- public/blastResult.js
 - public/css/bootstrap.min.css
 - public/css/custom.css
 - public/js/jquery.js
@@ -75,8 +74,6 @@ files:
 - public/js/sequenceserver.js
 - public/js/jquery.activity.js
 - public/js/sequenceserver.blast.js
-- public/js/bootstrap-modal.js
-- public/js/bootstrap-alerts.js
 - tests/test_sequencehelpers.rb
 - tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
 - tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
@@ -124,3 +121,4 @@ signing_key:
 specification_version: 3
 summary: iPod of BLAST searching
 test_files: []
+has_rdoc: 

data/public/blastResult.js

@@ -1,99 +0,0 @@
-
-function finalSubmit(dbIsNt, targetForm, inputName, submitFormName, dbType){
-  var formArr=targetForm.split(":");
-  var idArray=new Array();
-  if(dbType == 0){
-      if(dbIsNt==1){
-          document.forms[submitFormName].db.value="Nucleotide";
-      }
-      else{
-          document.forms[submitFormName].db.value="Protein";
-      }
-  }
-  for(j=0; j<formArr.length; j++){
-    for(var i=0; i<document.forms[formArr[j]].elements.length; i++){
-      var theElem=document.forms[formArr[j]].elements[i];
-      if(theElem.type=="checkbox"&&theElem.name==inputName&&theElem.checked){
-        if(!isIdIn(theElem.value, idArray)){
-     
-         idArray[idArray.length]=theElem.value;
-         }
-      }
-    }
-    if(dbType == 0){
-        document.forms[submitFormName].term.value="";
-        for(i=0; i<idArray.length; i++){  
-            if(i ==0 ) {
-                document.forms[submitFormName].term.value += idArray[i];
-            } else {
-                document.forms[submitFormName].term.value += "," + idArray[i];
-            }
-	}	
-    } else if (dbType == 1){
-        document.forms[submitFormName].val.value="";
-        for(i=0; i<idArray.length; i++){    
-            if(i ==0 ) {
-                document.forms[submitFormName].val.value += idArray[i];
-            } else {   
-                document.forms[submitFormName].val.value += "," + idArray[i];
-            }
-	}	
-    }
-  }
-    document.forms[submitFormName].submit();
-}
-
-function isIdIn(id, idArray){
-  var idSeen=false;
-
-  for(i=0; i<idArray.length; i++){
-    if(id==idArray[i]){
-      idSeen=true;
-      break;
-    }
-  }
-  return idSeen;
-}
-
-function handleCheckAll(mode, targetForm, inputName){
- 
-  var formArr=targetForm.split(":");
-  for(j=0; j<formArr.length; j++){
-    for(var i=0; i<document.forms[formArr[j]].elements.length; i++){
-      var theElem=document.forms[formArr[j]].elements[i];
-      if(theElem.type=="checkbox"&&theElem.name==inputName){
-        if(mode=="select"){
-          theElem.checked=true;
-        }
-        else if(mode=="deselect"){
-          theElem.checked=false;
-        }
-      }
-    }
-  }
- 
-}
-
-function synchronizeCheck(id, formName, inputName, isChecked){
- 
-  for(var i=0; i<document.forms[formName].elements.length; i++){
-    var theElem=document.forms[formName].elements[i];
-    if(theElem.type=="checkbox"&&theElem.name==inputName&&id==theElem.value){    
-        theElem.checked=isChecked; 
-       
-    }
-  }
-
-}
-
-
-function uncheckable(formName, inputName){
-  for(var i=0; i<document.forms[formName].elements.length; i++){
-    var theElem=document.forms[formName].elements[i];
-    if(theElem.type=="checkbox"&&theElem.name==inputName){    
-        theElem.checked=0; 
-       
-    }
-  }
-
-}

data/public/js/bootstrap-alerts.js

@@ -1,113 +0,0 @@
-/* ==========================================================
- * bootstrap-alerts.js v1.4.0
- * http://twitter.github.com/bootstrap/javascript.html#alerts
- * ==========================================================
- * Copyright 2011 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function( $ ){
-
-  "use strict"
-
-  /* CSS TRANSITION SUPPORT (https://gist.github.com/373874)
-   * ======================================================= */
-
-   var transitionEnd
-
-   $(document).ready(function () {
-
-     $.support.transition = (function () {
-       var thisBody = document.body || document.documentElement
-         , thisStyle = thisBody.style
-         , support = thisStyle.transition !== undefined || thisStyle.WebkitTransition !== undefined || thisStyle.MozTransition !== undefined || thisStyle.MsTransition !== undefined || thisStyle.OTransition !== undefined
-       return support
-     })()
-
-     // set CSS transition event type
-     if ( $.support.transition ) {
-       transitionEnd = "TransitionEnd"
-       if ( $.browser.webkit ) {
-        transitionEnd = "webkitTransitionEnd"
-       } else if ( $.browser.mozilla ) {
-        transitionEnd = "transitionend"
-       } else if ( $.browser.opera ) {
-        transitionEnd = "oTransitionEnd"
-       }
-     }
-
-   })
-
- /* ALERT CLASS DEFINITION
-  * ====================== */
-
-  var Alert = function ( content, options ) {
-    this.settings = $.extend({}, $.fn.alert.defaults, options)
-    this.$element = $(content)
-      .delegate(this.settings.selector, 'click', this.close)
-  }
-
-  Alert.prototype = {
-
-    close: function (e) {
-      var $element = $(this).parent('.alert-message')
-
-      e && e.preventDefault()
-      $element.removeClass('in')
-
-      function removeElement () {
-        $element.remove()
-      }
-
-      $.support.transition && $element.hasClass('fade') ?
-        $element.bind(transitionEnd, removeElement) :
-        removeElement()
-    }
-
-  }
-
-
- /* ALERT PLUGIN DEFINITION
-  * ======================= */
-
-  $.fn.alert = function ( options ) {
-
-    if ( options === true ) {
-      return this.data('alert')
-    }
-
-    return this.each(function () {
-      var $this = $(this)
-
-      if ( typeof options == 'string' ) {
-        return $this.data('alert')[options]()
-      }
-
-      $(this).data('alert', new Alert( this, options ))
-
-    })
-  }
-
-  $.fn.alert.defaults = {
-    selector: '.close'
-  }
-
-  $(document).ready(function () {
-    new Alert($('body'), {
-      selector: '.alert-message[data-alert] .close'
-    })
-  })
-
-}( window.jQuery || window.ender );

data/public/js/bootstrap-modal.js

@@ -1,260 +0,0 @@
-/* =========================================================
- * bootstrap-modal.js v1.4.0
- * http://twitter.github.com/bootstrap/javascript.html#modal
- * =========================================================
- * Copyright 2011 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================= */
-
-
-!function( $ ){
-
-  "use strict"
-
- /* CSS TRANSITION SUPPORT (https://gist.github.com/373874)
-  * ======================================================= */
-
-  var transitionEnd
-
-  $(document).ready(function () {
-
-    $.support.transition = (function () {
-      var thisBody = document.body || document.documentElement
-        , thisStyle = thisBody.style
-        , support = thisStyle.transition !== undefined || thisStyle.WebkitTransition !== undefined || thisStyle.MozTransition !== undefined || thisStyle.MsTransition !== undefined || thisStyle.OTransition !== undefined
-      return support
-    })()
-
-    // set CSS transition event type
-    if ( $.support.transition ) {
-      transitionEnd = "TransitionEnd"
-      if ( $.browser.webkit ) {
-      	transitionEnd = "webkitTransitionEnd"
-      } else if ( $.browser.mozilla ) {
-      	transitionEnd = "transitionend"
-      } else if ( $.browser.opera ) {
-      	transitionEnd = "oTransitionEnd"
-      }
-    }
-
-  })
-
-
- /* MODAL PUBLIC CLASS DEFINITION
-  * ============================= */
-
-  var Modal = function ( content, options ) {
-    this.settings = $.extend({}, $.fn.modal.defaults, options)
-    this.$element = $(content)
-      .delegate('.close', 'click.modal', $.proxy(this.hide, this))
-
-    if ( this.settings.show ) {
-      this.show()
-    }
-
-    return this
-  }
-
-  Modal.prototype = {
-
-      toggle: function () {
-        return this[!this.isShown ? 'show' : 'hide']()
-      }
-
-    , show: function () {
-        var that = this
-        this.isShown = true
-        this.$element.trigger('show')
-
-        escape.call(this)
-        backdrop.call(this, function () {
-          var transition = $.support.transition && that.$element.hasClass('fade')
-
-          that.$element
-            .appendTo(document.body)
-            .show()
-
-          if (transition) {
-            that.$element[0].offsetWidth // force reflow
-          }
-
-          that.$element.addClass('in')
-
-          transition ?
-            that.$element.one(transitionEnd, function () { that.$element.trigger('shown') }) :
-            that.$element.trigger('shown')
-
-        })
-
-        return this
-      }
-
-    , hide: function (e) {
-        e && e.preventDefault()
-
-        if ( !this.isShown ) {
-          return this
-        }
-
-        var that = this
-        this.isShown = false
-
-        escape.call(this)
-
-        this.$element
-          .trigger('hide')
-          .removeClass('in')
-
-        $.support.transition && this.$element.hasClass('fade') ?
-          hideWithTransition.call(this) :
-          hideModal.call(this)
-
-        return this
-      }
-
-  }
-
-
- /* MODAL PRIVATE METHODS
-  * ===================== */
-
-  function hideWithTransition() {
-    // firefox drops transitionEnd events :{o
-    var that = this
-      , timeout = setTimeout(function () {
-          that.$element.unbind(transitionEnd)
-          hideModal.call(that)
-        }, 500)
-
-    this.$element.one(transitionEnd, function () {
-      clearTimeout(timeout)
-      hideModal.call(that)
-    })
-  }
-
-  function hideModal (that) {
-    this.$element
-      .hide()
-      .trigger('hidden')
-
-    backdrop.call(this)
-  }
-
-  function backdrop ( callback ) {
-    var that = this
-      , animate = this.$element.hasClass('fade') ? 'fade' : ''
-    if ( this.isShown && this.settings.backdrop ) {
-      var doAnimate = $.support.transition && animate
-
-      this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
-        .appendTo(document.body)
-
-      if ( this.settings.backdrop != 'static' ) {
-        this.$backdrop.click($.proxy(this.hide, this))
-      }
-
-      if ( doAnimate ) {
-        this.$backdrop[0].offsetWidth // force reflow
-      }
-
-      this.$backdrop.addClass('in')
-
-      doAnimate ?
-        this.$backdrop.one(transitionEnd, callback) :
-        callback()
-
-    } else if ( !this.isShown && this.$backdrop ) {
-      this.$backdrop.removeClass('in')
-
-      $.support.transition && this.$element.hasClass('fade')?
-        this.$backdrop.one(transitionEnd, $.proxy(removeBackdrop, this)) :
-        removeBackdrop.call(this)
-
-    } else if ( callback ) {
-       callback()
-    }
-  }
-
-  function removeBackdrop() {
-    this.$backdrop.remove()
-    this.$backdrop = null
-  }
-
-  function escape() {
-    var that = this
-    if ( this.isShown && this.settings.keyboard ) {
-      $(document).bind('keyup.modal', function ( e ) {
-        if ( e.which == 27 ) {
-          that.hide()
-        }
-      })
-    } else if ( !this.isShown ) {
-      $(document).unbind('keyup.modal')
-    }
-  }
-
-
- /* MODAL PLUGIN DEFINITION
-  * ======================= */
-
-  $.fn.modal = function ( options ) {
-    var modal = this.data('modal')
-
-    if (!modal) {
-
-      if (typeof options == 'string') {
-        options = {
-          show: /show|toggle/.test(options)
-        }
-      }
-
-      return this.each(function () {
-        $(this).data('modal', new Modal(this, options))
-      })
-    }
-
-    if ( options === true ) {
-      return modal
-    }
-
-    if ( typeof options == 'string' ) {
-      modal[options]()
-    } else if ( modal ) {
-      modal.toggle()
-    }
-
-    return this
-  }
-
-  $.fn.modal.Modal = Modal
-
-  $.fn.modal.defaults = {
-    backdrop: false
-  , keyboard: false
-  , show: false
-  }
-
-
- /* MODAL DATA- IMPLEMENTATION
-  * ========================== */
-
-  $(document).ready(function () {
-    $('body').delegate('[data-controls-modal]', 'click', function (e) {
-      e.preventDefault()
-      var $this = $(this).data('show', true)
-      $('#' + $this.attr('data-controls-modal')).modal( $this.data() )
-    })
-  })
-
-}( window.jQuery || window.ender );