bio 1.5.1 → 2.0.2

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Files changed (128) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +35 -36
  3. data/ChangeLog +911 -2554
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
  5. data/KNOWN_ISSUES.rdoc +10 -13
  6. data/LEGAL +0 -10
  7. data/README.rdoc +40 -96
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +118 -234
  10. data/Rakefile +13 -43
  11. data/appveyor.yml +29 -0
  12. data/bioruby.gemspec +18 -81
  13. data/bioruby.gemspec.erb +8 -28
  14. data/doc/ChangeLog-1.5.0 +2919 -0
  15. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  16. data/doc/Tutorial.rd +6 -108
  17. data/doc/Tutorial.rd.html +19 -98
  18. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  19. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  20. data/gemfiles/Gemfile.travis-rbx +0 -3
  21. data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
  22. data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
  23. data/gemfiles/Gemfile.windows +6 -0
  24. data/gemfiles/prepare-gemspec.rb +4 -0
  25. data/lib/bio.rb +0 -10
  26. data/lib/bio/appl/blast/genomenet.rb +4 -4
  27. data/lib/bio/appl/blast/report.rb +40 -8
  28. data/lib/bio/appl/fasta/format10.rb +2 -1
  29. data/lib/bio/command.rb +10 -0
  30. data/lib/bio/data/codontable.rb +99 -3
  31. data/lib/bio/db/aaindex.rb +74 -5
  32. data/lib/bio/db/gff.rb +3 -1
  33. data/lib/bio/db/kegg/common.rb +14 -0
  34. data/lib/bio/db/kegg/genes.rb +26 -0
  35. data/lib/bio/db/kegg/pathway.rb +5 -11
  36. data/lib/bio/db/soft.rb +2 -2
  37. data/lib/bio/io/flatfile/autodetection.rb +5 -0
  38. data/lib/bio/io/togows.rb +5 -5
  39. data/lib/bio/map.rb +4 -4
  40. data/lib/bio/sequence/format.rb +1 -0
  41. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
  42. data/lib/bio/util/sirna.rb +2 -0
  43. data/lib/bio/version.rb +6 -8
  44. data/sample/color_scheme_aa.rb +82 -0
  45. data/sample/color_scheme_na.rb +5 -6
  46. data/sample/fastq2html.cwl +23 -0
  47. data/sample/fastq2html.rb +94 -0
  48. data/sample/fastq2html.testdata.yaml +5 -0
  49. data/sample/na2aa.cwl +23 -0
  50. data/sample/na2aa.rb +11 -25
  51. data/sample/na2aa.testdata.yaml +7 -0
  52. data/sample/rev_comp.cwl +23 -0
  53. data/sample/rev_comp.rb +20 -0
  54. data/sample/rev_comp.testdata.yaml +7 -0
  55. data/sample/test_restriction_enzyme_long.rb +1 -1
  56. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  57. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  58. data/test/unit/bio/data/test_codontable.rb +3 -0
  59. data/test/unit/bio/db/test_gff.rb +5 -0
  60. data/test/unit/bio/test_alignment.rb +2 -2
  61. metadata +20 -77
  62. data/bin/bioruby +0 -47
  63. data/bin/br_biofetch.rb +0 -71
  64. data/bin/br_bioflat.rb +0 -293
  65. data/bin/br_biogetseq.rb +0 -45
  66. data/bin/br_pmfetch.rb +0 -422
  67. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  68. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  69. data/lib/bio/db/biosql/sequence.rb +0 -444
  70. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  71. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  72. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  73. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  74. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  75. data/lib/bio/io/biosql/biosql.rb +0 -39
  76. data/lib/bio/io/biosql/config/database.yml +0 -21
  77. data/lib/bio/io/sql.rb +0 -79
  78. data/lib/bio/shell.rb +0 -44
  79. data/lib/bio/shell/core.rb +0 -578
  80. data/lib/bio/shell/demo.rb +0 -146
  81. data/lib/bio/shell/interface.rb +0 -217
  82. data/lib/bio/shell/irb.rb +0 -94
  83. data/lib/bio/shell/object.rb +0 -71
  84. data/lib/bio/shell/plugin/blast.rb +0 -42
  85. data/lib/bio/shell/plugin/codon.rb +0 -218
  86. data/lib/bio/shell/plugin/das.rb +0 -58
  87. data/lib/bio/shell/plugin/emboss.rb +0 -23
  88. data/lib/bio/shell/plugin/entry.rb +0 -137
  89. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  90. data/lib/bio/shell/plugin/midi.rb +0 -430
  91. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  92. data/lib/bio/shell/plugin/obda.rb +0 -45
  93. data/lib/bio/shell/plugin/psort.rb +0 -56
  94. data/lib/bio/shell/plugin/seq.rb +0 -248
  95. data/lib/bio/shell/plugin/togows.rb +0 -40
  96. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  97. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  98. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  99. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  100. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  101. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  102. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  103. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  104. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  105. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  106. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  107. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  108. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  109. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  110. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  111. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  112. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  113. data/lib/bio/shell/script.rb +0 -25
  114. data/lib/bio/shell/setup.rb +0 -108
  115. data/lib/bio/shell/web.rb +0 -102
  116. data/sample/test_phyloxml_big.rb +0 -205
  117. data/setup.rb +0 -1600
  118. data/test/data/phyloxml/apaf.xml +0 -666
  119. data/test/data/phyloxml/bcl_2.xml +0 -2097
  120. data/test/data/phyloxml/made_up.xml +0 -144
  121. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  122. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  123. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  124. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  125. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  126. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  127. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  128. data/test/unit/bio/test_shell.rb +0 -20
@@ -1,29 +0,0 @@
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- class BiorubyGenerator < Rails::Generator::Base
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- def manifest
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- record do |m|
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- m.directory 'app/controllers'
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- m.directory 'app/helpers'
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- m.directory 'app/views/bioruby'
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- m.directory 'app/views/layouts'
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- m.directory 'public/images/bioruby'
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- m.directory 'public/stylesheets'
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- m.file 'bioruby_controller.rb', 'app/controllers/bioruby_controller.rb'
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- m.file 'bioruby_helper.rb', 'app/helpers/bioruby_helper.rb'
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- m.file '_methods.rhtml', 'app/views/bioruby/_methods.rhtml'
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- m.file '_classes.rhtml', 'app/views/bioruby/_classes.rhtml'
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- m.file '_modules.rhtml', 'app/views/bioruby/_modules.rhtml'
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- m.file '_log.rhtml', 'app/views/bioruby/_log.rhtml'
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- m.file '_variables.rhtml', 'app/views/bioruby/_variables.rhtml'
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- m.file 'commands.rhtml', 'app/views/bioruby/commands.rhtml'
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- m.file 'history.rhtml', 'app/views/bioruby/history.rhtml'
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- m.file 'index.rhtml', 'app/views/bioruby/index.rhtml'
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- m.file 'bioruby.rhtml', 'app/views/layouts/bioruby.rhtml'
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- m.file 'spinner.gif', 'public/images/bioruby/spinner.gif'
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- m.file 'bioruby-gem.png', 'public/images/bioruby/gem.png'
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- m.file 'bioruby-link.gif', 'public/images/bioruby/link.gif'
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- m.file 'bioruby-bg.gif', 'public/images/bioruby/bg.gif'
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- m.file 'bioruby.css', 'public/stylesheets/bioruby.css'
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- end
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- end
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- end
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-
@@ -1,4 +0,0 @@
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- [ <%= @class %> ]
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- <div id="class_list">
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- <%= @classes.map{ |x| reference_link(x) }.join(" > ") %>
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- </div>
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- <div id="log_<%= @number %>" class="log">
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- <div class="input">
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- Input: [<%= link_to_remote @number, :url => {:action => "reload_script", :number => @number} %>]
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- <pre class="script">
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- <%=h @script %>
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- </pre>
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- <div class="output">
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- Result:
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- [<%= link_to_remote "methods", :url => {:action => "list_methods", :number => @number} %>]
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- [<%= link_to_remote "classes", :url => {:action => "list_classes", :number => @number} %>]
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- [<%= link_to_remote "modules", :url => {:action => "list_modules", :number => @number} %>]
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- <div id="methods_<%= @number %>" class="methods"></div>
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- <div id="classes_<%= @number %>" class="classes"></div>
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- <div id="modules_<%= @number %>" class="modules"></div>
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- <pre class="result">
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- <%=h @result %>
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- </pre>
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- <% if @output %>
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- Output:
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- <pre class="output">
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- <%=h @output %>
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- </pre>
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- <% end %>
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- </div>
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- </div>
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- </div>
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-
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- [ <%= @class %> ]
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- <div id="method_list">
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- <table>
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- <tr>
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- <%- step = @methods.size / 4 + 1 -%>
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- <%- 0.step(@methods.size, step) do |i| -%>
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- <td><%= @methods[i, step].join("<br>") %></td>
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- <%- end -%>
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- </tr>
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- </table>
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- </div>
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- [ <%= @class %> ]
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- <div id="module_list">
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- <%= @modules.map {|x| reference_link(x) }.sort.join("<br>") %>
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- </div>
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- <div id="variables">
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- <ul>
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- <% local_variables.each do |var| %>
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- <li><%= link_to_remote var, :update => "index", :url => {:action => "evaluate", :script => var} %></li>
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- <% end %>
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- </ul>
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- </div>
@@ -1,368 +0,0 @@
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- /* body */
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-
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- body {
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- margin: 0;
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- color: #555555;
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- background: url("/images/bioruby/bg.gif") repeat-y center;
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- font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
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- font-size: 12px;
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- }
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-
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- div#content {
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- width: 750px;
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- height: auto;
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- margin: 0 auto 0 auto;
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- text-align: left;
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- }
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-
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- /* title */
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-
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- div#title {
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- width: 550px;
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- padding-right: 200px;
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- margin-bottom: 20px;
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- text-align: left;
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- background: url("/images/bioruby/gem.png") no-repeat left bottom;
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- }
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-
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- div#title .titletop {
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- color: #736451;
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- font-size: 30px;
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- font-weight: normal;
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- text-align: left;
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- text-indent: 70px;
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- margin: 0;
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- padding: 0;
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- padding-top: 20px;
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- margin-bottom: 10px;
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- }
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-
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- div#title .titlesub {
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- color: #000000;
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- font-size: 15px;
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- font-weight: normal;
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- text-align: left;
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- text-indent: 70px;
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- margin: 0;
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- padding: 0;
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- border-bottom: 1px solid #eeeeee;
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- }
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-
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- /* main */
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-
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- div#main {
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- width: 550px;
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- background-color: #ffffff;
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- padding-top: 0px;
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- padding-left: 10px;
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- }
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-
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- div#notice {
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- background-color: #fcc;
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- border: 1px solid #f00;
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- }
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-
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- div#notice p {
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- margin: 0;
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- padding: 10px;
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- }
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-
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- pre {
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- color: #6e8377;
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- background-color: #eaedeb;
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- border-color: #6e8377;
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- border-style: dashed;
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- border-width: 1px;
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- padding: 5px;
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- width: 500px;
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- overflow: auto;
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- }
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-
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- div.log {
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- width: 500px;
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- margin-top: 15px;
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- padding-top: 5px;
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- border-top: 1px dotted #333333;
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- }
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-
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- div.log div.input pre.script {
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- background-color: #ffffeb;
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- border-style: solid;
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- }
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-
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- div.log div.output div.methods {
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- padding: 5px;
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- background-color: #ffffdd;
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- border: 1px solid #ffcc00;
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- }
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-
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- div.log div.output div.classes {
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- padding: 5px;
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- background-color: #ccffcc;
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- border: 1px solid #00ff00;
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- }
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-
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- div.log div.output div.modules {
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- padding: 5px;
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- background-color: #ffcccc;
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- border: 1px solid #ff0000;
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- }
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-
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- div.log div.output pre.result {
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- border-style: dashed;
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- }
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-
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- div.log div.output pre.output {
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- border-style: dashed;
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- }
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-
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- div.log hr.log {
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- border-style: dotted none none none;
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- border-top-width: 1px;
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- border-color: #6e8377;
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- width: 200px;
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- height: 1px;
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- }
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-
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- /* side */
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-
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- div#side {
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- width: 150px;
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- float: right;
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- margin-top: 20px;
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- text-align: left;
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- font-size: 12px;
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- color: #e44268;
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- }
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-
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- div#side div.title {
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- font-weight: normal;
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- color: #e44268;
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- text-align: left;
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- border-width: 0px 0px 1px 0px;
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- border-bottom: 1px solid #e44268;
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- }
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-
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- div#side a:link {
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- color: #ffffff;
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- text-decoration: none;
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- }
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-
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- div#side a:visited {
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- color: #ffffff;
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- text-decoration: none;
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- }
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-
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- div#side a:hover {
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- color: #cccccc;
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- text-decoration: underline;
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- }
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-
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- div#side ol,ul {
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- margin: 10px;
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- padding-left: 10px;
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- }
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-
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- div#side li {
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- color: #e44268;
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- }
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-
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- div#side img {
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- padding: 5px;
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- /* centering */
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- display: block;
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- margin-left: auto;
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- margin-right: auto;
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- border: 0px;
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- }
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-
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- /* history */
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-
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- div#history {
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- width: 500px;
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- }
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-
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- div#history div.histtime {
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- background-color: #eaedeb;
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- padding: 5px;
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- }
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-
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- div#history div.histline {
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- background-color: #ffffeb;
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- padding: 5px;
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- font-family: monospace;
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- white-space: pre;
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- }
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-
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- /* command */
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-
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- div#command {
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- width: 500px;
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- }
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-
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- /* image */
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-
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- img {
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- }
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-
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- /* em */
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-
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- em {
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- color: #6e8377;
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- font-style: normal;
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- }
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-
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- /* link */
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-
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- a {
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- text-decoration: none;
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- }
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-
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- a:link {
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- color: #669933;
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- }
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-
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- a:visited {
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- color: #669933;
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- }
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-
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- a:hover {
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- text-decoration: underline;
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- }
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-
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- /* header */
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-
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- h1 {
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- font-size: 180%;
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- color: #ffffff;
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- background-color: #6e8377;
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- line-height: 64px;
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- text-align: left;
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- padding-left: 20px;
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- }
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-
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- h2 {
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- font-size: 160%;
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- color: #6e8377;
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- border-color: #b9c3be;
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- border-style: dashed;
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- border-width: 0px 0px 1px 0px;
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- }
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-
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- h3 {
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- font-size: 140%;
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- color: #6e8377;
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- border-color: #b9c3be;
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- border-style: dotted;
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- border-width: 0px 0px 1px 0px;
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- }
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-
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- h4 {
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- font-size: 130%;
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- color: #6e8377;
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- border-color: #b9c3be;
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- border-style: solid;
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- border-width: 0px 0px 1px 0px;
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- }
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-
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- h5 {
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- font-size: 120%;
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- color: #6e8377;
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- }
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-
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- h6 {
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- font-size: 110%;
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- color: #6e8377;
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- }
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-
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- /* list */
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-
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- dt {
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- color: #6e8377;
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- border-color: #b9c3be;
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- border-style: dashed;
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- border-width: 1px;
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- padding: 5px;
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- }
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-
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- ul {
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- color: #6e8377;
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- }
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-
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- /* table */
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-
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- table {
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- border: 1px solid #cccccc;
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- border-collapse: collapse;
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- }
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-
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- th {
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- vertical-align: top;
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- padding: 5px;
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- }
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-
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- td {
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- vertical-align: top;
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- padding: 5px;
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- }
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-
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- div#method_list table {
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- border: none;
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- }
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-
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-
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- /* form */
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-
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- input {
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- background-color: #FFFFFF;
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- padding: 2px;
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- font-size: 10px;
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- color: #666666;
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- border: 1px solid #611022;
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- margin-bottom: 2px;
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- }
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-
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- input[type=submit] {
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- background-color: #FFFFFF;
327
- padding: 2px;
328
- font-size: 10px;
329
- color: #ffffff;
330
- border: 1px solid #611022;
331
- background-color: #E44268;
332
- margin-bottom: 2px;
333
- }
334
-
335
- /* textarea */
336
-
337
- textarea {
338
- background-color: #eaedeb;
339
- font-family: monospace;
340
- font-size: 12px;
341
- overflow: auto;
342
- width: 500px;
343
- padding: 5px;
344
- }
345
-
346
-
347
- /* blockquote */
348
-
349
- blockquote {
350
- color: #6e8377;
351
- background-color: #eaedeb;
352
- border-color: #6e8377;
353
- border-style: dashed;
354
- border-width: 1px;
355
- }
356
-
357
- /* media */
358
-
359
- @media print {
360
- div#main { margin-left: 0px; }
361
- div#side { display: none; }
362
- }
363
-
364
- @media screen {
365
- div#main { margin-left: 0px; }
366
- div#side { display: block; }
367
- }
368
-