genevalidator 1.6.1 → 1.6.2

Sign up to get free protection for your applications and to get access to all the features.
Files changed (131) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -1
  3. data/.travis.yml +2 -0
  4. data/README.md +78 -30
  5. data/Rakefile +11 -8
  6. data/aux/app_template_footer.erb +1 -6
  7. data/aux/app_template_header.erb +12 -32
  8. data/aux/files/css/style.css +2 -8
  9. data/aux/files/js/plots.js +564 -576
  10. data/aux/files/js/script.js +10 -0
  11. data/aux/json_footer.erb +8 -0
  12. data/aux/json_header.erb +19 -0
  13. data/aux/json_query.erb +14 -0
  14. data/aux/template_footer.erb +9 -58
  15. data/aux/template_header.erb +18 -58
  16. data/aux/template_query.erb +8 -36
  17. data/bin/genevalidator +45 -32
  18. data/genevalidator.gemspec +11 -7
  19. data/lib/genevalidator.rb +75 -455
  20. data/lib/genevalidator/arg_validation.rb +78 -107
  21. data/lib/genevalidator/blast.rb +57 -60
  22. data/lib/genevalidator/clusterization.rb +15 -15
  23. data/lib/genevalidator/exceptions.rb +32 -5
  24. data/lib/genevalidator/get_raw_sequences.rb +70 -33
  25. data/lib/genevalidator/hsp.rb +1 -4
  26. data/lib/genevalidator/json_to_gv_results.rb +109 -0
  27. data/lib/genevalidator/output.rb +177 -185
  28. data/lib/genevalidator/pool.rb +2 -1
  29. data/lib/genevalidator/sequences.rb +3 -3
  30. data/lib/genevalidator/tabular_parser.rb +24 -18
  31. data/lib/genevalidator/validation.rb +279 -0
  32. data/lib/genevalidator/validation_alignment.rb +31 -47
  33. data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
  34. data/lib/genevalidator/validation_duplication.rb +23 -19
  35. data/lib/genevalidator/validation_gene_merge.rb +30 -65
  36. data/lib/genevalidator/validation_length_cluster.rb +14 -53
  37. data/lib/genevalidator/validation_length_rank.rb +10 -11
  38. data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
  39. data/lib/genevalidator/validation_report.rb +2 -5
  40. data/lib/genevalidator/validation_test.rb +8 -4
  41. data/lib/genevalidator/version.rb +1 -1
  42. data/test/test_all_validations.rb +51 -66
  43. data/test/test_blast.rb +68 -51
  44. data/test/test_clusterization.rb +1 -1
  45. data/test/test_clusterization_2d.rb +19 -13
  46. data/test/test_extended_array_methods.rb +1 -1
  47. data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
  48. data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
  49. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
  50. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
  51. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
  52. data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
  53. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
  54. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
  55. data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
  56. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
  57. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
  58. data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
  59. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
  60. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
  61. data/test/test_sequences.rb +46 -41
  62. data/test/test_validation_open_reading_frame.rb +318 -202
  63. data/test/test_validations.rb +48 -32
  64. metadata +76 -102
  65. data/doc/AliasDuplicationError.html +0 -134
  66. data/doc/AlignmentValidation.html +0 -1687
  67. data/doc/AlignmentValidationOutput.html +0 -659
  68. data/doc/Blast.html +0 -1905
  69. data/doc/BlastRFValidationOutput.html +0 -545
  70. data/doc/BlastReadingFrameValidation.html +0 -370
  71. data/doc/BlastUtils.html +0 -875
  72. data/doc/ClasspathError.html +0 -134
  73. data/doc/Cluster.html +0 -1316
  74. data/doc/DuplciationValidationOutput.html +0 -564
  75. data/doc/DuplicationValidation.html +0 -920
  76. data/doc/DuplicationValidationOutput.html +0 -564
  77. data/doc/FileNotFoundException.html +0 -134
  78. data/doc/GeneMergeValidation.html +0 -935
  79. data/doc/GeneMergeValidationOutput.html +0 -652
  80. data/doc/HierarchicalClusterization.html +0 -994
  81. data/doc/Hsp.html +0 -1485
  82. data/doc/InconsistentTabularFormat.html +0 -135
  83. data/doc/LengthClusterValidation.html +0 -982
  84. data/doc/LengthClusterValidationOutput.html +0 -515
  85. data/doc/LengthRankValidation.html +0 -496
  86. data/doc/LengthRankValidationOutput.html +0 -517
  87. data/doc/NoInternetError.html +0 -135
  88. data/doc/NoMafftInstallationError.html +0 -134
  89. data/doc/NoPIdentError.html +0 -134
  90. data/doc/NoValidationError.html +0 -134
  91. data/doc/NotEnoughHitsError.html +0 -135
  92. data/doc/ORFValidationOutput.html +0 -593
  93. data/doc/OpenReadingFrameValidation.html +0 -1107
  94. data/doc/OtherError.html +0 -123
  95. data/doc/Output.html +0 -1540
  96. data/doc/Pair.html +0 -309
  97. data/doc/PairCluster.html +0 -767
  98. data/doc/Plot.html +0 -837
  99. data/doc/QueryError.html +0 -134
  100. data/doc/ReportClassError.html +0 -135
  101. data/doc/Sequence.html +0 -1299
  102. data/doc/SequenceTypeError.html +0 -135
  103. data/doc/TabularEntry.html +0 -837
  104. data/doc/TabularParser.html +0 -1104
  105. data/doc/Validation.html +0 -2147
  106. data/doc/ValidationClassError.html +0 -134
  107. data/doc/ValidationOutput.html +0 -460
  108. data/doc/ValidationReport.html +0 -940
  109. data/doc/ValidationTest.html +0 -939
  110. data/doc/_index.html +0 -449
  111. data/doc/class_list.html +0 -54
  112. data/doc/css/common.css +0 -1
  113. data/doc/css/full_list.css +0 -57
  114. data/doc/css/style.css +0 -338
  115. data/doc/file.README.html +0 -151
  116. data/doc/file_list.html +0 -56
  117. data/doc/frames.html +0 -26
  118. data/doc/index.html +0 -151
  119. data/doc/js/app.js +0 -214
  120. data/doc/js/full_list.js +0 -178
  121. data/doc/js/jquery.js +0 -4
  122. data/doc/method_list.html +0 -1505
  123. data/doc/top-level-namespace.html +0 -112
  124. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
  125. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
  126. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
  127. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
  128. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
  129. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
  130. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
  131. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751
data/doc/file_list.html DELETED
@@ -1,56 +0,0 @@
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 DELETED
@@ -1,26 +0,0 @@
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 0.8.7.2</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 DELETED
@@ -1,151 +0,0 @@
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=US-ASCII" />
6
- <title>
7
- File: README
8
-
9
- &mdash; Documentation by YARD 0.8.7.2
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#!" + escape(window.location.href);
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> &raquo;
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'><h1>Identify problems with predicted genes</h1>
65
-
66
- <p>This is a GSoC 2013 project.<br>
67
- Details about the project&#39;s progress during the <strong>Coding period</strong> can be found <a href="https://github.com/monicadragan/gene_prediction/wiki/Project-Diary">here</a>.<br>
68
- We also have a <a href="http://gene-prediction.blogspot.ro/">blog</a>.<br><br>
69
- <h3><div align = center><font color="blue">Please note that some of the functionalities<br> of this tool are still under development.<br> So, stay tunned!</font></div></h3>
70
- <br><br></p>
71
-
72
- <h3>Authors</h3>
73
-
74
- <ul>
75
- <li>GSoC student: <a href="http://swarm.cs.pub.ro/%7Emdragan/gsoc2013/Monica_Dragan_CV.pdf">Monica Dragan</a> (<a href="mailto:monica.dragan@cti.pub.ro">email</a>)</li>
76
- <li>Mentors: <a href="https://plus.google.com/114122400102590087616/about">Anurag Priyam</a>(<a href="mailto:anurag08priyam@gmail.com">email</a>) and <a href="http://yannick.poulet.org/">Yannick Wurm</a>(<a href="mailto:y.wurm@qmul.ac.uk">email</a>)</li>
77
- </ul>
78
-
79
- <h3>Abstract</h3>
80
-
81
- <p>The goal of GeneValidator is to identify problems with gene predictions and provide useful information based on the similarities to genes in public databases.The results of the prediction validation will make evidence about how the sequencing curation may be done and can be useful in improving / trying new approaches for gene prediction tools. The main target users of this tool are the Biologists who want to validate the data obtained in their own laboratories.</p>
82
-
83
- <h3>Current Validations</h3>
84
-
85
- <ul>
86
- <li>Length validation by clusterization</li>
87
- <li>Length validation by ranking</li>
88
- <li>Reading frame validation</li>
89
- <li>Check gene merge</li>
90
- <li>Check duplications</li>
91
- <li>Main ORF validation (for nucleotides)</li>
92
- <li>Validation based on multiple alignment ~ under development</li>
93
- <li>Codon coverage ~ under development</li>
94
- </ul>
95
-
96
- <h3>Requirements</h3>
97
-
98
- <ul>
99
- <li>Ruby (&gt;= 1.9.3)</li>
100
- <li>R (&gt;= 2.14.2)</li>
101
- <li>RubyGems (&gt;= 1.3.6)</li>
102
- <li>NCBI BLAST+ (&gt;= 2.2.25+)</li>
103
- <li>MAFFT installation (download it from : <a href="http://mafft.cbrc.jp/alignment/software/">http://mafft.cbrc.jp/alignment/software/</a> ).<br>
104
- Linux and MacOS are officially supported!</li>
105
- </ul>
106
-
107
- <h3>Installation</h3>
108
-
109
- <ol>
110
- <li><p>Get the source code<br>
111
- <code>$ git clone git@github.com:monicadragan/gene_prediction.git</code></p></li>
112
- <li><p>Be sudo and build the gem<br>
113
- <code>$ sudo rake</code></p></li>
114
- <li><p>Run GeneValidation<br>
115
- <code>$ genevalidator [validations] [skip_blast] [start] [tabular] [mafft] [raw_seq] FILE</code> </p></li>
116
- </ol>
117
-
118
- <p>Example that emphasizes all the validations:<br>
119
- <code>$ genevalidator -x data/all_validations_prot/all_validations_prot.xml data/all_validations_prot/all_validations_prot.fasta</code></p>
120
-
121
- <p>Learn more:<br>
122
- <code>$ genevalidator -h</code></p>
123
-
124
- <h3>Outputs</h3>
125
-
126
- <p>By running GeneValidator on your dataset you get numbers and plots. Some relevant files will be generated at the same path with the input file. The results are available in 3 formats:
127
- * console table output
128
- * validation results in YAML format (the YAML file has the same name with the input file + YAML extension)
129
- * html output with plot visualization (the useful files will be generated in the &#39;html&#39; directory, at the same path with the input file)<br>
130
- ! Note: for the moment check the html output with Firefox browser only !</p>
131
-
132
- <p><a href="http://swarm.cs.pub.ro/%7Emdragan/gsoc2013/genevalidator">Have a look at our results!</a></p>
133
-
134
- <h3>Other things</h3>
135
-
136
- <ol>
137
- <li><p>Run unit tests<br>
138
- <code>$ rake test</code></p></li>
139
- <li><p>Generate documentation<br>
140
- <code>$ rake doc</code></p></li>
141
- </ol>
142
- </div></div>
143
-
144
- <div id="footer">
145
- Generated on Sat Sep 28 07:01:32 2013 by
146
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
147
- 0.8.7.2 (ruby-1.9.3).
148
- </div>
149
-
150
- </body>
151
- </html>
data/doc/js/app.js DELETED
@@ -1,214 +0,0 @@
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
- window.top.document.title = $('html head title').text();
82
- }
83
- else {
84
- $('#menu .noframes a').text('frames').attr('href', framesUrl);
85
- }
86
- }
87
-
88
- function keyboardShortcuts() {
89
- if (window.top.frames.main) return;
90
- $(document).keypress(function(evt) {
91
- if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
92
- if (typeof evt.target !== "undefined" &&
93
- (evt.target.nodeName == "INPUT" ||
94
- evt.target.nodeName == "TEXTAREA")) return;
95
- switch (evt.charCode) {
96
- case 67: case 99: $('#class_list_link').click(); break; // 'c'
97
- case 77: case 109: $('#method_list_link').click(); break; // 'm'
98
- case 70: case 102: $('#file_list_link').click(); break; // 'f'
99
- default: break;
100
- }
101
- });
102
- }
103
-
104
- function summaryToggle() {
105
- $('.summary_toggle').click(function() {
106
- if (localStorage) {
107
- localStorage.summaryCollapsed = $(this).text();
108
- }
109
- $('.summary_toggle').each(function() {
110
- $(this).text($(this).text() == "collapse" ? "expand" : "collapse");
111
- var next = $(this).parent().parent().nextAll('ul.summary').first();
112
- if (next.hasClass('compact')) {
113
- next.toggle();
114
- next.nextAll('ul.summary').first().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
- });
128
- return false;
129
- });
130
- if (localStorage) {
131
- if (localStorage.summaryCollapsed == "collapse") {
132
- $('.summary_toggle').first().click();
133
- }
134
- else localStorage.summaryCollapsed = "expand";
135
- }
136
- }
137
-
138
- function fixOutsideWorldLinks() {
139
- $('a').each(function() {
140
- if (window.location.host != this.host) this.target = '_parent';
141
- });
142
- }
143
-
144
- function generateTOC() {
145
- if ($('#filecontents').length === 0) return;
146
- var _toc = $('<ol class="top"></ol>');
147
- var show = false;
148
- var toc = _toc;
149
- var counter = 0;
150
- var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
151
- var i;
152
- if ($('#filecontents h1').length > 1) tags.unshift('h1');
153
- for (i = 0; i < tags.length; i++) { tags[i] = '#filecontents ' + tags[i]; }
154
- var lastTag = parseInt(tags[0][1], 10);
155
- $(tags.join(', ')).each(function() {
156
- if ($(this).parents('.method_details .docstring').length != 0) return;
157
- if (this.id == "filecontents") return;
158
- show = true;
159
- var thisTag = parseInt(this.tagName[1], 10);
160
- if (this.id.length === 0) {
161
- var proposedId = $(this).attr('toc-id');
162
- if (typeof(proposedId) != "undefined") this.id = proposedId;
163
- else {
164
- var proposedId = $(this).text().replace(/[^a-z0-9-]/ig, '_');
165
- if ($('#' + proposedId).length > 0) { proposedId += counter; counter++; }
166
- this.id = proposedId;
167
- }
168
- }
169
- if (thisTag > lastTag) {
170
- for (i = 0; i < thisTag - lastTag; i++) {
171
- var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
172
- }
173
- }
174
- if (thisTag < lastTag) {
175
- for (i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
176
- }
177
- var title = $(this).attr('toc-title');
178
- if (typeof(title) == "undefined") title = $(this).text();
179
- toc.append('<li><a href="#' + this.id + '">' + title + '</a></li>');
180
- lastTag = thisTag;
181
- });
182
- if (!show) return;
183
- 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>';
184
- $('#content').prepend(html);
185
- $('#toc').append(_toc);
186
- $('#toc .hide_toc').toggle(function() {
187
- $('#toc .top').slideUp('fast');
188
- $('#toc').toggleClass('hidden');
189
- $('#toc .title small').toggle();
190
- }, function() {
191
- $('#toc .top').slideDown('fast');
192
- $('#toc').toggleClass('hidden');
193
- $('#toc .title small').toggle();
194
- });
195
- $('#toc .float_toc').toggle(function() {
196
- $(this).text('float');
197
- $('#toc').toggleClass('nofloat');
198
- }, function() {
199
- $(this).text('left');
200
- $('#toc').toggleClass('nofloat');
201
- });
202
- }
203
-
204
- $(framesInit);
205
- $(createSourceLinks);
206
- $(createDefineLinks);
207
- $(createFullTreeLinks);
208
- $(fixBoxInfoHeights);
209
- $(searchFrameLinks);
210
- $(linkSummaries);
211
- $(keyboardShortcuts);
212
- $(summaryToggle);
213
- $(fixOutsideWorldLinks);
214
- $(generateTOC);