sequenceserver 3.0 → 3.1.0

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Files changed (57) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +2 -2
  3. data/lib/sequenceserver/api_errors.rb +1 -1
  4. data/lib/sequenceserver/blast/job.rb +20 -3
  5. data/lib/sequenceserver/blast/report.rb +74 -86
  6. data/lib/sequenceserver/blast/tasks.rb +38 -0
  7. data/lib/sequenceserver/config.rb +54 -20
  8. data/lib/sequenceserver/makeblastdb.rb +16 -2
  9. data/lib/sequenceserver/report.rb +0 -6
  10. data/lib/sequenceserver/routes.rb +32 -21
  11. data/lib/sequenceserver/version.rb +1 -1
  12. data/lib/sequenceserver.rb +1 -1
  13. data/public/css/app.css +121 -0
  14. data/public/css/app.min.css +1 -0
  15. data/public/css/sequenceserver.css +0 -148
  16. data/public/css/sequenceserver.min.css +3 -3
  17. data/public/js/circos.js +2 -2
  18. data/public/js/collapse_preferences.js +37 -0
  19. data/public/js/databases.js +65 -37
  20. data/public/js/databases_tree.js +2 -1
  21. data/public/js/dnd.js +37 -50
  22. data/public/js/form.js +78 -50
  23. data/public/js/grapher.js +23 -37
  24. data/public/js/hits_overview.js +2 -2
  25. data/public/js/kablammo.js +2 -2
  26. data/public/js/length_distribution.js +3 -3
  27. data/public/js/null_plugins/grapher/histogram.js +25 -0
  28. data/public/js/null_plugins/options.js +3 -0
  29. data/public/js/null_plugins/query_stats.js +11 -0
  30. data/public/js/null_plugins/report_plugins.js +6 -1
  31. data/public/js/null_plugins/search_header_plugin.js +4 -0
  32. data/public/js/options.js +161 -56
  33. data/public/js/query.js +85 -59
  34. data/public/js/report.js +1 -1
  35. data/public/js/search.js +2 -0
  36. data/public/js/search_button.js +67 -56
  37. data/public/js/sidebar.js +1 -1
  38. data/public/js/tests/database.spec.js +5 -5
  39. data/public/js/tests/{advanced_parameters.spec.js → form.spec.js} +35 -1
  40. data/public/js/tests/mock_data/databases.json +5 -5
  41. data/public/js/tests/mocks/circos.js +6 -0
  42. data/public/js/tests/report.spec.js +4 -3
  43. data/public/js/tests/search_query.spec.js +5 -6
  44. data/public/sequenceserver-report.min.js +45 -23
  45. data/public/sequenceserver-search.min.js +57 -13
  46. data/public/sequenceserver_logo.webp +0 -0
  47. data/views/blastn_options.erb +66 -66
  48. data/views/blastp_options.erb +59 -59
  49. data/views/blastx_options.erb +68 -68
  50. data/views/layout.erb +60 -3
  51. data/views/search.erb +33 -38
  52. data/views/search_layout.erb +152 -0
  53. data/views/tblastn_options.erb +57 -57
  54. data/views/tblastx_options.erb +64 -64
  55. metadata +31 -22
  56. data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +0 -345
  57. data/public/SequenceServer_logo.png +0 -0
data/public/sequenceserver_logo.webp ADDED
Binary file
data/views/blastn_options.erb CHANGED
@@ -4,67 +4,67 @@
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  characters per line to preserve formatting.
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  %>
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- <h5>General Search Options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">General Search Options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'>
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  Task to execute
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  Default = 'megablast'|%></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-evalue <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-evalue <Real>
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  Expectation value (E) threshold for saving hits
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  Default = '10' (1000 for blastn-short)| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-word_size <Integer, >=2>
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  Word size for wordfinder algorithm (length of best perfect match)| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapopen <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapopen <Integer>
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  Cost to open a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapextend <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapextend <Integer>
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  Cost to extend a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-penalty <Integer, <=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-penalty <Integer, <=0>
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  Penalty for a nucleotide mismatch| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-reward <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-reward <Integer, >=0>
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  Reward for a nucleotide match| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-use_index <Boolean>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-use_index <Boolean>
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  Use MegaBLAST database index
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  Default = 'false'| %></pre>
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  </li>
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  </ul>
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  <br />
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- <h5>Formatting Options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Formatting Options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-show_gis
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-show_gis
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  Show NCBI GIs in deflines?| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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  Number of database sequences to show one-line descriptions for
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  Not applicable for outfmt > 4
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  Default = '500'
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  * Incompatible with: max_target_seqs| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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  Number of database sequences to show alignments for
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  Default = '250'
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  * Incompatible with: max_target_seqs| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -line_length <Integer, >=1>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -line_length <Integer, >=1>
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  Line length for formatting alignments
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  Not applicable for outfmt > 4
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  Default = '60'| %></pre>
@@ -73,52 +73,52 @@
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  <br/>
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- <h5>Query filtering options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Query filtering options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-dust <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-dust <String>
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  Filter query sequence with DUST (Format: 'yes', 'level window linker', or
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- 'no' to disable)
81
+ 'no' to disable)
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  Default = '20 64 1' ('no' for blastn-short)| %></pre>
83
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  </li>
84
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  <li>
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- <pre><%= ERB::Util.h %q|-soft_masking <Boolean>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-soft_masking <Boolean>
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  Apply filtering locations as soft masks
87
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  Default = 'true'| %></pre>
88
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  </li>
89
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  <li>
90
- <pre><%= ERB::Util.h %q|-lcase_masking
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-lcase_masking
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  Use lower case filtering in query and subject sequence(s)?| %></pre>
92
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  </li>
93
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  </ul>
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  <br/>
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- <h5>Restrict search or results</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Restrict search or results</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-gilist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gilist <String>
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  Restrict search of database to list of GIs
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  * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
105
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-seqidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seqidlist <String>
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  Restrict search of database to list of SeqIDs
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  * Incompatible with: gilist, taxids, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_gilist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_gilist <String>
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  Restrict search of database to everything except the specified GIs
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_seqidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_seqidlist <String>
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  Restrict search of database to everything except the specified SeqIDs
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
@@ -126,82 +126,82 @@
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  </li>
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  <li>
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  <li>
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- <pre><%= ERB::Util.h %q|-taxids <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxids <String>
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  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
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  * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
134
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_taxids <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxids <String>
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  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-taxidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxidlist <String>
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  Restrict search of database to include only the specified taxonomy IDs
145
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  * Incompatible with: gilist, seqidlist, taxids, negative_gilist,
146
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
147
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  subject_loc| %></pre>
148
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  </li>
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  <li>
150
- <pre><%= ERB::Util.h %q|-negative_taxidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxidlist <String>
151
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  Restrict search of database to everything except the specified taxonomy IDs
152
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
153
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  negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
154
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  subject_loc| %></pre>
155
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  </li>
156
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  <li>
157
- <pre><%= ERB::Util.h %q|-entrez_query <String>
157
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-entrez_query <String>
158
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  Restrict search with the given Entrez query
159
159
  * Requires: remote| %></pre>
160
160
  </li>
161
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  <li>
162
- <pre><%= ERB::Util.h %q|-db_soft_mask <String>
162
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_soft_mask <String>
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163
  Filtering algorithm ID to apply to the BLAST database as soft masking
164
164
  * Incompatible with: db_hard_mask, subject, subject_loc| %></pre>
165
165
  </li>
166
166
  <li>
167
- <pre><%= ERB::Util.h %q|-db_hard_mask <String>
167
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_hard_mask <String>
168
168
  Filtering algorithm ID to apply to the BLAST database as hard masking
169
169
  * Incompatible with: db_soft_mask, subject, subject_loc| %></pre>
170
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  </li>
171
171
  <li>
172
- <pre><%= ERB::Util.h %q|-perc_identity <Real, 0..100>
172
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-perc_identity <Real, 0..100>
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173
  Percent identity| %></pre>
174
174
  </li>
175
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  <li>
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- <pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
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177
  Percent query coverage per hsp| %></pre>
178
178
  </li>
179
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  <li>
180
- <pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
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181
  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
182
182
  </li>
183
183
  <li>
184
- <pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
184
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
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185
  If the query range of a hit is enveloped by that of at least this
186
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  many higher-scoring hits, delete the hit
187
187
  * Incompatible with: best_hit_overhang, best_hit_score_edge| %></pre>
188
188
  </li>
189
189
  <li>
190
- <pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
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191
  Best Hit algorithm overhang value (recommended value: 0.1)
192
192
  * Incompatible with: culling_limit| %></pre>
193
193
  </li>
194
194
  <li>
195
- <pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
195
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
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196
  Best Hit algorithm score edge value (recommended value: 0.1)
197
197
  * Incompatible with: culling_limit| %></pre>
198
198
  </li>
199
199
  <li>
200
- <pre><%= ERB::Util.h %q|-subject_besthit
200
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-subject_besthit
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201
  Turn on best hit per subject sequence| %></pre>
202
202
  </li>
203
203
  <li>
204
- <pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
204
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
205
205
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
206
206
  Default = '500'
207
207
  * Incompatible with: num_descriptions, num_alignments| %></pre>
@@ -210,15 +210,15 @@
210
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211
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  <br/>
212
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213
- <h5>Discontiguous MegaBLAST options</h5>
214
- <ul class="list-unstyled">
213
+ <h5 class="text-lg py-4 font-medium">Discontiguous MegaBLAST options</h5>
214
+ <ul class="list-unstyled space-y-2">
215
215
  <li>
216
- <pre><%= ERB::Util.h %q|-template_type <String, `coding', `coding_and_optimal', `optimal'>
216
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-template_type <String, `coding', `coding_and_optimal', `optimal'>
217
217
  Discontiguous MegaBLAST template type
218
218
  * Requires: template_length| %></pre>
219
219
  </li>
220
220
  <li>
221
- <pre><%= ERB::Util.h %q|-template_length <Integer, Permissible values: '16' '18' '21' >
221
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-template_length <Integer, Permissible values: '16' '18' '21' >
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  Discontiguous MegaBLAST template length
223
223
  * Requires: template_type| %></pre>
224
224
  </li>
@@ -227,65 +227,65 @@
227
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228
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  <br/>
229
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230
- <h5>Statistical options</h5>
231
- <ul class="list-unstyled">
230
+ <h5 class="text-lg py-4 font-medium">Statistical options</h5>
231
+ <ul class="list-unstyled space-y-2">
232
232
  <li>
233
- <pre><%= ERB::Util.h %q|-dbsize <Int8>
233
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-dbsize <Int8>
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  Effective length of the database| %></pre>
235
235
  </li>
236
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  <li>
237
- <pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
237
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-searchsp <Int8, >=0>
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  Effective length of the search space| %></pre>
239
239
  </li>
240
240
  </ul>
241
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242
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  <br/>
243
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244
- <h5>Extension options</h5>
245
- <ul class="list-unstyled">
244
+ <h5 class="text-lg py-4 font-medium">Extension options</h5>
245
+ <ul class="list-unstyled space-y-2">
246
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_ungap <Real>
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  X-dropoff value (in bits) for ungapped extensions| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap <Real>
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  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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  X-dropoff value (in bits) for final gapped alignment| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-no_greedy
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-no_greedy
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  Use non-greedy dynamic programming extension| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-min_raw_gapped_score <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-min_raw_gapped_score <Integer>
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  Minimum raw gapped score to keep an alignment in the preliminary gapped and
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  traceback stages| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-ungapped
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-ungapped
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  Perform ungapped alignment only?| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-window_size <Integer, >=0>
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  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-off_diagonal_range <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-off_diagonal_range <Integer, >=0>
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  Number of off-diagonals to search for the 2nd hit, use 0 to turn off
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  Default = `0'| %></pre>
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  </li>
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-
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+
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  </ul>
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  <br/>
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- <h5>Miscellaneous options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Miscellaneous options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-parse_deflines <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-parse_deflines <Real>
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  Should the query and subject defline(s) be parsed?| %></pre>
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  </li>
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-
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+
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  </ul>