genevalidator 1.6.1 → 1.6.2

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.
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
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347
- </div></span>
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- </ul>
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-
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- Class Method Summary
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- </h2>
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- <ul class="summary">
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-
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- <span class="summary_signature">
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-
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- <a href="#overall_evaluation-class_method" title="overall_evaluation (class method)">+ (Object) <strong>overall_evaluation</strong>(all_query_outputs) </a>
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- </span>
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-
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- <span class="summary_desc"><div class='inline'>
383
- <p>Calculates an overall evaluation of the output Params:
384
- <tt>all_query_outputs</tt>: Array of <tt>ValidationTest</tt> objects Output
385
- Array of Strigs with the reports.</p>
386
- </div></span>
387
-
388
- </li>
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-
390
-
391
- <li class="public ">
392
- <span class="summary_signature">
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-
394
- <a href="#print_footer-class_method" title="print_footer (class method)">+ (Object) <strong>print_footer</strong>(all_query_outputs, html_path) </a>
395
-
396
-
397
-
398
- </span>
399
-
400
-
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-
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-
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-
404
-
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-
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- <span class="summary_desc"><div class='inline'>
409
- <p>Class that closes the gas in the html file and writes the overall
410
- evaluation Param: <tt>all_query_outputs</tt>: array with
411
- <tt>ValidationTest</tt> objects <tt>html_path</tt>: path of the html
412
- folder.</p>
413
- </div></span>
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-
415
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-
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-
418
- </ul>
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-
420
- <h2>
421
- Instance Method Summary
422
- <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
423
- </h2>
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-
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- <ul class="summary">
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-
427
- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#generate_html-instance_method" title="#generate_html (instance method)">- (Object) <strong>generate_html</strong> </a>
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-
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-
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-
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- </span>
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-
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-
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-
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- <span class="summary_desc"><div class='inline'></div></span>
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- </li>
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-
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-
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- <li class="public ">
450
- <span class="summary_signature">
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-
452
- <a href="#initialize-instance_method" title="#initialize (instance method)">- (Output) <strong>initialize</strong>(filename, html_path, yaml_path, idx = 0, start_idx = 0) </a>
453
-
454
-
455
-
456
- </span>
457
-
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-
459
- <span class="note title constructor">constructor</span>
460
-
461
-
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-
463
-
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-
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-
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-
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-
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- <span class="summary_desc"><div class='inline'>
469
- <p>Initilizes the object Params: <tt>filename</tt>: name of the fasta input
470
- file <tt>html_path</tt>: path of the html folder <tt>yaml_path</tt>: path
471
- where the yaml output wil be saved <tt>idx</tt>: idnex of the current query
472
- <tt>start_idx</tt>: number of the sequence from the file to start with.</p>
473
- </div></span>
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- </li>
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-
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-
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- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#print_output_console-instance_method" title="#print_output_console (instance method)">- (Object) <strong>print_output_console</strong> </a>
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-
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-
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-
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- </span>
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-
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-
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-
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-
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-
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-
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-
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- <span class="summary_desc"><div class='inline'></div></span>
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- </li>
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-
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-
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- <li class="public ">
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- <span class="summary_signature">
502
-
503
- <a href="#print_output_file_yaml-instance_method" title="#print_output_file_yaml (instance method)">- (Object) <strong>print_output_file_yaml</strong> </a>
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-
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-
506
-
507
- </span>
508
-
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-
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-
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-
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-
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-
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-
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- <span class="summary_desc"><div class='inline'></div></span>
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-
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- </li>
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-
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-
522
- </ul>
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-
524
-
525
- <div id="constructor_details" class="method_details_list">
526
- <h2>Constructor Details</h2>
527
-
528
- <div class="method_details first">
529
- <h3 class="signature first" id="initialize-instance_method">
530
-
531
- - (<tt><span class='object_link'><a href="" title="Output (class)">Output</a></span></tt>) <strong>initialize</strong>(filename, html_path, yaml_path, idx = 0, start_idx = 0)
532
-
533
-
534
-
535
-
536
-
537
- </h3><div class="docstring">
538
- <div class="discussion">
539
-
540
- <p>Initilizes the object Params: <tt>filename</tt>: name of the fasta input
541
- file <tt>html_path</tt>: path of the html folder <tt>yaml_path</tt>: path
542
- where the yaml output wil be saved <tt>idx</tt>: idnex of the current query
543
- <tt>start_idx</tt>: number of the sequence from the file to start with</p>
544
-
545
-
546
- </div>
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- </div>
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- <div class="tags">
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-
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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569
- 40</pre>
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- </td>
571
- <td>
572
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 28</span>
573
-
574
- <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_html_path'>html_path</span><span class='comma'>,</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span><span class='comma'>,</span> <span class='id identifier rubyid_idx'>idx</span> <span class='op'>=</span> <span class='int'>0</span><span class='comma'>,</span> <span class='id identifier rubyid_start_idx'>start_idx</span> <span class='op'>=</span> <span class='int'>0</span><span class='rparen'>)</span>
575
-
576
- <span class='ivar'>@prediction_len</span> <span class='op'>=</span> <span class='int'>0</span>
577
- <span class='ivar'>@prediction_def</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>no_definition</span><span class='tstring_end'>&quot;</span></span>
578
- <span class='ivar'>@nr_hits</span> <span class='op'>=</span> <span class='int'>0</span>
579
-
580
- <span class='ivar'>@filename</span> <span class='op'>=</span> <span class='id identifier rubyid_filename'>filename</span>
581
- <span class='ivar'>@html_path</span> <span class='op'>=</span> <span class='id identifier rubyid_html_path'>html_path</span>
582
- <span class='ivar'>@yaml_path</span> <span class='op'>=</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span>
583
- <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='id identifier rubyid_idx'>idx</span>
584
- <span class='ivar'>@start_idx</span> <span class='op'>=</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
585
-
586
- <span class='kw'>end</span></pre>
587
- </td>
588
- </tr>
589
- </table>
590
- </div>
591
-
592
- </div>
593
-
594
- <div id="instance_attr_details" class="attr_details">
595
- <h2>Instance Attribute Details</h2>
596
-
597
-
598
- <span id="filename=-instance_method"></span>
599
- <div class="method_details first">
600
- <h3 class="signature first" id="filename-instance_method">
601
-
602
- - (<tt>Object</tt>) <strong>filename</strong>
603
-
604
-
605
-
606
-
607
-
608
- </h3><div class="docstring">
609
- <div class="discussion">
610
-
611
- <p>Returns the value of attribute filename</p>
612
-
613
-
614
- </div>
615
- </div>
616
- <div class="tags">
617
-
618
-
619
- </div><table class="source_code">
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- <tr>
621
- <td>
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- <pre class="lines">
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-
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-
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- 14
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- 15
627
- 16</pre>
628
- </td>
629
- <td>
630
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 14</span>
631
-
632
- <span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
633
- <span class='ivar'>@filename</span>
634
- <span class='kw'>end</span></pre>
635
- </td>
636
- </tr>
637
- </table>
638
- </div>
639
-
640
-
641
- <span id="html_path=-instance_method"></span>
642
- <div class="method_details ">
643
- <h3 class="signature " id="html_path-instance_method">
644
-
645
- - (<tt>Object</tt>) <strong>html_path</strong>
646
-
647
-
648
-
649
-
650
-
651
- </h3><div class="docstring">
652
- <div class="discussion">
653
-
654
- <p>Returns the value of attribute html_path</p>
655
-
656
-
657
- </div>
658
- </div>
659
- <div class="tags">
660
-
661
-
662
- </div><table class="source_code">
663
- <tr>
664
- <td>
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- <pre class="lines">
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-
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-
668
- 15
669
- 16
670
- 17</pre>
671
- </td>
672
- <td>
673
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 15</span>
674
-
675
- <span class='kw'>def</span> <span class='id identifier rubyid_html_path'>html_path</span>
676
- <span class='ivar'>@html_path</span>
677
- <span class='kw'>end</span></pre>
678
- </td>
679
- </tr>
680
- </table>
681
- </div>
682
-
683
-
684
- <span id="idx=-instance_method"></span>
685
- <div class="method_details ">
686
- <h3 class="signature " id="idx-instance_method">
687
-
688
- - (<tt>Object</tt>) <strong>idx</strong>
689
-
690
-
691
-
692
-
693
-
694
- </h3><div class="docstring">
695
- <div class="discussion">
696
-
697
- <p>Returns the value of attribute idx</p>
698
-
699
-
700
- </div>
701
- </div>
702
- <div class="tags">
703
-
704
-
705
- </div><table class="source_code">
706
- <tr>
707
- <td>
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- <pre class="lines">
709
-
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-
711
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712
- 18
713
- 19</pre>
714
- </td>
715
- <td>
716
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 17</span>
717
-
718
- <span class='kw'>def</span> <span class='id identifier rubyid_idx'>idx</span>
719
- <span class='ivar'>@idx</span>
720
- <span class='kw'>end</span></pre>
721
- </td>
722
- </tr>
723
- </table>
724
- </div>
725
-
726
-
727
- <span id="nr_hits=-instance_method"></span>
728
- <div class="method_details ">
729
- <h3 class="signature " id="nr_hits-instance_method">
730
-
731
- - (<tt>Object</tt>) <strong>nr_hits</strong>
732
-
733
-
734
-
735
-
736
-
737
- </h3><div class="docstring">
738
- <div class="discussion">
739
-
740
- <p>Returns the value of attribute nr_hits</p>
741
-
742
-
743
- </div>
744
- </div>
745
- <div class="tags">
746
-
747
-
748
- </div><table class="source_code">
749
- <tr>
750
- <td>
751
- <pre class="lines">
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-
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-
754
- 9
755
- 10
756
- 11</pre>
757
- </td>
758
- <td>
759
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 9</span>
760
-
761
- <span class='kw'>def</span> <span class='id identifier rubyid_nr_hits'>nr_hits</span>
762
- <span class='ivar'>@nr_hits</span>
763
- <span class='kw'>end</span></pre>
764
- </td>
765
- </tr>
766
- </table>
767
- </div>
768
-
769
-
770
- <span id="prediction_def=-instance_method"></span>
771
- <div class="method_details ">
772
- <h3 class="signature " id="prediction_def-instance_method">
773
-
774
- - (<tt>Object</tt>) <strong>prediction_def</strong>
775
-
776
-
777
-
778
-
779
-
780
- </h3><div class="docstring">
781
- <div class="discussion">
782
-
783
- <p>Returns the value of attribute prediction_def</p>
784
-
785
-
786
- </div>
787
- </div>
788
- <div class="tags">
789
-
790
-
791
- </div><table class="source_code">
792
- <tr>
793
- <td>
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- <pre class="lines">
795
-
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-
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- 8
798
- 9
799
- 10</pre>
800
- </td>
801
- <td>
802
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 8</span>
803
-
804
- <span class='kw'>def</span> <span class='id identifier rubyid_prediction_def'>prediction_def</span>
805
- <span class='ivar'>@prediction_def</span>
806
- <span class='kw'>end</span></pre>
807
- </td>
808
- </tr>
809
- </table>
810
- </div>
811
-
812
-
813
- <span id="prediction_len=-instance_method"></span>
814
- <div class="method_details ">
815
- <h3 class="signature " id="prediction_len-instance_method">
816
-
817
- - (<tt>Object</tt>) <strong>prediction_len</strong>
818
-
819
-
820
-
821
-
822
-
823
- </h3><div class="docstring">
824
- <div class="discussion">
825
-
826
- <p>Returns the value of attribute prediction_len</p>
827
-
828
-
829
- </div>
830
- </div>
831
- <div class="tags">
832
-
833
-
834
- </div><table class="source_code">
835
- <tr>
836
- <td>
837
- <pre class="lines">
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-
839
-
840
- 7
841
- 8
842
- 9</pre>
843
- </td>
844
- <td>
845
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 7</span>
846
-
847
- <span class='kw'>def</span> <span class='id identifier rubyid_prediction_len'>prediction_len</span>
848
- <span class='ivar'>@prediction_len</span>
849
- <span class='kw'>end</span></pre>
850
- </td>
851
- </tr>
852
- </table>
853
- </div>
854
-
855
-
856
- <span id="start_idx=-instance_method"></span>
857
- <div class="method_details ">
858
- <h3 class="signature " id="start_idx-instance_method">
859
-
860
- - (<tt>Object</tt>) <strong>start_idx</strong>
861
-
862
-
863
-
864
-
865
-
866
- </h3><div class="docstring">
867
- <div class="discussion">
868
-
869
- <p>Returns the value of attribute start_idx</p>
870
-
871
-
872
- </div>
873
- </div>
874
- <div class="tags">
875
-
876
-
877
- </div><table class="source_code">
878
- <tr>
879
- <td>
880
- <pre class="lines">
881
-
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-
883
- 18
884
- 19
885
- 20</pre>
886
- </td>
887
- <td>
888
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 18</span>
889
-
890
- <span class='kw'>def</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
891
- <span class='ivar'>@start_idx</span>
892
- <span class='kw'>end</span></pre>
893
- </td>
894
- </tr>
895
- </table>
896
- </div>
897
-
898
-
899
- <span id="validations=-instance_method"></span>
900
- <div class="method_details ">
901
- <h3 class="signature " id="validations-instance_method">
902
-
903
- - (<tt>Object</tt>) <strong>validations</strong>
904
-
905
-
906
-
907
-
908
-
909
- </h3><div class="docstring">
910
- <div class="discussion">
911
-
912
- <p>list of <tt>ValidationReport</tt> objects</p>
913
-
914
-
915
- </div>
916
- </div>
917
- <div class="tags">
918
-
919
-
920
- </div><table class="source_code">
921
- <tr>
922
- <td>
923
- <pre class="lines">
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-
925
-
926
- 12
927
- 13
928
- 14</pre>
929
- </td>
930
- <td>
931
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 12</span>
932
-
933
- <span class='kw'>def</span> <span class='id identifier rubyid_validations'>validations</span>
934
- <span class='ivar'>@validations</span>
935
- <span class='kw'>end</span></pre>
936
- </td>
937
- </tr>
938
- </table>
939
- </div>
940
-
941
-
942
- <span id="yaml_path=-instance_method"></span>
943
- <div class="method_details ">
944
- <h3 class="signature " id="yaml_path-instance_method">
945
-
946
- - (<tt>Object</tt>) <strong>yaml_path</strong>
947
-
948
-
949
-
950
-
951
-
952
- </h3><div class="docstring">
953
- <div class="discussion">
954
-
955
- <p>Returns the value of attribute yaml_path</p>
956
-
957
-
958
- </div>
959
- </div>
960
- <div class="tags">
961
-
962
-
963
- </div><table class="source_code">
964
- <tr>
965
- <td>
966
- <pre class="lines">
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-
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-
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- 16
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- 17
971
- 18</pre>
972
- </td>
973
- <td>
974
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 16</span>
975
-
976
- <span class='kw'>def</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span>
977
- <span class='ivar'>@yaml_path</span>
978
- <span class='kw'>end</span></pre>
979
- </td>
980
- </tr>
981
- </table>
982
- </div>
983
-
984
- </div>
985
-
986
-
987
- <div id="class_method_details" class="method_details_list">
988
- <h2>Class Method Details</h2>
989
-
990
-
991
- <div class="method_details first">
992
- <h3 class="signature first" id="overall_evaluation-class_method">
993
-
994
- + (<tt>Object</tt>) <strong>overall_evaluation</strong>(all_query_outputs)
995
-
996
-
997
-
998
-
999
-
1000
- </h3><div class="docstring">
1001
- <div class="discussion">
1002
-
1003
- <p>Calculates an overall evaluation of the output Params:
1004
- <tt>all_query_outputs</tt>: Array of <tt>ValidationTest</tt> objects Output
1005
- Array of Strigs with the reports</p>
1006
-
1007
-
1008
- </div>
1009
- </div>
1010
- <div class="tags">
1011
-
1012
-
1013
- </div><table class="source_code">
1014
- <tr>
1015
- <td>
1016
- <pre class="lines">
1017
-
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-
1019
- 148
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- 149
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1039
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1064
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1069
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1100
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1101
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1103
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1104
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1105
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1106
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1107
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1108
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1109
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1110
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1111
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1112
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1113
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1114
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1115
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1116
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1117
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1119
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1120
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1121
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1122
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1123
- 252</pre>
1124
- </td>
1125
- <td>
1126
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 148</span>
1127
-
1128
- <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='rparen'>)</span>
1129
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1130
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Query score evaluation:</span><span class='tstring_end'>&quot;</span></span>
1131
-
1132
- <span class='comment'># count the cases of &quot;not enough evidence&quot;
1133
- </span> <span class='id identifier rubyid_no_evidence'>no_evidence</span> <span class='op'>=</span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
1134
- <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='symbol'>:unapplicable</span> <span class='kw'>or</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='symbol'>:warning</span><span class='rbrace'>}</span> <span class='op'>==</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
1135
- <span class='rbrace'>}</span>
1136
-
1137
- <span class='comment'># print at the console
1138
- </span> <span class='id identifier rubyid_scores'>scores</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
1139
- <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>=</span> <span class='int'>0</span>
1140
- <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>=</span> <span class='int'>0</span>
1141
-
1142
- <span class='comment'># how many genes are good
1143
- </span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
1144
- <span class='id identifier rubyid_successes'>successes</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
1145
- <span class='id identifier rubyid_fails'>fails</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span> <span class='kw'>and</span>
1146
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>!=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
1147
- <span class='id identifier rubyid_overall_score'>overall_score</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span><span class='op'>*</span><span class='int'>100</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span> <span class='op'>+</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
1148
- <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='id identifier rubyid_overall_score'>overall_score</span>
1149
-
1150
- <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
1151
- <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span> <span class='op'>!=</span> <span class='kw'>nil</span>
1152
- <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>+=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span> <span class='op'>==</span> <span class='const'>NoMafftInstallationError</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
1153
- <span class='kw'>end</span>
1154
- <span class='kw'>end</span>
1155
-
1156
- <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
1157
- <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span> <span class='op'>!=</span> <span class='kw'>nil</span>
1158
- <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>+=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span> <span class='op'>==</span> <span class='const'>NoInternetError</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
1159
- <span class='kw'>end</span>
1160
- <span class='kw'>end</span>
1161
- <span class='kw'>end</span>
1162
-
1163
- <span class='id identifier rubyid_good_scores'>good_scores</span> <span class='op'>=</span> <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span> <span class='op'>&gt;</span> <span class='int'>75</span><span class='rbrace'>}</span>
1164
- <span class='id identifier rubyid_bad_scores'>bad_scores</span> <span class='op'>=</span> <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_good_scores'>good_scores</span>
1165
-
1166
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nThere were validated </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbrace'>}</span><span class='tstring_content'> predictions from which:</span><span class='tstring_end'>&quot;</span></span>
1167
- <span class='kw'>if</span> <span class='id identifier rubyid_good_scores'>good_scores</span> <span class='op'>==</span> <span class='int'>1</span>
1168
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nOne good prediction</span><span class='tstring_end'>&quot;</span></span>
1169
- <span class='kw'>else</span>
1170
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_good_scores'>good_scores</span><span class='rbrace'>}</span><span class='tstring_content'> are good predictions</span><span class='tstring_end'>&quot;</span></span>
1171
- <span class='kw'>end</span>
1172
- <span class='kw'>if</span> <span class='id identifier rubyid_bad_scores'>bad_scores</span> <span class='op'>==</span> <span class='int'>1</span>
1173
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nOne possibly weak prediction</span><span class='tstring_end'>&quot;</span></span>
1174
- <span class='kw'>else</span>
1175
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_bad_scores'>bad_scores</span><span class='rbrace'>}</span><span class='tstring_content'> are possibly weak predictions</span><span class='tstring_end'>&quot;</span></span>
1176
- <span class='kw'>end</span>
1177
-
1178
- <span class='kw'>if</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span> <span class='op'>!=</span> <span class='int'>0</span>
1179
- <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rbrace'>}</span><span class='tstring_content'> of them couldn't be evaluated because of low evidence</span><span class='tstring_end'>&quot;</span></span>
1180
- <span class='kw'>end</span>
1181
-
1182
- <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1183
- <span class='comment'># errors per validation
1184
- </span> <span class='id identifier rubyid_validations'>validations</span> <span class='op'>=</span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span>
1185
- <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='comma'>,</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
1186
- <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>=</span> <span class='int'>0</span>
1187
- <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
1188
- <span class='kw'>if</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>==</span> <span class='symbol'>:error</span>
1189
- <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>+=</span> <span class='int'>1</span>
1190
- <span class='kw'>end</span>
1191
- <span class='kw'>end</span>
1192
- <span class='kw'>if</span> <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>!=</span> <span class='int'>0</span>
1193
- <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't run </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbrace'>}</span><span class='tstring_content'> Validation for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_no_errors'>no_errors</span><span class='rbrace'>}</span><span class='tstring_content'> queries</span><span class='tstring_end'>&quot;</span></span>
1194
- <span class='kw'>end</span>
1195
- <span class='kw'>end</span>
1196
-
1197
- <span class='kw'>if</span> <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>&gt;=</span> <span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rparen'>)</span>
1198
- <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't run MAFFT multiple alignment</span><span class='tstring_end'>&quot;</span></span>
1199
- <span class='kw'>end</span>
1200
- <span class='kw'>if</span> <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>&gt;=</span> <span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rparen'>)</span>
1201
- <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't make use of your internet connection</span><span class='tstring_end'>&quot;</span></span>
1202
- <span class='kw'>end</span>
1203
-
1204
- <span class='comment'># Running time statistics
1205
- </span> <span class='id identifier rubyid_running_times'>running_times</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
1206
- <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
1207
- <span class='id identifier rubyid_running_times'>running_times</span><span class='lbracket'>[</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
1208
- <span class='kw'>end</span>
1209
-
1210
- <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_output'>output</span><span class='op'>|</span>
1211
- <span class='id identifier rubyid_output'>output</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
1212
- <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span> <span class='op'>!=</span> <span class='int'>0</span> <span class='kw'>and</span>
1213
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span>
1214
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span>
1215
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span>
1216
- <span class='id identifier rubyid_running_times'>running_times</span><span class='lbracket'>[</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span>
1217
- <span class='kw'>end</span>
1218
- <span class='kw'>end</span>
1219
- <span class='kw'>end</span>
1220
-
1221
- <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1222
- <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nRunning Time:</span><span class='tstring_end'>&quot;</span></span>
1223
- <span class='id identifier rubyid_running_times'>running_times</span> <span class='op'>=</span> <span class='id identifier rubyid_running_times'>running_times</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>!=</span><span class='int'>0</span><span class='rbrace'>}</span>
1224
- <span class='id identifier rubyid_running_times'>running_times</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_key'>key</span><span class='comma'>,</span> <span class='id identifier rubyid_array'>array</span><span class='op'>|</span>
1225
- <span class='id identifier rubyid_average_time'>average_time</span> <span class='op'>=</span> <span class='id identifier rubyid_array'>array</span><span class='period'>.</span><span class='id identifier rubyid_inject'>inject</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_el'>el</span><span class='op'>|</span> <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='id identifier rubyid_el'>el</span> <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span> <span class='op'>/</span> <span class='id identifier rubyid_array'>array</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span>
1226
- <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nAverage running time for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='rbrace'>}</span><span class='tstring_content'> Validation: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_average_time'>average_time</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>3</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='tstring_content'>s per validation</span><span class='tstring_end'>&quot;</span></span>
1227
- <span class='kw'>end</span>
1228
-
1229
- <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='id identifier rubyid_score_evaluation'>score_evaluation</span><span class='comma'>,</span> <span class='id identifier rubyid_error_evaluation'>error_evaluation</span><span class='comma'>,</span> <span class='id identifier rubyid_time_evaluation'>time_evaluation</span><span class='rbracket'>]</span>
1230
- <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span><span class='op'>!=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span>
1231
- <span class='kw'>return</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span>
1232
- <span class='kw'>end</span></pre>
1233
- </td>
1234
- </tr>
1235
- </table>
1236
- </div>
1237
-
1238
- <div class="method_details ">
1239
- <h3 class="signature " id="print_footer-class_method">
1240
-
1241
- + (<tt>Object</tt>) <strong>print_footer</strong>(all_query_outputs, html_path)
1242
-
1243
-
1244
-
1245
-
1246
-
1247
- </h3><div class="docstring">
1248
- <div class="discussion">
1249
-
1250
- <p>Class that closes the gas in the html file and writes the overall
1251
- evaluation Param: <tt>all_query_outputs</tt>: array with
1252
- <tt>ValidationTest</tt> objects <tt>html_path</tt>: path of the html folder</p>
1253
-
1254
-
1255
- </div>
1256
- </div>
1257
- <div class="tags">
1258
-
1259
-
1260
- </div><table class="source_code">
1261
- <tr>
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- <td>
1263
- <pre class="lines">
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1280
- 140</pre>
1281
- </td>
1282
- <td>
1283
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 126</span>
1284
-
1285
- <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_print_footer'>print_footer</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='comma'>,</span> <span class='id identifier rubyid_html_path'>html_path</span><span class='rparen'>)</span>
1286
- <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='rparen'>)</span>
1287
- <span class='comment'># print to console
1288
- </span> <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1289
- <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_e'>e</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span>
1290
- <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_evaluation'>evaluation</span>
1291
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1292
- <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_evaluation'>evaluation</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>&lt;br&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1293
-
1294
- <span class='comment'># print to html
1295
- </span> <span class='id identifier rubyid_index_file'>index_file</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_html_path'>html_path</span><span class='rbrace'>}</span><span class='tstring_content'>/index.html</span><span class='tstring_end'>&quot;</span></span>
1296
- <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_footer.htm.erb</span><span class='tstring_end'>&quot;</span></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_read'>read</span>
1297
- <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
1298
- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>a+</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
1299
- <span class='kw'>end</span></pre>
1300
- </td>
1301
- </tr>
1302
- </table>
1303
- </div>
1304
-
1305
- </div>
1306
-
1307
- <div id="instance_method_details" class="method_details_list">
1308
- <h2>Instance Method Details</h2>
1309
-
1310
-
1311
- <div class="method_details first">
1312
- <h3 class="signature first" id="generate_html-instance_method">
1313
-
1314
- - (<tt>Object</tt>) <strong>generate_html</strong>
1315
-
1316
-
1317
-
1318
-
1319
-
1320
- </h3><table class="source_code">
1321
- <tr>
1322
- <td>
1323
- <pre class="lines">
1324
-
1325
-
1326
- 88
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- 89
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- 91
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- 93
1332
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1353
- 115
1354
- 116
1355
- 117
1356
- 118
1357
- 119</pre>
1358
- </td>
1359
- <td>
1360
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 88</span>
1361
-
1362
- <span class='kw'>def</span> <span class='id identifier rubyid_generate_html'>generate_html</span>
1363
-
1364
- <span class='id identifier rubyid_successes'>successes</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span>
1365
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
1366
- <span class='id identifier rubyid_fails'>fails</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span>
1367
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span> <span class='kw'>and</span>
1368
- <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>!=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
1369
- <span class='id identifier rubyid_unknown'>unknown</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_successes'>successes</span> <span class='op'>-</span> <span class='id identifier rubyid_fails'>fails</span>
1370
- <span class='id identifier rubyid_overall_score'>overall_score</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span><span class='op'>*</span><span class='int'>100</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span> <span class='op'>+</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
1371
-
1372
- <span class='kw'>if</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>==</span> <span class='int'>0</span>
1373
- <span class='id identifier rubyid_bg_icon'>bg_icon</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>success</span><span class='tstring_end'>&quot;</span></span>
1374
- <span class='kw'>else</span>
1375
- <span class='id identifier rubyid_bg_icon'>bg_icon</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>danger</span><span class='tstring_end'>&quot;</span></span>
1376
- <span class='kw'>end</span>
1377
-
1378
- <span class='id identifier rubyid_index_file'>index_file</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@html_path</span><span class='rbrace'>}</span><span class='tstring_content'>/index.html</span><span class='tstring_end'>&quot;</span></span>
1379
-
1380
- <span class='comment'># if it's the first time I write in the html file
1381
- </span> <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
1382
- <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_header.htm.erb</span><span class='tstring_end'>&quot;</span></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_read'>read</span>
1383
- <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
1384
- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>w+</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
1385
- <span class='kw'>end</span>
1386
-
1387
- <span class='id identifier rubyid_toggle'>toggle</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>toggle</span><span class='embexpr_beg'>#{</span><span class='ivar'>@idx</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1388
-
1389
- <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_query.htm.erb</span><span class='tstring_end'>&quot;</span></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_read'>read</span>
1390
- <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
1391
-
1392
- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>a</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
1393
- <span class='kw'>end</span></pre>
1394
- </td>
1395
- </tr>
1396
- </table>
1397
- </div>
1398
-
1399
- <div class="method_details ">
1400
- <h3 class="signature " id="print_output_console-instance_method">
1401
-
1402
- - (<tt>Object</tt>) <strong>print_output_console</strong>
1403
-
1404
-
1405
-
1406
-
1407
-
1408
- </h3><table class="source_code">
1409
- <tr>
1410
- <td>
1411
- <pre class="lines">
1412
-
1413
-
1414
- 43
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- 44
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- 45
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- 46
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- 47
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- 48
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- 51
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1436
- 65
1437
- 66</pre>
1438
- </td>
1439
- <td>
1440
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 43</span>
1441
-
1442
- <span class='kw'>def</span> <span class='id identifier rubyid_print_output_console'>print_output_console</span>
1443
-
1444
- <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
1445
- <span class='id identifier rubyid_header'>header</span> <span class='op'>=</span><span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%3s|%20s|%5s</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>No</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Identifier</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>No_Hits</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1446
- <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
1447
- <span class='id identifier rubyid_header'>header</span><span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>|</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1448
- <span class='kw'>end</span>
1449
- <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_header'>header</span>
1450
- <span class='kw'>end</span>
1451
-
1452
- <span class='id identifier rubyid_short_def'>short_def</span> <span class='op'>=</span> <span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
1453
- <span class='id identifier rubyid_short_def'>short_def</span> <span class='op'>=</span> <span class='id identifier rubyid_short_def'>short_def</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='lbracket'>[</span><span class='int'>20</span><span class='comma'>,</span><span class='id identifier rubyid_short_def'>short_def</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_min'>min</span><span class='rbracket'>]</span>
1454
- <span class='id identifier rubyid_validation_outputs'>validation_outputs</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span><span class='rbrace'>}</span>
1455
-
1456
- <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%3s|%20s|%5s|</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@idx</span><span class='comma'>,</span> <span class='id identifier rubyid_short_def'>short_def</span><span class='comma'>,</span> <span class='ivar'>@nr_hits</span><span class='rparen'>)</span>
1457
- <span class='id identifier rubyid_validation_outputs'>validation_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_item'>item</span><span class='op'>|</span>
1458
- <span class='id identifier rubyid_item_padd'>item_padd</span> <span class='op'>=</span> <span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%17s</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_item'>item</span><span class='rparen'>)</span><span class='semicolon'>;</span>
1459
- <span class='id identifier rubyid_output'>output</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_item'>item</span>
1460
- <span class='id identifier rubyid_output'>output</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>|</span><span class='tstring_end'>&quot;</span></span>
1461
- <span class='kw'>end</span>
1462
-
1463
- <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_output'>output</span>
1464
-
1465
- <span class='kw'>end</span></pre>
1466
- </td>
1467
- </tr>
1468
- </table>
1469
- </div>
1470
-
1471
- <div class="method_details ">
1472
- <h3 class="signature " id="print_output_file_yaml-instance_method">
1473
-
1474
- - (<tt>Object</tt>) <strong>print_output_file_yaml</strong>
1475
-
1476
-
1477
-
1478
-
1479
-
1480
- </h3><table class="source_code">
1481
- <tr>
1482
- <td>
1483
- <pre class="lines">
1484
-
1485
-
1486
- 69
1487
- 70
1488
- 71
1489
- 72
1490
- 73
1491
- 74
1492
- 75
1493
- 76
1494
- 77
1495
- 78
1496
- 79
1497
- 80
1498
- 81
1499
- 82
1500
- 83
1501
- 84
1502
- 85</pre>
1503
- </td>
1504
- <td>
1505
- <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 69</span>
1506
-
1507
- <span class='kw'>def</span> <span class='id identifier rubyid_print_output_file_yaml'>print_output_file_yaml</span>
1508
-
1509
- <span class='id identifier rubyid_file_yaml'>file_yaml</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@yaml_path</span><span class='rbrace'>}</span><span class='tstring_content'>/</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>.yaml</span><span class='tstring_end'>&quot;</span></span>
1510
- <span class='id identifier rubyid_report'>report</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='rbrace'>}</span>
1511
- <span class='kw'>unless</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
1512
- <span class='id identifier rubyid_hsh'>hsh</span> <span class='op'>=</span> <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_load_file'>load_file</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='rparen'>)</span>
1513
- <span class='id identifier rubyid_hsh'>hsh</span><span class='lbracket'>[</span><span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span>
1514
- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_f'>f</span><span class='op'>|</span>
1515
- <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_dump'>dump</span><span class='lparen'>(</span><span class='id identifier rubyid_hsh'>hsh</span><span class='comma'>,</span> <span class='id identifier rubyid_f'>f</span><span class='rparen'>)</span>
1516
- <span class='kw'>end</span>
1517
- <span class='kw'>else</span>
1518
- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_f'>f</span><span class='op'>|</span>
1519
- <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_dump'>dump</span><span class='lparen'>(</span><span class='lbrace'>{</span><span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_report'>report</span><span class='rbrace'>}</span><span class='comma'>,</span><span class='id identifier rubyid_f'>f</span><span class='rparen'>)</span>
1520
- <span class='kw'>end</span>
1521
- <span class='kw'>end</span>
1522
-
1523
- <span class='kw'>end</span></pre>
1524
- </td>
1525
- </tr>
1526
- </table>
1527
- </div>
1528
-
1529
- </div>
1530
-
1531
- </div>
1532
-
1533
- <div id="footer">
1534
- Generated on Sat Sep 28 07:01:32 2013 by
1535
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
1536
- 0.8.7.2 (ruby-1.9.3).
1537
- </div>
1538
-
1539
- </body>
1540
- </html>