complearn 0.6.2

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Files changed (104) hide show
  1. data/AUTHORS +13 -0
  2. data/COPYING +340 -0
  3. data/ChangeLog +0 -0
  4. data/INSTALL +231 -0
  5. data/Makefile +352 -0
  6. data/Makefile.am +76 -0
  7. data/Makefile.in +352 -0
  8. data/NEWS +7 -0
  9. data/README +0 -0
  10. data/aclocal.m4 +104 -0
  11. data/bin/Makefile +209 -0
  12. data/bin/Makefile.am +8 -0
  13. data/bin/Makefile.in +209 -0
  14. data/bin/labeltree +68 -0
  15. data/bin/labeltree.in +68 -0
  16. data/bin/makesvm +70 -0
  17. data/bin/makesvm.in +70 -0
  18. data/bin/maketree +98 -0
  19. data/bin/maketree.in +98 -0
  20. data/bin/ncd +43 -0
  21. data/bin/ncd.in +43 -0
  22. data/bin/ncdmatrix +54 -0
  23. data/bin/ncdmatrix.in +54 -0
  24. data/bin/ncdvector +50 -0
  25. data/bin/ncdvector.in +50 -0
  26. data/complearn-0.6.2.gem +0 -0
  27. data/complearn.gemspec +57 -0
  28. data/config.log +597 -0
  29. data/config.status +1082 -0
  30. data/configure +4922 -0
  31. data/configure.ac +91 -0
  32. data/confstat5FpLBf/config.h +65 -0
  33. data/confstat5FpLBf/subs-1.sed +50 -0
  34. data/confstat5FpLBf/subs-2.sed +13 -0
  35. data/confstat5FpLBf/subs.frag +0 -0
  36. data/confstat5FpLBf/subs.sed +59 -0
  37. data/confstat5FpLBf/undefs.sed +24 -0
  38. data/doc/FAQ.txt +67 -0
  39. data/doc/Makefile +286 -0
  40. data/doc/Makefile.am +11 -0
  41. data/doc/Makefile.in +286 -0
  42. data/doc/devguide.txt +15 -0
  43. data/doc/example.complearnrc +14 -0
  44. data/doc/examples.txt +35 -0
  45. data/doc/man/Makefile +255 -0
  46. data/doc/man/Makefile.am +11 -0
  47. data/doc/man/Makefile.in +255 -0
  48. data/doc/man/complearn.5 +91 -0
  49. data/doc/man/labeltree.1 +35 -0
  50. data/doc/man/makesvm.1 +60 -0
  51. data/doc/man/maketree.1 +58 -0
  52. data/doc/man/ncd.1 +51 -0
  53. data/doc/man/ncdmatrix.1 +40 -0
  54. data/doc/man/ncdvector.1 +42 -0
  55. data/doc/readme.txt +101 -0
  56. data/doc/userguide.txt +46 -0
  57. data/examples/genes/blueWhale.txt +1 -0
  58. data/examples/genes/cat.txt +1 -0
  59. data/examples/genes/chimpanzee.txt +1 -0
  60. data/examples/genes/finWhale.txt +1 -0
  61. data/examples/genes/graySeal.txt +1 -0
  62. data/examples/genes/harborSeal.txt +1 -0
  63. data/examples/genes/horse.txt +1 -0
  64. data/examples/genes/human.txt +1 -0
  65. data/examples/genes/mouse.txt +1 -0
  66. data/examples/genes/rat.txt +1 -0
  67. data/ext/Makefile +167 -0
  68. data/ext/Quartet.c +399 -0
  69. data/ext/Quartet.h +62 -0
  70. data/ext/TreeScore.c +244 -0
  71. data/ext/TreeScore.h +3 -0
  72. data/ext/config.h +65 -0
  73. data/ext/config.h.in +64 -0
  74. data/ext/extconf.rb +3 -0
  75. data/ext/lib/CompLearnLib/CLConfig.rb +241 -0
  76. data/ext/lib/CompLearnLib/CompressionObject.rb +59 -0
  77. data/ext/lib/CompLearnLib/CompressionTask.rb +99 -0
  78. data/ext/lib/CompLearnLib/DistMatrix.rb +18 -0
  79. data/ext/lib/CompLearnLib/FoundComp.rb +10 -0
  80. data/ext/lib/CompLearnLib/FoundComp.rb.in +10 -0
  81. data/ext/lib/CompLearnLib/Ncd.rb +248 -0
  82. data/ext/lib/CompLearnLib/RunEnv.rb +150 -0
  83. data/ext/lib/CompLearnLib/Task.rb +39 -0
  84. data/ext/lib/CompLearnLib/TaskMaster.rb +13 -0
  85. data/ext/lib/CompLearnLib/TaskMasterMPI.rb +112 -0
  86. data/ext/lib/CompLearnLib/TaskMasterSingle.rb +39 -0
  87. data/ext/lib/CompLearnLib/Tree.rb +300 -0
  88. data/install-sh +294 -0
  89. data/missing +336 -0
  90. data/mkinstalldirs +111 -0
  91. data/o +24 -0
  92. data/scripts/CompLearn.iss +89 -0
  93. data/scripts/CompLearn.iss.in +89 -0
  94. data/scripts/debian/changelog +6 -0
  95. data/scripts/debian/control +14 -0
  96. data/scripts/makeSetup.sh +23 -0
  97. data/scripts/makeSetup.sh.in +23 -0
  98. data/scripts/makedeb.zsh +46 -0
  99. data/scripts/makedeb.zsh.in +46 -0
  100. data/tests/alltests.rb +2 -0
  101. data/tests/bz2test.rb +516 -0
  102. data/tests/sshagent-test.rb +48 -0
  103. data/tests/tests.rb +275 -0
  104. metadata +164 -0
@@ -0,0 +1,48 @@
1
+ require 'test/unit'
2
+ require 'CompLearnLib/RunEnv'
3
+ include MRunEnv
4
+ require 'CompLearnLib/CLConfig'
5
+ require 'CompLearnLib/Task'
6
+ include MTask
7
+
8
+ class TaskMasterParTestTask < Task
9
+ attr_reader :misc
10
+ def initialize(i) @i = i end
11
+ def execute() reply(@i * @i) end
12
+ end
13
+
14
+ class TC_SSHAgentTest < Test::Unit::TestCase
15
+ def test_SSHAgent
16
+ assert(ENV.has_key?('SSH_AGENT_PID'), 'ssh-agent is not available')
17
+ end
18
+ def test_livingHosts
19
+ cfg = CLConfig.getDefaultCLConfig()
20
+ assert(cfg.hosts != nil)
21
+ assert(cfg.hosts.size >= 1)
22
+ if (cfg.hosts.size > 1)
23
+ h = cfg.hosts[1]
24
+ cmd = 'echo testing-party'
25
+ result = SSHAgent.runAt(cmd, h)
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+ assert(result =~ /testing-party/, "Cannot run command #{cmd} on #{h}")
27
+ end
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+ end
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+
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+ # This test may work, but not until LAM/MPI is installed
31
+ def test_MPI
32
+ if CLConfig.getDefaultCLConfig().hosts.size > 1 && !CLConfig.getDefaultCLConfig().isSingleProcess?()
33
+ TaskMaster.init
34
+ sum = 0
35
+ todo = 4
36
+ 4.times { |i|
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+ TaskMaster.enqueue(TaskMasterParTestTask.new(i)) { |s, t, src|
38
+ sum += s
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+ todo -= 1
40
+ }
41
+ }
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+ while todo > 0
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+ TaskMaster.waitForSlave()
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+ end
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+ assert(sum == 14, "TaskMaster parallel-threading is not working")
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+ end
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+ end
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+ end
@@ -0,0 +1,275 @@
1
+ ##########################################################################
2
+ #
3
+ # Test suite for CompLearn system
4
+ #
5
+ # Invoke with
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+ # ruby tests/tests.rb # normal test suite
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+ # ruby tests/alltests.rb # run all tests, including ssh-agent (password req'd)
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+ #
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+
10
+ require 'test/unit'
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+
12
+ require 'CompLearn'
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+ require 'CompLearnLib/CLConfig'
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+ require 'CompLearnLib/Tree'
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+ require 'CompLearnLib/RunEnv'
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+ require 'CompLearnLib/DistMatrix'
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+
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+ #require 'bz2'
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+ require 'CompLearnLib/Task'
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+
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+ include MRunEnv
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+ include MTree
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+ include MTask
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+
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+ class TaskMasterTestTask < Task
26
+ attr_reader :misc
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+ def initialize(i) @i = i end
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+ def execute() reply(@i * @i) end
29
+ end
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+
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+ class TC_TaskMasterTest < Test::Unit::TestCase
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+ def test_TaskMasterSingle
33
+ CLConfig.setSingleUser
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+ TaskMaster.init
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+ sum = 0
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+ 4.times { |i|
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+ TaskMaster.enqueue(TaskMasterTestTask.new(i)) { |s, t, src|
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+ sum += s
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+ }
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+ }
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+ assert(sum == 14, "TaskMaster single-threading is not working")
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+ end
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+ end
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+
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+ class TC_EnvironmentTest < Test::Unit::TestCase
46
+ def test_configFile
47
+ cfg = CLConfig.getDefaultCLConfig()
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+ assert(cfg != nil)
49
+ assert(cfg.hosts.size >= 1)
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+ end
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+ # def test_BZ2
52
+ # a = 'the best coders are the lazy ones.'
53
+ # b = BZ2.compress(a)
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+ # c = BZ2.decompress(b)
55
+ # assert(c == a)
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+ # end
57
+ end
58
+
59
+ class TC_CLConfigFileParserTest < Test::Unit::TestCase
60
+ def test_CLConfigFileParser
61
+ fname = RunEnv.getTemporaryFilename()
62
+ assert(fname, "Cannot get temporary filename")
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+ f = File.open(fname, "w")
64
+ assert(f, "Cannot open #{fname} for writing")
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+ f.write <<EOF
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+ #
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+ # Test config file used by testconfig.rb
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+ #
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+ # $Id: tests.rb,v 1.6 2004/04/06 11:38:27 cilibrar Exp $
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+
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+ # comment
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+ InputDir: testInputDir
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+ OutputDir: testOutputDir
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+ WorkDir: testWorkDir
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+
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+ Symmetric: false
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+
78
+ Hosts:
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+ - host1
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+ - host2
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+ - host3
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+
83
+ EOF
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+ f.close
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+
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+ cfg = CLConfig.new(fname)
87
+
88
+ assert("testInputDir" == cfg.inputDir, "Error with InputDir")
89
+ assert("testOutputDir"== cfg.outputDir, "Error with OutputDir")
90
+ assert("testWorkDir" == cfg.workDir, "Error with WorkDir")
91
+ assert(!cfg.symmetric, "Error reading Symmetric")
92
+ assert(["host1","host2","host3"] == cfg.hosts, "Error with hosts")
93
+
94
+ File.unlink(fname)
95
+
96
+ cfg = CLConfig.getDefaultCLConfig
97
+
98
+ end
99
+
100
+ end
101
+
102
+ class TC_Tree < Test::Unit::TestCase
103
+ def test_TreeScore
104
+ dm = [
105
+ [ 0.1, 0.5, 0.1, 0.1],
106
+ [ 0.5, 0.1, 0.1, 0.1],
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+ [ 0.1, 0.1, 0.1, 0.1],
108
+ [ 0.1, 0.1, 0.1, 0.1],
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+ ]
110
+ t = TreeScore.makeFullList(dm)
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+ assert(t.best == -0.2, "Best tree score is not -0.2 like it should be; got #{t.best}.")
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+ assert(t.worst == -0.6, "Worst tree score is not -0.6 like it should be; got #{t.worst}.")
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+ end
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+ def test_TreeBasics
115
+ t = Tree.randomTree(8)
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+ assert(t.verifyTree)
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+ ot = t.clone()
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+ assert((ot <=> t) == 0)
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+ assert(t.getSpeciesCount() == 8)
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+ assert(t.getKernelCount() == 6)
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+ assert(t.getNodeCount() == 14)
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+ k = t.randomKernelNodes(3)
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+ k.each { |n| assert(t.isKernel?(n)) }
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+ s = t.randomSpeciesNodes(5)
125
+ s.each { |n| assert(t.isSpecies?(n)) }
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+ a = t.randomNode()
127
+ p = t.findPath(a,a)
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+ assert(p.size == 1)
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+ assert(p[0] == a)
130
+ 20.times {
131
+ a,b = t.randomNodes(2)
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+ p = t.findPath(a,b)
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+ assert(p[0] == a)
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+ assert(p[-1] == b)
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+ (p.size-1).times { |n|
136
+ assert(p[n] != p[n+1])
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+ assert(t.connected?(p[n],p[n+1]))
138
+ }
139
+ }
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+ 50.times { # should n3v3r be the sam3 aft3r a mut4t10n
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+ t = ot.clone
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+ assert((ot <=> t) == 0)
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+ t.mutateSpecies
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+ assert((ot <=> t) != 0)
145
+ assert(t.verifyTree())
146
+ t = ot.clone
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+ t.mutateSubtreeInterchange
148
+ assert(t.verifyTree())
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+ assert((ot <=> t) != 0)
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+ t = ot.clone
151
+ t.mutateSubtreeTransfer
152
+ assert((ot <=> t) != 0)
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+ assert(t.verifyTree())
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+ t = ot.clone
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+ t.mutateRandom
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+ assert((ot <=> t) != 0)
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+ assert(t.verifyTree())
158
+ t = ot.clone
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+ t.mutateComplex
160
+ assert((ot <=> t) != 0)
161
+ assert(t.verifyTree())
162
+ }
163
+ t = ot.clone
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+ t.mutateSpecies
165
+ begin
166
+ z = t.clone
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+ z.mutateSpecies
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+ end until ((ot <=> z) == 0) # should be able to mutate back
169
+ t = ot.clone
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+ t.mutateSubtreeInterchange
171
+ begin
172
+ z = t.clone
173
+ z.mutateSubtreeInterchange
174
+ end until ((ot <=> z) == 0)
175
+ 5.times {
176
+ t = ot.clone
177
+ t.mutateSubtreeTransfer
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+ counter=0
179
+ begin
180
+ counter += 1
181
+ z = t.clone
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+ z.mutateSubtreeTransfer
183
+ end until ((ot <=> z) == 0)
184
+ }
185
+ t = ot.clone
186
+ t.mutateRandom
187
+ begin
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+ z = t.clone
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+ z.mutateComplex
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+ end until ((ot <=> z) == 0)
191
+ end
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+
193
+ class TC_RunEnv < Test::Unit::TestCase
194
+ def test_tmpnames
195
+ a,b,c = RunEnv.getTemporaryFilenames(3)
196
+ assert( (a <= b) != 0 )
197
+ assert( (b <=> c) != 0 )
198
+ assert( (a <=> c) != 0 )
199
+ f = File.open(a, "wb")
200
+ f.write("hi!\n")
201
+ f.close()
202
+ end
203
+ end
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+
205
+ class TC_DistMatrix < Test::Unit::TestCase
206
+ def test_distmatrix()
207
+ a,b,c = RunEnv.getTemporaryFilenames(3)
208
+ f = File.open(a, "wb")
209
+ f.write <<EOF
210
+ 20
211
+ BlueWhale 0.000000 0.956323 0.972438 0.933378 0.602634 0.976144 0.979629 0.952030 0.951910 0.944889 0.969844 0.976034 0.981995 0.977991 0.982811 0.974382 0.972313 0.976209 0.982206 0.945881
212
+ Cat 0.956323 0.000000 0.974313 0.944650 0.956363 0.975953 0.975125 0.926396 0.928524 0.932140 0.964397 0.977328 0.979132 0.977075 0.982982 0.974569 0.964113 0.979347 0.976386 0.937550
213
+ Chimpanzee 0.972438 0.974313 0.000000 0.970806 0.977246 0.873617 0.727796 0.972297 0.971715 0.968993 0.981926 0.657387 0.985329 0.851432 0.987256 0.428991 0.976425 0.850383 0.986032 0.969842
214
+ Cow 0.933378 0.944650 0.970806 0.000000 0.938797 0.972798 0.972197 0.941317 0.942067 0.940301 0.967403 0.973620 0.978456 0.973127 0.980380 0.970828 0.969176 0.977041 0.973974 0.933010
215
+ FinbackWhale 0.602634 0.956363 0.977246 0.938797 0.000000 0.981417 0.979665 0.957940 0.958546 0.947599 0.976451 0.980493 0.981616 0.978559 0.982824 0.979584 0.970869 0.980316 0.982494 0.948306
216
+ Gibbon 0.976144 0.975953 0.873617 0.972798 0.981417 0.000000 0.880709 0.973661 0.976154 0.969450 0.981696 0.880203 0.984314 0.891729 0.990322 0.875655 0.979186 0.891283 0.985513 0.968633
217
+ Gorilla 0.979629 0.975125 0.727796 0.972197 0.979665 0.880709 0.000000 0.975026 0.974955 0.973320 0.982952 0.732325 0.986312 0.857432 0.986569 0.720617 0.982154 0.854869 0.986469 0.969977
218
+ GreySeal 0.952030 0.926396 0.972297 0.941317 0.957940 0.973661 0.975026 0.000000 0.428044 0.938868 0.968053 0.975760 0.979947 0.978015 0.981756 0.975585 0.967721 0.976995 0.977296 0.933762
219
+ HarborSeal 0.951910 0.928524 0.971715 0.942067 0.958546 0.976154 0.974955 0.428044 0.000000 0.934823 0.965112 0.974737 0.980340 0.978275 0.981906 0.974849 0.966301 0.975989 0.977183 0.934832
220
+ Horse 0.944889 0.932140 0.968993 0.940301 0.947599 0.969450 0.973320 0.938868 0.934823 0.000000 0.972751 0.971558 0.977220 0.975414 0.984268 0.970180 0.964328 0.975455 0.978211 0.879802
221
+ HouseMouse 0.969844 0.964397 0.981926 0.967403 0.976451 0.981696 0.982952 0.968053 0.965112 0.972751 0.000000 0.980400 0.974406 0.983850 0.981355 0.980623 0.901139 0.983575 0.973949 0.968500
222
+ Human 0.976034 0.977328 0.657387 0.973620 0.980493 0.880203 0.732325 0.975760 0.974737 0.971558 0.980400 0.000000 0.986243 0.847139 0.988041 0.654234 0.981715 0.841775 0.985926 0.973694
223
+ Opossum 0.981995 0.979132 0.985329 0.978456 0.981616 0.984314 0.986312 0.979947 0.980340 0.977220 0.974406 0.986243 0.000000 0.987712 0.984083 0.985832 0.979062 0.986586 0.942194 0.979566
224
+ Orangutan 0.977991 0.977075 0.851432 0.973127 0.978559 0.891729 0.857432 0.978015 0.978275 0.975414 0.983850 0.847139 0.987712 0.000000 0.990018 0.849235 0.982004 0.569297 0.986478 0.978454
225
+ Platypus 0.982811 0.982982 0.987256 0.980380 0.982824 0.990322 0.986569 0.981756 0.981906 0.984268 0.981355 0.988041 0.984083 0.990018 0.000000 0.987128 0.983857 0.989407 0.981747 0.986069
226
+ PygmyChimpanzee 0.974382 0.974569 0.428991 0.970828 0.979584 0.875655 0.720617 0.975585 0.974849 0.970180 0.980623 0.654234 0.985832 0.849235 0.987128 0.000000 0.976925 0.849978 0.984617 0.971307
227
+ Rat 0.972313 0.964113 0.976425 0.969176 0.970869 0.979186 0.982154 0.967721 0.966301 0.964328 0.901139 0.981715 0.979062 0.982004 0.983857 0.976925 0.000000 0.979808 0.976307 0.964887
228
+ SumatranOrangutan 0.976209 0.979347 0.850383 0.977041 0.980316 0.891283 0.854869 0.976995 0.975989 0.975455 0.983575 0.841775 0.986586 0.569297 0.989407 0.849978 0.979808 0.000000 0.988176 0.975742
229
+ Wallaroo 0.982206 0.976386 0.986032 0.973974 0.982494 0.985513 0.986469 0.977296 0.977183 0.978211 0.973949 0.985926 0.942194 0.986478 0.981747 0.984617 0.976307 0.988176 0.000000 0.972083
230
+ WhiteRhino 0.945881 0.937550 0.969842 0.933010 0.948306 0.968633 0.969977 0.933762 0.934832 0.879802 0.968500 0.973694 0.979566 0.978454 0.986069 0.971307 0.964887 0.975742 0.972083 0.000000
231
+ EOF
232
+ f.close
233
+
234
+ # dm, names = DistMatrix.readFile(a)
235
+ # DistMatrix.writeFile(b, dm, names)
236
+ # dm2, names2 = DistMatrix.readFile(b)
237
+ # DistMatrix.writeFile(c, dm2, names2)
238
+ # dm3, names3 = DistMatrix.readFile(c)
239
+ # assert(names.size == 20)
240
+ # assert(names2.size == 20)
241
+ # assert(names3.size == 20)
242
+ # assert((dm2 <=> dm3) == 0)
243
+ # [a,b,c].each { |n| File.unlink(n) }
244
+ # ts = TreeScore.makeFullList(dm)
245
+ # randtree = Tree.randomTree(dm.size)
246
+ # assert(randtree.verifyTree)
247
+ # score = ts.score(randtree)
248
+ # assert(score >= 0.0 && score <= 1.0)
249
+ #DistMatrix.makeFromDir("/ufs/cilibrar/src/mpicquart/data/genres", "genresdist.txt")
250
+ end
251
+ end
252
+
253
+ end
254
+
255
+ class TC_WholeSystem < Test::Unit::TestCase
256
+ def test_wholesystem
257
+ exampledir = "../examples/genes"
258
+ a,b,treename = RunEnv.getTemporaryFilenames(3)
259
+ `ncdmatrix #{exampledir} >#{a}`
260
+ assert( File.exist?(a) && File.stat(a).size > 100, "Distance Matrix file #{a} problem!" )
261
+ `maketree #{a} #{treename} >#{b}`
262
+ lastscore = nil
263
+ File.open(b, 'r') { |f|
264
+ while line = f.gets
265
+ lastscore = $1.to_f if line =~ /([0-9.]+)\s*$/
266
+ end
267
+ }
268
+ assert(lastscore > 0.7, "Final tree score too low: #{lastscore}")
269
+ assert(File.exist?(treename), "No #{treename} file created!")
270
+ File.unlink(a)
271
+ File.unlink(b)
272
+ File.unlink(treename)
273
+ end
274
+ end
275
+
metadata ADDED
@@ -0,0 +1,164 @@
1
+ --- !ruby/object:Gem::Specification
2
+ rubygems_version: 0.8.1
3
+ specification_version: 1
4
+ name: complearn
5
+ version: !ruby/object:Gem::Version
6
+ version: 0.6.2
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+ date: 2004-10-02
8
+ summary: The CompLearn Toolkit enables you to do data mining using data compression. It also allows you to do Quartet Tree Reconstruction as well as Support Vector Machine experiments with these techniques.
9
+ require_paths:
10
+ - lib
11
+ author: Rudi Cilibrasi
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+ email: cilibrar@ofb.net
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+ homepage: http://complearn.sourceforge.net/
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+ rubyforge_project: complearn
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+ description: "Using this package, you can do powerful pattern recognition easily from your
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+ shell command line using a simple suite of tools. Applications include music
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+ cateogrization, text classification, handwritten digit recognition, and
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+ evolutionary tree reconstruction. The technique is based on a very general
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+ theoretical notion of Kolmogorov Complexity, and so is undoubtedly applicable to
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+ many as yet unknown disciplines. See the webpage for research papers explaining
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+ the math behind these techniques."
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+ autorequire:
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+ default_executable: ncd
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+ bindir: bin
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+ has_rdoc: true
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+ required_ruby_version: !ruby/object:Gem::Version::Requirement
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+ requirements:
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+ -
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+ - ">"
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+ - !ruby/object:Gem::Version
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+ version: 0.0.0
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+ version:
33
+ platform: ruby
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+ files:
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+ - AUTHORS
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+ - COPYING
37
+ - ChangeLog
38
+ - INSTALL
39
+ - Makefile.am
40
+ - Makefile.in
41
+ - NEWS
42
+ - README
43
+ - aclocal.m4
44
+ - bin
45
+ - configure
46
+ - configure.ac
47
+ - doc
48
+ - examples
49
+ - ext
50
+ - install-sh
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+ - missing
52
+ - mkinstalldirs
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+ - scripts
54
+ - tests
55
+ - complearn.gemspec
56
+ - complearn-0.6.2.gem
57
+ - config.log
58
+ - o
59
+ - config.status
60
+ - Makefile
61
+ - confstat5FpLBf
62
+ - bin/Makefile.am
63
+ - bin/Makefile.in
64
+ - bin/labeltree.in
65
+ - bin/makesvm.in
66
+ - bin/maketree.in
67
+ - bin/ncd.in
68
+ - bin/ncdmatrix.in
69
+ - bin/ncdvector.in
70
+ - bin/Makefile
71
+ - bin/ncd
72
+ - bin/ncdvector
73
+ - bin/ncdmatrix
74
+ - bin/labeltree
75
+ - bin/maketree
76
+ - bin/makesvm
77
+ - doc/FAQ.txt
78
+ - doc/Makefile.am
79
+ - doc/Makefile.in
80
+ - doc/devguide.txt
81
+ - doc/example.complearnrc
82
+ - doc/examples.txt
83
+ - doc/man
84
+ - doc/readme.txt
85
+ - doc/userguide.txt
86
+ - doc/Makefile
87
+ - doc/man/Makefile.am
88
+ - doc/man/Makefile.in
89
+ - doc/man/complearn.5
90
+ - doc/man/labeltree.1
91
+ - doc/man/makesvm.1
92
+ - doc/man/maketree.1
93
+ - doc/man/ncd.1
94
+ - doc/man/ncdmatrix.1
95
+ - doc/man/ncdvector.1
96
+ - doc/man/Makefile
97
+ - examples/genes
98
+ - examples/genes/blueWhale.txt
99
+ - examples/genes/cat.txt
100
+ - examples/genes/chimpanzee.txt
101
+ - examples/genes/finWhale.txt
102
+ - examples/genes/graySeal.txt
103
+ - examples/genes/harborSeal.txt
104
+ - examples/genes/horse.txt
105
+ - examples/genes/human.txt
106
+ - examples/genes/mouse.txt
107
+ - examples/genes/rat.txt
108
+ - ext/Quartet.c
109
+ - ext/Quartet.h
110
+ - ext/TreeScore.c
111
+ - ext/TreeScore.h
112
+ - ext/config.h.in
113
+ - ext/extconf.rb
114
+ - ext/lib
115
+ - ext/config.h
116
+ - ext/Makefile
117
+ - ext/lib/CompLearnLib
118
+ - ext/lib/CompLearnLib/CompressionObject.rb
119
+ - ext/lib/CompLearnLib/CompressionTask.rb
120
+ - ext/lib/CompLearnLib/FoundComp.rb
121
+ - ext/lib/CompLearnLib/DistMatrix.rb
122
+ - ext/lib/CompLearnLib/FoundComp.rb.in
123
+ - ext/lib/CompLearnLib/Ncd.rb
124
+ - ext/lib/CompLearnLib/RunEnv.rb
125
+ - ext/lib/CompLearnLib/Task.rb
126
+ - ext/lib/CompLearnLib/TaskMaster.rb
127
+ - ext/lib/CompLearnLib/TaskMasterMPI.rb
128
+ - ext/lib/CompLearnLib/TaskMasterSingle.rb
129
+ - ext/lib/CompLearnLib/Tree.rb
130
+ - ext/lib/CompLearnLib/CLConfig.rb
131
+ - scripts/CompLearn.iss.in
132
+ - scripts/debian
133
+ - scripts/makeSetup.sh.in
134
+ - scripts/makedeb.zsh.in
135
+ - scripts/CompLearn.iss
136
+ - scripts/makeSetup.sh
137
+ - scripts/makedeb.zsh
138
+ - scripts/debian/changelog
139
+ - scripts/debian/control
140
+ - tests/alltests.rb
141
+ - tests/bz2test.rb
142
+ - tests/sshagent-test.rb
143
+ - tests/tests.rb
144
+ - confstat5FpLBf/subs.sed
145
+ - confstat5FpLBf/subs.frag
146
+ - confstat5FpLBf/subs-1.sed
147
+ - confstat5FpLBf/subs-2.sed
148
+ - confstat5FpLBf/undefs.sed
149
+ - confstat5FpLBf/config.h
150
+ test_files: []
151
+ rdoc_options: []
152
+ extra_rdoc_files: []
153
+ executables:
154
+ - ncd
155
+ - ncdvector
156
+ - ncdmatrix
157
+ - maketree
158
+ - makesvm
159
+ - labeltree
160
+ extensions:
161
+ - ext/extconf.rb
162
+ requirements:
163
+ - "Data compressors such as bzip, gzip, or ppmz"
164
+ dependencies: []