sequenceserver 0.7.9 → 0.8.0

data/public/js/bootstrap.dropdown.js

@@ -0,0 +1,92 @@
+/* ============================================================
+ * bootstrap-dropdown.js v2.0.2
+ * http://twitter.github.com/bootstrap/javascript.html#dropdowns
+ * ============================================================
+ * Copyright 2012 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"
+
+ /* DROPDOWN CLASS DEFINITION
+  * ========================= */
+
+  var toggle = '[data-toggle="dropdown"]'
+    , Dropdown = function ( element ) {
+        var $el = $(element).on('click.dropdown.data-api', this.toggle)
+        $('html').on('click.dropdown.data-api', function () {
+          $el.parent().removeClass('open')
+        })
+      }
+
+  Dropdown.prototype = {
+
+    constructor: Dropdown
+
+  , toggle: function ( e ) {
+      var $this = $(this)
+        , selector = $this.attr('data-target')
+        , $parent
+        , isActive
+
+      if (!selector) {
+        selector = $this.attr('href')
+        selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+      }
+
+      $parent = $(selector)
+      $parent.length || ($parent = $this.parent())
+
+      isActive = $parent.hasClass('open')
+
+      clearMenus()
+      !isActive && $parent.toggleClass('open')
+
+      return false
+    }
+
+  }
+
+  function clearMenus() {
+    $(toggle).parent().removeClass('open')
+  }
+
+
+  /* DROPDOWN PLUGIN DEFINITION
+   * ========================== */
+
+  $.fn.dropdown = function ( option ) {
+    return this.each(function () {
+      var $this = $(this)
+        , data = $this.data('dropdown')
+      if (!data) $this.data('dropdown', (data = new Dropdown(this)))
+      if (typeof option == 'string') data[option].call($this)
+    })
+  }
+
+  $.fn.dropdown.Constructor = Dropdown
+
+
+  /* APPLY TO STANDARD DROPDOWN ELEMENTS
+   * =================================== */
+
+  $(function () {
+    $('html').on('click.dropdown.data-api', clearMenus)
+    $('body').on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle)
+  })
+
+}( window.jQuery );

data/public/js/bootstrap.modal.js

@@ -0,0 +1,7 @@
+/**
+* Bootstrap.js by @fat & @mdo
+* plugins: bootstrap-modal.js
+* Copyright 2012 Twitter, Inc.
+* http://www.apache.org/licenses/LICENSE-2.0.txt
+*/
+!function(a){function c(){var b=this,c=setTimeout(function(){b.$element.off(a.support.transition.end),d.call(b)},500);this.$element.one(a.support.transition.end,function(){clearTimeout(c),d.call(b)})}function d(a){this.$element.hide().trigger("hidden"),e.call(this)}function e(b){var c=this,d=this.$element.hasClass("fade")?"fade":"";if(this.isShown&&this.options.backdrop){var e=a.support.transition&&d;this.$backdrop=a('<div class="modal-backdrop '+d+'" />').appendTo(document.body),this.options.backdrop!="static"&&this.$backdrop.click(a.proxy(this.hide,this)),e&&this.$backdrop[0].offsetWidth,this.$backdrop.addClass("in"),e?this.$backdrop.one(a.support.transition.end,b):b()}else!this.isShown&&this.$backdrop?(this.$backdrop.removeClass("in"),a.support.transition&&this.$element.hasClass("fade")?this.$backdrop.one(a.support.transition.end,a.proxy(f,this)):f.call(this)):b&&b()}function f(){this.$backdrop.remove(),this.$backdrop=null}function g(){var b=this;this.isShown&&this.options.keyboard?a(document).on("keyup.dismiss.modal",function(a){a.which==27&&b.hide()}):this.isShown||a(document).off("keyup.dismiss.modal")}var b=function(b,c){this.options=c,this.$element=a(b).delegate('[data-dismiss="modal"]',"click.dismiss.modal",a.proxy(this.hide,this))};b.prototype={constructor:b,toggle:function(){return this[this.isShown?"hide":"show"]()},show:function(){var b=this,c=a.Event("show");this.$element.trigger(c);if(this.isShown||c.isDefaultPrevented())return;a("body").addClass("modal-open"),this.isShown=!0,g.call(this),e.call(this,function(){var c=a.support.transition&&b.$element.hasClass("fade");b.$element.parent().length||b.$element.appendTo(document.body),b.$element.show(),c&&b.$element[0].offsetWidth,b.$element.addClass("in"),c?b.$element.one(a.support.transition.end,function(){b.$element.trigger("shown")}):b.$element.trigger("shown")})},hide:function(b){b&&b.preventDefault();var e=this;b=a.Event("hide"),this.$element.trigger(b);if(!this.isShown||b.isDefaultPrevented())return;this.isShown=!1,a("body").removeClass("modal-open"),g.call(this),this.$element.removeClass("in"),a.support.transition&&this.$element.hasClass("fade")?c.call(this):d.call(this)}},a.fn.modal=function(c){return this.each(function(){var d=a(this),e=d.data("modal"),f=a.extend({},a.fn.modal.defaults,d.data(),typeof c=="object"&&c);e||d.data("modal",e=new b(this,f)),typeof c=="string"?e[c]():f.show&&e.show()})},a.fn.modal.defaults={backdrop:!0,keyboard:!0,show:!0},a.fn.modal.Constructor=b,a(function(){a("body").on("click.modal.data-api",'[data-toggle="modal"]',function(b){var c=a(this),d,e=a(c.attr("data-target")||(d=c.attr("href"))&&d.replace(/.*(?=#[^\s]+$)/,"")),f=e.data("modal")?"toggle":a.extend({},e.data(),c.data());b.preventDefault(),e.modal(f)})})}(window.jQuery)

data/public/js/bootstrap.transition.js

@@ -0,0 +1,7 @@
+/**
+* Bootstrap.js by @fat & @mdo
+* plugins: bootstrap-transition.js
+* Copyright 2012 Twitter, Inc.
+* http://www.apache.org/licenses/LICENSE-2.0.txt
+*/
+!function(a){a(function(){a.support.transition=function(){var a=function(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in b)if(a.style[c]!==undefined)return b[c]}();return a&&{end:a}}()})}(window.jQuery)

data/public/js/jquery.index.js

@@ -0,0 +1,67 @@
+;(function ($) {
+    var defaults = {
+        threshold: 1
+    };
+
+    /*
+        Generate an index from the selected elements and add to or replace it
+        in the given container element.
+
+        Events:
+
+            add.index:
+
+                After the index has been created and added to the container.
+
+            remove.index:
+
+                When an index on the selected element is removed.
+
+        Options:
+
+            threshold:
+
+                Maximum number of elements selected with 'map' for which no
+                index is to be created.  Or the index should be deleted if
+                already exists.
+
+            container:
+
+                A jQuery selector.  The index is appended to or deleted from
+                the container.
+
+        Usage:
+
+            $('.resultn').index({container: '.results'})
+
+    */
+    $.fn.index = function (options) {
+        var options   = $.extend({}, defaults, options);
+        var container = $(options.container);
+
+        if (this.length > options.threshold) {
+            var entries = this.map(function () {
+                var id  = $(this).attr('id');
+                var sid = (id.length > 25) ? (id.slice(0, 22) + ' ...') : id // sid => short/display id :P
+                return '<li><a href="#' + id + '" title="' + id + '">' + sid + '</a></li>';
+            });
+
+            var index = $('<ul class="index">' + entries.get().join('') + '</ul>');
+
+            // remove previous index if any
+            container.find('.index').remove();
+            container.trigger('remove.index');
+
+            // add the new one
+            container.append(index);
+            container.trigger('add.index', index);
+        }
+        else {
+            // remove previous index if any
+            container.find('.index').remove();
+            container.trigger('remove.index');
+        }
+
+        return this;
+    }
+})(jQuery);

data/public/js/jquery.scrollspy.js

@@ -0,0 +1,74 @@
+;(function ($) {
+    var defaults = {
+        approach:   0,
+        overtravel: 0
+    };
+
+    /*
+        Trigger appropriate events when the selected element is scrolled in or
+        out of view.
+
+        An element is considered to be in view if the length of document
+        scrolled is greater than or equal to the offset of the element relative
+        to the top of the document and within the vertical span of the element.
+        (its height).
+
+        Vertical span of the element can be modified by adding required
+        'approach' and 'overtravel' length.
+
+        Events:
+
+            enter.scrollspy:
+
+                When the selected element scrolls into the view.
+
+            leave.scrollspy:
+
+                When the selected element scrolls out of the view.
+
+        Options:
+
+            approach:
+
+                Extend vertical span of the element from top.  It can be
+                positive or negative.
+
+            overtravel:
+
+                Extend vertical span of the element from bottom.  It can be
+                positive or negative.
+
+            The terminology: approach and overtravel, are borrowed from
+            Machining :).
+
+        Usage:
+
+            $('.resultn').scrollspy();
+
+    */
+    $.fn.scrollspy = function (options) {
+        var elements = this;
+        var options  = $.extend({}, defaults, options);
+
+        $(window).scroll(function() {
+            var scrolled = $(this).scrollTop();
+
+            elements.each(function() {
+                var element = $(this);
+
+                //compute threshold
+                var start = element.offset().top - options.approach;
+                var end   = start + element.height() + options.overtravel;
+
+                if (scrolled >= start && scrolled <= end){
+                    element.trigger('enter.scrollspy');
+                }
+                else {
+                    element.trigger('leave.scrollspy');
+                }
+            });
+        });
+
+        return this;
+    }
+})(jQuery);

data/public/js/jquery.ui.js

@@ -0,0 +1,57 @@
+/*! jQuery UI - v1.8.19 - 2012-04-16
+* https://github.com/jquery/jquery-ui
+* Includes: jquery.effects.core.js
+* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */
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+* Includes: jquery.effects.slide.js
+* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */
+(function(a,b){a.effects.slide=function(b){return this.queue(function(){var c=a(this),d=["position","top","bottom","left","right"],e=a.effects.setMode(c,b.options.mode||"show"),f=b.options.direction||"left";a.effects.save(c,d),c.show(),a.effects.createWrapper(c).css({overflow:"hidden"});var g=f=="up"||f=="down"?"top":"left",h=f=="up"||f=="left"?"pos":"neg",i=b.options.distance||(g=="top"?c.outerHeight({margin:!0}):c.outerWidth({margin:!0}));e=="show"&&c.css(g,h=="pos"?isNaN(i)?"-"+i:-i:i);var j={};j[g]=(e=="show"?h=="pos"?"+=":"-=":h=="pos"?"-=":"+=")+i,c.animate(j,{queue:!1,duration:b.duration,easing:b.options.easing,complete:function(){e=="hide"&&c.hide(),a.effects.restore(c,d),a.effects.removeWrapper(c),b.callback&&b.callback.apply(this,arguments),c.dequeue()}})})}})(jQuery);/*! jQuery UI - v1.8.19 - 2012-04-16
+* https://github.com/jquery/jquery-ui
+* Includes: jquery.effects.transfer.js
+* Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */
+(function(a,b){a.effects.transfer=function(b){return this.queue(function(){var c=a(this),d=a(b.options.to),e=d.offset(),f={top:e.top,left:e.left,height:d.innerHeight(),width:d.innerWidth()},g=c.offset(),h=a('<div class="ui-effects-transfer"></div>').appendTo(document.body).addClass(b.options.className).css({top:g.top,left:g.left,height:c.innerHeight(),width:c.innerWidth(),position:"absolute"}).animate(f,b.duration,b.options.easing,function(){h.remove(),b.callback&&b.callback.apply(c[0],arguments),c.dequeue()})})}})(jQuery);

data/public/js/sequenceserver.blast.js

@@ -15,11 +15,11 @@
         sequence_type_changed:
             When the type (nucleotide or protein) of the input sequence changes.
 
-        blast_valid:
-            If the current user input is sufficient to launch a BLAST
+        database_type_changed:
+            When a user selects one type of database (nucleotide or protein) over the other.
 
-        blast_invalid:
-            If the current user input is not sufficient to launch a BLAST
+        blast_method_changed:
+            When the change in input parameters lead to a change in the preferred blast method.
 
     TODO: should (probably) access UI objects through some sort of interface
 */
@@ -29,18 +29,16 @@ SS.blast = (function () {
     // 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
-        }
+        // can't determine the type of ultrashort queries
+        if (sequence.length < 10) { return undefined }
+
+        var putative_NA_count, threshold, i;
+        putative_NA_count = 0;
+        threshold = 0.9 * sequence.length;
 
         // count the number of putative NA
         for (i = 0; i < sequence.length; i++) {
@@ -49,13 +47,11 @@ SS.blast = (function () {
             }
         }
 
-        threshold = 0.9 * sequence.length
-
         return putative_NA_count > threshold ? 'nucleotide' : 'protein'
     }
 
     var type_of_sequences = function () {
-        var sequences = $('#sequence').val().split(/>.*/)
+        var sequences = $('#sequence').val().split(/>.*/);
         var type, tmp, i;
 
         for (i = 0; i < sequences.length; i++) {
@@ -70,27 +66,27 @@ SS.blast = (function () {
             }
             else if (tmp !== type) {
               // user has mixed different type of sequences
-              return undefined
+              return 'mixed'
             }
         }
 
         return type;
     }
 
+    /* */
+    var type_of_databases = function () {
+        return $('.databases input:checked').data('type');
+    }
+
     /*
         check if blast is valid (sufficient input to blast or not)
     */
-    var is_valid = function () {
+    var required_params_present = function () {
         // must enter a query
         if (!$('#sequence').val()) {
             return false;
         }
 
-        // must select a blast method
-        if (!$('.blastmethods input:checked').val()) {
-            return false;
-        }
-
         // must select atleast one database
         if (!$('.databases input:checked').val()) {
             return false;
@@ -100,20 +96,6 @@ SS.blast = (function () {
         return true;
     }
 
-    /*
-        signal blast's validity (sufficient input to blast or not)
-    */
-    var signal_blast_validity = function () {
-        $('#sequence, .blastmethods, .databases').change(function () {
-          if (is_valid()) {
-              $('form').trigger('blast_valid');
-          }
-          else {
-              $('form').trigger('blast_invalid');
-          }
-        });
-    }
-
     /*
         determine input sequence type, and trigger 'sequence_type_changed'
         event if the input sequence type has changed
@@ -133,6 +115,82 @@ SS.blast = (function () {
         });
     };
 
+    /* determine */
+    var signal_database_type_changed = function () {
+        var type = type_of_databases(), tmp;
+
+        $('.databases input').change(function () {
+            tmp = type_of_databases();
+
+            if (tmp != type) {
+                type = tmp;
+
+                //notify listeners
+                $(this).trigger('database_type_changed', type);
+            }
+        });
+    }
+
+    /* */
+    var signal_blast_method_changed = function () {
+        var method, tmp;
+
+        $('#blast').on('sequence_type_changed database_type_changed',
+            function (event) {
+                  tmp = determine_blast_method();
+
+                  if (tmp != method) {
+                      method = tmp;
+
+                      //notify listeners
+                      $(this).trigger('blast_method_changed', [method]);
+                  }
+            });
+    }
+
+    /*
+        Return a BLAST method to use for the selected database and input
+        sequence type.
+
+             database       method
+            ------------------------
+             protein        blastx
+             protein        blastp
+            ------------------------
+             nucleotide     tblastx
+             nucleotide     tblastn
+             nucleotide     blastn
+    */
+    var determine_blast_method = function () {
+        if (!required_params_present()) {
+            return
+        }
+
+        var database_type = type_of_databases();
+        var sequence_type = type_of_sequences();
+
+        //database type is always known
+        switch (database_type) {
+            case 'protein':
+                switch (sequence_type) {
+                    case undefined:
+                      return ['blastp', 'blastx'];
+                    case 'protein':
+                        return ['blastp'];
+                    case 'nucleotide':
+                        return ['blastx'];
+                }
+            case 'nucleotide':
+                switch (sequence_type) {
+                    case undefined:
+                      return ['tblastn', 'blastn', 'tblastx'];
+                    case 'protein':
+                        return ['tblastn'];
+                    case 'nucleotide':
+                        return ['blastn', 'tblastx'];
+                }
+        }
+    }
 
     /* public interface */
 
@@ -142,7 +200,8 @@ SS.blast = (function () {
 
     blast.init = function () {
         signal_sequence_type_changed();
-        signal_blast_validity();
+        signal_database_type_changed();
+        signal_blast_method_changed();
     }
 
     return blast;