bio-band 0.1.0
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- data/Gemfile +20 -0
- data/Gemfile.lock +79 -0
- data/Jarfile +9 -0
- data/Jarfile.lock +10 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +54 -0
- data/Rakefile +54 -0
- data/VERSION +1 -0
- data/bin/bio-band +83 -0
- data/bio-band.gemspec +129 -0
- data/ext/mkrf_conf.rb +74 -0
- data/features/create_dataset.feature +12 -0
- data/features/step_definitions/create_dataset.rb +40 -0
- data/features/step_definitions/weka_classifiers.rb +42 -0
- data/features/step_definitions/weka_clustering.rb +30 -0
- data/features/step_definitions/weka_filters.rb +29 -0
- data/features/step_definitions/weka_parsers.rb +45 -0
- data/features/support/env.rb +3 -0
- data/features/weka_classifiers.feature +16 -0
- data/features/weka_clustering.feature +14 -0
- data/features/weka_filters.feature +12 -0
- data/features/weka_parsers.feature +18 -0
- data/features/weka_pipeline.feature +13 -0
- data/lib/bio-band.rb +10 -0
- data/lib/bio-band/apache.rb +1 -0
- data/lib/bio-band/apache/stat/inference.rb +145 -0
- data/lib/bio-band/core.rb +6 -0
- data/lib/bio-band/core/parser/parser.rb +23 -0
- data/lib/bio-band/core/type/apache_matrices.rb +35 -0
- data/lib/bio-band/core/type/attribute.rb +53 -0
- data/lib/bio-band/core/type/instance.rb +10 -0
- data/lib/bio-band/core/type/instances.rb +332 -0
- data/lib/bio-band/core/type/utils.rb +31 -0
- data/lib/bio-band/weka.rb +11 -0
- data/lib/bio-band/weka/classifiers/bayes/bayes.rb +75 -0
- data/lib/bio-band/weka/classifiers/bayes/bayes_utils.rb +42 -0
- data/lib/bio-band/weka/classifiers/evaluation.rb +12 -0
- data/lib/bio-band/weka/classifiers/functions/functions.rb +23 -0
- data/lib/bio-band/weka/classifiers/functions/functions_utils.rb +39 -0
- data/lib/bio-band/weka/classifiers/lazy/lazy.rb +23 -0
- data/lib/bio-band/weka/classifiers/lazy/lazy_utils.rb +39 -0
- data/lib/bio-band/weka/classifiers/trees/trees.rb +48 -0
- data/lib/bio-band/weka/classifiers/trees/trees_utils.rb +42 -0
- data/lib/bio-band/weka/clusterers/clusterers.rb +32 -0
- data/lib/bio-band/weka/clusterers/clusterers_utils.rb +49 -0
- data/lib/bio-band/weka/db/DatabaseUtils_mysql +280 -0
- data/lib/bio-band/weka/db/DatabaseUtils_postgresql +594 -0
- data/lib/bio-band/weka/db/db.rb +74 -0
- data/lib/bio-band/weka/filters/supervised/attribute/attribute.rb +25 -0
- data/lib/bio-band/weka/filters/supervised/instance/instance.rb +17 -0
- data/lib/bio-band/weka/filters/supervised/supervised_utils.rb +32 -0
- data/lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb +70 -0
- data/lib/bio-band/weka/filters/unsupervised/instance/instance.rb +48 -0
- data/lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb +33 -0
- data/resources/weather.csv +15 -0
- data/resources/weather.numeric.arff +23 -0
- data/spec/bio-band_spec.rb +7 -0
- data/spec/spec_helper.rb +12 -0
- metadata +302 -0
data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "rdoc", "~> 3.12"
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gem "bundler", "~> 1.3.5"
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gem "jeweler", "~> 1.8.4"
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gem "simplecov", ">= 0"
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gem "jbundler"
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gem "ruport"
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gem "cucumber"
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gem "rspec"
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gem "json"
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gem "bio", ">= 1.4.2"
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end
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data/Gemfile.lock
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GEM
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remote: http://rubygems.org/
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specs:
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activesupport (3.2.13)
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i18n (= 0.6.1)
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multi_json (~> 1.0)
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bio (1.4.3.0001)
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builder (3.2.2)
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color (1.4.2)
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cucumber (1.3.2)
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builder (>= 2.1.2)
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diff-lcs (>= 1.1.3)
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gherkin (~> 2.12.0)
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multi_json (~> 1.3)
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diff-lcs (1.2.4)
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fastercsv (1.5.5)
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gherkin (2.12.0-java)
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multi_json (~> 1.3)
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git (1.2.5)
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i18n (0.6.1)
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jbundler (0.4.2)
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maven-tools (~> 0.32.1)
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ruby-maven (~> 3.0.4)
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jeweler (1.8.4)
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bundler (~> 1.0)
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git (>= 1.2.5)
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rake
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rdoc
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json (1.8.0-java)
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maven-tools (0.32.4)
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multi_json (1.7.4)
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pdf-writer (1.1.8)
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color (>= 1.4.0)
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transaction-simple (~> 1.3)
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rake (10.1.0)
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rdoc (3.12.2)
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json (~> 1.4)
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rspec (2.13.0)
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rspec-core (~> 2.13.0)
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rspec-expectations (~> 2.13.0)
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rspec-mocks (~> 2.13.0)
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rspec-core (2.13.1)
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rspec-expectations (2.13.0)
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diff-lcs (>= 1.1.3, < 2.0)
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rspec-mocks (2.13.1)
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ruby-maven (3.0.4.1.4)
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maven-tools (~> 0.32.3)
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thor (>= 0.14.6, < 2.0)
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ruport (1.6.3)
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fastercsv
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pdf-writer (= 1.1.8)
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shoulda (3.5.0)
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shoulda-context (~> 1.0, >= 1.0.1)
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shoulda-matchers (>= 1.4.1, < 3.0)
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shoulda-context (1.1.2)
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shoulda-matchers (2.1.0)
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activesupport (>= 3.0.0)
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simplecov (0.7.1)
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multi_json (~> 1.0)
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simplecov-html (~> 0.7.1)
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simplecov-html (0.7.1)
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thor (0.18.1)
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transaction-simple (1.4.0.2)
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PLATFORMS
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java
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DEPENDENCIES
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bio (>= 1.4.2)
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bundler (~> 1.3.5)
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cucumber
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jbundler
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jeweler (~> 1.8.4)
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json
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rdoc (~> 3.12)
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rspec
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ruport
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shoulda
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simplecov
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data/Jarfile
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jar 'nz.ac.waikato.cms.weka:weka-stable','3.6.9'
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jar 'org.apache.commons:commons-math3','3.0'
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jar 'junit:junit','3.8.1'
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jar 'mysql:mysql-connector-java','5.1.6'
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jar 'postgresql:postgresql','9.1-901.jdbc4'
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jar 'org.xerial:sqlite-jdbc','3.7.2'
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jar 'hsqldb:hsqldb','1.8.0.7'
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jar 'idb:idb','3.26'
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jar 'mckoi:mckoi','0.93'
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data/Jarfile.lock
ADDED
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nz.ac.waikato.cms.weka:weka-stable:jar:3.6.9
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net.sf.squirrel-sql.thirdparty-non-maven:java-cup:jar:0.11a
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org.apache.commons:commons-math3:jar:3.0
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junit:junit:jar:3.8.1
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mysql:mysql-connector-java:jar:5.1.6
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postgresql:postgresql:jar:9.1-901.jdbc4
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org.xerial:sqlite-jdbc:jar:3.7.2
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hsqldb:hsqldb:jar:1.8.0.7
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idb:idb:jar:3.26
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mckoi:mckoi:jar:0.93
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data/LICENSE.txt
ADDED
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Copyright (c) 2013 Alberto Arrigoni
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
ADDED
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= bio-band
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Data mining and machine learning algorithms for Ruby
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== Installation
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Install 'bundle' for JRuby before trying to install the 'bio-band' gem.
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Maven is also required for .jars automatic download and installation. On
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Ubuntu/Debian Maven should already be installed and on OSX system you can get
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it from Brew
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If you want to use 'bio-band' APIs without installing the gem you need
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to run command 'rake -T' once before requiring the gem in your script
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(this is necessary for jbundler to download the '.jar' files and subsequently
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set the Java classpath).
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Otherwise use:
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gem install bio-band
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== Usage
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== Developers
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To use the library
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require 'bio-band'
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The API doc is online. For more code examples see also the test files in
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the source tree.
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== Project home page
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Information on the source tree, documentation, issues and how to contribute, see
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http://github.com/arrigonialberto86/bioruby-band
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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== Cite
|
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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== Biogems.info
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This Biogem is published at http://biogems.info/index.html#bio-band
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== Copyright
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Copyright (c) 2013 arrigonialberto86. See LICENSE.txt for
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further details.
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data/Rakefile
ADDED
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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require 'jbundler'
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `jruby -S bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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gem.name = "bio-band"
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gem.homepage = "http://github.com/arrigonialberto86/bioruby-band"
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gem.license = "MIT"
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gem.summary = %Q{Data mining algorithms for JRuby}
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gem.description = %Q{Data mining and machine learning algorithms for JRuby }
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gem.email = "arrigonialberto86@gmail.com"
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gem.authors = ["arrigonialberto86"]
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gem.extensions = ["ext/mkrf_conf.rb"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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|
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#require 'rcov/rcovtask'
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#Rcov::RcovTask.new do |test|
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# test.libs << 'test'
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# test.pattern = 'test/**/test_*.rb'
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# test.verbose = true
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# test.rcov_opts << '--exclude "gems/*"'
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#end
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task :default => :test
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-band #{version}"
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rdoc.rdoc_files.include('README*')
|
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
ADDED
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0.1.0
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data/bin/bio-band
ADDED
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#!/usr/bin/env ruby
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#
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# BioRuby bio-band Plugin BioBand
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# Author:: arrigonialberto86
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# Copyright:: 2013
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USAGE = "Describe bio-band"
|
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|
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gempath = File.dirname(File.dirname(__FILE__))
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$: << File.join(gempath,'lib')
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|
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VERSION_FILENAME=File.join(gempath,'VERSION')
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version = File.new(VERSION_FILENAME).read.chomp
|
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# print banner
|
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print "bio-band #{version} by arrigonialberto86 2013\n"
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|
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if ARGV.size == 0
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print USAGE
|
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end
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|
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require 'bio-band'
|
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require 'optparse'
|
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|
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# Uncomment when using the bio-logger
|
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# require 'bio-logger'
|
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# Bio::Log::CLI.logger('stderr')
|
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# Bio::Log::CLI.trace('info')
|
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|
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options = {:example_switch=>false,:show_help=>false}
|
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opts = OptionParser.new do |o|
|
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o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
|
33
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+
|
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+
o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
|
35
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+
# TODO: your logic here, below an example
|
36
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+
options[:example_parameter] = 'this is a parameter'
|
37
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+
end
|
38
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+
|
39
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+
o.separator ""
|
40
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+
o.on("--switch-example", 'TODO: put a description for the SWITCH') do
|
41
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+
# TODO: your logic here, below an example
|
42
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+
self[:example_switch] = true
|
43
|
+
end
|
44
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+
|
45
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# Uncomment the following when using the bio-logger
|
46
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+
# o.separator ""
|
47
|
+
# o.on("--logger filename",String,"Log to file (default stderr)") do | name |
|
48
|
+
# Bio::Log::CLI.logger(name)
|
49
|
+
# end
|
50
|
+
#
|
51
|
+
# o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
|
52
|
+
# Bio::Log::CLI.trace(s)
|
53
|
+
# end
|
54
|
+
#
|
55
|
+
# o.on("-q", "--quiet", "Run quietly") do |q|
|
56
|
+
# Bio::Log::CLI.trace('error')
|
57
|
+
# end
|
58
|
+
#
|
59
|
+
# o.on("-v", "--verbose", "Run verbosely") do |v|
|
60
|
+
# Bio::Log::CLI.trace('info')
|
61
|
+
# end
|
62
|
+
#
|
63
|
+
# o.on("--debug", "Show debug messages") do |v|
|
64
|
+
# Bio::Log::CLI.trace('debug')
|
65
|
+
# end
|
66
|
+
|
67
|
+
o.separator ""
|
68
|
+
o.on_tail('-h', '--help', 'display this help and exit') do
|
69
|
+
options[:show_help] = true
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
73
|
+
begin
|
74
|
+
opts.parse!(ARGV)
|
75
|
+
|
76
|
+
# Uncomment the following when using the bio-logger
|
77
|
+
# Bio::Log::CLI.configure('bio-band')
|
78
|
+
|
79
|
+
# TODO: your code here
|
80
|
+
# use options for your logic
|
81
|
+
rescue OptionParser::InvalidOption => e
|
82
|
+
options[:invalid_argument] = e.message
|
83
|
+
end
|
data/bio-band.gemspec
ADDED
@@ -0,0 +1,129 @@
|
|
1
|
+
# Generated by jeweler
|
2
|
+
# DO NOT EDIT THIS FILE DIRECTLY
|
3
|
+
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
4
|
+
# -*- encoding: utf-8 -*-
|
5
|
+
|
6
|
+
Gem::Specification.new do |s|
|
7
|
+
s.name = "bio-band"
|
8
|
+
s.version = "0.1.0"
|
9
|
+
|
10
|
+
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
|
+
s.authors = ["arrigonialberto86"]
|
12
|
+
s.date = "2013-07-25"
|
13
|
+
s.description = "Data mining and machine learning algorithms for JRuby "
|
14
|
+
s.email = "arrigonialberto86@gmail.com"
|
15
|
+
s.executables = ["bio-band"]
|
16
|
+
s.extensions = ["ext/mkrf_conf.rb"]
|
17
|
+
s.extra_rdoc_files = [
|
18
|
+
"LICENSE.txt",
|
19
|
+
"README.rdoc"
|
20
|
+
]
|
21
|
+
s.files = [
|
22
|
+
"Gemfile",
|
23
|
+
"Gemfile.lock",
|
24
|
+
"Jarfile",
|
25
|
+
"Jarfile.lock",
|
26
|
+
"LICENSE.txt",
|
27
|
+
"README.rdoc",
|
28
|
+
"Rakefile",
|
29
|
+
"VERSION",
|
30
|
+
"bin/bio-band",
|
31
|
+
"bio-band.gemspec",
|
32
|
+
"ext/mkrf_conf.rb",
|
33
|
+
"features/create_dataset.feature",
|
34
|
+
"features/step_definitions/create_dataset.rb",
|
35
|
+
"features/step_definitions/weka_classifiers.rb",
|
36
|
+
"features/step_definitions/weka_clustering.rb",
|
37
|
+
"features/step_definitions/weka_filters.rb",
|
38
|
+
"features/step_definitions/weka_parsers.rb",
|
39
|
+
"features/support/env.rb",
|
40
|
+
"features/weka_classifiers.feature",
|
41
|
+
"features/weka_clustering.feature",
|
42
|
+
"features/weka_filters.feature",
|
43
|
+
"features/weka_parsers.feature",
|
44
|
+
"features/weka_pipeline.feature",
|
45
|
+
"lib/bio-band.rb",
|
46
|
+
"lib/bio-band/apache.rb",
|
47
|
+
"lib/bio-band/apache/stat/inference.rb",
|
48
|
+
"lib/bio-band/core.rb",
|
49
|
+
"lib/bio-band/core/parser/parser.rb",
|
50
|
+
"lib/bio-band/core/type/apache_matrices.rb",
|
51
|
+
"lib/bio-band/core/type/attribute.rb",
|
52
|
+
"lib/bio-band/core/type/instance.rb",
|
53
|
+
"lib/bio-band/core/type/instances.rb",
|
54
|
+
"lib/bio-band/core/type/utils.rb",
|
55
|
+
"lib/bio-band/weka.rb",
|
56
|
+
"lib/bio-band/weka/classifiers/bayes/bayes.rb",
|
57
|
+
"lib/bio-band/weka/classifiers/bayes/bayes_utils.rb",
|
58
|
+
"lib/bio-band/weka/classifiers/evaluation.rb",
|
59
|
+
"lib/bio-band/weka/classifiers/functions/functions.rb",
|
60
|
+
"lib/bio-band/weka/classifiers/functions/functions_utils.rb",
|
61
|
+
"lib/bio-band/weka/classifiers/lazy/lazy.rb",
|
62
|
+
"lib/bio-band/weka/classifiers/lazy/lazy_utils.rb",
|
63
|
+
"lib/bio-band/weka/classifiers/trees/trees.rb",
|
64
|
+
"lib/bio-band/weka/classifiers/trees/trees_utils.rb",
|
65
|
+
"lib/bio-band/weka/clusterers/clusterers.rb",
|
66
|
+
"lib/bio-band/weka/clusterers/clusterers_utils.rb",
|
67
|
+
"lib/bio-band/weka/db/DatabaseUtils_mysql",
|
68
|
+
"lib/bio-band/weka/db/DatabaseUtils_postgresql",
|
69
|
+
"lib/bio-band/weka/db/db.rb",
|
70
|
+
"lib/bio-band/weka/filters/supervised/attribute/attribute.rb",
|
71
|
+
"lib/bio-band/weka/filters/supervised/instance/instance.rb",
|
72
|
+
"lib/bio-band/weka/filters/supervised/supervised_utils.rb",
|
73
|
+
"lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb",
|
74
|
+
"lib/bio-band/weka/filters/unsupervised/instance/instance.rb",
|
75
|
+
"lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb",
|
76
|
+
"resources/weather.csv",
|
77
|
+
"resources/weather.numeric.arff",
|
78
|
+
"spec/bio-band_spec.rb",
|
79
|
+
"spec/spec_helper.rb"
|
80
|
+
]
|
81
|
+
s.homepage = "http://github.com/arrigonialberto86/bioruby-band"
|
82
|
+
s.licenses = ["MIT"]
|
83
|
+
s.require_paths = ["lib"]
|
84
|
+
s.rubygems_version = "1.8.24"
|
85
|
+
s.summary = "Data mining algorithms for JRuby"
|
86
|
+
|
87
|
+
if s.respond_to? :specification_version then
|
88
|
+
s.specification_version = 3
|
89
|
+
|
90
|
+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
91
|
+
s.add_development_dependency(%q<shoulda>, [">= 0"])
|
92
|
+
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
|
93
|
+
s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
|
94
|
+
s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
|
95
|
+
s.add_development_dependency(%q<simplecov>, [">= 0"])
|
96
|
+
s.add_development_dependency(%q<jbundler>, [">= 0"])
|
97
|
+
s.add_development_dependency(%q<ruport>, [">= 0"])
|
98
|
+
s.add_development_dependency(%q<cucumber>, [">= 0"])
|
99
|
+
s.add_development_dependency(%q<rspec>, [">= 0"])
|
100
|
+
s.add_development_dependency(%q<json>, [">= 0"])
|
101
|
+
s.add_development_dependency(%q<bio>, [">= 1.4.2"])
|
102
|
+
else
|
103
|
+
s.add_dependency(%q<shoulda>, [">= 0"])
|
104
|
+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
105
|
+
s.add_dependency(%q<bundler>, ["~> 1.3.5"])
|
106
|
+
s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
|
107
|
+
s.add_dependency(%q<simplecov>, [">= 0"])
|
108
|
+
s.add_dependency(%q<jbundler>, [">= 0"])
|
109
|
+
s.add_dependency(%q<ruport>, [">= 0"])
|
110
|
+
s.add_dependency(%q<cucumber>, [">= 0"])
|
111
|
+
s.add_dependency(%q<rspec>, [">= 0"])
|
112
|
+
s.add_dependency(%q<json>, [">= 0"])
|
113
|
+
s.add_dependency(%q<bio>, [">= 1.4.2"])
|
114
|
+
end
|
115
|
+
else
|
116
|
+
s.add_dependency(%q<shoulda>, [">= 0"])
|
117
|
+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
118
|
+
s.add_dependency(%q<bundler>, ["~> 1.3.5"])
|
119
|
+
s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
|
120
|
+
s.add_dependency(%q<simplecov>, [">= 0"])
|
121
|
+
s.add_dependency(%q<jbundler>, [">= 0"])
|
122
|
+
s.add_dependency(%q<ruport>, [">= 0"])
|
123
|
+
s.add_dependency(%q<cucumber>, [">= 0"])
|
124
|
+
s.add_dependency(%q<rspec>, [">= 0"])
|
125
|
+
s.add_dependency(%q<json>, [">= 0"])
|
126
|
+
s.add_dependency(%q<bio>, [">= 1.4.2"])
|
127
|
+
end
|
128
|
+
end
|
129
|
+
|