parse_fasta 0.0.5 → 1.0.0
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.
- checksums.yaml +4 -4
- data/.gitignore +0 -1
- data/COPYING +674 -0
- data/README.md +56 -6
- data/Rakefile +6 -0
- data/doc/FastaFile.html +292 -0
- data/doc/File.html +212 -0
- data/doc/ParseFasta.html +144 -0
- data/doc/Sequence.html +361 -0
- data/doc/_index.html +136 -0
- data/doc/class_list.html +54 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +57 -0
- data/doc/css/style.css +339 -0
- data/doc/file.README.html +161 -0
- data/doc/file_list.html +56 -0
- data/doc/frames.html +26 -0
- data/doc/index.html +161 -0
- data/doc/js/app.js +219 -0
- data/doc/js/full_list.js +178 -0
- data/doc/js/jquery.js +4 -0
- data/doc/method_list.html +71 -0
- data/doc/top-level-namespace.html +114 -0
- data/lib/parse_fasta/fasta_file.rb +46 -0
- data/lib/parse_fasta/sequence.rb +55 -0
- data/lib/parse_fasta/version.rb +19 -1
- data/lib/parse_fasta.rb +11 -21
- data/parse_fasta.gemspec +3 -0
- data/spec/lib/fasta_file_spec.rb +46 -0
- data/spec/lib/sequence_spec.rb +52 -0
- data/spec/spec_helper.rb +19 -0
- data/test_files/benchmark.rb +70 -0
- data/test_files/test.fa +9 -0
- metadata +75 -5
- data/LICENSE.txt +0 -22
- data/benchmark.rb +0 -22
data/doc/file_list.html
ADDED
|
@@ -0,0 +1,56 @@
|
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
2
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
3
|
+
<html>
|
|
4
|
+
<head>
|
|
5
|
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
6
|
+
|
|
7
|
+
<link rel="stylesheet" href="css/full_list.css" type="text/css" media="screen" charset="utf-8" />
|
|
8
|
+
|
|
9
|
+
<link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
|
|
13
|
+
<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
|
|
14
|
+
|
|
15
|
+
<script type="text/javascript" charset="utf-8" src="js/full_list.js"></script>
|
|
16
|
+
|
|
17
|
+
|
|
18
|
+
<title>File List</title>
|
|
19
|
+
<base id="base_target" target="_parent" />
|
|
20
|
+
</head>
|
|
21
|
+
<body>
|
|
22
|
+
<script type="text/javascript" charset="utf-8">
|
|
23
|
+
if (window.top.frames.main) {
|
|
24
|
+
document.getElementById('base_target').target = 'main';
|
|
25
|
+
document.body.className = 'frames';
|
|
26
|
+
}
|
|
27
|
+
</script>
|
|
28
|
+
<div id="content">
|
|
29
|
+
<h1 id="full_list_header">File List</h1>
|
|
30
|
+
<div id="nav">
|
|
31
|
+
|
|
32
|
+
<span><a target="_self" href="class_list.html">
|
|
33
|
+
Classes
|
|
34
|
+
</a></span>
|
|
35
|
+
|
|
36
|
+
<span><a target="_self" href="method_list.html">
|
|
37
|
+
Methods
|
|
38
|
+
</a></span>
|
|
39
|
+
|
|
40
|
+
<span><a target="_self" href="file_list.html">
|
|
41
|
+
Files
|
|
42
|
+
</a></span>
|
|
43
|
+
|
|
44
|
+
</div>
|
|
45
|
+
<div id="search">Search: <input type="text" /></div>
|
|
46
|
+
|
|
47
|
+
<ul id="full_list" class="file">
|
|
48
|
+
|
|
49
|
+
|
|
50
|
+
<li class="r1"><span class="object_link"><a href="index.html" title="README">README</a></a></li>
|
|
51
|
+
|
|
52
|
+
|
|
53
|
+
</ul>
|
|
54
|
+
</div>
|
|
55
|
+
</body>
|
|
56
|
+
</html>
|
data/doc/frames.html
ADDED
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
|
|
2
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
|
|
3
|
+
|
|
4
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
5
|
+
<head>
|
|
6
|
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
|
|
7
|
+
<title>Documentation by YARD 0.8.7.4</title>
|
|
8
|
+
</head>
|
|
9
|
+
<script type="text/javascript" charset="utf-8">
|
|
10
|
+
window.onload = function() {
|
|
11
|
+
var match = unescape(window.location.hash).match(/^#!(.+)/);
|
|
12
|
+
var name = match ? match[1] : 'index.html';
|
|
13
|
+
name = name.replace(/^(\w+):\/\//, '').replace(/^\/\//, '');
|
|
14
|
+
document.writeln('<frameset cols="20%,*">' +
|
|
15
|
+
'<frame name="list" src="class_list.html" />' +
|
|
16
|
+
'<frame name="main" src="' + escape(name) + '" />' +
|
|
17
|
+
'</frameset>');
|
|
18
|
+
}
|
|
19
|
+
</script>
|
|
20
|
+
<noscript>
|
|
21
|
+
<frameset cols="20%,*">
|
|
22
|
+
<frame name="list" src="class_list.html" />
|
|
23
|
+
<frame name="main" src="index.html" />
|
|
24
|
+
</frameset>
|
|
25
|
+
</noscript>
|
|
26
|
+
</html>
|
data/doc/index.html
ADDED
|
@@ -0,0 +1,161 @@
|
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
2
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
3
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
4
|
+
<head>
|
|
5
|
+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
|
|
6
|
+
<title>
|
|
7
|
+
File: README
|
|
8
|
+
|
|
9
|
+
— Documentation by YARD 0.8.7.4
|
|
10
|
+
|
|
11
|
+
</title>
|
|
12
|
+
|
|
13
|
+
<link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
|
|
14
|
+
|
|
15
|
+
<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
|
|
16
|
+
|
|
17
|
+
<script type="text/javascript" charset="utf-8">
|
|
18
|
+
hasFrames = window.top.frames.main ? true : false;
|
|
19
|
+
relpath = '';
|
|
20
|
+
framesUrl = "frames.html#!file.README.html";
|
|
21
|
+
</script>
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
|
|
25
|
+
|
|
26
|
+
<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
|
|
27
|
+
|
|
28
|
+
|
|
29
|
+
</head>
|
|
30
|
+
<body>
|
|
31
|
+
<div id="header">
|
|
32
|
+
<div id="menu">
|
|
33
|
+
|
|
34
|
+
<a href="_index.html">Index</a> »
|
|
35
|
+
<span class="title">File: README</span>
|
|
36
|
+
|
|
37
|
+
|
|
38
|
+
<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
|
|
39
|
+
</div>
|
|
40
|
+
|
|
41
|
+
<div id="search">
|
|
42
|
+
|
|
43
|
+
<a class="full_list_link" id="class_list_link"
|
|
44
|
+
href="class_list.html">
|
|
45
|
+
Class List
|
|
46
|
+
</a>
|
|
47
|
+
|
|
48
|
+
<a class="full_list_link" id="method_list_link"
|
|
49
|
+
href="method_list.html">
|
|
50
|
+
Method List
|
|
51
|
+
</a>
|
|
52
|
+
|
|
53
|
+
<a class="full_list_link" id="file_list_link"
|
|
54
|
+
href="file_list.html">
|
|
55
|
+
File List
|
|
56
|
+
</a>
|
|
57
|
+
|
|
58
|
+
</div>
|
|
59
|
+
<div class="clear"></div>
|
|
60
|
+
</div>
|
|
61
|
+
|
|
62
|
+
<iframe id="search_frame"></iframe>
|
|
63
|
+
|
|
64
|
+
<div id="content"><div id='filecontents'>
|
|
65
|
+
<h1 id="label-parse_fasta">parse_fasta</h1>
|
|
66
|
+
|
|
67
|
+
<p>So you want to parse a fasta file…</p>
|
|
68
|
+
|
|
69
|
+
<h2 id="label-Installation">Installation</h2>
|
|
70
|
+
|
|
71
|
+
<p>Add this line to your application's Gemfile:</p>
|
|
72
|
+
|
|
73
|
+
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>'</span></span></code></pre>
|
|
74
|
+
|
|
75
|
+
<p>And then execute:</p>
|
|
76
|
+
|
|
77
|
+
<pre class="code ruby"><code class="ruby">$ bundle</code></pre>
|
|
78
|
+
|
|
79
|
+
<p>Or install it yourself as:</p>
|
|
80
|
+
|
|
81
|
+
<pre class="code ruby"><code class="ruby">$ gem install parse_fasta</code></pre>
|
|
82
|
+
|
|
83
|
+
<h2 id="label-Overview">Overview</h2>
|
|
84
|
+
|
|
85
|
+
<p>Provides the method <code>#each_record</code> for the <code>File</code>
|
|
86
|
+
class.</p>
|
|
87
|
+
|
|
88
|
+
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_each_record'>each_record</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span> <span class='id identifier rubyid_block'>block</span> <span class='rbrace'>}</span>
|
|
89
|
+
</code></pre>
|
|
90
|
+
|
|
91
|
+
<p>The whole file is not loaded into memory, so have no fear of giant fasta
|
|
92
|
+
files!</p>
|
|
93
|
+
|
|
94
|
+
<h2 id="label-Usage">Usage</h2>
|
|
95
|
+
|
|
96
|
+
<h3 id="label-Version+1.0.0+%28current%29">Version 1.0.0 (current)</h3>
|
|
97
|
+
|
|
98
|
+
<p>The monkey patch of the <code>File</code> class is no more! Here is the new
|
|
99
|
+
print length example:</p>
|
|
100
|
+
|
|
101
|
+
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>'</span></span>
|
|
102
|
+
|
|
103
|
+
<span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
|
|
104
|
+
<span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>\t</span><span class='tstring_end'>"</span></span><span class='rparen'>)</span>
|
|
105
|
+
<span class='kw'>end</span>
|
|
106
|
+
</code></pre>
|
|
107
|
+
|
|
108
|
+
<p>And here, a script to calculate GC content:</p>
|
|
109
|
+
|
|
110
|
+
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>'</span></span>
|
|
111
|
+
|
|
112
|
+
<span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
|
|
113
|
+
<span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>\t</span><span class='tstring_end'>"</span></span><span class='rparen'>)</span>
|
|
114
|
+
<span class='kw'>end</span>
|
|
115
|
+
</code></pre>
|
|
116
|
+
|
|
117
|
+
<h3 id="label-Version+0.0.5+%28old%29">Version 0.0.5 (old)</h3>
|
|
118
|
+
|
|
119
|
+
<p>An example that lists the length for each sequence. (Won't work in
|
|
120
|
+
version 1.0.0)</p>
|
|
121
|
+
|
|
122
|
+
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>'</span></span>
|
|
123
|
+
|
|
124
|
+
<span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
|
|
125
|
+
<span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>"</span><span class='tstring_content'>\t</span><span class='tstring_end'>"</span></span><span class='rparen'>)</span>
|
|
126
|
+
<span class='kw'>end</span>
|
|
127
|
+
</code></pre>
|
|
128
|
+
|
|
129
|
+
<h2 id="label-Benchmark">Benchmark</h2>
|
|
130
|
+
|
|
131
|
+
<p>Just for fun, I wanted to compare the execution time to that of BioRuby. I
|
|
132
|
+
calculated sequence length for each fasta record with both the
|
|
133
|
+
<code>each_record</code> method from this gem and using the
|
|
134
|
+
<code>FastaFormat</code> class from BioRuby. You can see the test script in
|
|
135
|
+
<code>benchmark.rb</code>.</p>
|
|
136
|
+
|
|
137
|
+
<p>The test file contained 2,009,897 illumina reads and the file size was 1.1
|
|
138
|
+
gigabytes. Here are the results from Ruby's <code>Benchmark</code>
|
|
139
|
+
class:</p>
|
|
140
|
+
|
|
141
|
+
<pre class="code ruby"><code class="ruby"> user system total real
|
|
142
|
+
parse_fasta 64.530000 1.740000 66.270000 ( 67.081502)
|
|
143
|
+
bioruby 116.250000 2.260000 118.510000 (120.223710)</code></pre>
|
|
144
|
+
|
|
145
|
+
<p>I just wanted a nice, clean way to parse fasta files, but being nearly
|
|
146
|
+
twice as fasta as BioRuby doesn't hurt either!</p>
|
|
147
|
+
|
|
148
|
+
<h2 id="label-Notes">Notes</h2>
|
|
149
|
+
|
|
150
|
+
<p>Currently in doesn't check whether your file is actually a fasta file
|
|
151
|
+
or anything, so watch out.</p>
|
|
152
|
+
</div></div>
|
|
153
|
+
|
|
154
|
+
<div id="footer">
|
|
155
|
+
Generated on Tue Jun 3 22:55:41 2014 by
|
|
156
|
+
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
|
157
|
+
0.8.7.4 (ruby-2.1.1).
|
|
158
|
+
</div>
|
|
159
|
+
|
|
160
|
+
</body>
|
|
161
|
+
</html>
|
data/doc/js/app.js
ADDED
|
@@ -0,0 +1,219 @@
|
|
|
1
|
+
function createSourceLinks() {
|
|
2
|
+
$('.method_details_list .source_code').
|
|
3
|
+
before("<span class='showSource'>[<a href='#' class='toggleSource'>View source</a>]</span>");
|
|
4
|
+
$('.toggleSource').toggle(function() {
|
|
5
|
+
$(this).parent().nextAll('.source_code').slideDown(100);
|
|
6
|
+
$(this).text("Hide source");
|
|
7
|
+
},
|
|
8
|
+
function() {
|
|
9
|
+
$(this).parent().nextAll('.source_code').slideUp(100);
|
|
10
|
+
$(this).text("View source");
|
|
11
|
+
});
|
|
12
|
+
}
|
|
13
|
+
|
|
14
|
+
function createDefineLinks() {
|
|
15
|
+
var tHeight = 0;
|
|
16
|
+
$('.defines').after(" <a href='#' class='toggleDefines'>more...</a>");
|
|
17
|
+
$('.toggleDefines').toggle(function() {
|
|
18
|
+
tHeight = $(this).parent().prev().height();
|
|
19
|
+
$(this).prev().show();
|
|
20
|
+
$(this).parent().prev().height($(this).parent().height());
|
|
21
|
+
$(this).text("(less)");
|
|
22
|
+
},
|
|
23
|
+
function() {
|
|
24
|
+
$(this).prev().hide();
|
|
25
|
+
$(this).parent().prev().height(tHeight);
|
|
26
|
+
$(this).text("more...");
|
|
27
|
+
});
|
|
28
|
+
}
|
|
29
|
+
|
|
30
|
+
function createFullTreeLinks() {
|
|
31
|
+
var tHeight = 0;
|
|
32
|
+
$('.inheritanceTree').toggle(function() {
|
|
33
|
+
tHeight = $(this).parent().prev().height();
|
|
34
|
+
$(this).parent().toggleClass('showAll');
|
|
35
|
+
$(this).text("(hide)");
|
|
36
|
+
$(this).parent().prev().height($(this).parent().height());
|
|
37
|
+
},
|
|
38
|
+
function() {
|
|
39
|
+
$(this).parent().toggleClass('showAll');
|
|
40
|
+
$(this).parent().prev().height(tHeight);
|
|
41
|
+
$(this).text("show all");
|
|
42
|
+
});
|
|
43
|
+
}
|
|
44
|
+
|
|
45
|
+
function fixBoxInfoHeights() {
|
|
46
|
+
$('dl.box dd.r1, dl.box dd.r2').each(function() {
|
|
47
|
+
$(this).prev().height($(this).height());
|
|
48
|
+
});
|
|
49
|
+
}
|
|
50
|
+
|
|
51
|
+
function searchFrameLinks() {
|
|
52
|
+
$('.full_list_link').click(function() {
|
|
53
|
+
toggleSearchFrame(this, $(this).attr('href'));
|
|
54
|
+
return false;
|
|
55
|
+
});
|
|
56
|
+
}
|
|
57
|
+
|
|
58
|
+
function toggleSearchFrame(id, link) {
|
|
59
|
+
var frame = $('#search_frame');
|
|
60
|
+
$('#search a').removeClass('active').addClass('inactive');
|
|
61
|
+
if (frame.attr('src') == link && frame.css('display') != "none") {
|
|
62
|
+
frame.slideUp(100);
|
|
63
|
+
$('#search a').removeClass('active inactive');
|
|
64
|
+
}
|
|
65
|
+
else {
|
|
66
|
+
$(id).addClass('active').removeClass('inactive');
|
|
67
|
+
frame.attr('src', link).slideDown(100);
|
|
68
|
+
}
|
|
69
|
+
}
|
|
70
|
+
|
|
71
|
+
function linkSummaries() {
|
|
72
|
+
$('.summary_signature').click(function() {
|
|
73
|
+
document.location = $(this).find('a').attr('href');
|
|
74
|
+
});
|
|
75
|
+
}
|
|
76
|
+
|
|
77
|
+
function framesInit() {
|
|
78
|
+
if (hasFrames) {
|
|
79
|
+
document.body.className = 'frames';
|
|
80
|
+
$('#menu .noframes a').attr('href', document.location);
|
|
81
|
+
try {
|
|
82
|
+
window.top.document.title = $('html head title').text();
|
|
83
|
+
} catch(error) {
|
|
84
|
+
// some browsers will not allow this when serving from file://
|
|
85
|
+
// but we don't want to stop the world.
|
|
86
|
+
}
|
|
87
|
+
}
|
|
88
|
+
else {
|
|
89
|
+
$('#menu .noframes a').text('frames').attr('href', framesUrl);
|
|
90
|
+
}
|
|
91
|
+
}
|
|
92
|
+
|
|
93
|
+
function keyboardShortcuts() {
|
|
94
|
+
if (window.top.frames.main) return;
|
|
95
|
+
$(document).keypress(function(evt) {
|
|
96
|
+
if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
|
|
97
|
+
if (typeof evt.target !== "undefined" &&
|
|
98
|
+
(evt.target.nodeName == "INPUT" ||
|
|
99
|
+
evt.target.nodeName == "TEXTAREA")) return;
|
|
100
|
+
switch (evt.charCode) {
|
|
101
|
+
case 67: case 99: $('#class_list_link').click(); break; // 'c'
|
|
102
|
+
case 77: case 109: $('#method_list_link').click(); break; // 'm'
|
|
103
|
+
case 70: case 102: $('#file_list_link').click(); break; // 'f'
|
|
104
|
+
default: break;
|
|
105
|
+
}
|
|
106
|
+
});
|
|
107
|
+
}
|
|
108
|
+
|
|
109
|
+
function summaryToggle() {
|
|
110
|
+
$('.summary_toggle').click(function() {
|
|
111
|
+
if (localStorage) {
|
|
112
|
+
localStorage.summaryCollapsed = $(this).text();
|
|
113
|
+
}
|
|
114
|
+
$('.summary_toggle').each(function() {
|
|
115
|
+
$(this).text($(this).text() == "collapse" ? "expand" : "collapse");
|
|
116
|
+
var next = $(this).parent().parent().nextAll('ul.summary').first();
|
|
117
|
+
if (next.hasClass('compact')) {
|
|
118
|
+
next.toggle();
|
|
119
|
+
next.nextAll('ul.summary').first().toggle();
|
|
120
|
+
}
|
|
121
|
+
else if (next.hasClass('summary')) {
|
|
122
|
+
var list = $('<ul class="summary compact" />');
|
|
123
|
+
list.html(next.html());
|
|
124
|
+
list.find('.summary_desc, .note').remove();
|
|
125
|
+
list.find('a').each(function() {
|
|
126
|
+
$(this).html($(this).find('strong').html());
|
|
127
|
+
$(this).parent().html($(this)[0].outerHTML);
|
|
128
|
+
});
|
|
129
|
+
next.before(list);
|
|
130
|
+
next.toggle();
|
|
131
|
+
}
|
|
132
|
+
});
|
|
133
|
+
return false;
|
|
134
|
+
});
|
|
135
|
+
if (localStorage) {
|
|
136
|
+
if (localStorage.summaryCollapsed == "collapse") {
|
|
137
|
+
$('.summary_toggle').first().click();
|
|
138
|
+
}
|
|
139
|
+
else localStorage.summaryCollapsed = "expand";
|
|
140
|
+
}
|
|
141
|
+
}
|
|
142
|
+
|
|
143
|
+
function fixOutsideWorldLinks() {
|
|
144
|
+
$('a').each(function() {
|
|
145
|
+
if (window.location.host != this.host) this.target = '_parent';
|
|
146
|
+
});
|
|
147
|
+
}
|
|
148
|
+
|
|
149
|
+
function generateTOC() {
|
|
150
|
+
if ($('#filecontents').length === 0) return;
|
|
151
|
+
var _toc = $('<ol class="top"></ol>');
|
|
152
|
+
var show = false;
|
|
153
|
+
var toc = _toc;
|
|
154
|
+
var counter = 0;
|
|
155
|
+
var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
|
|
156
|
+
var i;
|
|
157
|
+
if ($('#filecontents h1').length > 1) tags.unshift('h1');
|
|
158
|
+
for (i = 0; i < tags.length; i++) { tags[i] = '#filecontents ' + tags[i]; }
|
|
159
|
+
var lastTag = parseInt(tags[0][1], 10);
|
|
160
|
+
$(tags.join(', ')).each(function() {
|
|
161
|
+
if ($(this).parents('.method_details .docstring').length != 0) return;
|
|
162
|
+
if (this.id == "filecontents") return;
|
|
163
|
+
show = true;
|
|
164
|
+
var thisTag = parseInt(this.tagName[1], 10);
|
|
165
|
+
if (this.id.length === 0) {
|
|
166
|
+
var proposedId = $(this).attr('toc-id');
|
|
167
|
+
if (typeof(proposedId) != "undefined") this.id = proposedId;
|
|
168
|
+
else {
|
|
169
|
+
var proposedId = $(this).text().replace(/[^a-z0-9-]/ig, '_');
|
|
170
|
+
if ($('#' + proposedId).length > 0) { proposedId += counter; counter++; }
|
|
171
|
+
this.id = proposedId;
|
|
172
|
+
}
|
|
173
|
+
}
|
|
174
|
+
if (thisTag > lastTag) {
|
|
175
|
+
for (i = 0; i < thisTag - lastTag; i++) {
|
|
176
|
+
var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
|
|
177
|
+
}
|
|
178
|
+
}
|
|
179
|
+
if (thisTag < lastTag) {
|
|
180
|
+
for (i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
|
|
181
|
+
}
|
|
182
|
+
var title = $(this).attr('toc-title');
|
|
183
|
+
if (typeof(title) == "undefined") title = $(this).text();
|
|
184
|
+
toc.append('<li><a href="#' + this.id + '">' + title + '</a></li>');
|
|
185
|
+
lastTag = thisTag;
|
|
186
|
+
});
|
|
187
|
+
if (!show) return;
|
|
188
|
+
html = '<div id="toc"><p class="title"><a class="hide_toc" href="#"><strong>Table of Contents</strong></a> <small>(<a href="#" class="float_toc">left</a>)</small></p></div>';
|
|
189
|
+
$('#content').prepend(html);
|
|
190
|
+
$('#toc').append(_toc);
|
|
191
|
+
$('#toc .hide_toc').toggle(function() {
|
|
192
|
+
$('#toc .top').slideUp('fast');
|
|
193
|
+
$('#toc').toggleClass('hidden');
|
|
194
|
+
$('#toc .title small').toggle();
|
|
195
|
+
}, function() {
|
|
196
|
+
$('#toc .top').slideDown('fast');
|
|
197
|
+
$('#toc').toggleClass('hidden');
|
|
198
|
+
$('#toc .title small').toggle();
|
|
199
|
+
});
|
|
200
|
+
$('#toc .float_toc').toggle(function() {
|
|
201
|
+
$(this).text('float');
|
|
202
|
+
$('#toc').toggleClass('nofloat');
|
|
203
|
+
}, function() {
|
|
204
|
+
$(this).text('left');
|
|
205
|
+
$('#toc').toggleClass('nofloat');
|
|
206
|
+
});
|
|
207
|
+
}
|
|
208
|
+
|
|
209
|
+
$(framesInit);
|
|
210
|
+
$(createSourceLinks);
|
|
211
|
+
$(createDefineLinks);
|
|
212
|
+
$(createFullTreeLinks);
|
|
213
|
+
$(fixBoxInfoHeights);
|
|
214
|
+
$(searchFrameLinks);
|
|
215
|
+
$(linkSummaries);
|
|
216
|
+
$(keyboardShortcuts);
|
|
217
|
+
$(summaryToggle);
|
|
218
|
+
$(fixOutsideWorldLinks);
|
|
219
|
+
$(generateTOC);
|
data/doc/js/full_list.js
ADDED
|
@@ -0,0 +1,178 @@
|
|
|
1
|
+
var inSearch = null;
|
|
2
|
+
var searchIndex = 0;
|
|
3
|
+
var searchCache = [];
|
|
4
|
+
var searchString = '';
|
|
5
|
+
var regexSearchString = '';
|
|
6
|
+
var caseSensitiveMatch = false;
|
|
7
|
+
var ignoreKeyCodeMin = 8;
|
|
8
|
+
var ignoreKeyCodeMax = 46;
|
|
9
|
+
var commandKey = 91;
|
|
10
|
+
|
|
11
|
+
RegExp.escape = function(text) {
|
|
12
|
+
return text.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&");
|
|
13
|
+
}
|
|
14
|
+
|
|
15
|
+
function fullListSearch() {
|
|
16
|
+
// generate cache
|
|
17
|
+
searchCache = [];
|
|
18
|
+
$('#full_list li').each(function() {
|
|
19
|
+
var link = $(this).find('.object_link a');
|
|
20
|
+
if (link.length === 0) return;
|
|
21
|
+
var fullName = link.attr('title').split(' ')[0];
|
|
22
|
+
searchCache.push({name:link.text(), fullName:fullName, node:$(this), link:link});
|
|
23
|
+
});
|
|
24
|
+
|
|
25
|
+
$('#search input').keyup(function(event) {
|
|
26
|
+
if ((event.keyCode > ignoreKeyCodeMin && event.keyCode < ignoreKeyCodeMax)
|
|
27
|
+
|| event.keyCode == commandKey)
|
|
28
|
+
return;
|
|
29
|
+
searchString = this.value;
|
|
30
|
+
caseSensitiveMatch = searchString.match(/[A-Z]/) != null;
|
|
31
|
+
regexSearchString = RegExp.escape(searchString);
|
|
32
|
+
if (caseSensitiveMatch) {
|
|
33
|
+
regexSearchString += "|" +
|
|
34
|
+
$.map(searchString.split(''), function(e) { return RegExp.escape(e); }).
|
|
35
|
+
join('.+?');
|
|
36
|
+
}
|
|
37
|
+
if (searchString === "") {
|
|
38
|
+
clearTimeout(inSearch);
|
|
39
|
+
inSearch = null;
|
|
40
|
+
$('ul .search_uncollapsed').removeClass('search_uncollapsed');
|
|
41
|
+
$('#full_list, #content').removeClass('insearch');
|
|
42
|
+
$('#full_list li').removeClass('found').each(function() {
|
|
43
|
+
|
|
44
|
+
var link = $(this).find('.object_link a');
|
|
45
|
+
if (link.length > 0) link.text(link.text());
|
|
46
|
+
});
|
|
47
|
+
if (clicked) {
|
|
48
|
+
clicked.parents('ul').each(function() {
|
|
49
|
+
$(this).removeClass('collapsed').prev().removeClass('collapsed');
|
|
50
|
+
});
|
|
51
|
+
}
|
|
52
|
+
highlight();
|
|
53
|
+
}
|
|
54
|
+
else {
|
|
55
|
+
if (inSearch) clearTimeout(inSearch);
|
|
56
|
+
searchIndex = 0;
|
|
57
|
+
lastRowClass = '';
|
|
58
|
+
$('#full_list, #content').addClass('insearch');
|
|
59
|
+
$('#noresults').text('');
|
|
60
|
+
searchItem();
|
|
61
|
+
}
|
|
62
|
+
});
|
|
63
|
+
|
|
64
|
+
$('#search input').focus();
|
|
65
|
+
$('#full_list').after("<div id='noresults'></div>");
|
|
66
|
+
}
|
|
67
|
+
|
|
68
|
+
var lastRowClass = '';
|
|
69
|
+
function searchItem() {
|
|
70
|
+
for (var i = 0; i < searchCache.length / 50; i++) {
|
|
71
|
+
var item = searchCache[searchIndex];
|
|
72
|
+
var searchName = (searchString.indexOf('::') != -1 ? item.fullName : item.name);
|
|
73
|
+
var matchString = regexSearchString;
|
|
74
|
+
var matchRegexp = new RegExp(matchString, caseSensitiveMatch ? "" : "i");
|
|
75
|
+
if (searchName.match(matchRegexp) == null) {
|
|
76
|
+
item.node.removeClass('found');
|
|
77
|
+
}
|
|
78
|
+
else {
|
|
79
|
+
item.node.css('padding-left', '10px').addClass('found');
|
|
80
|
+
item.node.parents().addClass('search_uncollapsed');
|
|
81
|
+
item.node.removeClass(lastRowClass).addClass(lastRowClass == 'r1' ? 'r2' : 'r1');
|
|
82
|
+
lastRowClass = item.node.hasClass('r1') ? 'r1' : 'r2';
|
|
83
|
+
item.link.html(item.name.replace(matchRegexp, "<strong>$&</strong>"));
|
|
84
|
+
}
|
|
85
|
+
|
|
86
|
+
if (searchCache.length === searchIndex + 1) {
|
|
87
|
+
searchDone();
|
|
88
|
+
return;
|
|
89
|
+
}
|
|
90
|
+
else {
|
|
91
|
+
searchIndex++;
|
|
92
|
+
}
|
|
93
|
+
}
|
|
94
|
+
inSearch = setTimeout('searchItem()', 0);
|
|
95
|
+
}
|
|
96
|
+
|
|
97
|
+
function searchDone() {
|
|
98
|
+
highlight(true);
|
|
99
|
+
if ($('#full_list li:visible').size() === 0) {
|
|
100
|
+
$('#noresults').text('No results were found.').hide().fadeIn();
|
|
101
|
+
}
|
|
102
|
+
else {
|
|
103
|
+
$('#noresults').text('');
|
|
104
|
+
}
|
|
105
|
+
$('#content').removeClass('insearch');
|
|
106
|
+
clearTimeout(inSearch);
|
|
107
|
+
inSearch = null;
|
|
108
|
+
}
|
|
109
|
+
|
|
110
|
+
clicked = null;
|
|
111
|
+
function linkList() {
|
|
112
|
+
$('#full_list li, #full_list li a:last').click(function(evt) {
|
|
113
|
+
if ($(this).hasClass('toggle')) return true;
|
|
114
|
+
if (this.tagName.toLowerCase() == "li") {
|
|
115
|
+
if ($(this).find('.object_link a').length === 0) {
|
|
116
|
+
$(this).children('a.toggle').click();
|
|
117
|
+
return false;
|
|
118
|
+
}
|
|
119
|
+
var toggle = $(this).children('a.toggle');
|
|
120
|
+
if (toggle.size() > 0 && evt.pageX < toggle.offset().left) {
|
|
121
|
+
toggle.click();
|
|
122
|
+
return false;
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
if (clicked) clicked.removeClass('clicked');
|
|
126
|
+
var win = window.top.frames.main ? window.top.frames.main : window.parent;
|
|
127
|
+
if (this.tagName.toLowerCase() == "a") {
|
|
128
|
+
clicked = $(this).parents('li').addClass('clicked');
|
|
129
|
+
win.location = this.href;
|
|
130
|
+
}
|
|
131
|
+
else {
|
|
132
|
+
clicked = $(this).addClass('clicked');
|
|
133
|
+
win.location = $(this).find('a:last').attr('href');
|
|
134
|
+
}
|
|
135
|
+
return false;
|
|
136
|
+
});
|
|
137
|
+
}
|
|
138
|
+
|
|
139
|
+
function collapse() {
|
|
140
|
+
if (!$('#full_list').hasClass('class')) return;
|
|
141
|
+
$('#full_list.class a.toggle').click(function() {
|
|
142
|
+
$(this).parent().toggleClass('collapsed').next().toggleClass('collapsed');
|
|
143
|
+
highlight();
|
|
144
|
+
return false;
|
|
145
|
+
});
|
|
146
|
+
$('#full_list.class ul').each(function() {
|
|
147
|
+
$(this).addClass('collapsed').prev().addClass('collapsed');
|
|
148
|
+
});
|
|
149
|
+
$('#full_list.class').children().removeClass('collapsed');
|
|
150
|
+
highlight();
|
|
151
|
+
}
|
|
152
|
+
|
|
153
|
+
function highlight(no_padding) {
|
|
154
|
+
var n = 1;
|
|
155
|
+
$('#full_list li:visible').each(function() {
|
|
156
|
+
var next = n == 1 ? 2 : 1;
|
|
157
|
+
$(this).removeClass("r" + next).addClass("r" + n);
|
|
158
|
+
if (!no_padding && $('#full_list').hasClass('class')) {
|
|
159
|
+
$(this).css('padding-left', (10 + $(this).parents('ul').size() * 15) + 'px');
|
|
160
|
+
}
|
|
161
|
+
n = next;
|
|
162
|
+
});
|
|
163
|
+
}
|
|
164
|
+
|
|
165
|
+
function escapeShortcut() {
|
|
166
|
+
$(document).keydown(function(evt) {
|
|
167
|
+
if (evt.which == 27) {
|
|
168
|
+
$('#search_frame', window.top.document).slideUp(100);
|
|
169
|
+
$('#search a', window.top.document).removeClass('active inactive');
|
|
170
|
+
$(window.top).focus();
|
|
171
|
+
}
|
|
172
|
+
});
|
|
173
|
+
}
|
|
174
|
+
|
|
175
|
+
$(escapeShortcut);
|
|
176
|
+
$(fullListSearch);
|
|
177
|
+
$(linkList);
|
|
178
|
+
$(collapse);
|