ulla 0.9.3

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 (91) hide show
  1. data/.git/COMMIT_EDITMSG +13 -0
  2. data/.git/HEAD +1 -0
  3. data/.git/config +11 -0
  4. data/.git/description +1 -0
  5. data/.git/hooks/applypatch-msg.sample +15 -0
  6. data/.git/hooks/commit-msg.sample +24 -0
  7. data/.git/hooks/post-commit.sample +8 -0
  8. data/.git/hooks/post-receive.sample +15 -0
  9. data/.git/hooks/post-update.sample +8 -0
  10. data/.git/hooks/pre-applypatch.sample +14 -0
  11. data/.git/hooks/pre-commit.sample +18 -0
  12. data/.git/hooks/pre-rebase.sample +169 -0
  13. data/.git/hooks/prepare-commit-msg.sample +36 -0
  14. data/.git/hooks/update.sample +107 -0
  15. data/.git/index +0 -0
  16. data/.git/info/exclude +6 -0
  17. data/.git/logs/HEAD +3 -0
  18. data/.git/logs/refs/heads/master +3 -0
  19. data/.git/logs/refs/remotes/origin/HEAD +1 -0
  20. data/.git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e +0 -0
  21. data/.git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069 +0 -0
  22. data/.git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b +0 -0
  23. data/.git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c +0 -0
  24. data/.git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca +0 -0
  25. data/.git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace +2 -0
  26. data/.git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05 +4 -0
  27. data/.git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb +3 -0
  28. data/.git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029 +0 -0
  29. data/.git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96 +2 -0
  30. data/.git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e +2 -0
  31. data/.git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152 +0 -0
  32. data/.git/objects/a6/578c95f2f474303464b572e9dac716432472b2 +0 -0
  33. data/.git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723 +0 -0
  34. data/.git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4 +0 -0
  35. data/.git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d +0 -0
  36. data/.git/objects/c2/fb6afc000952b56354fe195682645000d2aea2 +0 -0
  37. data/.git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 +2 -0
  38. data/.git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753 +5 -0
  39. data/.git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9 +0 -0
  40. data/.git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396 +0 -0
  41. data/.git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44 +0 -0
  42. data/.git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4 +0 -0
  43. data/.git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278 +0 -0
  44. data/.git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f +0 -0
  45. data/.git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da +0 -0
  46. data/.git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac +0 -0
  47. data/.git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12 +0 -0
  48. data/.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx +0 -0
  49. data/.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack +0 -0
  50. data/.git/packed-refs +8 -0
  51. data/.git/refs/heads/master +1 -0
  52. data/.git/refs/remotes/origin/HEAD +1 -0
  53. data/.gitignore +8 -0
  54. data/History.txt +42 -0
  55. data/Manifest.txt +90 -0
  56. data/PostInstall.txt +5 -0
  57. data/README.rdoc +259 -0
  58. data/Rakefile +32 -0
  59. data/bin/ulla +10 -0
  60. data/config/website.yml +2 -0
  61. data/config/website.yml.sample +2 -0
  62. data/lib/math_extensions.rb +7 -0
  63. data/lib/narray_extensions.rb +22 -0
  64. data/lib/nmatrix_extensions.rb +245 -0
  65. data/lib/string_extensions.rb +17 -0
  66. data/lib/ulla/cli.rb +1742 -0
  67. data/lib/ulla/environment.rb +34 -0
  68. data/lib/ulla/environment_class_hash.rb +20 -0
  69. data/lib/ulla/environment_feature.rb +26 -0
  70. data/lib/ulla/environment_feature_array.rb +12 -0
  71. data/lib/ulla/heatmap_array.rb +111 -0
  72. data/lib/ulla.rb +6 -0
  73. data/script/console +10 -0
  74. data/script/destroy +14 -0
  75. data/script/generate +14 -0
  76. data/script/txt2html +71 -0
  77. data/test/test_helper.rb +2 -0
  78. data/test/test_math_extensions.rb +11 -0
  79. data/test/test_narray_extensions.rb +14 -0
  80. data/test/test_nmatrix_extensions.rb +16 -0
  81. data/test/test_string_extensions.rb +11 -0
  82. data/test/test_ulla.rb +11 -0
  83. data/test/ulla/test_cli.rb +9 -0
  84. data/test/ulla/test_environment_class_hash.rb +25 -0
  85. data/test/ulla/test_environment_feature.rb +29 -0
  86. data/website/index.html +16 -0
  87. data/website/index.txt +217 -0
  88. data/website/javascripts/rounded_corners_lite.inc.js +285 -0
  89. data/website/stylesheets/screen.css +158 -0
  90. data/website/template.html.erb +57 -0
  91. metadata +215 -0
data/website/template.html.erb ADDED
@@ -0,0 +1,57 @@
1
+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <link rel="stylesheet" href="stylesheets/screen.css" type="text/css" media="screen" />
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ <%= title %>
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+ </title>
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+ <script src="javascripts/rounded_corners_lite.inc.js" type="text/javascript"></script>
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+ <style>
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+
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+ </style>
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+ <script type="text/javascript">
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+ window.onload = function() {
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+ settings = {
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+ tl: { radius: 10 },
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+ tr: { radius: 10 },
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+ bl: { radius: 10 },
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+ br: { radius: 10 },
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+ antiAlias: true,
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+ autoPad: true,
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+ validTags: ["div"]
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+ }
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+ var versionBox = new curvyCorners(settings, document.getElementById("version"));
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+ versionBox.applyCornersToAll();
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+ }
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+ </script>
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+ </head>
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+ <body>
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+ <div id="main">
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+
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+ <h1><%= title %></h1>
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+ <div class="sidebar">
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+ <div id="version" class="clickable" onclick='document.location = "<%= download %>"; return false'>
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+ <p>Get Version</p>
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+ <a href="<%= download %>" class="numbers"><%= version %></a>
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+ </div>
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+ </div>
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+ <%= body %>
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+ <p class="coda">
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+ Semin Lee, <%= modified.pretty %><br>
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+ Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
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+ </p>
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+ </div>
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+
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+ <!-- insert site tracking codes here, like Google Urchin -->
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+ <script type="text/javascript">
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+ var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
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+ document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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+ </script>
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+ <script type="text/javascript">
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+ var pageTracker = _gat._getTracker("UA-6291956-1");
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+ pageTracker._trackPageview();
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+ </script>
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+ </body>
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+ </html>
metadata ADDED
@@ -0,0 +1,215 @@
1
+ --- !ruby/object:Gem::Specification
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+ name: ulla
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+ version: !ruby/object:Gem::Version
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+ version: 0.9.3
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+ platform: ruby
6
+ authors:
7
+ - Semin Lee
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+ autorequire:
9
+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2009-02-23 00:00:00 +00:00
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+ default_executable:
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+ dependencies:
15
+ - !ruby/object:Gem::Dependency
16
+ name: narray
17
+ type: :runtime
18
+ version_requirement:
19
+ version_requirements: !ruby/object:Gem::Requirement
20
+ requirements:
21
+ - - ">="
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+ - !ruby/object:Gem::Version
23
+ version: 0.5.9.5
24
+ version:
25
+ - !ruby/object:Gem::Dependency
26
+ name: bio
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+ type: :runtime
28
+ version_requirement:
29
+ version_requirements: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: 1.2.1
34
+ version:
35
+ - !ruby/object:Gem::Dependency
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+ name: facets
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+ type: :runtime
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+ version_requirement:
39
+ version_requirements: !ruby/object:Gem::Requirement
40
+ requirements:
41
+ - - ">="
42
+ - !ruby/object:Gem::Version
43
+ version: 2.4.5
44
+ version:
45
+ - !ruby/object:Gem::Dependency
46
+ name: rmagick
47
+ type: :runtime
48
+ version_requirement:
49
+ version_requirements: !ruby/object:Gem::Requirement
50
+ requirements:
51
+ - - ">="
52
+ - !ruby/object:Gem::Version
53
+ version: 2.9.1
54
+ version:
55
+ - !ruby/object:Gem::Dependency
56
+ name: newgem
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+ type: :development
58
+ version_requirement:
59
+ version_requirements: !ruby/object:Gem::Requirement
60
+ requirements:
61
+ - - ">="
62
+ - !ruby/object:Gem::Version
63
+ version: 1.2.3
64
+ version:
65
+ - !ruby/object:Gem::Dependency
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+ name: hoe
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+ type: :development
68
+ version_requirement:
69
+ version_requirements: !ruby/object:Gem::Requirement
70
+ requirements:
71
+ - - ">="
72
+ - !ruby/object:Gem::Version
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+ version: 1.8.0
74
+ version:
75
+ description: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
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+ email:
77
+ - seminlee@gmail.com
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+ executables:
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+ - ulla
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+ extensions: []
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+
82
+ extra_rdoc_files:
83
+ - History.txt
84
+ - Manifest.txt
85
+ - PostInstall.txt
86
+ - README.rdoc
87
+ - website/index.txt
88
+ files:
89
+ - .git/COMMIT_EDITMSG
90
+ - .git/HEAD
91
+ - .git/config
92
+ - .git/description
93
+ - .git/hooks/applypatch-msg.sample
94
+ - .git/hooks/commit-msg.sample
95
+ - .git/hooks/post-commit.sample
96
+ - .git/hooks/post-receive.sample
97
+ - .git/hooks/post-update.sample
98
+ - .git/hooks/pre-applypatch.sample
99
+ - .git/hooks/pre-commit.sample
100
+ - .git/hooks/pre-rebase.sample
101
+ - .git/hooks/prepare-commit-msg.sample
102
+ - .git/hooks/update.sample
103
+ - .git/index
104
+ - .git/info/exclude
105
+ - .git/logs/HEAD
106
+ - .git/logs/refs/heads/master
107
+ - .git/logs/refs/remotes/origin/HEAD
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+ - .git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
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+ - .git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
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+ - .git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
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+ - .git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
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+ - .git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
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+ - .git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
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+ - .git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
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+ - .git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
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+ - .git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
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+ - .git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
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+ - .git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
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+ - .git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
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+ - .git/objects/a6/578c95f2f474303464b572e9dac716432472b2
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+ - .git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
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+ - .git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
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+ - .git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
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+ - .git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
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+ - .git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
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+ - .git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
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+ - .git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
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+ - .git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
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+ - .git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
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+ - .git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
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+ - .git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
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+ - .git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
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+ - .git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
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+ - .git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
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+ - .git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
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+ - .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
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+ - .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
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+ - .git/packed-refs
139
+ - .git/refs/heads/master
140
+ - .git/refs/remotes/origin/HEAD
141
+ - .gitignore
142
+ - History.txt
143
+ - Manifest.txt
144
+ - PostInstall.txt
145
+ - README.rdoc
146
+ - Rakefile
147
+ - bin/ulla
148
+ - config/website.yml
149
+ - config/website.yml.sample
150
+ - lib/math_extensions.rb
151
+ - lib/narray_extensions.rb
152
+ - lib/nmatrix_extensions.rb
153
+ - lib/string_extensions.rb
154
+ - lib/ulla.rb
155
+ - lib/ulla/cli.rb
156
+ - lib/ulla/environment.rb
157
+ - lib/ulla/environment_class_hash.rb
158
+ - lib/ulla/environment_feature.rb
159
+ - lib/ulla/environment_feature_array.rb
160
+ - lib/ulla/heatmap_array.rb
161
+ - script/console
162
+ - script/destroy
163
+ - script/generate
164
+ - script/txt2html
165
+ - test/test_helper.rb
166
+ - test/test_math_extensions.rb
167
+ - test/test_narray_extensions.rb
168
+ - test/test_nmatrix_extensions.rb
169
+ - test/test_string_extensions.rb
170
+ - test/test_ulla.rb
171
+ - test/ulla/test_cli.rb
172
+ - test/ulla/test_environment_class_hash.rb
173
+ - test/ulla/test_environment_feature.rb
174
+ - website/index.html
175
+ - website/index.txt
176
+ - website/javascripts/rounded_corners_lite.inc.js
177
+ - website/stylesheets/screen.css
178
+ - website/template.html.erb
179
+ has_rdoc: true
180
+ homepage: http://www-cryst.bioc.cam.ac.uk/ulla
181
+ post_install_message: PostInstall.txt
182
+ rdoc_options:
183
+ - --main
184
+ - README.rdoc
185
+ require_paths:
186
+ - lib
187
+ required_ruby_version: !ruby/object:Gem::Requirement
188
+ requirements:
189
+ - - ">="
190
+ - !ruby/object:Gem::Version
191
+ version: "0"
192
+ version:
193
+ required_rubygems_version: !ruby/object:Gem::Requirement
194
+ requirements:
195
+ - - ">="
196
+ - !ruby/object:Gem::Version
197
+ version: "0"
198
+ version:
199
+ requirements: []
200
+
201
+ rubyforge_project: ulla
202
+ rubygems_version: 1.3.1
203
+ signing_key:
204
+ specification_version: 2
205
+ summary: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
206
+ test_files:
207
+ - test/test_math_extensions.rb
208
+ - test/test_narray_extensions.rb
209
+ - test/test_nmatrix_extensions.rb
210
+ - test/test_string_extensions.rb
211
+ - test/ulla/test_cli.rb
212
+ - test/ulla/test_environment_class_hash.rb
213
+ - test/ulla/test_environment_feature.rb
214
+ - test/test_helper.rb
215
+ - test/test_ulla.rb