sequenceserver 1.0.0.pre.1 → 1.0.0.pre.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b4b6422d0e86b47690118cf32a0633609fd8e545
-  data.tar.gz: 01dda58ef4ab7bac5c889508361be848482cfc75
+  metadata.gz: 3f26e8eac4c55a9a2a0997d2ab6e922c88ded0d8
+  data.tar.gz: 60684bb5f9291fcbbfefd410517ea3892df9ff5c
 SHA512:
-  metadata.gz: c469b959e1fa91763766a7584b2b8ba6950c057d68319cb5ffc7e7dffe8b903bdff88037264ff9a6e71a6b2914a8c733e061b0c065c6934af6f41e633f01e889
-  data.tar.gz: 6cc6dcf46bbf6e4d93437e284102083de62fb30e35e18f0a6f63461dfbaa27f1fe9e7a019b2bcab48ca84d67b787598dc7fde277dcb9ffaad9c507f64e76b89c
+  metadata.gz: a51d9aff1dc67c12898295dbbc36452216820c22695a0e2b1507fa977d49fe8cf235f2da44762b0a5229bce2e59266b00358f40b51a072fbb9de007b9b60bef0
+  data.tar.gz: 8042ec1559d3719d2f910681c8cb4988d6cf0fe81d4205d5b596929be31045b0309ec44ad3bd335a457fae2c3ad0c1d80dc0be4c3322fc5d07501af494210695

data/public/css/custom.css

@@ -182,6 +182,7 @@ a.disabled:hover {
 .label-reset {
   color: inherit;
   line-height: inherit;
+  font-weight: normal;
 }
 
 /**
@@ -309,11 +310,12 @@ h1,h2,h3,h4,h5,h6,.page-header {
 }
 
 .main {
-  border-right: 1px solid #ddd;
+  /*border-right: 1px solid #ddd;*/
 }
 
 .sidebar > .page-header > h4 {
-  padding: 8px 0px 0px 8px;
+  padding: 10px 0px 0px 0px;
+  font-size: 14px;
 }
 
 .sidebar.affix {
@@ -393,6 +395,14 @@ svg:not(:root) {
   letter-spacing: 1px;
 }
 
+.fastan > .page-header {
+  padding-bottom: 8px;
+}
+.fastan > .page-content {
+  padding-top: 8px;
+  padding-left: 0;
+}
+
 .footer a:first-child {
   vertical-align: super;
 }
@@ -453,21 +463,8 @@ svg:not(:root) {
 }
 
 .glow {
-  -webkit-transform: translateZ(0);
-  transform: translateZ(0);
-  box-shadow: 0 0 1px rgba(0, 0, 0, 0);
-  -webkit-backface-visibility: hidden;
-  backface-visibility: hidden;
-  -moz-osx-font-smoothing: grayscale;
-  -webkit-transition-duration: 0.3s;
-  transition-duration: 0.3s;
-  -webkit-transition-property: box-shadow;
-  transition-property: box-shadow;
-  box-shadow: 0 0 8px rgba(0, 0, 0, 0.6);
+  box-shadow: 0 0 2px rgba(0, 0, 0, 0.6);
+  border-left: 2px solid #f0ad4e;
   padding-left: 16px;
   padding-right: 16px;
 }
-
-.pos-marker {
-  display: none;
-}

data/public/js/sequence.js

@@ -275,10 +275,7 @@ Sequence = Class(
 		this._buildFormatSelector();
 		
 		// DIV for the sequence
-		this._contentDiv = jQuery('<div></div>').appendTo(this._container);
-		this._contentDiv.css({
-				'text-align': 'left'
-			});
+		this._contentDiv = jQuery('<div/>').appendTo(this._container);
 		
 		// Initialize highlighting 
 		this._highlights = this.opt.highlights;
@@ -836,21 +833,18 @@ Sequence = Class(
      * Inputs: -
      */
 	_drawCodata : function() {
-		
-		var self = this;
-		var a = this.opt.sequence.toUpperCase().split('');
-		var pre = jQuery('<pre/>').appendTo(this._contentDiv);
+		var seq = this.opt.sequence.toUpperCase().split('');
 
-		var i = 0;
-		var str = 'ENTRY           ' + this.opt.id + '<br/>';
-		str += 'SEQUENCE<br/>';
+		// Add header.
 		if ( this.opt.formatOptions !== undefined ){
 			if(this.opt.formatOptions.title !== undefined ){
-				if (this.opt.formatOptions.title == false) {
-					str = '';
-				}			
+				if (this.opt.formatOptions.title != false) {
+					var header =
+						$('<pre/>').addClass('header').appendTo(this._contentDiv);
+					header.html('ENTRY           ' + this.opt.id +
+								'<br/>SEQUENCE<br/>'); }			
 			}
-		} 
+		}
 		
 		/* Correct column size in case the sequence is as small peptide */
 		var numCols = this.opt.columns.size;
@@ -868,19 +862,18 @@ Sequence = Class(
 			    numColsForSpace: 0,
 			    spaceBetweenChars: true
 		};
+		this._drawSequence(seq, opt);
 		
-		str += this._drawSequence(a, opt);
-		
-		var footer = '<br/>///';
+		// Add footer.
 		if (this.opt.formatOptions !== undefined) {
 			if (this.opt.formatOptions.footer !== undefined) {
-				if (this.opt.formatOptions.footer == false) {
-					footer = '';
+				if (this.opt.formatOptions.footer != false) {
+					var footer =
+						$('<pre/>').addClass('footer').appendTo(this._contentDiv);
+					footer.html('<br/>///');
 				}
 			}
 		}
-		str += footer;
-		pre.html(str);
 		
 		this._drawAnnotations(opt);
 	},
@@ -1066,9 +1059,7 @@ Sequence = Class(
      * Inputs: -
      */
 	_drawPride : function() {
-		var self = this;
-		var a = this.opt.sequence.toUpperCase().split('');
-		var pre = jQuery('<pre></pre>').appendTo(this._contentDiv);
+		var seq = this.opt.sequence.toUpperCase().split('');
 		
 		/* Correct column size in case the sequence is as small peptide */
 		var numCols = this.opt.columns.size;
@@ -1079,18 +1070,14 @@ Sequence = Class(
 		opt = {
 			numLeft: true,
 			numLeftSize: 5,
-			numLeftPad:'0',
-			numRight: true,
+			numLeftPad: ' ',
+			numRight: false,
 			numRightSize: 5,
-			numRightPad: '0',
+			numRightPad: '',
 			numCols: numCols,
-		    numColsForSpace: self.opt.columns.spacedEach
+		    numColsForSpace: this.opt.columns.spacedEach
 		};
-		
-		pre.html(
-			this._drawSequence(a, opt)
-		);
-		
+		this._drawSequence(seq, opt);
 		this._drawAnnotations(opt);
 	},
 	/* 
@@ -1101,34 +1088,38 @@ Sequence = Class(
      * 			 opt -> {Object} opt The CUSTOM format.
      */
 	_drawSequence : function(a, opt) {
-		var str = '';
+        var indL = '';
+		var indT = '';
+		var indR = '\n';
+		var str  = '';
 
 		// Index at top?
 		if( opt.numTop )
 		{
-			str += '<span class="numTop pos-marker">'
+			indT += '<span class="numTop pos-marker">'
 			var size = (opt.spaceBetweenChars)? opt.numTopEach*2: opt.numTopEach;
 			
 			if (opt.numLeft) {
-				str += this._formatIndex(' ', opt.numLeftSize, ' ');
+				indT += this._formatIndex(' ', opt.numLeftSize, ' ');
 			}
 			
-			str += this._formatIndex(' ', size, ' ');
+			indT += this._formatIndex(' ', size, ' ');
 			
 			for(var x = opt.numTopEach; x < opt.numCols; x += opt.numTopEach) {
-				str += this._formatIndex(x, size, ' ', true);
+				indT += this._formatIndex(x, size, ' ', true);
 			}
-			str += '</span>'
+			indT += '</span>'
 		}
 		
 		
 		// Index at the left?
 		if (opt.numLeft) {
-			str += '<span id="numLeft_' + this.getId() + '_' + 0 + '"';
-			str += 'class="pos-marker">'
-			str += this._formatIndex(1, opt.numLeftSize, opt.numLeftPad);
-			str += '  ';
-			str += '</span>';
+			indL += '<span id="numLeft_' + this.getId() + '_' + 0 + '"';
+			indL += 'class="pos-marker">'
+			indL += this._formatIndex(1, opt.numLeftSize, opt.numLeftPad);
+			indL += '  ';
+			indL += '</span>';
+            indL += '\n';
 		}
 
 		var j=1;
@@ -1138,30 +1129,33 @@ Sequence = Class(
 				str += '<span class="sequence" id="' + this.getId() + '_' + i + '">' + a[i-1] + '</span>';
 				
 				if (opt.numRight) {
-					str += '<span id="numRight_' + this.getId() + '_' + i + '"';
-					str += 'class="pos-marker">'
-					str += '  ';
-					str += this._formatIndex(i, opt.numRightSize, opt.numRightPad);	
-					str += '</span>';
+					indR += '<span id="numRight_' + this.getId() + '_' + i + '"';
+					indR += 'class="pos-marker">'
+					indR += '  ';
+					indR += this._formatIndex(i, opt.numRightSize, opt.numRightPad);	
+					indR += '</span>';
+					indR += '\n';
 				}
 				
 				str += '<br/>';
 				
 				var aaRemaining = a.length - i;
 				if (opt.numLeft && aaRemaining > 0) {
-					str += '<span id="numLeft_' + this.getId() + '_' + i + '"';
-					str += 'class="pos-marker">'
-					str += this._formatIndex(i+1, opt.numLeftSize, opt.numLeftPad);
-					str += '  ';
-					str += '</span>';
-				}
+					indL += '<span id="numLeft_' + this.getId() + '_' + i + '"';
+					indL += 'class="pos-marker">'
+					indL += this._formatIndex(i+1, opt.numLeftSize, opt.numLeftPad);
+					indL += '  ';
+					indL += '</span>';
+                    indL += '\n';
+                }
 				
 				j = 1;
 				
 			} else {
-                str += '<span class="sequence" id="' + this.getId() + '_' + i + '">' + a[i-1];
-				str += ( j % opt.numColsForSpace == 0)? ' ' : '';
-				str += (opt.spaceBetweenChars)? ' ' : '';
+                str += '<span class="sequence" id="' + this.getId() + '_' + i + '"';
+				str += (j % opt.numColsForSpace == 0)? ' style="letter-spacing: 1em;"' : '';
+				str += (opt.spaceBetweenChars)? ' style="letter-spacing: 1em;"' : '';
+				str += '">' + a[i-1];
 				str += '</span>';
 				j++;
 			}
@@ -1173,6 +1167,47 @@ Sequence = Class(
 			str = "<pre>" + str + "</pre>";
 		}	
 			
+
+		var ret = [];
+		if (opt.numTop) {
+			$('<pre/>')
+			.html(indT)
+			.addClass('indT')
+			.css({
+				color: '#aaa'
+			})
+			.appendTo(this._contentDiv);
+		}
+		if (opt.numLeft) {
+			$('<pre/>')
+			.html(indL)
+			.addClass('indL')
+			.css({
+				color: '#aaa',
+				display: 'inline-block'
+			})
+			.appendTo(this._contentDiv);
+		}
+
+		$('<pre/>')
+		.html(str)
+		.addClass('seqF')
+		.css({
+			display: 'inline-block'
+		})
+		.appendTo(this._contentDiv);
+
+		if (opt.numRight) {
+			$('<pre/>')
+			.html(indR)
+			.addClass('indR')
+			.css({
+				color: '#aaa',
+				display: 'inline-block'
+			})
+			.appendTo(this._contentDiv);
+		}
+
 		return str;
 	},
 	/* 

data/public/js/sequenceserver.js

@@ -55,16 +55,15 @@
 
 (function ($) {
     $.fn.poll = function () {
-        var that, val, tmp;
-
-        that = this;
-        val  = that.val();
+        var that = this;
+        var val  = null;
+        var newval;
 
         (function ping () {
-            tmp = that.val();
+            newval = that.val();
 
-            if (tmp != val){
-                val = tmp;
+            if (newval != val){
+                val = newval;
                 that.change();
             }
 
@@ -266,8 +265,6 @@ if (!SS) {
         this.$sequenceFile = $('#sequence-file');
         this.$sequenceControls = $('.sequence-controls');
 
-        this.$sequence.poll();
-
         SS.blast.init();
     };
 
@@ -280,7 +277,7 @@ if (!SS) {
 SS.selectHit = function (checkbox) {
     if (!checkbox || !checkbox.value) return;
 
-    var $hitn = $('.hitn[data-hit-def="' + checkbox.value + '"]');
+    var $hitn = $($(checkbox).data('target'));
 
     // Highlight selected hit and sync checkboxes if sequence viewer is open.
     if(checkbox.checked) {
@@ -361,9 +358,10 @@ SS.showSequenceViewer = (function () {
         var widget = new Sequence({
             sequence: sequence.value,
             target: widgetId,
-            format: 'CODATA',
+            format: 'PRIDE',
             columns: {
-                size: 35
+                size: 40,
+                spacedEach: 5
             },
             formatOptions: {
                 title: false,
@@ -725,4 +723,6 @@ $(document).ready(function(){
 
         return false;
     });
+
+    SS.$sequence.poll();
 });

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '1.0.0-1'
+  s.version     = '1.0.0-2'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Vivek Rai', 'Yannick Wurm']
   s.email       = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
   s.homepage    = 'http://sequenceserver.com'

data/views/result.erb

@@ -109,7 +109,7 @@
                   <div class="hit-links text-right">
                     <label>
                       <input
-                      type="checkbox" value=<%="#{ hit.accession }"%>>
+                      type="checkbox" value="<%= hit.accession %>" data-target="<%= "#Query_#{query.number}_hit_#{hit.number}" %>">
                       Select
                     </label>
                     <% report.link_per_hit(hit.accession).each do |link| %>
@@ -142,18 +142,15 @@ Total letters in queried databases: <%= report.stats[1] %>
 
   <% unless report.queries.length == 1 && report.queries.first.hits.empty? %>
     <div
-      class="side col-md-3">
+      class="side col-md-3 hidden-xs hidden-sm">
       <div
         class="sidebar">
         <div
           class="page-header">
           <h4>
-            <i class="fa fa-street-view"></i>
-            <small>
-              <%= report.queries.length %> <%= report.queries.length > 1 ? 'queries' : 'query' %>,
-              <%= report.querydb.length %> <%= report.querydb.length > 1 ? 'databases' : 'database' %>,
-              <%= report.program.upcase %>
-            </small>
+            <%= report.program.upcase %>:
+            <%= report.queries.length %> <%= report.queries.length > 1 ? 'queries' : 'query' %>,
+            <%= report.querydb.length %> <%= report.querydb.length > 1 ? 'databases' : 'database' %>
           </h4>
         </div>
         <ul
@@ -176,10 +173,7 @@ Total letters in queried databases: <%= report.stats[1] %>
         <div
           class="page-header">
           <h4>
-            <i class="fa fa-download"></i>
-            <small>
-              FASTA, XML, TSV
-            </small>
+            Download FASTA, XML, TSV
           </h4>
         </div>
         <ul

data/views/search.erb

@@ -16,9 +16,9 @@
 
   <link href='http://fonts.googleapis.com/css?family=Roboto:400' rel='stylesheet' type='text/css'>
   <link href='http://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
-  <link rel="stylesheet" media="screen" type="text/css" href="css/bootstrap.min.css"/>
-  <link rel="stylesheet" media="screen" type="text/css" href="css/font-awesome.min.css"/>
-  <link rel="stylesheet" media="screen" type="text/css" href="css/custom.css"/>
+  <link rel="stylesheet" media="screen,print" type="text/css" href="css/bootstrap.min.css"/>
+  <link rel="stylesheet" media="screen,print" type="text/css" href="css/font-awesome.min.css"/>
+  <link rel="stylesheet" media="screen,print" type="text/css" href="css/custom.css"/>
 </head>
 
 <body>
@@ -235,8 +235,7 @@
             <button
               type="submit"
               id="method" class="btn btn-primary col-md-12"
-              title="Use Ctrl+Enter as shortcut."
-              disabled="disabled">
+              title="Use Ctrl+Enter as shortcut.">
               blast
             </button>
           </div>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.0.0.pre.1
+  version: 1.0.0.pre.2
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-27 00:00:00.000000000 Z
+date: 2015-01-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thin