sequenceserver 1.0.0.pre.1 → 1.0.0.pre.2
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- checksums.yaml +4 -4
- data/public/css/custom.css +14 -17
- data/public/js/sequence.js +94 -59
- data/public/js/sequenceserver.js +12 -12
- data/sequenceserver.gemspec +1 -1
- data/views/result.erb +6 -12
- data/views/search.erb +4 -5
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 3f26e8eac4c55a9a2a0997d2ab6e922c88ded0d8
|
4
|
+
data.tar.gz: 60684bb5f9291fcbbfefd410517ea3892df9ff5c
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: a51d9aff1dc67c12898295dbbc36452216820c22695a0e2b1507fa977d49fe8cf235f2da44762b0a5229bce2e59266b00358f40b51a072fbb9de007b9b60bef0
|
7
|
+
data.tar.gz: 8042ec1559d3719d2f910681c8cb4988d6cf0fe81d4205d5b596929be31045b0309ec44ad3bd335a457fae2c3ad0c1d80dc0be4c3322fc5d07501af494210695
|
data/public/css/custom.css
CHANGED
@@ -182,6 +182,7 @@ a.disabled:hover {
|
|
182
182
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.label-reset {
|
183
183
|
color: inherit;
|
184
184
|
line-height: inherit;
|
185
|
+
font-weight: normal;
|
185
186
|
}
|
186
187
|
|
187
188
|
/**
|
@@ -309,11 +310,12 @@ h1,h2,h3,h4,h5,h6,.page-header {
|
|
309
310
|
}
|
310
311
|
|
311
312
|
.main {
|
312
|
-
border-right: 1px solid #ddd
|
313
|
+
/*border-right: 1px solid #ddd;*/
|
313
314
|
}
|
314
315
|
|
315
316
|
.sidebar > .page-header > h4 {
|
316
|
-
padding:
|
317
|
+
padding: 10px 0px 0px 0px;
|
318
|
+
font-size: 14px;
|
317
319
|
}
|
318
320
|
|
319
321
|
.sidebar.affix {
|
@@ -393,6 +395,14 @@ svg:not(:root) {
|
|
393
395
|
letter-spacing: 1px;
|
394
396
|
}
|
395
397
|
|
398
|
+
.fastan > .page-header {
|
399
|
+
padding-bottom: 8px;
|
400
|
+
}
|
401
|
+
.fastan > .page-content {
|
402
|
+
padding-top: 8px;
|
403
|
+
padding-left: 0;
|
404
|
+
}
|
405
|
+
|
396
406
|
.footer a:first-child {
|
397
407
|
vertical-align: super;
|
398
408
|
}
|
@@ -453,21 +463,8 @@ svg:not(:root) {
|
|
453
463
|
}
|
454
464
|
|
455
465
|
.glow {
|
456
|
-
-
|
457
|
-
|
458
|
-
box-shadow: 0 0 1px rgba(0, 0, 0, 0);
|
459
|
-
-webkit-backface-visibility: hidden;
|
460
|
-
backface-visibility: hidden;
|
461
|
-
-moz-osx-font-smoothing: grayscale;
|
462
|
-
-webkit-transition-duration: 0.3s;
|
463
|
-
transition-duration: 0.3s;
|
464
|
-
-webkit-transition-property: box-shadow;
|
465
|
-
transition-property: box-shadow;
|
466
|
-
box-shadow: 0 0 8px rgba(0, 0, 0, 0.6);
|
466
|
+
box-shadow: 0 0 2px rgba(0, 0, 0, 0.6);
|
467
|
+
border-left: 2px solid #f0ad4e;
|
467
468
|
padding-left: 16px;
|
468
469
|
padding-right: 16px;
|
469
470
|
}
|
470
|
-
|
471
|
-
.pos-marker {
|
472
|
-
display: none;
|
473
|
-
}
|
data/public/js/sequence.js
CHANGED
@@ -275,10 +275,7 @@ Sequence = Class(
|
|
275
275
|
this._buildFormatSelector();
|
276
276
|
|
277
277
|
// DIV for the sequence
|
278
|
-
this._contentDiv = jQuery('<div
|
279
|
-
this._contentDiv.css({
|
280
|
-
'text-align': 'left'
|
281
|
-
});
|
278
|
+
this._contentDiv = jQuery('<div/>').appendTo(this._container);
|
282
279
|
|
283
280
|
// Initialize highlighting
|
284
281
|
this._highlights = this.opt.highlights;
|
@@ -836,21 +833,18 @@ Sequence = Class(
|
|
836
833
|
* Inputs: -
|
837
834
|
*/
|
838
835
|
_drawCodata : function() {
|
839
|
-
|
840
|
-
var self = this;
|
841
|
-
var a = this.opt.sequence.toUpperCase().split('');
|
842
|
-
var pre = jQuery('<pre/>').appendTo(this._contentDiv);
|
836
|
+
var seq = this.opt.sequence.toUpperCase().split('');
|
843
837
|
|
844
|
-
|
845
|
-
var str = 'ENTRY ' + this.opt.id + '<br/>';
|
846
|
-
str += 'SEQUENCE<br/>';
|
838
|
+
// Add header.
|
847
839
|
if ( this.opt.formatOptions !== undefined ){
|
848
840
|
if(this.opt.formatOptions.title !== undefined ){
|
849
|
-
if (this.opt.formatOptions.title
|
850
|
-
|
851
|
-
|
841
|
+
if (this.opt.formatOptions.title != false) {
|
842
|
+
var header =
|
843
|
+
$('<pre/>').addClass('header').appendTo(this._contentDiv);
|
844
|
+
header.html('ENTRY ' + this.opt.id +
|
845
|
+
'<br/>SEQUENCE<br/>'); }
|
852
846
|
}
|
853
|
-
}
|
847
|
+
}
|
854
848
|
|
855
849
|
/* Correct column size in case the sequence is as small peptide */
|
856
850
|
var numCols = this.opt.columns.size;
|
@@ -868,19 +862,18 @@ Sequence = Class(
|
|
868
862
|
numColsForSpace: 0,
|
869
863
|
spaceBetweenChars: true
|
870
864
|
};
|
865
|
+
this._drawSequence(seq, opt);
|
871
866
|
|
872
|
-
|
873
|
-
|
874
|
-
var footer = '<br/>///';
|
867
|
+
// Add footer.
|
875
868
|
if (this.opt.formatOptions !== undefined) {
|
876
869
|
if (this.opt.formatOptions.footer !== undefined) {
|
877
|
-
if (this.opt.formatOptions.footer
|
878
|
-
footer =
|
870
|
+
if (this.opt.formatOptions.footer != false) {
|
871
|
+
var footer =
|
872
|
+
$('<pre/>').addClass('footer').appendTo(this._contentDiv);
|
873
|
+
footer.html('<br/>///');
|
879
874
|
}
|
880
875
|
}
|
881
876
|
}
|
882
|
-
str += footer;
|
883
|
-
pre.html(str);
|
884
877
|
|
885
878
|
this._drawAnnotations(opt);
|
886
879
|
},
|
@@ -1066,9 +1059,7 @@ Sequence = Class(
|
|
1066
1059
|
* Inputs: -
|
1067
1060
|
*/
|
1068
1061
|
_drawPride : function() {
|
1069
|
-
var
|
1070
|
-
var a = this.opt.sequence.toUpperCase().split('');
|
1071
|
-
var pre = jQuery('<pre></pre>').appendTo(this._contentDiv);
|
1062
|
+
var seq = this.opt.sequence.toUpperCase().split('');
|
1072
1063
|
|
1073
1064
|
/* Correct column size in case the sequence is as small peptide */
|
1074
1065
|
var numCols = this.opt.columns.size;
|
@@ -1079,18 +1070,14 @@ Sequence = Class(
|
|
1079
1070
|
opt = {
|
1080
1071
|
numLeft: true,
|
1081
1072
|
numLeftSize: 5,
|
1082
|
-
numLeftPad:'
|
1083
|
-
numRight:
|
1073
|
+
numLeftPad: ' ',
|
1074
|
+
numRight: false,
|
1084
1075
|
numRightSize: 5,
|
1085
|
-
numRightPad: '
|
1076
|
+
numRightPad: '',
|
1086
1077
|
numCols: numCols,
|
1087
|
-
numColsForSpace:
|
1078
|
+
numColsForSpace: this.opt.columns.spacedEach
|
1088
1079
|
};
|
1089
|
-
|
1090
|
-
pre.html(
|
1091
|
-
this._drawSequence(a, opt)
|
1092
|
-
);
|
1093
|
-
|
1080
|
+
this._drawSequence(seq, opt);
|
1094
1081
|
this._drawAnnotations(opt);
|
1095
1082
|
},
|
1096
1083
|
/*
|
@@ -1101,34 +1088,38 @@ Sequence = Class(
|
|
1101
1088
|
* opt -> {Object} opt The CUSTOM format.
|
1102
1089
|
*/
|
1103
1090
|
_drawSequence : function(a, opt) {
|
1104
|
-
|
1091
|
+
var indL = '';
|
1092
|
+
var indT = '';
|
1093
|
+
var indR = '\n';
|
1094
|
+
var str = '';
|
1105
1095
|
|
1106
1096
|
// Index at top?
|
1107
1097
|
if( opt.numTop )
|
1108
1098
|
{
|
1109
|
-
|
1099
|
+
indT += '<span class="numTop pos-marker">'
|
1110
1100
|
var size = (opt.spaceBetweenChars)? opt.numTopEach*2: opt.numTopEach;
|
1111
1101
|
|
1112
1102
|
if (opt.numLeft) {
|
1113
|
-
|
1103
|
+
indT += this._formatIndex(' ', opt.numLeftSize, ' ');
|
1114
1104
|
}
|
1115
1105
|
|
1116
|
-
|
1106
|
+
indT += this._formatIndex(' ', size, ' ');
|
1117
1107
|
|
1118
1108
|
for(var x = opt.numTopEach; x < opt.numCols; x += opt.numTopEach) {
|
1119
|
-
|
1109
|
+
indT += this._formatIndex(x, size, ' ', true);
|
1120
1110
|
}
|
1121
|
-
|
1111
|
+
indT += '</span>'
|
1122
1112
|
}
|
1123
1113
|
|
1124
1114
|
|
1125
1115
|
// Index at the left?
|
1126
1116
|
if (opt.numLeft) {
|
1127
|
-
|
1128
|
-
|
1129
|
-
|
1130
|
-
|
1131
|
-
|
1117
|
+
indL += '<span id="numLeft_' + this.getId() + '_' + 0 + '"';
|
1118
|
+
indL += 'class="pos-marker">'
|
1119
|
+
indL += this._formatIndex(1, opt.numLeftSize, opt.numLeftPad);
|
1120
|
+
indL += ' ';
|
1121
|
+
indL += '</span>';
|
1122
|
+
indL += '\n';
|
1132
1123
|
}
|
1133
1124
|
|
1134
1125
|
var j=1;
|
@@ -1138,30 +1129,33 @@ Sequence = Class(
|
|
1138
1129
|
str += '<span class="sequence" id="' + this.getId() + '_' + i + '">' + a[i-1] + '</span>';
|
1139
1130
|
|
1140
1131
|
if (opt.numRight) {
|
1141
|
-
|
1142
|
-
|
1143
|
-
|
1144
|
-
|
1145
|
-
|
1132
|
+
indR += '<span id="numRight_' + this.getId() + '_' + i + '"';
|
1133
|
+
indR += 'class="pos-marker">'
|
1134
|
+
indR += ' ';
|
1135
|
+
indR += this._formatIndex(i, opt.numRightSize, opt.numRightPad);
|
1136
|
+
indR += '</span>';
|
1137
|
+
indR += '\n';
|
1146
1138
|
}
|
1147
1139
|
|
1148
1140
|
str += '<br/>';
|
1149
1141
|
|
1150
1142
|
var aaRemaining = a.length - i;
|
1151
1143
|
if (opt.numLeft && aaRemaining > 0) {
|
1152
|
-
|
1153
|
-
|
1154
|
-
|
1155
|
-
|
1156
|
-
|
1157
|
-
|
1144
|
+
indL += '<span id="numLeft_' + this.getId() + '_' + i + '"';
|
1145
|
+
indL += 'class="pos-marker">'
|
1146
|
+
indL += this._formatIndex(i+1, opt.numLeftSize, opt.numLeftPad);
|
1147
|
+
indL += ' ';
|
1148
|
+
indL += '</span>';
|
1149
|
+
indL += '\n';
|
1150
|
+
}
|
1158
1151
|
|
1159
1152
|
j = 1;
|
1160
1153
|
|
1161
1154
|
} else {
|
1162
|
-
str += '<span class="sequence" id="' + this.getId() + '_' + i + '"
|
1163
|
-
str += (
|
1164
|
-
str += (opt.spaceBetweenChars)? ' ' : '';
|
1155
|
+
str += '<span class="sequence" id="' + this.getId() + '_' + i + '"';
|
1156
|
+
str += (j % opt.numColsForSpace == 0)? ' style="letter-spacing: 1em;"' : '';
|
1157
|
+
str += (opt.spaceBetweenChars)? ' style="letter-spacing: 1em;"' : '';
|
1158
|
+
str += '">' + a[i-1];
|
1165
1159
|
str += '</span>';
|
1166
1160
|
j++;
|
1167
1161
|
}
|
@@ -1173,6 +1167,47 @@ Sequence = Class(
|
|
1173
1167
|
str = "<pre>" + str + "</pre>";
|
1174
1168
|
}
|
1175
1169
|
|
1170
|
+
|
1171
|
+
var ret = [];
|
1172
|
+
if (opt.numTop) {
|
1173
|
+
$('<pre/>')
|
1174
|
+
.html(indT)
|
1175
|
+
.addClass('indT')
|
1176
|
+
.css({
|
1177
|
+
color: '#aaa'
|
1178
|
+
})
|
1179
|
+
.appendTo(this._contentDiv);
|
1180
|
+
}
|
1181
|
+
if (opt.numLeft) {
|
1182
|
+
$('<pre/>')
|
1183
|
+
.html(indL)
|
1184
|
+
.addClass('indL')
|
1185
|
+
.css({
|
1186
|
+
color: '#aaa',
|
1187
|
+
display: 'inline-block'
|
1188
|
+
})
|
1189
|
+
.appendTo(this._contentDiv);
|
1190
|
+
}
|
1191
|
+
|
1192
|
+
$('<pre/>')
|
1193
|
+
.html(str)
|
1194
|
+
.addClass('seqF')
|
1195
|
+
.css({
|
1196
|
+
display: 'inline-block'
|
1197
|
+
})
|
1198
|
+
.appendTo(this._contentDiv);
|
1199
|
+
|
1200
|
+
if (opt.numRight) {
|
1201
|
+
$('<pre/>')
|
1202
|
+
.html(indR)
|
1203
|
+
.addClass('indR')
|
1204
|
+
.css({
|
1205
|
+
color: '#aaa',
|
1206
|
+
display: 'inline-block'
|
1207
|
+
})
|
1208
|
+
.appendTo(this._contentDiv);
|
1209
|
+
}
|
1210
|
+
|
1176
1211
|
return str;
|
1177
1212
|
},
|
1178
1213
|
/*
|
data/public/js/sequenceserver.js
CHANGED
@@ -55,16 +55,15 @@
|
|
55
55
|
|
56
56
|
(function ($) {
|
57
57
|
$.fn.poll = function () {
|
58
|
-
var that
|
59
|
-
|
60
|
-
|
61
|
-
val = that.val();
|
58
|
+
var that = this;
|
59
|
+
var val = null;
|
60
|
+
var newval;
|
62
61
|
|
63
62
|
(function ping () {
|
64
|
-
|
63
|
+
newval = that.val();
|
65
64
|
|
66
|
-
if (
|
67
|
-
val =
|
65
|
+
if (newval != val){
|
66
|
+
val = newval;
|
68
67
|
that.change();
|
69
68
|
}
|
70
69
|
|
@@ -266,8 +265,6 @@ if (!SS) {
|
|
266
265
|
this.$sequenceFile = $('#sequence-file');
|
267
266
|
this.$sequenceControls = $('.sequence-controls');
|
268
267
|
|
269
|
-
this.$sequence.poll();
|
270
|
-
|
271
268
|
SS.blast.init();
|
272
269
|
};
|
273
270
|
|
@@ -280,7 +277,7 @@ if (!SS) {
|
|
280
277
|
SS.selectHit = function (checkbox) {
|
281
278
|
if (!checkbox || !checkbox.value) return;
|
282
279
|
|
283
|
-
var $hitn = $(
|
280
|
+
var $hitn = $($(checkbox).data('target'));
|
284
281
|
|
285
282
|
// Highlight selected hit and sync checkboxes if sequence viewer is open.
|
286
283
|
if(checkbox.checked) {
|
@@ -361,9 +358,10 @@ SS.showSequenceViewer = (function () {
|
|
361
358
|
var widget = new Sequence({
|
362
359
|
sequence: sequence.value,
|
363
360
|
target: widgetId,
|
364
|
-
format: '
|
361
|
+
format: 'PRIDE',
|
365
362
|
columns: {
|
366
|
-
size:
|
363
|
+
size: 40,
|
364
|
+
spacedEach: 5
|
367
365
|
},
|
368
366
|
formatOptions: {
|
369
367
|
title: false,
|
@@ -725,4 +723,6 @@ $(document).ready(function(){
|
|
725
723
|
|
726
724
|
return false;
|
727
725
|
});
|
726
|
+
|
727
|
+
SS.$sequence.poll();
|
728
728
|
});
|
data/sequenceserver.gemspec
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
# meta
|
3
3
|
s.name = 'sequenceserver'
|
4
|
-
s.version = '1.0.0-
|
4
|
+
s.version = '1.0.0-2'
|
5
5
|
s.authors = ['Anurag Priyam', 'Ben J Woodcroft', 'Vivek Rai', 'Yannick Wurm']
|
6
6
|
s.email = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
|
7
7
|
s.homepage = 'http://sequenceserver.com'
|
data/views/result.erb
CHANGED
@@ -109,7 +109,7 @@
|
|
109
109
|
<div class="hit-links text-right">
|
110
110
|
<label>
|
111
111
|
<input
|
112
|
-
type="checkbox" value
|
112
|
+
type="checkbox" value="<%= hit.accession %>" data-target="<%= "#Query_#{query.number}_hit_#{hit.number}" %>">
|
113
113
|
Select
|
114
114
|
</label>
|
115
115
|
<% report.link_per_hit(hit.accession).each do |link| %>
|
@@ -142,18 +142,15 @@ Total letters in queried databases: <%= report.stats[1] %>
|
|
142
142
|
|
143
143
|
<% unless report.queries.length == 1 && report.queries.first.hits.empty? %>
|
144
144
|
<div
|
145
|
-
class="side col-md-3">
|
145
|
+
class="side col-md-3 hidden-xs hidden-sm">
|
146
146
|
<div
|
147
147
|
class="sidebar">
|
148
148
|
<div
|
149
149
|
class="page-header">
|
150
150
|
<h4>
|
151
|
-
|
152
|
-
|
153
|
-
|
154
|
-
<%= report.querydb.length %> <%= report.querydb.length > 1 ? 'databases' : 'database' %>,
|
155
|
-
<%= report.program.upcase %>
|
156
|
-
</small>
|
151
|
+
<%= report.program.upcase %>:
|
152
|
+
<%= report.queries.length %> <%= report.queries.length > 1 ? 'queries' : 'query' %>,
|
153
|
+
<%= report.querydb.length %> <%= report.querydb.length > 1 ? 'databases' : 'database' %>
|
157
154
|
</h4>
|
158
155
|
</div>
|
159
156
|
<ul
|
@@ -176,10 +173,7 @@ Total letters in queried databases: <%= report.stats[1] %>
|
|
176
173
|
<div
|
177
174
|
class="page-header">
|
178
175
|
<h4>
|
179
|
-
|
180
|
-
<small>
|
181
|
-
FASTA, XML, TSV
|
182
|
-
</small>
|
176
|
+
Download FASTA, XML, TSV
|
183
177
|
</h4>
|
184
178
|
</div>
|
185
179
|
<ul
|
data/views/search.erb
CHANGED
@@ -16,9 +16,9 @@
|
|
16
16
|
|
17
17
|
<link href='http://fonts.googleapis.com/css?family=Roboto:400' rel='stylesheet' type='text/css'>
|
18
18
|
<link href='http://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
|
19
|
-
<link rel="stylesheet" media="screen" type="text/css" href="css/bootstrap.min.css"/>
|
20
|
-
<link rel="stylesheet" media="screen" type="text/css" href="css/font-awesome.min.css"/>
|
21
|
-
<link rel="stylesheet" media="screen" type="text/css" href="css/custom.css"/>
|
19
|
+
<link rel="stylesheet" media="screen,print" type="text/css" href="css/bootstrap.min.css"/>
|
20
|
+
<link rel="stylesheet" media="screen,print" type="text/css" href="css/font-awesome.min.css"/>
|
21
|
+
<link rel="stylesheet" media="screen,print" type="text/css" href="css/custom.css"/>
|
22
22
|
</head>
|
23
23
|
|
24
24
|
<body>
|
@@ -235,8 +235,7 @@
|
|
235
235
|
<button
|
236
236
|
type="submit"
|
237
237
|
id="method" class="btn btn-primary col-md-12"
|
238
|
-
title="Use Ctrl+Enter as shortcut."
|
239
|
-
disabled="disabled">
|
238
|
+
title="Use Ctrl+Enter as shortcut.">
|
240
239
|
blast
|
241
240
|
</button>
|
242
241
|
</div>
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequenceserver
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.0.0.pre.
|
4
|
+
version: 1.0.0.pre.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Anurag Priyam
|
@@ -11,7 +11,7 @@ authors:
|
|
11
11
|
autorequire:
|
12
12
|
bindir: bin
|
13
13
|
cert_chain: []
|
14
|
-
date: 2015-01-
|
14
|
+
date: 2015-01-29 00:00:00.000000000 Z
|
15
15
|
dependencies:
|
16
16
|
- !ruby/object:Gem::Dependency
|
17
17
|
name: thin
|