bio-bwa 0.2.0
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- data/.document +5 -0
- data/Gemfile +15 -0
- data/Gemfile.lock +28 -0
- data/LICENSE.txt +35 -0
- data/README.rdoc +33 -0
- data/Rakefile +56 -0
- data/VERSION +1 -0
- data/bio-bwa.gemspec +152 -0
- data/doc/Bio.html +93 -0
- data/doc/Bio/BWA.html +2884 -0
- data/doc/Bio/BWA/Library.html +229 -0
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- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +53 -0
- data/doc/css/style.css +310 -0
- data/doc/file.LICENSE.html +88 -0
- data/doc/file.README.html +119 -0
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- data/doc/frames.html +13 -0
- data/doc/index.html +119 -0
- data/doc/js/app.js +203 -0
- data/doc/js/full_list.js +149 -0
- data/doc/js/jquery.js +154 -0
- data/doc/method_list.html +171 -0
- data/doc/top-level-namespace.html +88 -0
- data/ext/COPYING +674 -0
- data/ext/ChangeLog +3864 -0
- data/ext/NEWS +555 -0
- data/ext/README +29 -0
- data/ext/bamlite.c +155 -0
- data/ext/bamlite.h +94 -0
- data/ext/bntseq.c +303 -0
- data/ext/bntseq.h +80 -0
- data/ext/bwa.1 +562 -0
- data/ext/bwape.c +807 -0
- data/ext/bwase.c +686 -0
- data/ext/bwase.h +27 -0
- data/ext/bwaseqio.c +222 -0
- data/ext/bwt.c +250 -0
- data/ext/bwt.h +105 -0
- data/ext/bwt_gen/Makefile +23 -0
- data/ext/bwt_gen/QSufSort.c +496 -0
- data/ext/bwt_gen/QSufSort.h +40 -0
- data/ext/bwt_gen/bwt_gen.c +1547 -0
- data/ext/bwt_gen/bwt_gen.h +105 -0
- data/ext/bwt_lite.c +94 -0
- data/ext/bwt_lite.h +29 -0
- data/ext/bwtaln.c +345 -0
- data/ext/bwtaln.h +150 -0
- data/ext/bwtgap.c +264 -0
- data/ext/bwtgap.h +38 -0
- data/ext/bwtindex.c +186 -0
- data/ext/bwtio.c +77 -0
- data/ext/bwtmisc.c +269 -0
- data/ext/bwtsw2.h +51 -0
- data/ext/bwtsw2_aux.c +650 -0
- data/ext/bwtsw2_chain.c +107 -0
- data/ext/bwtsw2_core.c +594 -0
- data/ext/bwtsw2_main.c +100 -0
- data/ext/cs2nt.c +191 -0
- data/ext/is.c +218 -0
- data/ext/khash.h +506 -0
- data/ext/kseq.h +208 -0
- data/ext/ksort.h +269 -0
- data/ext/kstring.c +35 -0
- data/ext/kstring.h +46 -0
- data/ext/kvec.h +90 -0
- data/ext/main.c +63 -0
- data/ext/main.h +29 -0
- data/ext/mkrf_conf.rb +49 -0
- data/ext/qualfa2fq.pl +27 -0
- data/ext/simple_dp.c +162 -0
- data/ext/simpletest.c +23 -0
- data/ext/solid2fastq.pl +111 -0
- data/ext/stdaln.c +1072 -0
- data/ext/stdaln.h +162 -0
- data/ext/utils.c +82 -0
- data/ext/utils.h +54 -0
- data/lib/bio-bwa.rb +7 -0
- data/lib/bio/bwa.rb +312 -0
- data/lib/bio/bwa/library.rb +42 -0
- data/test/data/testdata.fa +602 -0
- data/test/data/testdata.long.fa +175 -0
- data/test/data/testdata.short.fa +2 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-bwa_basic.rb +62 -0
- data/test/test_bio-bwa_make_index.rb +42 -0
- data/test/test_bio-bwa_run_aln.rb +49 -0
- data/test/test_bio-bwa_sam_conversion.rb +49 -0
- metadata +218 -0
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<div id="content"><div id='filecontents'><pre>Copyright (c) 2011 Francesco Strozzi - for Ruby Code and binding
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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IMPORTANT NOTE:
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This package includes the BWA source code and pre-compiled shared libraries.
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The full BWA package is distributed under GPLv3 as it uses source codes from BWT-SW which is covered by GPL.
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Sorting, hash table, BWT and IS libraries are distributed under the MIT license.
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Please check http://bio-bwa.sourceforge.net/ for further details.
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Burrows-Wheeler Aligner REFERENCES:
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Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
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Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505]
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</pre></div></div>
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<div id="footer">
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Generated on Thu Feb 10 16:31:16 2011 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.6.4 (ruby-1.9.2).
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<div id="content"><div id='filecontents'><h1>bio-bwa</h1>
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<p>
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Ruby binding to BWA fast mapping software. Built using Ruby FFI library.
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</p>
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<h2>Contributing to bio-bwa</h2>
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<pre class="code">
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</pre>
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<ul>
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<li><p>
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Check out the latest master to make sure the feature hasn’t been
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implemented or the bug hasn’t been fixed yet
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</p>
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<li><p>
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Check out the issue tracker to make sure someone already hasn’t
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requested it and/or contributed it
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</p>
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Fork the project
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<li><p>
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Start a feature/bugfix branch
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</p>
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<li><p>
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Commit and push until you are happy with your contribution
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<li><p>
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Make sure to add tests for it. This is important so I don’t break it
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in a future version unintentionally.
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</p>
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</li>
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<li><p>
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Please try not to mess with the Rakefile, version, or history. If you want
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to have your own version, or is otherwise necessary, that is fine, but
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please isolate to its own commit so I can cherry-pick around it.
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</p>
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</li>
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</ul>
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<h2>Copyright</h2>
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<p>
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Copyright © 2011 Francesco Strozzi. See LICENSE.txt for further
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details.
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</p>
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<h2>Citations</h2>
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<p>
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If you use this package please cite the following references:
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</p>
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<p>
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For short read alignment:
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</p>
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<p>
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Li H. and Durbin R. (2009) Fast and accurate short read alignment with
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Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
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</p>
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<p>
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For long read alignment:
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</p>
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<p>
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Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
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Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505]
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</p>
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</div></div>
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<div id="footer">
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Generated on Thu Feb 10 16:31:16 2011 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.6.4 (ruby-1.9.2).
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<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
|
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+
<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
|
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+
|
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</head>
|
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<body>
|
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<script type="text/javascript" charset="utf-8">
|
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if (window.top.frames.main) document.body.className = 'frames';
|
21
|
+
</script>
|
22
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+
|
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+
<div id="header">
|
24
|
+
<div id="menu">
|
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|
+
|
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|
+
<a href="_index.html" title="Index">Index</a> »
|
27
|
+
<span class="title">File: README</span>
|
28
|
+
|
29
|
+
|
30
|
+
<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
|
31
|
+
</div>
|
32
|
+
|
33
|
+
<div id="search">
|
34
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+
<a id="class_list_link" href="#">Class List</a>
|
35
|
+
<a id="method_list_link" href="#">Method List</a>
|
36
|
+
<a id ="file_list_link" href="#">File List</a>
|
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+
</div>
|
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+
|
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+
<div class="clear"></div>
|
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</div>
|
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+
|
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+
<iframe id="search_frame"></iframe>
|
43
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+
|
44
|
+
<div id="content"><div id='filecontents'><h1>bio-bwa</h1>
|
45
|
+
<p>
|
46
|
+
Ruby binding to BWA fast mapping software. Built using Ruby FFI library.
|
47
|
+
</p>
|
48
|
+
<h2>Contributing to bio-bwa</h2>
|
49
|
+
<pre class="code">
|
50
|
+
|
51
|
+
</pre>
|
52
|
+
<ul>
|
53
|
+
<li><p>
|
54
|
+
Check out the latest master to make sure the feature hasn’t been
|
55
|
+
implemented or the bug hasn’t been fixed yet
|
56
|
+
</p>
|
57
|
+
</li>
|
58
|
+
<li><p>
|
59
|
+
Check out the issue tracker to make sure someone already hasn’t
|
60
|
+
requested it and/or contributed it
|
61
|
+
</p>
|
62
|
+
</li>
|
63
|
+
<li><p>
|
64
|
+
Fork the project
|
65
|
+
</p>
|
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|
+
</li>
|
67
|
+
<li><p>
|
68
|
+
Start a feature/bugfix branch
|
69
|
+
</p>
|
70
|
+
</li>
|
71
|
+
<li><p>
|
72
|
+
Commit and push until you are happy with your contribution
|
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|
+
</p>
|
74
|
+
</li>
|
75
|
+
<li><p>
|
76
|
+
Make sure to add tests for it. This is important so I don’t break it
|
77
|
+
in a future version unintentionally.
|
78
|
+
</p>
|
79
|
+
</li>
|
80
|
+
<li><p>
|
81
|
+
Please try not to mess with the Rakefile, version, or history. If you want
|
82
|
+
to have your own version, or is otherwise necessary, that is fine, but
|
83
|
+
please isolate to its own commit so I can cherry-pick around it.
|
84
|
+
</p>
|
85
|
+
</li>
|
86
|
+
</ul>
|
87
|
+
<h2>Copyright</h2>
|
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+
<p>
|
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|
+
Copyright © 2011 Francesco Strozzi. See LICENSE.txt for further
|
90
|
+
details.
|
91
|
+
</p>
|
92
|
+
<h2>Citations</h2>
|
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|
+
<p>
|
94
|
+
If you use this package please cite the following references:
|
95
|
+
</p>
|
96
|
+
<p>
|
97
|
+
For short read alignment:
|
98
|
+
</p>
|
99
|
+
<p>
|
100
|
+
Li H. and Durbin R. (2009) Fast and accurate short read alignment with
|
101
|
+
Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
|
102
|
+
</p>
|
103
|
+
<p>
|
104
|
+
For long read alignment:
|
105
|
+
</p>
|
106
|
+
<p>
|
107
|
+
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
|
108
|
+
Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505]
|
109
|
+
</p>
|
110
|
+
</div></div>
|
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|
+
|
112
|
+
<div id="footer">
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|
+
Generated on Thu Feb 10 16:31:16 2011 by
|
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|
+
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
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|
+
0.6.4 (ruby-1.9.2).
|
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+
</div>
|
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|
+
|
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|
+
</body>
|
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|
+
</html>
|
data/doc/js/app.js
ADDED
@@ -0,0 +1,203 @@
|
|
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().next().slideDown(100);
|
6
|
+
$(this).text("Hide source");
|
7
|
+
},
|
8
|
+
function() {
|
9
|
+
$(this).parent().next().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() {
|
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|
+
tHeight = $(this).parent().prev().height();
|
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|
+
$(this).prev().show();
|
20
|
+
$(this).parent().prev().height($(this).parent().height());
|
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|
+
$(this).text("(less)");
|
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|
+
},
|
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|
+
function() {
|
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|
+
$(this).prev().hide();
|
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|
+
$(this).parent().prev().height(tHeight);
|
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+
$(this).text("more...")
|
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|
+
});
|
28
|
+
}
|
29
|
+
|
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|
+
function createFullTreeLinks() {
|
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|
+
var tHeight = 0;
|
32
|
+
$('.inheritanceTree').toggle(function() {
|
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|
+
tHeight = $(this).parent().prev().height();
|
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|
+
$(this).parent().toggleClass('showAll');
|
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|
+
$(this).text("(hide)");
|
36
|
+
$(this).parent().prev().height($(this).parent().height());
|
37
|
+
},
|
38
|
+
function() {
|
39
|
+
$(this).parent().toggleClass('showAll');
|
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|
+
$(this).parent().prev().height(tHeight);
|
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|
+
$(this).text("show all")
|
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|
+
});
|
43
|
+
}
|
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|
+
|
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|
+
function fixBoxInfoHeights() {
|
46
|
+
$('dl.box dd.r1, dl.box dd.r2').each(function() {
|
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|
+
$(this).prev().height($(this).height());
|
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|
+
});
|
49
|
+
}
|
50
|
+
|
51
|
+
function searchFrameLinks() {
|
52
|
+
$('#method_list_link').click(function() {
|
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|
+
toggleSearchFrame(this, relpath + 'method_list.html');
|
54
|
+
});
|
55
|
+
|
56
|
+
$('#class_list_link').click(function() {
|
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|
+
toggleSearchFrame(this, relpath + 'class_list.html');
|
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|
+
});
|
59
|
+
|
60
|
+
$('#file_list_link').click(function() {
|
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+
toggleSearchFrame(this, relpath + 'file_list.html');
|
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|
+
});
|
63
|
+
}
|
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|
+
|
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|
+
function toggleSearchFrame(id, link) {
|
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+
var frame = $('#search_frame');
|
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+
$('#search a').removeClass('active').addClass('inactive');
|
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|
+
if (frame.attr('src') == link && frame.css('display') != "none") {
|
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|
+
frame.slideUp(100);
|
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+
$('#search a').removeClass('active inactive');
|
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+
}
|
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+
else {
|
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+
$(id).addClass('active').removeClass('inactive');
|
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+
frame.attr('src', link).slideDown(100);
|
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+
}
|
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|
+
}
|
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+
|
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+
function linkSummaries() {
|
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+
$('.summary_signature').click(function() {
|
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+
document.location = $(this).find('a').attr('href');
|
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+
});
|
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+
}
|
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+
|
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+
function framesInit() {
|
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+
if (window.top.frames.main) {
|
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+
document.body.className = 'frames';
|
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+
$('#menu .noframes a').attr('href', document.location);
|
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+
$('html head title', window.parent.document).text($('html head title').text());
|
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+
}
|
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|
+
}
|
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+
|
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+
function keyboardShortcuts() {
|
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+
if (window.top.frames.main) return;
|
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+
$(document).keypress(function(evt) {
|
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+
if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
|
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+
if (typeof evt.orignalTarget !== "undefined" &&
|
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+
(evt.originalTarget.nodeName == "INPUT" ||
|
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|
+
evt.originalTarget.nodeName == "TEXTAREA")) return;
|
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|
+
switch (evt.charCode) {
|
100
|
+
case 67: case 99: $('#class_list_link').click(); break; // 'c'
|
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|
+
case 77: case 109: $('#method_list_link').click(); break; // 'm'
|
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|
+
case 70: case 102: $('#file_list_link').click(); break; // 'f'
|
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|
+
}
|
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|
+
});
|
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|
+
}
|
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|
+
|
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|
+
function summaryToggle() {
|
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|
+
$('.summary_toggle').click(function() {
|
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|
+
localStorage.summaryCollapsed = $(this).text();
|
110
|
+
$(this).text($(this).text() == "collapse" ? "expand" : "collapse");
|
111
|
+
var next = $(this).parent().parent().next();
|
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|
+
if (next.hasClass('compact')) {
|
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+
next.toggle();
|
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|
+
next.next().toggle();
|
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|
+
}
|
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|
+
else if (next.hasClass('summary')) {
|
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|
+
var list = $('<ul class="summary compact" />');
|
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|
+
list.html(next.html());
|
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|
+
list.find('.summary_desc, .note').remove();
|
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|
+
list.find('a').each(function() {
|
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|
+
$(this).html($(this).find('strong').html());
|
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|
+
$(this).parent().html($(this)[0].outerHTML);
|
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|
+
});
|
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+
next.before(list);
|
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+
next.toggle();
|
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|
+
}
|
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|
+
return false;
|
128
|
+
});
|
129
|
+
if (localStorage) {
|
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|
+
if (localStorage.summaryCollapsed == "collapse") $('.summary_toggle').click();
|
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|
+
else localStorage.summaryCollapsed = "expand";
|
132
|
+
}
|
133
|
+
}
|
134
|
+
|
135
|
+
function fixOutsideWorldLinks() {
|
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|
+
$('a').each(function() {
|
137
|
+
if (window.location.host != this.host) this.target = '_parent';
|
138
|
+
});
|
139
|
+
}
|
140
|
+
|
141
|
+
function generateTOC() {
|
142
|
+
if ($('#filecontents').length == 0) return;
|
143
|
+
var _toc = $('<ol class="top"></ol>');
|
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|
+
var show = false;
|
145
|
+
var toc = _toc;
|
146
|
+
var counter = 0;
|
147
|
+
var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
|
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|
+
if ($('#filecontents h1').length > 1) tags.unshift('h1');
|
149
|
+
for (i in tags) { tags[i] = '#filecontents ' + tags[i] }
|
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|
+
var lastTag = parseInt(tags[0][1]);
|
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|
+
$(tags.join(', ')).each(function() {
|
152
|
+
if (this.id == "filecontents") return;
|
153
|
+
show = true;
|
154
|
+
var thisTag = parseInt(this.tagName[1]);
|
155
|
+
if (this.id.length == 0) {
|
156
|
+
var proposedId = $(this).text().replace(/[^a-z0-9:\.()=-]/ig, '_');
|
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|
+
if ($('#' + proposedId).length > 0) proposedId += counter++;
|
158
|
+
this.id = proposedId;
|
159
|
+
}
|
160
|
+
if (thisTag > lastTag) {
|
161
|
+
for (var i = 0; i < thisTag - lastTag; i++) {
|
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|
+
var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
|
163
|
+
}
|
164
|
+
}
|
165
|
+
if (thisTag < lastTag) {
|
166
|
+
for (var i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
|
167
|
+
}
|
168
|
+
toc.append('<li><a href="#' + this.id + '">' + $(this).text() + '</a></li>');
|
169
|
+
lastTag = thisTag;
|
170
|
+
});
|
171
|
+
if (!show) return;
|
172
|
+
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>';
|
173
|
+
$('#content').prepend(html);
|
174
|
+
$('#toc').append(_toc);
|
175
|
+
$('#toc .hide_toc').toggle(function() {
|
176
|
+
$('#toc .top').slideUp('fast');
|
177
|
+
$('#toc').toggleClass('hidden');
|
178
|
+
$('#toc .title small').toggle();
|
179
|
+
}, function() {
|
180
|
+
$('#toc .top').slideDown('fast');
|
181
|
+
$('#toc').toggleClass('hidden');
|
182
|
+
$('#toc .title small').toggle();
|
183
|
+
});
|
184
|
+
$('#toc .float_toc').toggle(function() {
|
185
|
+
$(this).text('float');
|
186
|
+
$('#toc').toggleClass('nofloat');
|
187
|
+
}, function() {
|
188
|
+
$(this).text('left')
|
189
|
+
$('#toc').toggleClass('nofloat');
|
190
|
+
});
|
191
|
+
}
|
192
|
+
|
193
|
+
$(framesInit);
|
194
|
+
$(createSourceLinks);
|
195
|
+
$(createDefineLinks);
|
196
|
+
$(createFullTreeLinks);
|
197
|
+
$(fixBoxInfoHeights);
|
198
|
+
$(searchFrameLinks);
|
199
|
+
$(linkSummaries);
|
200
|
+
$(keyboardShortcuts);
|
201
|
+
$(summaryToggle);
|
202
|
+
$(fixOutsideWorldLinks);
|
203
|
+
$(generateTOC);
|