bio-band 0.1.0

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.3.5"
+  gem "jeweler", "~> 1.8.4"
+  gem "simplecov", ">= 0"
+  gem "jbundler"
+  gem "ruport"
+  gem "cucumber"
+  gem "rspec"
+  gem "json"
+  gem "bio", ">= 1.4.2"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.2.13)
+      i18n (= 0.6.1)
+      multi_json (~> 1.0)
+    bio (1.4.3.0001)
+    builder (3.2.2)
+    color (1.4.2)
+    cucumber (1.3.2)
+      builder (>= 2.1.2)
+      diff-lcs (>= 1.1.3)
+      gherkin (~> 2.12.0)
+      multi_json (~> 1.3)
+    diff-lcs (1.2.4)
+    fastercsv (1.5.5)
+    gherkin (2.12.0-java)
+      multi_json (~> 1.3)
+    git (1.2.5)
+    i18n (0.6.1)
+    jbundler (0.4.2)
+      maven-tools (~> 0.32.1)
+      ruby-maven (~> 3.0.4)
+    jeweler (1.8.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+      rdoc
+    json (1.8.0-java)
+    maven-tools (0.32.4)
+    multi_json (1.7.4)
+    pdf-writer (1.1.8)
+      color (>= 1.4.0)
+      transaction-simple (~> 1.3)
+    rake (10.1.0)
+    rdoc (3.12.2)
+      json (~> 1.4)
+    rspec (2.13.0)
+      rspec-core (~> 2.13.0)
+      rspec-expectations (~> 2.13.0)
+      rspec-mocks (~> 2.13.0)
+    rspec-core (2.13.1)
+    rspec-expectations (2.13.0)
+      diff-lcs (>= 1.1.3, < 2.0)
+    rspec-mocks (2.13.1)
+    ruby-maven (3.0.4.1.4)
+      maven-tools (~> 0.32.3)
+      thor (>= 0.14.6, < 2.0)
+    ruport (1.6.3)
+      fastercsv
+      pdf-writer (= 1.1.8)
+    shoulda (3.5.0)
+      shoulda-context (~> 1.0, >= 1.0.1)
+      shoulda-matchers (>= 1.4.1, < 3.0)
+    shoulda-context (1.1.2)
+    shoulda-matchers (2.1.0)
+      activesupport (>= 3.0.0)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    thor (0.18.1)
+    transaction-simple (1.4.0.2)
+
+PLATFORMS
+  java
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.3.5)
+  cucumber
+  jbundler
+  jeweler (~> 1.8.4)
+  json
+  rdoc (~> 3.12)
+  rspec
+  ruport
+  shoulda
+  simplecov

data/Jarfile

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+jar 'nz.ac.waikato.cms.weka:weka-stable','3.6.9'
+jar 'org.apache.commons:commons-math3','3.0'
+jar 'junit:junit','3.8.1'
+jar 'mysql:mysql-connector-java','5.1.6'
+jar 'postgresql:postgresql','9.1-901.jdbc4'
+jar 'org.xerial:sqlite-jdbc','3.7.2'
+jar 'hsqldb:hsqldb','1.8.0.7'
+jar 'idb:idb','3.26'
+jar 'mckoi:mckoi','0.93'

data/Jarfile.lock

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+nz.ac.waikato.cms.weka:weka-stable:jar:3.6.9
+net.sf.squirrel-sql.thirdparty-non-maven:java-cup:jar:0.11a
+org.apache.commons:commons-math3:jar:3.0
+junit:junit:jar:3.8.1
+mysql:mysql-connector-java:jar:5.1.6
+postgresql:postgresql:jar:9.1-901.jdbc4
+org.xerial:sqlite-jdbc:jar:3.7.2
+hsqldb:hsqldb:jar:1.8.0.7
+idb:idb:jar:3.26
+mckoi:mckoi:jar:0.93

data/LICENSE.txt

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+Copyright (c) 2013 Alberto Arrigoni
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-band
+
+Data mining and machine learning algorithms for Ruby
+
+== Installation
+
+Install 'bundle' for JRuby before trying to install the 'bio-band' gem.
+Maven is also required for .jars automatic download and installation. On
+Ubuntu/Debian Maven should already be installed and on OSX system you can get
+it from Brew
+
+If you want to use 'bio-band' APIs without installing the gem you need
+to run command 'rake -T' once before requiring the gem in your script
+(this is necessary for jbundler to download the '.jar' files and subsequently
+set the Java classpath).
+Otherwise use:
+
+        gem install bio-band
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-band'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/arrigonialberto86/bioruby-band
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-band
+
+== Copyright
+
+Copyright (c) 2013 arrigonialberto86. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+  require 'jbundler'
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `jruby -S bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-band"
+  gem.homepage = "http://github.com/arrigonialberto86/bioruby-band"
+  gem.license = "MIT"
+  gem.summary = %Q{Data mining algorithms for JRuby}
+  gem.description = %Q{Data mining and machine learning algorithms for JRuby }
+  gem.email = "arrigonialberto86@gmail.com"
+  gem.authors = ["arrigonialberto86"]
+  gem.extensions = ["ext/mkrf_conf.rb"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |test|
+#  test.libs << 'test'
+#  test.pattern = 'test/**/test_*.rb'
+#  test.verbose = true
+#  test.rcov_opts << '--exclude "gems/*"'
+#end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-band #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bin/bio-band

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-band Plugin BioBand
+# Author:: arrigonialberto86
+# Copyright:: 2013
+
+USAGE = "Describe bio-band"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+# print banner
+print "bio-band #{version} by arrigonialberto86 2013\n"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-band'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+  
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment the following when using the bio-logger 
+  # Bio::Log::CLI.configure('bio-band')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/bio-band.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-band"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["arrigonialberto86"]
+  s.date = "2013-07-25"
+  s.description = "Data mining and machine learning algorithms for JRuby "
+  s.email = "arrigonialberto86@gmail.com"
+  s.executables = ["bio-band"]
+  s.extensions = ["ext/mkrf_conf.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    "Gemfile",
+    "Gemfile.lock",
+    "Jarfile",
+    "Jarfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/bio-band",
+    "bio-band.gemspec",
+    "ext/mkrf_conf.rb",
+    "features/create_dataset.feature",
+    "features/step_definitions/create_dataset.rb",
+    "features/step_definitions/weka_classifiers.rb",
+    "features/step_definitions/weka_clustering.rb",
+    "features/step_definitions/weka_filters.rb",
+    "features/step_definitions/weka_parsers.rb",
+    "features/support/env.rb",
+    "features/weka_classifiers.feature",
+    "features/weka_clustering.feature",
+    "features/weka_filters.feature",
+    "features/weka_parsers.feature",
+    "features/weka_pipeline.feature",
+    "lib/bio-band.rb",
+    "lib/bio-band/apache.rb",
+    "lib/bio-band/apache/stat/inference.rb",
+    "lib/bio-band/core.rb",
+    "lib/bio-band/core/parser/parser.rb",
+    "lib/bio-band/core/type/apache_matrices.rb",
+    "lib/bio-band/core/type/attribute.rb",
+    "lib/bio-band/core/type/instance.rb",
+    "lib/bio-band/core/type/instances.rb",
+    "lib/bio-band/core/type/utils.rb",
+    "lib/bio-band/weka.rb",
+    "lib/bio-band/weka/classifiers/bayes/bayes.rb",
+    "lib/bio-band/weka/classifiers/bayes/bayes_utils.rb",
+    "lib/bio-band/weka/classifiers/evaluation.rb",
+    "lib/bio-band/weka/classifiers/functions/functions.rb",
+    "lib/bio-band/weka/classifiers/functions/functions_utils.rb",
+    "lib/bio-band/weka/classifiers/lazy/lazy.rb",
+    "lib/bio-band/weka/classifiers/lazy/lazy_utils.rb",
+    "lib/bio-band/weka/classifiers/trees/trees.rb",
+    "lib/bio-band/weka/classifiers/trees/trees_utils.rb",
+    "lib/bio-band/weka/clusterers/clusterers.rb",
+    "lib/bio-band/weka/clusterers/clusterers_utils.rb",
+    "lib/bio-band/weka/db/DatabaseUtils_mysql",
+    "lib/bio-band/weka/db/DatabaseUtils_postgresql",
+    "lib/bio-band/weka/db/db.rb",
+    "lib/bio-band/weka/filters/supervised/attribute/attribute.rb",
+    "lib/bio-band/weka/filters/supervised/instance/instance.rb",
+    "lib/bio-band/weka/filters/supervised/supervised_utils.rb",
+    "lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb",
+    "lib/bio-band/weka/filters/unsupervised/instance/instance.rb",
+    "lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb",
+    "resources/weather.csv",
+    "resources/weather.numeric.arff",
+    "spec/bio-band_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://github.com/arrigonialberto86/bioruby-band"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.24"
+  s.summary = "Data mining algorithms for JRuby"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<jbundler>, [">= 0"])
+      s.add_development_dependency(%q<ruport>, [">= 0"])
+      s.add_development_dependency(%q<cucumber>, [">= 0"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
+      s.add_development_dependency(%q<json>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.3.5"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<jbundler>, [">= 0"])
+      s.add_dependency(%q<ruport>, [">= 0"])
+      s.add_dependency(%q<cucumber>, [">= 0"])
+      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<json>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.3.5"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<jbundler>, [">= 0"])
+    s.add_dependency(%q<ruport>, [">= 0"])
+    s.add_dependency(%q<cucumber>, [">= 0"])
+    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<json>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+