sequenceserver 0.7.9 → 0.8.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- data/lib/sequenceserver.rb +55 -57
- data/lib/sequenceserver/blast.rb +51 -158
- data/lib/sequenceserver/database.rb +8 -2
- data/lib/sequenceserver/helpers.rb +14 -12
- data/lib/sequenceserver/options.rb +132 -0
- data/lib/sequenceserver/sequencehelpers.rb +4 -30
- data/public/css/bootstrap.dropdown.css +29 -0
- data/public/css/bootstrap.icons.css +155 -0
- data/public/css/bootstrap.min.css +399 -314
- data/public/css/bootstrap.modal.css +28 -0
- data/public/css/custom.css +183 -23
- data/public/img/glyphicons-halflings-white.png +0 -0
- data/public/img/glyphicons-halflings.png +0 -0
- data/public/js/bootstrap-typeahead.js +298 -0
- data/public/js/bootstrap.dropdown.js +92 -0
- data/public/js/bootstrap.modal.js +7 -0
- data/public/js/bootstrap.transition.js +7 -0
- data/public/js/jquery.index.js +67 -0
- data/public/js/jquery.scrollspy.js +74 -0
- data/public/js/jquery.ui.js +57 -0
- data/public/js/sequenceserver.blast.js +96 -37
- data/public/js/sequenceserver.js +157 -85
- data/public/js/store.min.js +2 -0
- data/public/js/yaml.js +24 -0
- data/sequenceserver.gemspec +5 -2
- data/tests/run +26 -0
- data/tests/test_sequencehelpers.rb +10 -18
- data/tests/test_sequenceserver_blast.rb +60 -0
- data/views/_options.erb +144 -0
- data/views/search.erb +133 -145
- metadata +135 -52
@@ -0,0 +1,28 @@
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/*!
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* Bootstrap v2.0.3
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*
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* Copyright 2012 Twitter, Inc
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* Licensed under the Apache License v2.0
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Designed and built with all the love in the world @twitter by @mdo and @fat.
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*/
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.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}
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.clearfix:after{clear:both;}
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.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}
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.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;}
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.modal-open .dropdown-menu{z-index:2050;}
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.modal-open .dropdown.open{*z-index:2050;}
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.modal-open .popover{z-index:2060;}
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.modal-open .tooltip{z-index:2070;}
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.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;}
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.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);}
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.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%;}
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.modal.fade.in{top:50%;}
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.modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;}
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.modal-body{overflow-y:auto;max-height:400px;padding:15px;}
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.modal-form{margin-bottom:0;}
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.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:"";}
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.modal-footer:after{clear:both;}
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.modal-footer .btn+.btn{margin-left:5px;margin-bottom:0;}
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.modal-footer .btn-group .btn+.btn{margin-left:-1px;}
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data/public/css/custom.css
CHANGED
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/* generic */
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html, body{
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height: 100%;
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}
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pre {
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font-family: Monospace;
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}
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br.large {
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line-height: 28px;
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}
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.control-group {
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margin-bottom: 0px;
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}
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.nojs-error {
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margin-top: 10px;
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padding: 10px;
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color: white;
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background-color: red;
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}
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.offset-left {
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margin-left: 20px;
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}
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fieldset legend {
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padding-left: 2%;
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margin-bottom: 0px;
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font-size: 16px;
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font-weight: bold;
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border: 0px;
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}
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/* contextual */
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body {
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background-color: #2B3E42;
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}
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.page {
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border-radius: 10px 10px 10px 10px;
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border-radius: 6px 6px 6px 6px;
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margin: 50px 0px;
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}
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#banner {
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background: #EBCD7B;
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padding: 2%;
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border-radius:
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border-radius: 6px 6px 0px 0px;
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text-align: center;
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}
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#blast {
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background-color: white;
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padding-top: 20px;
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padding-bottom: 20px;
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margin: 0px;
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}
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.detached-top {
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border-top-left-radius: 6px;
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border-top-right-radius: 6px;
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}
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.detached-bottom {
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border-radius: 0px 0px 6px 6px;
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}
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#sequence {
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height: 198px;
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width: 890px;
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display: block;
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margin: 0 auto;
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}
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.notifications {
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height: 0px;
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position: relative;
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top: -12px;
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}
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.notification {
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margin: 0 auto;
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z-index: 1050;
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border-radius: 6px;
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-webkit-border-radius: 6px;
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-moz-border-radius: 6px;
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box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
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-webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
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-moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
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font-size: 14px;
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font-weight: bold;
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text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
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text-align: center;
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padding: 6px 12px 6px 12px;
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}
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#sequence-type {
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font-style: italic;
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}
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#nucleotide-sequence-notification, #protein-sequence-notification {
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width: 250px;
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}
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#mixed-sequence-notification {
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width: 740px;
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}
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.databases {
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padding-bottom: 10px;
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}
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span.highlight {
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font-weight: bold;
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}
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.advanced label {
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display: inline-block;
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font-size: 16px;
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font-weight: bold;
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padding-left: 2%;
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}
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.advanced input {
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width: 440px;
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margin: 1% 1%;
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}
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.advanced
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margin: 0% 1% 1%;
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.advanced span {
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cursor: pointer;
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}
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.hover-focus {
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background-color: #FFC;
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}
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#method, #methods li {
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text-transform: uppercase;
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}
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#methods li {
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font-size: 15px;
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text-align: center;
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padding-top: 4px;
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padding-bottom: 4px;
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cursor: pointer;
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}
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.dropdown-menu li {
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border-bottom: 1px solid #ccc;
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}
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.dropdown-menu li:last-child {
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border-bottom: 0px;
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}
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#methods > button {
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height: 38px;
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}
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.results {
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background-color: #2B3E42;
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padding-top: 20px;
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padding-bottom: 20px;
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}
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#result {
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padding: 20px;
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background-color: white;
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border-radius: 6px;
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-moz-border-radius: 6px;
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}
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.resultn{
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.resultn {
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background-color: #dfefe6;
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margin: 18px 0px 18px 0px;
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border-radius: 6px;
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border: 1px solid transparent;
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}
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.
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ul.index {
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list-style: none;
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position: fixed;
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margin-left: 710px;
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padding: 15px;
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width: 200px;
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top: 5px;
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}
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ul.index li {
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padding: 3%;
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}
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ul.index li.focussed {
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background-color: #08C;
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}
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ul.index li.focussed a {
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color: white;
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text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2);
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}
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ul.index li:visited {
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}
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div.focussed {
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border: 1px solid black;
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}
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#underbar {
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background: #EBCD7B;
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padding: 1%;
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border-radius:
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border-bottom-right-radius: 6px;
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border-bottom-left-radius: 6px;
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text-align: center;
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}
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#spinner {
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color: gray;
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background-color: transparent;
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border: none;
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box-shadow: none;
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overflow: hidden;
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}
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#spinner > div {
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height: 200px;
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}
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#social p {
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font-size: 14px;
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}
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#social .buttons {
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width: 268px;
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margin: 0px auto;
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}
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.button-container {
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width: 74px;
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height: 32px;
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float: left;
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margin-right: 20px;
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text-align: center;
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}
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/* =============================================================
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* bootstrap-typeahead.js v2.0.3
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* http://twitter.github.com/bootstrap/javascript.html#typeahead
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* =============================================================
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* Copyright 2012 Twitter, Inc.
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* ============================================================ */
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!function($){
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"use strict"; // jshint ;_;
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/* TYPEAHEAD PUBLIC CLASS DEFINITION
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* ================================= */
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var Typeahead = function (element, options) {
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this.$element = $(element)
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this.options = $.extend({}, $.fn.typeahead.defaults, options)
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this.matcher = this.options.matcher || this.matcher
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this.sorter = this.options.sorter || this.sorter
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this.highlighter = this.options.highlighter || this.highlighter
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this.updater = this.options.updater || this.updater
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this.$menu = $(this.options.menu).appendTo('body')
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this.source = this.options.source
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this.shown = false
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this.listen()
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}
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Typeahead.prototype = {
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constructor: Typeahead
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, select: function () {
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var val = this.$menu.find('.active').attr('data-value')
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this.$element
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.val(this.updater(val))
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.change()
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return this.hide()
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}
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, updater: function (item) {
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return item
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}
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, show: function () {
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var pos = $.extend({}, this.$element.offset(), {
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height: this.$element[0].offsetHeight
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})
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this.$menu.css({
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top: pos.top + pos.height
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, left: pos.left
|
66
|
+
})
|
67
|
+
|
68
|
+
this.$menu.show()
|
69
|
+
this.shown = true
|
70
|
+
return this
|
71
|
+
}
|
72
|
+
|
73
|
+
, hide: function () {
|
74
|
+
this.$menu.hide()
|
75
|
+
this.shown = false
|
76
|
+
return this
|
77
|
+
}
|
78
|
+
|
79
|
+
, lookup: function (event) {
|
80
|
+
var that = this
|
81
|
+
, items
|
82
|
+
, q
|
83
|
+
|
84
|
+
this.query = this.$element.val()
|
85
|
+
|
86
|
+
if (!this.query) {
|
87
|
+
return this.shown ? this.hide() : this
|
88
|
+
}
|
89
|
+
|
90
|
+
//console.log(that.matcher);
|
91
|
+
|
92
|
+
items = $.grep(this.source, function (item) {
|
93
|
+
//console.log(item.toLowerCase());
|
94
|
+
//console.log(this);
|
95
|
+
//console.log(~item.toLowerCase().indexOf(this.query.toLowerCase()));
|
96
|
+
//console.log(that.matcher(item));
|
97
|
+
return that.matcher(item)
|
98
|
+
})
|
99
|
+
|
100
|
+
//console.log(typeof(this.query.toLowerCase()));
|
101
|
+
console.log(items);
|
102
|
+
|
103
|
+
items = this.sorter(items)
|
104
|
+
|
105
|
+
if (!items.length) {
|
106
|
+
return this.shown ? this.hide() : this
|
107
|
+
}
|
108
|
+
|
109
|
+
return this.render(items.slice(0, this.options.items)).show()
|
110
|
+
}
|
111
|
+
|
112
|
+
, matcher: function (item) {
|
113
|
+
console.log(item.toLowerCase());
|
114
|
+
console.log(this.query.toLowerCase());
|
115
|
+
var val = item.toLowerCase().indexOf(this.query.toLowerCase());
|
116
|
+
console.log(val);
|
117
|
+
return ~val;
|
118
|
+
}
|
119
|
+
|
120
|
+
, sorter: function (items) {
|
121
|
+
var beginswith = []
|
122
|
+
, caseSensitive = []
|
123
|
+
, caseInsensitive = []
|
124
|
+
, item
|
125
|
+
|
126
|
+
while (item = items.shift()) {
|
127
|
+
if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item)
|
128
|
+
else if (~item.indexOf(this.query)) caseSensitive.push(item)
|
129
|
+
else caseInsensitive.push(item)
|
130
|
+
}
|
131
|
+
|
132
|
+
return beginswith.concat(caseSensitive, caseInsensitive)
|
133
|
+
}
|
134
|
+
|
135
|
+
, highlighter: function (item) {
|
136
|
+
var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&')
|
137
|
+
return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) {
|
138
|
+
return '<strong>' + match + '</strong>'
|
139
|
+
})
|
140
|
+
}
|
141
|
+
|
142
|
+
, render: function (items) {
|
143
|
+
var that = this
|
144
|
+
|
145
|
+
items = $(items).map(function (i, item) {
|
146
|
+
i = $(that.options.item).attr('data-value', item)
|
147
|
+
i.find('a').html(that.highlighter(item))
|
148
|
+
return i[0]
|
149
|
+
})
|
150
|
+
|
151
|
+
items.first().addClass('active')
|
152
|
+
this.$menu.html(items)
|
153
|
+
return this
|
154
|
+
}
|
155
|
+
|
156
|
+
, next: function (event) {
|
157
|
+
var active = this.$menu.find('.active').removeClass('active')
|
158
|
+
, next = active.next()
|
159
|
+
|
160
|
+
if (!next.length) {
|
161
|
+
next = $(this.$menu.find('li')[0])
|
162
|
+
}
|
163
|
+
|
164
|
+
next.addClass('active')
|
165
|
+
}
|
166
|
+
|
167
|
+
, prev: function (event) {
|
168
|
+
var active = this.$menu.find('.active').removeClass('active')
|
169
|
+
, prev = active.prev()
|
170
|
+
|
171
|
+
if (!prev.length) {
|
172
|
+
prev = this.$menu.find('li').last()
|
173
|
+
}
|
174
|
+
|
175
|
+
prev.addClass('active')
|
176
|
+
}
|
177
|
+
|
178
|
+
, listen: function () {
|
179
|
+
this.$element
|
180
|
+
.on('blur', $.proxy(this.blur, this))
|
181
|
+
.on('keypress', $.proxy(this.keypress, this))
|
182
|
+
.on('keyup', $.proxy(this.keyup, this))
|
183
|
+
|
184
|
+
if ($.browser.webkit || $.browser.msie) {
|
185
|
+
this.$element.on('keydown', $.proxy(this.keypress, this))
|
186
|
+
}
|
187
|
+
|
188
|
+
this.$menu
|
189
|
+
.on('click', $.proxy(this.click, this))
|
190
|
+
.on('mouseenter', 'li', $.proxy(this.mouseenter, this))
|
191
|
+
}
|
192
|
+
|
193
|
+
, keyup: function (e) {
|
194
|
+
switch(e.keyCode) {
|
195
|
+
case 40: // down arrow
|
196
|
+
case 38: // up arrow
|
197
|
+
break
|
198
|
+
|
199
|
+
case 9: // tab
|
200
|
+
case 13: // enter
|
201
|
+
if (!this.shown) return
|
202
|
+
this.select()
|
203
|
+
break
|
204
|
+
|
205
|
+
case 27: // escape
|
206
|
+
if (!this.shown) return
|
207
|
+
this.hide()
|
208
|
+
break
|
209
|
+
|
210
|
+
default:
|
211
|
+
this.lookup()
|
212
|
+
}
|
213
|
+
|
214
|
+
e.stopPropagation()
|
215
|
+
e.preventDefault()
|
216
|
+
}
|
217
|
+
|
218
|
+
, keypress: function (e) {
|
219
|
+
if (!this.shown) return
|
220
|
+
|
221
|
+
switch(e.keyCode) {
|
222
|
+
case 9: // tab
|
223
|
+
case 13: // enter
|
224
|
+
case 27: // escape
|
225
|
+
e.preventDefault()
|
226
|
+
break
|
227
|
+
|
228
|
+
case 38: // up arrow
|
229
|
+
if (e.type != 'keydown') break
|
230
|
+
e.preventDefault()
|
231
|
+
this.prev()
|
232
|
+
break
|
233
|
+
|
234
|
+
case 40: // down arrow
|
235
|
+
if (e.type != 'keydown') break
|
236
|
+
e.preventDefault()
|
237
|
+
this.next()
|
238
|
+
break
|
239
|
+
}
|
240
|
+
|
241
|
+
e.stopPropagation()
|
242
|
+
}
|
243
|
+
|
244
|
+
, blur: function (e) {
|
245
|
+
var that = this
|
246
|
+
setTimeout(function () { that.hide() }, 150)
|
247
|
+
}
|
248
|
+
|
249
|
+
, click: function (e) {
|
250
|
+
e.stopPropagation()
|
251
|
+
e.preventDefault()
|
252
|
+
this.select()
|
253
|
+
}
|
254
|
+
|
255
|
+
, mouseenter: function (e) {
|
256
|
+
this.$menu.find('.active').removeClass('active')
|
257
|
+
$(e.currentTarget).addClass('active')
|
258
|
+
}
|
259
|
+
|
260
|
+
}
|
261
|
+
|
262
|
+
|
263
|
+
/* TYPEAHEAD PLUGIN DEFINITION
|
264
|
+
* =========================== */
|
265
|
+
|
266
|
+
$.fn.typeahead = function (option) {
|
267
|
+
return this.each(function () {
|
268
|
+
var $this = $(this)
|
269
|
+
, data = $this.data('typeahead')
|
270
|
+
, options = typeof option == 'object' && option
|
271
|
+
if (!data) $this.data('typeahead', (data = new Typeahead(this, options)))
|
272
|
+
if (typeof option == 'string') data[option]()
|
273
|
+
})
|
274
|
+
}
|
275
|
+
|
276
|
+
$.fn.typeahead.defaults = {
|
277
|
+
source: []
|
278
|
+
, items: 8
|
279
|
+
, menu: '<ul class="typeahead dropdown-menu"></ul>'
|
280
|
+
, item: '<li><a href="#"></a></li>'
|
281
|
+
}
|
282
|
+
|
283
|
+
$.fn.typeahead.Constructor = Typeahead
|
284
|
+
|
285
|
+
|
286
|
+
/* TYPEAHEAD DATA-API
|
287
|
+
* ================== */
|
288
|
+
|
289
|
+
$(function () {
|
290
|
+
$('body').on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) {
|
291
|
+
var $this = $(this)
|
292
|
+
if ($this.data('typeahead')) return
|
293
|
+
e.preventDefault()
|
294
|
+
$this.typeahead($this.data())
|
295
|
+
})
|
296
|
+
})
|
297
|
+
|
298
|
+
}(window.jQuery);
|