sequenceserver 0.7.8 → 0.7.9
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- data/lib/sequenceserver.rb +0 -6
- data/public/css/custom.css +4 -0
- data/public/js/sequenceserver.blast.js +65 -28
- data/public/js/sequenceserver.js +37 -8
- data/sequenceserver.gemspec +1 -1
- data/views/search.erb +10 -1
- metadata +9 -11
- data/public/blastResult.js +0 -99
- data/public/js/bootstrap-alerts.js +0 -113
- data/public/js/bootstrap-modal.js +0 -260
data/lib/sequenceserver.rb
CHANGED
@@ -229,12 +229,6 @@ module SequenceServer
|
|
229
229
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# evaluate empty sequence as nil, otherwise as fasta
|
230
230
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sequence = sequence.empty? ? nil : to_fasta(sequence)
|
231
231
|
|
232
|
-
# TODO: detect sequence type in the browser itself (no AJAX)
|
233
|
-
if request.xhr?
|
234
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-
# if the AJAX request didn't specify a blast method, it must be interested in sequence type only
|
235
|
-
return (sequence && type_of_sequences(sequence)).to_s unless method
|
236
|
-
end
|
237
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-
|
238
232
|
# Raise ArgumentError if there is no database selected
|
239
233
|
if db_type_param.nil?
|
240
234
|
raise ArgumentError, "No BLAST database selected"
|
data/public/css/custom.css
CHANGED
@@ -26,6 +26,57 @@
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|
26
26
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SS.blast = (function () {
|
27
27
|
/* private methods */
|
28
28
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|
29
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+
// TODO: embedding magic numbers in the code is bad
|
30
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+
// TODO: magic numbers in JS and Ruby should be in sync
|
31
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+
var guess_sequence_type = function (sequence) {
|
32
|
+
var putative_NA_count, threshold, i;
|
33
|
+
|
34
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+
putative_NA_count = 0;
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+
|
36
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+
// remove 'noisy' characters
|
37
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+
sequence = sequence.replace(/[^A-Z]/gi, '') // non-letter characters
|
38
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+
sequence = sequence.replace(/[NX]/gi, '') // ambiguous characters
|
39
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+
|
40
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+
// guessing the type of a small sequence is unsafe
|
41
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+
if (sequence.length < 10) {
|
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+
return undefined
|
43
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+
}
|
44
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+
|
45
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+
// count the number of putative NA
|
46
|
+
for (i = 0; i < sequence.length; i++) {
|
47
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+
if (sequence[i].match(/[ACGTU]/i)) {
|
48
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+
putative_NA_count += 1;
|
49
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+
}
|
50
|
+
}
|
51
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+
|
52
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+
threshold = 0.9 * sequence.length
|
53
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+
|
54
|
+
return putative_NA_count > threshold ? 'nucleotide' : 'protein'
|
55
|
+
}
|
56
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+
|
57
|
+
var type_of_sequences = function () {
|
58
|
+
var sequences = $('#sequence').val().split(/>.*/)
|
59
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+
var type, tmp, i;
|
60
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+
|
61
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+
for (i = 0; i < sequences.length; i++) {
|
62
|
+
tmp = guess_sequence_type(sequences[i]);
|
63
|
+
|
64
|
+
// could not guess the sequence type; try the next sequence
|
65
|
+
if (!tmp) { continue }
|
66
|
+
|
67
|
+
if (!type) {
|
68
|
+
// successfully guessed the type of atleast one sequence
|
69
|
+
type = tmp
|
70
|
+
}
|
71
|
+
else if (tmp !== type) {
|
72
|
+
// user has mixed different type of sequences
|
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+
return undefined
|
74
|
+
}
|
75
|
+
}
|
76
|
+
|
77
|
+
return type;
|
78
|
+
}
|
79
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+
|
29
80
|
/*
|
30
81
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check if blast is valid (sufficient input to blast or not)
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82
|
*/
|
@@ -64,36 +115,22 @@ SS.blast = (function () {
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64
115
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}
|
65
116
|
|
66
117
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/*
|
67
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-
determine input sequence type,
|
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-
|
69
|
-
(TODO: the method is doing too much; split it)
|
118
|
+
determine input sequence type, and trigger 'sequence_type_changed'
|
119
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+
event if the input sequence type has changed
|
70
120
|
*/
|
71
121
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var signal_sequence_type_changed = function () {
|
72
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-
var
|
73
|
-
|
74
|
-
(function
|
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|
-
|
76
|
-
|
77
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-
|
78
|
-
|
79
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-
|
80
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-
|
81
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-
|
82
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-
|
83
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-
|
84
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-
//get input sequence type from the server
|
85
|
-
$.post('', {sequence: seq}, function(seq_type){
|
86
|
-
if (seq_type != prev_seq_type){
|
87
|
-
prev_seq_type = seq_type;
|
88
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-
|
89
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-
//store sequence type and notify listeners
|
90
|
-
$('#sequence').data('sequence_type', seq_type).trigger('sequence_type_changed');
|
91
|
-
}
|
92
|
-
});
|
93
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-
}
|
94
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-
poll();
|
95
|
-
}, 100)
|
96
|
-
}());
|
122
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+
var type, tmp;
|
123
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+
|
124
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+
$('#sequence').change(function () {
|
125
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+
tmp = type_of_sequences();
|
126
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+
|
127
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+
if (tmp != type){
|
128
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+
type = tmp;
|
129
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+
|
130
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+
//notify listeners
|
131
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+
$(this).trigger('sequence_type_changed', type);
|
132
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+
}
|
133
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+
});
|
97
134
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};
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98
135
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|
99
136
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data/public/js/sequenceserver.js
CHANGED
@@ -52,6 +52,27 @@
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52
52
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};
|
53
53
|
})( jQuery );
|
54
54
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|
55
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+
(function ($) {
|
56
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+
$.fn.poll = function () {
|
57
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+
var that, val, tmp;
|
58
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+
|
59
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+
that = this;
|
60
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+
|
61
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+
(function ping () {
|
62
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+
tmp = that.val();
|
63
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+
|
64
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+
if (tmp != val){
|
65
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+
val = tmp;
|
66
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+
that.change();
|
67
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+
}
|
68
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+
|
69
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+
setTimeout(ping, 100);
|
70
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+
}());
|
71
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+
|
72
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+
return this;
|
73
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+
};
|
74
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+
}(jQuery));
|
75
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+
|
55
76
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/*
|
56
77
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SS - SequenceServer's JavaScript module
|
57
78
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|
@@ -80,6 +101,9 @@ if (!SS) {
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80
101
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}()); //end SS module
|
81
102
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|
82
103
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$(document).ready(function(){
|
104
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+
// poll the sequence textbox for a change in user input
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105
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+
$('#sequence').poll();
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106
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+
|
83
107
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// start SequenceServer's event loop
|
84
108
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SS.main();
|
85
109
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$('input:submit').disable();
|
@@ -92,17 +116,16 @@ $(document).ready(function(){
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92
116
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$('input:submit').disable();
|
93
117
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});
|
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118
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|
95
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-
$('#sequence').bind('sequence_type_changed', function(){
|
96
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-
|
97
|
-
if (seq_type == "nucleotide"){
|
119
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+
$('#sequence').bind('sequence_type_changed', function(event, type){
|
120
|
+
if (type == "nucleotide"){
|
98
121
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$("#blastn, #tblastx, #blastx").enable();
|
99
122
|
$("#blastp, #tblastn").uncheck().disable().first().change();
|
100
123
|
}
|
101
|
-
else if (
|
124
|
+
else if (type == "protein"){
|
102
125
|
$("#blastp, #tblastn").enable();
|
103
126
|
$("#blastn, #tblastx, #blastx").uncheck().disable().first().change();
|
104
127
|
}
|
105
|
-
else if (
|
128
|
+
else if (type == undefined){
|
106
129
|
//reset blast methods
|
107
130
|
$('.blastmethods input[type=radio]').enable().first().change();
|
108
131
|
}
|
@@ -148,7 +171,13 @@ $(document).ready(function(){
|
|
148
171
|
});
|
149
172
|
|
150
173
|
$('#blast').submit(function(){
|
151
|
-
|
174
|
+
//parse AJAX URL
|
175
|
+
var action = $(this).attr('action');
|
176
|
+
var index = action.indexOf('#');
|
177
|
+
var url = action.slice(0, index);
|
178
|
+
var hash = action.slice(index, action.length);
|
179
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+
|
180
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+
var button = $(this).find('input:submit');
|
152
181
|
|
153
182
|
//prevent submitting another query while this one is being processed
|
154
183
|
button.disable();
|
@@ -173,13 +202,13 @@ $(document).ready(function(){
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173
202
|
});
|
174
203
|
|
175
204
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// BLAST now
|
176
|
-
$.post(
|
205
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+
$.post(url, $('form').serialize()).
|
177
206
|
done(function (data) {
|
178
207
|
// BLASTed successfully
|
179
208
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|
180
209
|
// display the result
|
181
210
|
$('#result').html(data);
|
182
|
-
location.hash =
|
211
|
+
location.hash = hash;
|
183
212
|
}).
|
184
213
|
fail(function (jqXHR, status, error) {
|
185
214
|
// BLAST failed
|
data/sequenceserver.gemspec
CHANGED
data/views/search.erb
CHANGED
@@ -216,7 +216,16 @@
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216
216
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</div>
|
217
217
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|
218
218
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<div id="underbar">
|
219
|
-
<p
|
219
|
+
<p><strong><a href='http://www.sequenceserver.com'>
|
220
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+
<%= [ "© SequenceServer: BLAST search made easy!",
|
221
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+
"Custom BLAST web interface by SequenceServer.",
|
222
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+
"SequenceServer: Local BLAST with bespoke html interface.",
|
223
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+
"Set up custom BLAST interface with SequenceServer.",
|
224
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+
"Please cite: Priyam A, Woodcroft BJ, Wurm Y (<em>in prep</em>). " +
|
225
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+
"Sequenceserver: BLAST searching made easy."
|
226
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+
][rand(5)]
|
227
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+
%>
|
228
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+
</a></strong></p>
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220
229
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</div>
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221
230
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</div> <!-- /page -->
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231
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</div> <!-- /container -->
|
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: sequenceserver
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.7.
|
4
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+
version: 0.7.9
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5
5
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prerelease:
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6
6
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platform: ruby
|
7
7
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authors:
|
@@ -11,11 +11,11 @@ authors:
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11
11
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autorequire:
|
12
12
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bindir: bin
|
13
13
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cert_chain: []
|
14
|
-
date: 2012-
|
14
|
+
date: 2012-04-11 00:00:00.000000000Z
|
15
15
|
dependencies:
|
16
16
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- !ruby/object:Gem::Dependency
|
17
17
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name: bundler
|
18
|
-
requirement: &
|
18
|
+
requirement: &22947800 !ruby/object:Gem::Requirement
|
19
19
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none: false
|
20
20
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requirements:
|
21
21
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- - ! '>='
|
@@ -23,10 +23,10 @@ dependencies:
|
|
23
23
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version: '0'
|
24
24
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type: :runtime
|
25
25
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prerelease: false
|
26
|
-
version_requirements: *
|
26
|
+
version_requirements: *22947800
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: sinatra
|
29
|
-
requirement: &
|
29
|
+
requirement: &22947280 !ruby/object:Gem::Requirement
|
30
30
|
none: false
|
31
31
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requirements:
|
32
32
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- - ! '>='
|
@@ -34,10 +34,10 @@ dependencies:
|
|
34
34
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version: 1.2.0
|
35
35
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type: :runtime
|
36
36
|
prerelease: false
|
37
|
-
version_requirements: *
|
37
|
+
version_requirements: *22947280
|
38
38
|
- !ruby/object:Gem::Dependency
|
39
39
|
name: ptools
|
40
|
-
requirement: &
|
40
|
+
requirement: &22946860 !ruby/object:Gem::Requirement
|
41
41
|
none: false
|
42
42
|
requirements:
|
43
43
|
- - ! '>='
|
@@ -45,7 +45,7 @@ dependencies:
|
|
45
45
|
version: '0'
|
46
46
|
type: :runtime
|
47
47
|
prerelease: false
|
48
|
-
version_requirements: *
|
48
|
+
version_requirements: *22946860
|
49
49
|
description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
|
50
50
|
user interface for use locally or over the web.
|
51
51
|
|
@@ -67,7 +67,6 @@ files:
|
|
67
67
|
- views/search.erb
|
68
68
|
- views/500.erb
|
69
69
|
- public/favicon.ico
|
70
|
-
- public/blastResult.js
|
71
70
|
- public/css/bootstrap.min.css
|
72
71
|
- public/css/custom.css
|
73
72
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- public/js/jquery.js
|
@@ -75,8 +74,6 @@ files:
|
|
75
74
|
- public/js/sequenceserver.js
|
76
75
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- public/js/jquery.activity.js
|
77
76
|
- public/js/sequenceserver.blast.js
|
78
|
-
- public/js/bootstrap-modal.js
|
79
|
-
- public/js/bootstrap-alerts.js
|
80
77
|
- tests/test_sequencehelpers.rb
|
81
78
|
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
|
82
79
|
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
|
@@ -124,3 +121,4 @@ signing_key:
|
|
124
121
|
specification_version: 3
|
125
122
|
summary: iPod of BLAST searching
|
126
123
|
test_files: []
|
124
|
+
has_rdoc:
|
data/public/blastResult.js
DELETED
@@ -1,99 +0,0 @@
|
|
1
|
-
|
2
|
-
function finalSubmit(dbIsNt, targetForm, inputName, submitFormName, dbType){
|
3
|
-
var formArr=targetForm.split(":");
|
4
|
-
var idArray=new Array();
|
5
|
-
if(dbType == 0){
|
6
|
-
if(dbIsNt==1){
|
7
|
-
document.forms[submitFormName].db.value="Nucleotide";
|
8
|
-
}
|
9
|
-
else{
|
10
|
-
document.forms[submitFormName].db.value="Protein";
|
11
|
-
}
|
12
|
-
}
|
13
|
-
for(j=0; j<formArr.length; j++){
|
14
|
-
for(var i=0; i<document.forms[formArr[j]].elements.length; i++){
|
15
|
-
var theElem=document.forms[formArr[j]].elements[i];
|
16
|
-
if(theElem.type=="checkbox"&&theElem.name==inputName&&theElem.checked){
|
17
|
-
if(!isIdIn(theElem.value, idArray)){
|
18
|
-
|
19
|
-
idArray[idArray.length]=theElem.value;
|
20
|
-
}
|
21
|
-
}
|
22
|
-
}
|
23
|
-
if(dbType == 0){
|
24
|
-
document.forms[submitFormName].term.value="";
|
25
|
-
for(i=0; i<idArray.length; i++){
|
26
|
-
if(i ==0 ) {
|
27
|
-
document.forms[submitFormName].term.value += idArray[i];
|
28
|
-
} else {
|
29
|
-
document.forms[submitFormName].term.value += "," + idArray[i];
|
30
|
-
}
|
31
|
-
}
|
32
|
-
} else if (dbType == 1){
|
33
|
-
document.forms[submitFormName].val.value="";
|
34
|
-
for(i=0; i<idArray.length; i++){
|
35
|
-
if(i ==0 ) {
|
36
|
-
document.forms[submitFormName].val.value += idArray[i];
|
37
|
-
} else {
|
38
|
-
document.forms[submitFormName].val.value += "," + idArray[i];
|
39
|
-
}
|
40
|
-
}
|
41
|
-
}
|
42
|
-
}
|
43
|
-
document.forms[submitFormName].submit();
|
44
|
-
}
|
45
|
-
|
46
|
-
function isIdIn(id, idArray){
|
47
|
-
var idSeen=false;
|
48
|
-
|
49
|
-
for(i=0; i<idArray.length; i++){
|
50
|
-
if(id==idArray[i]){
|
51
|
-
idSeen=true;
|
52
|
-
break;
|
53
|
-
}
|
54
|
-
}
|
55
|
-
return idSeen;
|
56
|
-
}
|
57
|
-
|
58
|
-
function handleCheckAll(mode, targetForm, inputName){
|
59
|
-
|
60
|
-
var formArr=targetForm.split(":");
|
61
|
-
for(j=0; j<formArr.length; j++){
|
62
|
-
for(var i=0; i<document.forms[formArr[j]].elements.length; i++){
|
63
|
-
var theElem=document.forms[formArr[j]].elements[i];
|
64
|
-
if(theElem.type=="checkbox"&&theElem.name==inputName){
|
65
|
-
if(mode=="select"){
|
66
|
-
theElem.checked=true;
|
67
|
-
}
|
68
|
-
else if(mode=="deselect"){
|
69
|
-
theElem.checked=false;
|
70
|
-
}
|
71
|
-
}
|
72
|
-
}
|
73
|
-
}
|
74
|
-
|
75
|
-
}
|
76
|
-
|
77
|
-
function synchronizeCheck(id, formName, inputName, isChecked){
|
78
|
-
|
79
|
-
for(var i=0; i<document.forms[formName].elements.length; i++){
|
80
|
-
var theElem=document.forms[formName].elements[i];
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|
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|
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|
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transitionEnd = "webkitTransitionEnd"
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transitionEnd = "transitionend"
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|
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* ============================= */
|
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|
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var Modal = function ( content, options ) {
|
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|
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this.settings = $.extend({}, $.fn.modal.defaults, options)
|
59
|
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|
60
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.delegate('.close', 'click.modal', $.proxy(this.hide, this))
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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var that = this
|
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|
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|
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this.$element.trigger('show')
|
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|
80
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escape.call(this)
|
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backdrop.call(this, function () {
|
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var transition = $.support.transition && that.$element.hasClass('fade')
|
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that.$element
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|
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.show()
|
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|
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that.$element[0].offsetWidth // force reflow
|
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}
|
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|
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|
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|
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transition ?
|
95
|
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that.$element.one(transitionEnd, function () { that.$element.trigger('shown') }) :
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
104
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e && e.preventDefault()
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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.removeClass('in')
|
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|
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|
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|
122
|
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|
123
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-
return this
|
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|
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}
|
125
|
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|
126
|
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}
|
127
|
-
|
128
|
-
|
129
|
-
/* MODAL PRIVATE METHODS
|
130
|
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* ===================== */
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
139
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|
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|
-
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|
141
|
-
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|
142
|
-
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|
143
|
-
})
|
144
|
-
}
|
145
|
-
|
146
|
-
function hideModal (that) {
|
147
|
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this.$element
|
148
|
-
.hide()
|
149
|
-
.trigger('hidden')
|
150
|
-
|
151
|
-
backdrop.call(this)
|
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|
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|
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|
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|
154
|
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|
155
|
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|
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|
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|
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|
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|
158
|
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|
159
|
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|
160
|
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this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
|
161
|
-
.appendTo(document.body)
|
162
|
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|
163
|
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if ( this.settings.backdrop != 'static' ) {
|
164
|
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this.$backdrop.click($.proxy(this.hide, this))
|
165
|
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}
|
166
|
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|
167
|
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if ( doAnimate ) {
|
168
|
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this.$backdrop[0].offsetWidth // force reflow
|
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|
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}
|
170
|
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|
171
|
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|
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|
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|
173
|
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doAnimate ?
|
174
|
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this.$backdrop.one(transitionEnd, callback) :
|
175
|
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callback()
|
176
|
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|
177
|
-
} else if ( !this.isShown && this.$backdrop ) {
|
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|
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this.$backdrop.removeClass('in')
|
179
|
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|
180
|
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$.support.transition && this.$element.hasClass('fade')?
|
181
|
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this.$backdrop.one(transitionEnd, $.proxy(removeBackdrop, this)) :
|
182
|
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removeBackdrop.call(this)
|
183
|
-
|
184
|
-
} else if ( callback ) {
|
185
|
-
callback()
|
186
|
-
}
|
187
|
-
}
|
188
|
-
|
189
|
-
function removeBackdrop() {
|
190
|
-
this.$backdrop.remove()
|
191
|
-
this.$backdrop = null
|
192
|
-
}
|
193
|
-
|
194
|
-
function escape() {
|
195
|
-
var that = this
|
196
|
-
if ( this.isShown && this.settings.keyboard ) {
|
197
|
-
$(document).bind('keyup.modal', function ( e ) {
|
198
|
-
if ( e.which == 27 ) {
|
199
|
-
that.hide()
|
200
|
-
}
|
201
|
-
})
|
202
|
-
} else if ( !this.isShown ) {
|
203
|
-
$(document).unbind('keyup.modal')
|
204
|
-
}
|
205
|
-
}
|
206
|
-
|
207
|
-
|
208
|
-
/* MODAL PLUGIN DEFINITION
|
209
|
-
* ======================= */
|
210
|
-
|
211
|
-
$.fn.modal = function ( options ) {
|
212
|
-
var modal = this.data('modal')
|
213
|
-
|
214
|
-
if (!modal) {
|
215
|
-
|
216
|
-
if (typeof options == 'string') {
|
217
|
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options = {
|
218
|
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show: /show|toggle/.test(options)
|
219
|
-
}
|
220
|
-
}
|
221
|
-
|
222
|
-
return this.each(function () {
|
223
|
-
$(this).data('modal', new Modal(this, options))
|
224
|
-
})
|
225
|
-
}
|
226
|
-
|
227
|
-
if ( options === true ) {
|
228
|
-
return modal
|
229
|
-
}
|
230
|
-
|
231
|
-
if ( typeof options == 'string' ) {
|
232
|
-
modal[options]()
|
233
|
-
} else if ( modal ) {
|
234
|
-
modal.toggle()
|
235
|
-
}
|
236
|
-
|
237
|
-
return this
|
238
|
-
}
|
239
|
-
|
240
|
-
$.fn.modal.Modal = Modal
|
241
|
-
|
242
|
-
$.fn.modal.defaults = {
|
243
|
-
backdrop: false
|
244
|
-
, keyboard: false
|
245
|
-
, show: false
|
246
|
-
}
|
247
|
-
|
248
|
-
|
249
|
-
/* MODAL DATA- IMPLEMENTATION
|
250
|
-
* ========================== */
|
251
|
-
|
252
|
-
$(document).ready(function () {
|
253
|
-
$('body').delegate('[data-controls-modal]', 'click', function (e) {
|
254
|
-
e.preventDefault()
|
255
|
-
var $this = $(this).data('show', true)
|
256
|
-
$('#' + $this.attr('data-controls-modal')).modal( $this.data() )
|
257
|
-
})
|
258
|
-
})
|
259
|
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|
260
|
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}( window.jQuery || window.ender );
|