sequenceserver 0.7.2 → 0.7.3
Sign up to get free protection for your applications and to get access to all the features.
- data/public/js/sequenceserver.blast.js +112 -0
- data/public/js/{search.js → sequenceserver.js} +13 -47
- data/sequenceserver.gemspec +1 -1
- data/views/search.erb +2 -1
- metadata +5 -4
@@ -0,0 +1,112 @@
|
|
1
|
+
/*
|
2
|
+
SequenceServer's BLAST module/method
|
3
|
+
|
4
|
+
Adds `blast` method to `SS`.
|
5
|
+
|
6
|
+
blast():
|
7
|
+
not implemented
|
8
|
+
|
9
|
+
`blast` defines the following methods:
|
10
|
+
init():
|
11
|
+
initialize `blast` object
|
12
|
+
|
13
|
+
This module defines the following events:
|
14
|
+
|
15
|
+
sequence_type_changed:
|
16
|
+
When the type (nucleotide or protein) of the input sequence changes.
|
17
|
+
|
18
|
+
blast_valid:
|
19
|
+
If the current user input is sufficient to launch a BLAST
|
20
|
+
|
21
|
+
blast_invalid:
|
22
|
+
If the current user input is not sufficient to launch a BLAST
|
23
|
+
|
24
|
+
TODO: should (probably) access UI objects through some sort of interface
|
25
|
+
*/
|
26
|
+
SS.blast = (function () {
|
27
|
+
/* private methods */
|
28
|
+
|
29
|
+
/*
|
30
|
+
check if blast is valid (sufficient input to blast or not)
|
31
|
+
*/
|
32
|
+
var is_valid = function () {
|
33
|
+
// must enter a query
|
34
|
+
if (!$('#sequence').val()) {
|
35
|
+
return false;
|
36
|
+
}
|
37
|
+
|
38
|
+
// must select a blast method
|
39
|
+
if (!$('.blastmethods input:checked').val()) {
|
40
|
+
return false;
|
41
|
+
}
|
42
|
+
|
43
|
+
// must select atleast one database
|
44
|
+
if (!$('.databases input:checked').val()) {
|
45
|
+
return false;
|
46
|
+
}
|
47
|
+
|
48
|
+
// everything good
|
49
|
+
return true;
|
50
|
+
}
|
51
|
+
|
52
|
+
/*
|
53
|
+
signal blast's validity (sufficient input to blast or not)
|
54
|
+
*/
|
55
|
+
var signal_blast_validity = function () {
|
56
|
+
$('#sequence, .blastmethods, .databases').change(function () {
|
57
|
+
if (is_valid()) {
|
58
|
+
$('form').trigger('blast_valid');
|
59
|
+
}
|
60
|
+
else {
|
61
|
+
$('form').trigger('blast_invalid');
|
62
|
+
}
|
63
|
+
});
|
64
|
+
}
|
65
|
+
|
66
|
+
/*
|
67
|
+
determine input sequence type, store it, and trigger
|
68
|
+
'sequence_type_changed' event if the input sequence has changed
|
69
|
+
(TODO: the method is doing too much; split it)
|
70
|
+
*/
|
71
|
+
var signal_sequence_type_changed = function () {
|
72
|
+
var prev_seq = prev_seq_type = '';
|
73
|
+
|
74
|
+
(function poll () {
|
75
|
+
setTimeout(function (){
|
76
|
+
var seq, seq_type;
|
77
|
+
seq = $('#sequence').val();
|
78
|
+
|
79
|
+
//act only if user input has changed
|
80
|
+
if (seq != prev_seq){
|
81
|
+
prev_seq = seq;
|
82
|
+
$('#sequence').change();
|
83
|
+
|
84
|
+
//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
|
+
|
89
|
+
//store sequence type and notify listeners
|
90
|
+
$('#sequence').data('sequence_type', seq_type).trigger('sequence_type_changed');
|
91
|
+
}
|
92
|
+
});
|
93
|
+
}
|
94
|
+
poll();
|
95
|
+
}, 100)
|
96
|
+
}());
|
97
|
+
};
|
98
|
+
|
99
|
+
|
100
|
+
/* public interface */
|
101
|
+
|
102
|
+
var blast = function () {
|
103
|
+
return undefined;
|
104
|
+
}
|
105
|
+
|
106
|
+
blast.init = function () {
|
107
|
+
signal_sequence_type_changed();
|
108
|
+
signal_blast_validity();
|
109
|
+
}
|
110
|
+
|
111
|
+
return blast;
|
112
|
+
}());
|
@@ -59,14 +59,7 @@
|
|
59
59
|
following methods:
|
60
60
|
|
61
61
|
main():
|
62
|
-
SequenceServer's
|
63
|
-
input and triggers appropriate SequenceServer specific events.
|
64
|
-
|
65
|
-
|
66
|
-
SequenceServer defines the following events:
|
67
|
-
|
68
|
-
sequence_type_changed:
|
69
|
-
When the type (nucleotide or protein) of the input sequence changes.
|
62
|
+
Initializes SequenceServer's various modules.
|
70
63
|
*/
|
71
64
|
|
72
65
|
//define global SS object
|
@@ -78,53 +71,26 @@ if (!SS) {
|
|
78
71
|
//SS module
|
79
72
|
(function () {
|
80
73
|
|
81
|
-
/*
|
82
|
-
|
83
|
-
/* determine input sequence type, store it, and trigger
|
84
|
-
sequence_type_changed' event if the input sequence has changed
|
85
|
-
(TODO: the method is doing too much; split it)
|
86
|
-
*/
|
87
|
-
var check_sequence_type = function () {
|
88
|
-
var prev_seq = prev_seq_type = '';
|
89
|
-
|
90
|
-
(function poll () {
|
91
|
-
setTimeout(function (){
|
92
|
-
var seq, seq_type;
|
93
|
-
seq = $('#sequence').val();
|
94
|
-
|
95
|
-
//act only if user input has changed
|
96
|
-
if (seq != prev_seq){
|
97
|
-
prev_seq = seq;
|
98
|
-
|
99
|
-
//get input sequence type from the server
|
100
|
-
$.post('', {sequence: seq}, function(seq_type){
|
101
|
-
if (seq_type != prev_seq_type){
|
102
|
-
prev_seq_type = seq_type;
|
103
|
-
|
104
|
-
//store sequence type and notify listeners
|
105
|
-
$('#sequence').data('sequence_type', seq_type).trigger('sequence_type_changed');
|
106
|
-
}
|
107
|
-
});
|
108
|
-
}
|
109
|
-
poll();
|
110
|
-
}, 100)
|
111
|
-
}());
|
112
|
-
};
|
113
|
-
|
114
|
-
|
115
|
-
/* public methods */
|
116
|
-
|
117
|
-
/* setup listeners for user input changes that trigger appropriate
|
118
|
-
SequenceServer events
|
74
|
+
/*
|
75
|
+
ask each module to initialize itself
|
119
76
|
*/
|
120
77
|
SS.main = function () {
|
121
|
-
|
78
|
+
SS.blast.init();
|
122
79
|
}
|
123
80
|
}()); //end SS module
|
124
81
|
|
125
82
|
$(document).ready(function(){
|
126
83
|
// start SequenceServer's event loop
|
127
84
|
SS.main();
|
85
|
+
$('input:submit').disable();
|
86
|
+
|
87
|
+
$('form').on('blast_valid', function () {
|
88
|
+
$('input:submit').enable();
|
89
|
+
});
|
90
|
+
|
91
|
+
$('form').on('blast_invalid', function () {
|
92
|
+
$('input:submit').disable();
|
93
|
+
});
|
128
94
|
|
129
95
|
$('#sequence').bind('sequence_type_changed', function(){
|
130
96
|
var seq_type = $(this).data('sequence_type');
|
data/sequenceserver.gemspec
CHANGED
data/views/search.erb
CHANGED
@@ -11,7 +11,8 @@
|
|
11
11
|
<script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
|
12
12
|
<script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
|
13
13
|
<script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
|
14
|
-
<script type="text/javascript" src="<%= uri('/js/
|
14
|
+
<script type="text/javascript" src="<%= uri('/js/sequenceserver.js') %>"></script>
|
15
|
+
<script type="text/javascript" src="<%= uri('/js/sequenceserver.blast.js') %>"></script>
|
15
16
|
|
16
17
|
<%# without a space after erb's closing tag, a / gets appended to css' path %>
|
17
18
|
<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequenceserver
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 5
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 7
|
9
|
-
-
|
10
|
-
version: 0.7.
|
9
|
+
- 3
|
10
|
+
version: 0.7.3
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Anurag Priyam
|
@@ -89,8 +89,9 @@ files:
|
|
89
89
|
- public/css/custom.css
|
90
90
|
- public/js/jquery.js
|
91
91
|
- public/js/jquery.enablePlaceholder.min.js
|
92
|
-
- public/js/
|
92
|
+
- public/js/sequenceserver.js
|
93
93
|
- public/js/jquery.activity.js
|
94
|
+
- public/js/sequenceserver.blast.js
|
94
95
|
- public/js/bootstrap-modal.js
|
95
96
|
- public/js/bootstrap-alerts.js
|
96
97
|
- tests/test_sequencehelpers.rb
|