complearn 0.6.2

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  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
data/AUTHORS ADDED
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+ CompLearnLib
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+
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+ A toolkit for compression-based learning by Rudi Cilibrasi
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+
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+ Contact cilibrar@ofb.net for more information.
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+
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+ Please see the doc/ directory for more info, and enjoy!
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+
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+ Thanks also to:
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+
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+ julio b. (juliob@juliob.com) for Website Design
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+ Stephanie Wehner (_@r4k.net) for programming and CVS help
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+
data/COPYING ADDED
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+ GNU GENERAL PUBLIC LICENSE
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+ Version 2, June 1991
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data/INSTALL ADDED
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+ Please see the doc/ directory for more specific installation instructions.
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+ Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
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+ Basic Installation
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+ ==================
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+ to figure out how `configure' could check whether to do them, and mail
31
+ diffs or instructions to the address given in the `README' so they can
32
+ be considered for the next release. If you are using the cache, and at
33
+ some point `config.cache' contains results you don't want to keep, you
34
+ may remove or edit it.
35
+
36
+ The file `configure.ac' (or `configure.in') is used to create
37
+ `configure' by a program called `autoconf'. You only need
38
+ `configure.ac' if you want to change it or regenerate `configure' using
39
+ a newer version of `autoconf'.
40
+
41
+ The simplest way to compile this package is:
42
+
43
+ 1. `cd' to the directory containing the package's source code and type
44
+ `./configure' to configure the package for your system. If you're
45
+ using `csh' on an old version of System V, you might need to type
46
+ `sh ./configure' instead to prevent `csh' from trying to execute
47
+ `configure' itself.
48
+
49
+ Running `configure' takes awhile. While running, it prints some
50
+ messages telling which features it is checking for.
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+
52
+ 2. Type `make' to compile the package.
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+
54
+ 3. Optionally, type `make check' to run any self-tests that come with
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+ the package.
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+
57
+ 4. Type `make install' to install the programs and any data files and
58
+ documentation.
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+
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+ 5. You can remove the program binaries and object files from the
61
+ source code directory by typing `make clean'. To also remove the
62
+ files that `configure' created (so you can compile the package for
63
+ a different kind of computer), type `make distclean'. There is
64
+ also a `make maintainer-clean' target, but that is intended mainly
65
+ for the package's developers. If you use it, you may have to get
66
+ all sorts of other programs in order to regenerate files that came
67
+ with the distribution.
68
+
69
+ Compilers and Options
70
+ =====================
71
+
72
+ Some systems require unusual options for compilation or linking that
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+ the `configure' script does not know about. Run `./configure --help'
74
+ for details on some of the pertinent environment variables.
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+
76
+ You can give `configure' initial values for configuration parameters
77
+ by setting variables in the command line or in the environment. Here
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+ is an example:
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+
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+ ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
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+
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+ *Note Defining Variables::, for more details.
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+
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+ Compiling For Multiple Architectures
85
+ ====================================
86
+
87
+ You can compile the package for more than one kind of computer at the
88
+ same time, by placing the object files for each architecture in their
89
+ own directory. To do this, you must use a version of `make' that
90
+ supports the `VPATH' variable, such as GNU `make'. `cd' to the
91
+ directory where you want the object files and executables to go and run
92
+ the `configure' script. `configure' automatically checks for the
93
+ source code in the directory that `configure' is in and in `..'.
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+
95
+ If you have to use a `make' that does not support the `VPATH'
96
+ variable, you have to compile the package for one architecture at a
97
+ time in the source code directory. After you have installed the
98
+ package for one architecture, use `make distclean' before reconfiguring
99
+ for another architecture.
100
+
101
+ Installation Names
102
+ ==================
103
+
104
+ By default, `make install' will install the package's files in
105
+ `/usr/local/bin', `/usr/local/man', etc. You can specify an
106
+ installation prefix other than `/usr/local' by giving `configure' the
107
+ option `--prefix=PATH'.
108
+
109
+ You can specify separate installation prefixes for
110
+ architecture-specific files and architecture-independent files. If you
111
+ give `configure' the option `--exec-prefix=PATH', the package will use
112
+ PATH as the prefix for installing programs and libraries.
113
+ Documentation and other data files will still use the regular prefix.
114
+
115
+ In addition, if you use an unusual directory layout you can give
116
+ options like `--bindir=PATH' to specify different values for particular
117
+ kinds of files. Run `configure --help' for a list of the directories
118
+ you can set and what kinds of files go in them.
119
+
120
+ If the package supports it, you can cause programs to be installed
121
+ with an extra prefix or suffix on their names by giving `configure' the
122
+ option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
123
+
124
+ Optional Features
125
+ =================
126
+
127
+ Some packages pay attention to `--enable-FEATURE' options to
128
+ `configure', where FEATURE indicates an optional part of the package.
129
+ They may also pay attention to `--with-PACKAGE' options, where PACKAGE
130
+ is something like `gnu-as' or `x' (for the X Window System). The
131
+ `README' should mention any `--enable-' and `--with-' options that the
132
+ package recognizes.
133
+
134
+ For packages that use the X Window System, `configure' can usually
135
+ find the X include and library files automatically, but if it doesn't,
136
+ you can use the `configure' options `--x-includes=DIR' and
137
+ `--x-libraries=DIR' to specify their locations.
138
+
139
+ Specifying the System Type
140
+ ==========================
141
+
142
+ There may be some features `configure' cannot figure out
143
+ automatically, but needs to determine by the type of machine the package
144
+ will run on. Usually, assuming the package is built to be run on the
145
+ _same_ architectures, `configure' can figure that out, but if it prints
146
+ a message saying it cannot guess the machine type, give it the
147
+ `--build=TYPE' option. TYPE can either be a short name for the system
148
+ type, such as `sun4', or a canonical name which has the form:
149
+
150
+ CPU-COMPANY-SYSTEM
151
+
152
+ where SYSTEM can have one of these forms:
153
+
154
+ OS KERNEL-OS
155
+
156
+ See the file `config.sub' for the possible values of each field. If
157
+ `config.sub' isn't included in this package, then this package doesn't
158
+ need to know the machine type.
159
+
160
+ If you are _building_ compiler tools for cross-compiling, you should
161
+ use the `--target=TYPE' option to select the type of system they will
162
+ produce code for.
163
+
164
+ If you want to _use_ a cross compiler, that generates code for a
165
+ platform different from the build platform, you should specify the
166
+ "host" platform (i.e., that on which the generated programs will
167
+ eventually be run) with `--host=TYPE'.
168
+
169
+ Sharing Defaults
170
+ ================
171
+
172
+ If you want to set default values for `configure' scripts to share,
173
+ you can create a site shell script called `config.site' that gives
174
+ default values for variables like `CC', `cache_file', and `prefix'.
175
+ `configure' looks for `PREFIX/share/config.site' if it exists, then
176
+ `PREFIX/etc/config.site' if it exists. Or, you can set the
177
+ `CONFIG_SITE' environment variable to the location of the site script.
178
+ A warning: not all `configure' scripts look for a site script.
179
+
180
+ Defining Variables
181
+ ==================
182
+
183
+ Variables not defined in a site shell script can be set in the
184
+ environment passed to `configure'. However, some packages may run
185
+ configure again during the build, and the customized values of these
186
+ variables may be lost. In order to avoid this problem, you should set
187
+ them in the `configure' command line, using `VAR=value'. For example:
188
+
189
+ ./configure CC=/usr/local2/bin/gcc
190
+
191
+ will cause the specified gcc to be used as the C compiler (unless it is
192
+ overridden in the site shell script).
193
+
194
+ `configure' Invocation
195
+ ======================
196
+
197
+ `configure' recognizes the following options to control how it
198
+ operates.
199
+
200
+ `--help'
201
+ `-h'
202
+ Print a summary of the options to `configure', and exit.
203
+
204
+ `--version'
205
+ `-V'
206
+ Print the version of Autoconf used to generate the `configure'
207
+ script, and exit.
208
+
209
+ `--cache-file=FILE'
210
+ Enable the cache: use and save the results of the tests in FILE,
211
+ traditionally `config.cache'. FILE defaults to `/dev/null' to
212
+ disable caching.
213
+
214
+ `--config-cache'
215
+ `-C'
216
+ Alias for `--cache-file=config.cache'.
217
+
218
+ `--quiet'
219
+ `--silent'
220
+ `-q'
221
+ Do not print messages saying which checks are being made. To
222
+ suppress all normal output, redirect it to `/dev/null' (any error
223
+ messages will still be shown).
224
+
225
+ `--srcdir=DIR'
226
+ Look for the package's source code in directory DIR. Usually
227
+ `configure' can determine that directory automatically.
228
+
229
+ `configure' also accepts some other, not widely useful, options. Run
230
+ `configure --help' for more details.
231
+