bio-bwa 0.2.0

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  1. data/.document +5 -0
  2. data/Gemfile +15 -0
  3. data/Gemfile.lock +28 -0
  4. data/LICENSE.txt +35 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +56 -0
  7. data/VERSION +1 -0
  8. data/bio-bwa.gemspec +152 -0
  9. data/doc/Bio.html +93 -0
  10. data/doc/Bio/BWA.html +2884 -0
  11. data/doc/Bio/BWA/Library.html +229 -0
  12. data/doc/_index.html +119 -0
  13. data/doc/class_list.html +36 -0
  14. data/doc/css/common.css +1 -0
  15. data/doc/css/full_list.css +53 -0
  16. data/doc/css/style.css +310 -0
  17. data/doc/file.LICENSE.html +88 -0
  18. data/doc/file.README.html +119 -0
  19. data/doc/file_list.html +41 -0
  20. data/doc/frames.html +13 -0
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  22. data/doc/js/app.js +203 -0
  23. data/doc/js/full_list.js +149 -0
  24. data/doc/js/jquery.js +154 -0
  25. data/doc/method_list.html +171 -0
  26. data/doc/top-level-namespace.html +88 -0
  27. data/ext/COPYING +674 -0
  28. data/ext/ChangeLog +3864 -0
  29. data/ext/NEWS +555 -0
  30. data/ext/README +29 -0
  31. data/ext/bamlite.c +155 -0
  32. data/ext/bamlite.h +94 -0
  33. data/ext/bntseq.c +303 -0
  34. data/ext/bntseq.h +80 -0
  35. data/ext/bwa.1 +562 -0
  36. data/ext/bwape.c +807 -0
  37. data/ext/bwase.c +686 -0
  38. data/ext/bwase.h +27 -0
  39. data/ext/bwaseqio.c +222 -0
  40. data/ext/bwt.c +250 -0
  41. data/ext/bwt.h +105 -0
  42. data/ext/bwt_gen/Makefile +23 -0
  43. data/ext/bwt_gen/QSufSort.c +496 -0
  44. data/ext/bwt_gen/QSufSort.h +40 -0
  45. data/ext/bwt_gen/bwt_gen.c +1547 -0
  46. data/ext/bwt_gen/bwt_gen.h +105 -0
  47. data/ext/bwt_lite.c +94 -0
  48. data/ext/bwt_lite.h +29 -0
  49. data/ext/bwtaln.c +345 -0
  50. data/ext/bwtaln.h +150 -0
  51. data/ext/bwtgap.c +264 -0
  52. data/ext/bwtgap.h +38 -0
  53. data/ext/bwtindex.c +186 -0
  54. data/ext/bwtio.c +77 -0
  55. data/ext/bwtmisc.c +269 -0
  56. data/ext/bwtsw2.h +51 -0
  57. data/ext/bwtsw2_aux.c +650 -0
  58. data/ext/bwtsw2_chain.c +107 -0
  59. data/ext/bwtsw2_core.c +594 -0
  60. data/ext/bwtsw2_main.c +100 -0
  61. data/ext/cs2nt.c +191 -0
  62. data/ext/is.c +218 -0
  63. data/ext/khash.h +506 -0
  64. data/ext/kseq.h +208 -0
  65. data/ext/ksort.h +269 -0
  66. data/ext/kstring.c +35 -0
  67. data/ext/kstring.h +46 -0
  68. data/ext/kvec.h +90 -0
  69. data/ext/main.c +63 -0
  70. data/ext/main.h +29 -0
  71. data/ext/mkrf_conf.rb +49 -0
  72. data/ext/qualfa2fq.pl +27 -0
  73. data/ext/simple_dp.c +162 -0
  74. data/ext/simpletest.c +23 -0
  75. data/ext/solid2fastq.pl +111 -0
  76. data/ext/stdaln.c +1072 -0
  77. data/ext/stdaln.h +162 -0
  78. data/ext/utils.c +82 -0
  79. data/ext/utils.h +54 -0
  80. data/lib/bio-bwa.rb +7 -0
  81. data/lib/bio/bwa.rb +312 -0
  82. data/lib/bio/bwa/library.rb +42 -0
  83. data/test/data/testdata.fa +602 -0
  84. data/test/data/testdata.long.fa +175 -0
  85. data/test/data/testdata.short.fa +2 -0
  86. data/test/helper.rb +18 -0
  87. data/test/test_bio-bwa_basic.rb +62 -0
  88. data/test/test_bio-bwa_make_index.rb +42 -0
  89. data/test/test_bio-bwa_run_aln.rb +49 -0
  90. data/test/test_bio-bwa_sam_conversion.rb +49 -0
  91. metadata +218 -0
data/doc/file.LICENSE.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ <a href="_index.html" title="Index">Index</a> &raquo;
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+ <span class="title">File: LICENSE</span>
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ <iframe id="search_frame"></iframe>
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+
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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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+
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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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+
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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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+
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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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+
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+
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+
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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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+
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+ Burrows-Wheeler Aligner REFERENCES:
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+
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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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+
78
+
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+ </pre></div></div>
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+
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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>
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+
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+ </body>
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+ </html>
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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.
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&#8217;t been
55
+ implemented or the bug hasn&#8217;t been fixed yet
56
+ </p>
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+ </li>
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+ <li><p>
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+ Check out the issue tracker to make sure someone already hasn&#8217;t
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+ requested it and/or contributed it
61
+ </p>
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+ </li>
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+ <li><p>
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+ Fork the project
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+ </p>
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+ </li>
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+ <li><p>
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+ Start a feature/bugfix branch
69
+ </p>
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+ </li>
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+ <li><p>
72
+ Commit and push until you are happy with your contribution
73
+ </p>
74
+ </li>
75
+ <li><p>
76
+ Make sure to add tests for it. This is important so I don&#8217;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>
88
+ <p>
89
+ Copyright &#169; 2011 Francesco Strozzi. See LICENSE.txt for further
90
+ details.
91
+ </p>
92
+ <h2>Citations</h2>
93
+ <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>
111
+
112
+ <div id="footer">
113
+ Generated on Thu Feb 10 16:31:16 2011 by
114
+ <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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42
+ <iframe id="search_frame"></iframe>
43
+
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&#8217;t been
55
+ implemented or the bug hasn&#8217;t been fixed yet
56
+ </p>
57
+ </li>
58
+ <li><p>
59
+ Check out the issue tracker to make sure someone already hasn&#8217;t
60
+ requested it and/or contributed it
61
+ </p>
62
+ </li>
63
+ <li><p>
64
+ Fork the project
65
+ </p>
66
+ </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
73
+ </p>
74
+ </li>
75
+ <li><p>
76
+ Make sure to add tests for it. This is important so I don&#8217;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>
88
+ <p>
89
+ Copyright &#169; 2011 Francesco Strozzi. See LICENSE.txt for further
90
+ details.
91
+ </p>
92
+ <h2>Citations</h2>
93
+ <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>
111
+
112
+ <div id="footer">
113
+ Generated on Thu Feb 10 16:31:16 2011 by
114
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
115
+ 0.6.4 (ruby-1.9.2).
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+ 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
+ $('#method_list_link').click(function() {
53
+ toggleSearchFrame(this, relpath + 'method_list.html');
54
+ });
55
+
56
+ $('#class_list_link').click(function() {
57
+ toggleSearchFrame(this, relpath + 'class_list.html');
58
+ });
59
+
60
+ $('#file_list_link').click(function() {
61
+ toggleSearchFrame(this, relpath + 'file_list.html');
62
+ });
63
+ }
64
+
65
+ function toggleSearchFrame(id, link) {
66
+ var frame = $('#search_frame');
67
+ $('#search a').removeClass('active').addClass('inactive');
68
+ if (frame.attr('src') == link && frame.css('display') != "none") {
69
+ frame.slideUp(100);
70
+ $('#search a').removeClass('active inactive');
71
+ }
72
+ else {
73
+ $(id).addClass('active').removeClass('inactive');
74
+ frame.attr('src', link).slideDown(100);
75
+ }
76
+ }
77
+
78
+ function linkSummaries() {
79
+ $('.summary_signature').click(function() {
80
+ document.location = $(this).find('a').attr('href');
81
+ });
82
+ }
83
+
84
+ function framesInit() {
85
+ if (window.top.frames.main) {
86
+ document.body.className = 'frames';
87
+ $('#menu .noframes a').attr('href', document.location);
88
+ $('html head title', window.parent.document).text($('html head title').text());
89
+ }
90
+ }
91
+
92
+ function keyboardShortcuts() {
93
+ if (window.top.frames.main) return;
94
+ $(document).keypress(function(evt) {
95
+ if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
96
+ if (typeof evt.orignalTarget !== "undefined" &&
97
+ (evt.originalTarget.nodeName == "INPUT" ||
98
+ evt.originalTarget.nodeName == "TEXTAREA")) return;
99
+ switch (evt.charCode) {
100
+ case 67: case 99: $('#class_list_link').click(); break; // 'c'
101
+ case 77: case 109: $('#method_list_link').click(); break; // 'm'
102
+ case 70: case 102: $('#file_list_link').click(); break; // 'f'
103
+ }
104
+ });
105
+ }
106
+
107
+ function summaryToggle() {
108
+ $('.summary_toggle').click(function() {
109
+ localStorage.summaryCollapsed = $(this).text();
110
+ $(this).text($(this).text() == "collapse" ? "expand" : "collapse");
111
+ var next = $(this).parent().parent().next();
112
+ if (next.hasClass('compact')) {
113
+ next.toggle();
114
+ next.next().toggle();
115
+ }
116
+ else if (next.hasClass('summary')) {
117
+ var list = $('<ul class="summary compact" />');
118
+ list.html(next.html());
119
+ list.find('.summary_desc, .note').remove();
120
+ list.find('a').each(function() {
121
+ $(this).html($(this).find('strong').html());
122
+ $(this).parent().html($(this)[0].outerHTML);
123
+ });
124
+ next.before(list);
125
+ next.toggle();
126
+ }
127
+ return false;
128
+ });
129
+ if (localStorage) {
130
+ if (localStorage.summaryCollapsed == "collapse") $('.summary_toggle').click();
131
+ else localStorage.summaryCollapsed = "expand";
132
+ }
133
+ }
134
+
135
+ function fixOutsideWorldLinks() {
136
+ $('a').each(function() {
137
+ if (window.location.host != this.host) this.target = '_parent';
138
+ });
139
+ }
140
+
141
+ function generateTOC() {
142
+ if ($('#filecontents').length == 0) return;
143
+ var _toc = $('<ol class="top"></ol>');
144
+ var show = false;
145
+ var toc = _toc;
146
+ var counter = 0;
147
+ var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
148
+ if ($('#filecontents h1').length > 1) tags.unshift('h1');
149
+ for (i in tags) { tags[i] = '#filecontents ' + tags[i] }
150
+ var lastTag = parseInt(tags[0][1]);
151
+ $(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 = $(this).text().replace(/[^a-z0-9:\.()=-]/ig, '_');
157
+ if ($('#' + proposedId).length > 0) proposedId += counter++;
158
+ this.id = proposedId;
159
+ }
160
+ if (thisTag > lastTag) {
161
+ for (var i = 0; i < thisTag - lastTag; i++) {
162
+ 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);