bio-band 0.1.2 → 0.1.3

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Files changed (33) hide show
  1. data/VERSION +1 -1
  2. data/bio-band.gemspec +8 -3
  3. data/features/step_definitions/create_dataset.rb +16 -17
  4. data/features/step_definitions/weka_clustering.rb +2 -2
  5. data/features/step_definitions/weka_filters.rb +12 -9
  6. data/features/step_definitions/weka_parsers.rb +13 -13
  7. data/lib/bio-band/core/type/instances.rb +33 -14
  8. data/lib/bio-band/weka.rb +3 -1
  9. data/lib/bio-band/weka/attribute_selection/attribute_selection_utils.rb +18 -0
  10. data/lib/bio-band/weka/attribute_selection/evaluators.rb +21 -0
  11. data/lib/bio-band/weka/attribute_selection/search.rb +26 -0
  12. data/lib/bio-band/weka/classifiers/bayes/bayes.rb +74 -54
  13. data/lib/bio-band/weka/classifiers/bayes/bayes_utils.rb +43 -23
  14. data/lib/bio-band/weka/classifiers/evaluation.rb +1 -1
  15. data/lib/bio-band/weka/classifiers/functions/functions.rb +157 -2
  16. data/lib/bio-band/weka/classifiers/functions/functions_utils.rb +45 -25
  17. data/lib/bio-band/weka/classifiers/lazy/lazy.rb +69 -4
  18. data/lib/bio-band/weka/classifiers/lazy/lazy_utils.rb +48 -28
  19. data/lib/bio-band/weka/classifiers/mi/mi.rb +190 -0
  20. data/lib/bio-band/weka/classifiers/mi/mi_utils.rb +65 -0
  21. data/lib/bio-band/weka/classifiers/rules/rules.rb +190 -0
  22. data/lib/bio-band/weka/classifiers/rules/rules_utils.rb +45 -25
  23. data/lib/bio-band/weka/classifiers/trees/trees.rb +66 -0
  24. data/lib/bio-band/weka/classifiers/trees/trees_utils.rb +47 -27
  25. data/lib/bio-band/weka/clusterers/clusterers.rb +34 -0
  26. data/lib/bio-band/weka/clusterers/clusterers_utils.rb +2 -4
  27. data/lib/bio-band/weka/db/db.rb +67 -67
  28. data/lib/bio-band/weka/filters/supervised/attribute/attribute.rb +31 -1
  29. data/lib/bio-band/weka/filters/supervised/supervised_utils.rb +33 -31
  30. data/lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb +12 -0
  31. data/lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb +29 -29
  32. metadata +8 -3
  33. data/lib/bio-band/weka/classifiers/rules/rules.rb +0 -32
@@ -8,7 +8,9 @@ module Weka
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  module Attribute
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  java_import "weka.filters.unsupervised.attribute.Add"
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+ java_import "weka.filters.unsupervised.attribute.AddCluster"
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  java_import "weka.filters.unsupervised.attribute.Center"
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+ java_import "weka.filters.unsupervised.attribute.ClusterMembership"
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  java_import "weka.filters.unsupervised.attribute.Discretize"
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  java_import "weka.filters.unsupervised.attribute.NominalToString"
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  java_import "weka.filters.unsupervised.attribute.Normalize"
@@ -23,10 +25,18 @@ module Weka
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  include Unsupervised_Util
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  end
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+ class AddCluster
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+ include Unsupervised_Util
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+ end
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+
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  class Center
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  include Unsupervised_Util
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  end
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+ class ClusterMembership
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+ include Unsupervised_Util
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+ end
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+
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  class Discretize
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  include Unsupervised_Util
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  end
@@ -57,6 +67,8 @@ module Weka
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  Weka::Filter::Unsupervised::Attribute::PrincipalComponents.__persistent__ = true
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  Weka::Filter::Unsupervised::Attribute::Add.__persistent__ = true
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+ Weka::Filter::Unsupervised::Attribute::AddCluster.__persistent__ = true
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+ Weka::Filter::Unsupervised::Attribute::ClusterMembership.__persistent__ = true
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  Weka::Filter::Unsupervised::Attribute::Standardize.__persistent__ = true
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  Weka::Filter::Unsupervised::Attribute::Remove.__persistent__ = true
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  Weka::Filter::Unsupervised::Attribute::Normalize.__persistent__ = true
@@ -1,33 +1,33 @@
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  module Unsupervised_Util
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- java_import "weka.core.Utils"
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- java_import "weka.filters.Filter"
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-
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- #Instance methods list
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- def filter_options
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- begin
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- listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
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- rescue
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- puts "Sorry, list option is available for this filter"
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- end
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- end
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-
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- def set_filter_options(options_string)
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- options = Utils.splitOptions(options_string)
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- setOptions(options)
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- end
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-
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- def set_data(instances)
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- setInputFormat(instances)
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- @input = instances
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- end
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-
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- def description
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- begin; puts globalInfo; rescue; NoMethodError; puts "Sorry, no description available for this filter"; end
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- end
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-
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- def use
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- Filter.useFilter(@input,self)
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- end
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+ java_import "weka.core.Utils"
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+ java_import "weka.filters.Filter"
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+
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+ #Instance methods list
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+ def options_list
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+ listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
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+ end
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+
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+ def filter_options(options_string)
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+ options = Utils.splitOptions(options_string)
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+ setOptions(options)
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+ end
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+
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+ def data(instances)
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+ setInputFormat(instances)
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+ @input = instances
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+ end
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+
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+ def description
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+ globalInfo
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+ end
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+
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+ def use
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+ Filter.useFilter(@input,self)
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+ end
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+
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+ def set(&block)
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+ self.instance_eval(&block)
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+ end
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  end
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metadata CHANGED
@@ -2,14 +2,14 @@
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  name: bio-band
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  version: !ruby/object:Gem::Version
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  prerelease:
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- version: 0.1.2
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+ version: 0.1.3
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  platform: ruby
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  authors:
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  - arrigonialberto86
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-07-30 00:00:00.000000000 Z
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+ date: 2013-09-02 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: shoulda
@@ -247,6 +247,9 @@ files:
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  - lib/bio-band/core/type/instances.rb
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  - lib/bio-band/core/type/utils.rb
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  - lib/bio-band/weka.rb
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+ - lib/bio-band/weka/attribute_selection/attribute_selection_utils.rb
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+ - lib/bio-band/weka/attribute_selection/evaluators.rb
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+ - lib/bio-band/weka/attribute_selection/search.rb
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  - lib/bio-band/weka/classifiers/bayes/bayes.rb
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  - lib/bio-band/weka/classifiers/bayes/bayes_utils.rb
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  - lib/bio-band/weka/classifiers/evaluation.rb
@@ -254,7 +257,9 @@ files:
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  - lib/bio-band/weka/classifiers/functions/functions_utils.rb
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  - lib/bio-band/weka/classifiers/lazy/lazy.rb
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  - lib/bio-band/weka/classifiers/lazy/lazy_utils.rb
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- - ! 'lib/bio-band/weka/classifiers/rules/rules.rb '
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+ - lib/bio-band/weka/classifiers/mi/mi.rb
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+ - lib/bio-band/weka/classifiers/mi/mi_utils.rb
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+ - lib/bio-band/weka/classifiers/rules/rules.rb
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  - lib/bio-band/weka/classifiers/rules/rules_utils.rb
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  - lib/bio-band/weka/classifiers/trees/trees.rb
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  - lib/bio-band/weka/classifiers/trees/trees_utils.rb
@@ -1,32 +0,0 @@
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- $:.unshift File.dirname(__FILE__)
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- require 'rules_utils'
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-
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- module Weka
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- module Classifier
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- module Rules
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- java_import "weka.classifiers.rules.DecisionTable"
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- java_import "weka.classifiers.rules.DTNB"
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-
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- class DecisionTable
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- include Rules_utils
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- class Base < DecisionTable
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- def initialize
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- super
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- init_rules
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- end
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- end
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- end
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-
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- class DTNB
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- include Rules_utils
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- class Base < DTNB
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- def initialize
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- super
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- init_rules
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- end
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- end
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- end
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-
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- end
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- end
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- end