sequenceserver 0.7.9 → 0.8.0

data/public/css/bootstrap.modal.css

@@ -0,0 +1,28 @@
+/*!
+ * Bootstrap v2.0.3
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}
+.clearfix:after{clear:both;}
+.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}
+.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;}
+.modal-open .dropdown-menu{z-index:2050;}
+.modal-open .dropdown.open{*z-index:2050;}
+.modal-open .popover{z-index:2060;}
+.modal-open .tooltip{z-index:2070;}
+.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;}
+.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);}
+.modal{position:fixed;top:50%;left:50%;z-index:1050;overflow:auto;width:560px;margin:-250px 0 0 -280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-ms-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;}
+.modal.fade.in{top:50%;}
+.modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;}
+.modal-body{overflow-y:auto;max-height:400px;padding:15px;}
+.modal-form{margin-bottom:0;}
+.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";}
+.modal-footer:after{clear:both;}
+.modal-footer .btn+.btn{margin-left:5px;margin-bottom:0;}
+.modal-footer .btn-group .btn+.btn{margin-left:-1px;}

data/public/css/custom.css

@@ -1,8 +1,26 @@
-/* generic */
 html, body{
   height: 100%;
 }
 
+pre {
+  font-family: Monospace;
+}
+
+br.large {
+  line-height: 28px;
+}
+
+.control-group {
+  margin-bottom: 0px;
+}
+
+.nojs-error {
+  margin-top: 10px;
+  padding: 10px;
+  color: white;
+  background-color: red;
+}
+
 .offset-left {
   margin-left: 20px;
 }
@@ -19,52 +37,151 @@ html, body{
 
 fieldset legend {
   padding-left: 2%;
+  margin-bottom: 0px;
+  font-size: 16px;
+  font-weight: bold;
+  border: 0px;
 }
 
-/* contextual */
 body {
   background-color: #2B3E42;
 }
 
 .page {
-  background-color: white;
-  border-radius: 10px 10px 10px 10px;
+  border-radius: 6px 6px 6px 6px;
   margin: 50px 0px;
 }
 
 #banner {
   background: #EBCD7B;
   padding: 2%;
-  border-radius: 10px 10px 0px 0px;
+  border-radius: 6px 6px 0px 0px;
   text-align: center;
 }
 
+#blast {
+  background-color: white;
+  padding-top: 20px;
+  padding-bottom: 20px;
+  margin: 0px;
+}
+
+.detached-top {
+  border-top-left-radius: 6px;
+  border-top-right-radius: 6px;
+}
+
+.detached-bottom {
+  border-radius: 0px 0px 6px 6px;
+}
+
 #sequence {
-  width: 680px;
+  height: 198px;
+  width: 890px;
+  display: block;
+  margin: 0 auto;
+}
+
+.notifications {
+  height: 0px;
+  position: relative;
+  top: -12px;
+}
+
+.notification {
+  margin: 0 auto;
+  z-index: 1050;
+  border-radius: 6px;
+  -webkit-border-radius: 6px;
+  -moz-border-radius: 6px;
+  box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+  -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+  -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+  font-size: 14px;
+  font-weight: bold;
+  text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
+  text-align: center;
+  padding: 6px 12px 6px 12px;
+}
+
+#sequence-type {
+  font-style: italic;
+}
+
+#nucleotide-sequence-notification, #protein-sequence-notification {
+  width: 250px;
+}
+
+#mixed-sequence-notification {
+  width: 740px;
+}
+
+.databases {
+  padding-bottom: 10px;
+}
+
+span.highlight {
+  font-weight: bold;
 }
 
 .advanced label {
-  text-align: left;
-  padding: 0px;
-  width: auto;
-  cursor:pointer;
+  display: inline-block;
+  font-size: 16px;
+  font-weight: bold;
+  padding-left: 2%;
 }
 
 .advanced input {
+  width: 440px;
   margin: 1% 1%;
 }
 
-.advanced .help {
-  display: none;
-  margin: 0% 1% 1%;
+.advanced span {
+  cursor: pointer;
 }
 
-#result{
+.hover-focus {
+  background-color: #FFC;
+}
+
+#method, #methods li {
+  text-transform: uppercase;
+}
+
+#methods li {
+  font-size: 15px;
+  text-align: center;
+  padding-top: 4px;
+  padding-bottom: 4px;
+  cursor: pointer;
+}
+
+.dropdown-menu li {
+  border-bottom: 1px solid #ccc;
+}
+
+.dropdown-menu li:last-child {
+  border-bottom: 0px;
+}
+
+#methods > button {
+  height: 38px;
+}
+
+.results {
+  background-color: #2B3E42;
+  padding-top: 20px;
+  padding-bottom: 20px;
+}
+
+#result {
+  padding: 20px;
+  background-color: white;
   border-radius: 6px;
   -moz-border-radius: 6px;
 }
 
-.resultn{
+.resultn {
   background-color: #dfefe6;
   margin: 18px 0px 18px 0px;
   border-radius: 6px;
@@ -73,25 +190,68 @@ body {
   border: 1px solid transparent;
 }
 
-.focussed {
+ul.index {
+  list-style: none;
+  position: fixed;
+  margin-left: 710px;
+  padding: 15px;
+  width: 200px;
+  top: 5px;
+}
+
+ul.index li {
+  padding: 3%;
+}
+
+ul.index li.focussed {
+  background-color: #08C;
+}
+
+ul.index li.focussed a {
+  color: white;
+  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2);
+}
+
+ul.index li:visited {
+}
+
+div.focussed {
   border: 1px solid black;
 }
 
 #underbar {
   background: #EBCD7B;
   padding: 1%;
-  border-radius: 0px 0px 10px 10px;
+  border-bottom-right-radius: 6px;
+  border-bottom-left-radius: 6px;
   text-align: center;
 }
 
-.inputs-list {
-  padding-left: 3%;
+#spinner {
+  color: gray;
+  background-color: transparent;
+  border: none;
+  box-shadow: none;
+  overflow: hidden;
 }
 
-.inputs-list li {
-  padding: 1%;
+#spinner > div {
+  height: 200px;
+}
+
+#social p {
+  font-size: 14px;
 }
 
-fieldset {
-  padding-top: 0;
+#social .buttons {
+  width: 268px;
+  margin: 0px auto;
+}
+
+.button-container {
+  width: 74px;
+  height: 32px;
+  float: left;
+  margin-right: 20px;
+  text-align: center;
 }

data/public/js/bootstrap-typeahead.js

@@ -0,0 +1,298 @@
+/* =============================================================
+ * bootstrap-typeahead.js v2.0.3
+ * http://twitter.github.com/bootstrap/javascript.html#typeahead
+ * =============================================================
+ * 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($){
+
+  "use strict"; // jshint ;_;
+
+
+ /* TYPEAHEAD PUBLIC CLASS DEFINITION
+  * ================================= */
+
+  var Typeahead = function (element, options) {
+    this.$element = $(element)
+    this.options = $.extend({}, $.fn.typeahead.defaults, options)
+    this.matcher = this.options.matcher || this.matcher
+    this.sorter = this.options.sorter || this.sorter
+    this.highlighter = this.options.highlighter || this.highlighter
+    this.updater = this.options.updater || this.updater
+    this.$menu = $(this.options.menu).appendTo('body')
+    this.source = this.options.source
+    this.shown = false
+    this.listen()
+  }
+
+  Typeahead.prototype = {
+
+    constructor: Typeahead
+
+  , select: function () {
+      var val = this.$menu.find('.active').attr('data-value')
+      this.$element
+        .val(this.updater(val))
+        .change()
+      return this.hide()
+    }
+
+  , updater: function (item) {
+      return item
+    }
+
+  , show: function () {
+      var pos = $.extend({}, this.$element.offset(), {
+        height: this.$element[0].offsetHeight
+      })
+
+      this.$menu.css({
+        top: pos.top + pos.height
+      , left: pos.left
+      })
+
+      this.$menu.show()
+      this.shown = true
+      return this
+    }
+
+  , hide: function () {
+      this.$menu.hide()
+      this.shown = false
+      return this
+    }
+
+  , lookup: function (event) {
+      var that = this
+        , items
+        , q
+
+      this.query = this.$element.val()
+
+      if (!this.query) {
+        return this.shown ? this.hide() : this
+      }
+
+      //console.log(that.matcher);
+
+      items = $.grep(this.source, function (item) {
+        //console.log(item.toLowerCase());
+        //console.log(this);
+        //console.log(~item.toLowerCase().indexOf(this.query.toLowerCase()));
+        //console.log(that.matcher(item));
+        return that.matcher(item)
+      })
+
+      //console.log(typeof(this.query.toLowerCase()));
+      console.log(items);
+
+      items = this.sorter(items)
+
+      if (!items.length) {
+        return this.shown ? this.hide() : this
+      }
+
+      return this.render(items.slice(0, this.options.items)).show()
+    }
+
+  , matcher: function (item) {
+      console.log(item.toLowerCase());
+      console.log(this.query.toLowerCase());
+      var val = item.toLowerCase().indexOf(this.query.toLowerCase());
+      console.log(val);
+      return ~val;
+    }
+
+  , sorter: function (items) {
+      var beginswith = []
+        , caseSensitive = []
+        , caseInsensitive = []
+        , item
+
+      while (item = items.shift()) {
+        if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item)
+        else if (~item.indexOf(this.query)) caseSensitive.push(item)
+        else caseInsensitive.push(item)
+      }
+
+      return beginswith.concat(caseSensitive, caseInsensitive)
+    }
+
+  , highlighter: function (item) {
+      var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&')
+      return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) {
+        return '<strong>' + match + '</strong>'
+      })
+    }
+
+  , render: function (items) {
+      var that = this
+
+      items = $(items).map(function (i, item) {
+        i = $(that.options.item).attr('data-value', item)
+        i.find('a').html(that.highlighter(item))
+        return i[0]
+      })
+
+      items.first().addClass('active')
+      this.$menu.html(items)
+      return this
+    }
+
+  , next: function (event) {
+      var active = this.$menu.find('.active').removeClass('active')
+        , next = active.next()
+
+      if (!next.length) {
+        next = $(this.$menu.find('li')[0])
+      }
+
+      next.addClass('active')
+    }
+
+  , prev: function (event) {
+      var active = this.$menu.find('.active').removeClass('active')
+        , prev = active.prev()
+
+      if (!prev.length) {
+        prev = this.$menu.find('li').last()
+      }
+
+      prev.addClass('active')
+    }
+
+  , listen: function () {
+      this.$element
+        .on('blur',     $.proxy(this.blur, this))
+        .on('keypress', $.proxy(this.keypress, this))
+        .on('keyup',    $.proxy(this.keyup, this))
+
+      if ($.browser.webkit || $.browser.msie) {
+        this.$element.on('keydown', $.proxy(this.keypress, this))
+      }
+
+      this.$menu
+        .on('click', $.proxy(this.click, this))
+        .on('mouseenter', 'li', $.proxy(this.mouseenter, this))
+    }
+
+  , keyup: function (e) {
+      switch(e.keyCode) {
+        case 40: // down arrow
+        case 38: // up arrow
+          break
+
+        case 9: // tab
+        case 13: // enter
+          if (!this.shown) return
+          this.select()
+          break
+
+        case 27: // escape
+          if (!this.shown) return
+          this.hide()
+          break
+
+        default:
+          this.lookup()
+      }
+
+      e.stopPropagation()
+      e.preventDefault()
+  }
+
+  , keypress: function (e) {
+      if (!this.shown) return
+
+      switch(e.keyCode) {
+        case 9: // tab
+        case 13: // enter
+        case 27: // escape
+          e.preventDefault()
+          break
+
+        case 38: // up arrow
+          if (e.type != 'keydown') break
+          e.preventDefault()
+          this.prev()
+          break
+
+        case 40: // down arrow
+          if (e.type != 'keydown') break
+          e.preventDefault()
+          this.next()
+          break
+      }
+
+      e.stopPropagation()
+    }
+
+  , blur: function (e) {
+      var that = this
+      setTimeout(function () { that.hide() }, 150)
+    }
+
+  , click: function (e) {
+      e.stopPropagation()
+      e.preventDefault()
+      this.select()
+    }
+
+  , mouseenter: function (e) {
+      this.$menu.find('.active').removeClass('active')
+      $(e.currentTarget).addClass('active')
+    }
+
+  }
+
+
+  /* TYPEAHEAD PLUGIN DEFINITION
+   * =========================== */
+
+  $.fn.typeahead = function (option) {
+    return this.each(function () {
+      var $this = $(this)
+        , data = $this.data('typeahead')
+        , options = typeof option == 'object' && option
+      if (!data) $this.data('typeahead', (data = new Typeahead(this, options)))
+      if (typeof option == 'string') data[option]()
+    })
+  }
+
+  $.fn.typeahead.defaults = {
+    source: []
+  , items: 8
+  , menu: '<ul class="typeahead dropdown-menu"></ul>'
+  , item: '<li><a href="#"></a></li>'
+  }
+
+  $.fn.typeahead.Constructor = Typeahead
+
+
+ /* TYPEAHEAD DATA-API
+  * ================== */
+
+  $(function () {
+    $('body').on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) {
+      var $this = $(this)
+      if ($this.data('typeahead')) return
+      e.preventDefault()
+      $this.typeahead($this.data())
+    })
+  })
+
+}(window.jQuery);