bio-band 0.1.0

data/lib/bio-band/core/type/utils.rb

@@ -0,0 +1,31 @@
+require 'java'
+
+module Core
+ 	module Utils
+
+		# Convert a bidimensional RubyArray to a java double [][]
+		def Utils.bidimensional_to_double(ruby_array)
+			ruby_array.to_java Java::double[]
+		end
+
+    def Utils.bidimensional_to_long(ruby_array)
+      ruby_array.to_java Java::long[]
+    end
+
+		def Utils.double_to_a(java_array)
+			ruby_array = []
+			java_array.each {|val| ruby_array << val}
+			ruby_array
+		end
+
+  end
+end
+
+class Array
+  def is_2d?
+    self.each do |item|
+      return true if item.is_a? Array 
+    end
+    return false
+  end
+end

data/lib/bio-band/weka.rb

@@ -0,0 +1,11 @@
+require 'ruby_mining/weka/db/db'
+require 'ruby_mining/weka/filters/unsupervised/attribute/attribute.rb'
+require 'ruby_mining/weka/filters/unsupervised/instance/instance.rb'
+require 'ruby_mining/weka/filters/supervised/instance/instance.rb'
+require 'ruby_mining/weka/filters/supervised/attribute/attribute.rb'
+require 'ruby_mining/weka/classifiers/bayes/bayes.rb'
+require 'ruby_mining/weka/classifiers/evaluation.rb'
+require 'ruby_mining/weka/classifiers/functions/functions.rb'
+require 'ruby_mining/weka/classifiers/trees/trees.rb'
+require 'ruby_mining/weka/classifiers/lazy/lazy.rb'
+require 'ruby_mining/weka/clusterers/clusterers.rb'

data/lib/bio-band/weka/classifiers/bayes/bayes.rb

@@ -0,0 +1,75 @@
+$:.unshift File.dirname(__FILE__)
+require 'bayes_utils'
+
+module Weka
+	module Classifier
+		module Bayes
+			java_import "weka.classifiers.bayes.NaiveBayes"
+			java_import "weka.classifiers.bayes.BayesianLogisticRegression"
+			java_import "weka.classifiers.bayes.AODE"
+			java_import "weka.classifiers.bayes.ComplementNaiveBayes"
+			java_import "weka.classifiers.bayes.WAODE"
+
+			class NaiveBayes
+				include Bayes_utils
+				class Base < NaiveBayes
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+
+			class AODE
+				include Bayes_utils
+				class Base < AODE
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+
+			class BayesianLogisticRegression
+				include Bayes_utils
+				class Base < BayesianLogisticRegression
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+
+			class ComplementNaiveBayes
+				include Bayes_utils
+				class Base < ComplementNaiveBayes
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+
+			class WAODE
+				include Bayes_utils
+				class Base < WAODE
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+
+		end
+	end
+end

data/lib/bio-band/weka/classifiers/bayes/bayes_utils.rb

@@ -0,0 +1,42 @@
+#This module is used by the Bayesian classifiers from 'bayes.rb' 
+#to inherit the following methods (instance and class methods)
+module Bayes_utils
+	java_import "weka.core.Utils"
+
+	#Instance methods list
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  def set_options(options)
+  	options_inst = Utils.splitOptions(options)
+		setOptions(options_inst)
+  end
+
+	def list_options
+		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+	end
+
+	def description
+    puts globalInfo
+	end
+
+	#Class methods module
+	module ClassMethods
+		
+		def self.classifier_attr_accessor(*args)
+	    args.each do |arg|
+	      #Here's the getter
+	      self.class_eval("def #{arg};@#{arg};end")
+	      #Here's the setter
+	      self.class_eval("def set_#{arg}(val);@#{arg}=val;end")
+	  	end
+  	end
+
+		classifier_attr_accessor :options,:data,:class_index
+
+	end
+end
+
+
+

data/lib/bio-band/weka/classifiers/evaluation.rb

@@ -0,0 +1,12 @@
+module Weka
+	module Classifier
+		java_import 'weka.classifiers.Evaluation'
+
+		class Evaluation
+			def summary
+				puts toSummaryString
+			end
+
+		end
+	end
+end

data/lib/bio-band/weka/classifiers/functions/functions.rb

@@ -0,0 +1,23 @@
+$:.unshift File.dirname(__FILE__)
+require 'functions_utils'
+
+module Weka
+	module Classifier
+		module Functions
+      java_import 'weka.classifiers.functions.LinearRegression'
+
+      class LinearRegression
+        include Functions_utils
+        class Base < LinearRegression
+          def initialize
+            super
+            set_options(self.class.options) if self.class.options 
+            self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+            buildClassifier(self.class.data)
+          end
+        end
+      end
+
+    end
+  end
+end

data/lib/bio-band/weka/classifiers/functions/functions_utils.rb

@@ -0,0 +1,39 @@
+#This module is used by the 'functions' classifiers from 'functions.rb' 
+#to inherit the following methods (instance and class methods)
+module Functions_utils
+	java_import "weka.core.Utils"
+
+	#Instance methods list
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  def set_options(options)
+  	options_inst = Utils.splitOptions(options)
+		setOptions(options_inst)
+  end
+
+	def list_options
+		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+	end
+
+	def description
+    puts globalInfo
+	end
+
+	#Class methods module
+	module ClassMethods
+		
+		def self.classifier_attr_accessor(*args)
+	    args.each do |arg|
+	      #Here's the getter
+	      self.class_eval("def #{arg};@#{arg};end")
+	      #Here's the setter
+	      self.class_eval("def set_#{arg}(val);@#{arg}=val;end")
+	  	end
+  	end
+
+		classifier_attr_accessor :options,:data,:class_index
+
+	end
+end

data/lib/bio-band/weka/classifiers/lazy/lazy.rb

@@ -0,0 +1,23 @@
+$:.unshift File.dirname(__FILE__)
+require 'lazy_utils'
+
+module Weka
+	module Classifier
+		module Lazy
+
+      java_import 'weka.classifiers.lazy.KStar' 
+
+			class KStar
+				include Lazy_utils
+				class Base < KStar
+					def initialize
+						super
+						set_options(self.class.options) if self.class.options 
+						self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+						buildClassifier(self.class.data)
+					end
+				end
+			end
+    end
+  end
+end

data/lib/bio-band/weka/classifiers/lazy/lazy_utils.rb

@@ -0,0 +1,39 @@
+#This module is used by the 'lazy' classifiers from 'lazy.rb' 
+#to inherit the following methods (instance and class methods)
+module Lazy_utils
+	java_import "weka.core.Utils"
+
+	#Instance methods list
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  def set_options(options)
+  	options_inst = Utils.splitOptions(options)
+		setOptions(options_inst)
+  end
+
+	def list_options
+		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+	end
+
+	def description
+    puts globalInfo
+	end
+
+	#Class methods module
+	module ClassMethods
+		
+		def self.classifier_attr_accessor(*args)
+	    args.each do |arg|
+	      #Here's the getter
+	      self.class_eval("def #{arg};@#{arg};end")
+	      #Here's the setter
+	      self.class_eval("def set_#{arg}(val);@#{arg}=val;end")
+	  	end
+  	end
+
+		classifier_attr_accessor :options,:data,:class_index
+
+	end
+end

data/lib/bio-band/weka/classifiers/trees/trees.rb

@@ -0,0 +1,48 @@
+$:.unshift File.dirname(__FILE__)
+require 'trees_utils'
+
+module Weka
+	module Classifier
+		module Trees
+      java_import 'weka.classifiers.trees.J48'
+      java_import 'weka.classifiers.trees.RandomForest'
+
+      class FT
+        include Trees_utils
+        class Base < FT
+          def initialize
+            super
+            set_options(self.class.options) if self.class.options 
+            self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+            buildClassifier(self.class.data)
+          end
+        end
+      end
+
+      class J48
+        include Trees_utils
+        class Base < J48
+          def initialize
+            super
+            set_options(self.class.options) if self.class.options 
+            self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+            buildClassifier(self.class.data)
+          end
+        end
+      end
+
+      class RandomForest
+        include Trees_utils
+        class Base < RandomForest
+          def initialize
+            super
+            set_options(self.class.options) if self.class.options 
+            self.class.data.setClassIndex(self.class.class_index) if self.class.class_index
+            buildClassifier(self.class.data)
+          end
+        end
+      end
+
+		end
+  end
+end

data/lib/bio-band/weka/classifiers/trees/trees_utils.rb

@@ -0,0 +1,42 @@
+#This module is used by the 'trees' classifiers from 'trees.rb' 
+#to inherit the following methods (instance and class methods)
+module Trees_utils
+	java_import "weka.core.Utils"
+
+	#Instance methods list
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  def set_options(options)
+  	options_inst = Utils.splitOptions(options)
+		setOptions(options_inst)
+  end
+
+	def list_options
+		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+	end
+
+	def description
+    puts globalInfo
+	end
+
+	#Class methods module
+	module ClassMethods
+		
+		def self.classifier_attr_accessor(*args)
+	    args.each do |arg|
+	      #Here's the getter
+	      self.class_eval("def #{arg};@#{arg};end")
+	      #Here's the setter
+	      self.class_eval("def set_#{arg}(val);@#{arg}=val;end")
+	  	end
+  	end
+
+		classifier_attr_accessor :options,:data,:class_index
+
+	end
+end
+
+
+

data/lib/bio-band/weka/clusterers/clusterers.rb

@@ -0,0 +1,32 @@
+$:.unshift File.dirname(__FILE__)
+require 'clusterers_utils'
+
+module Weka
+	module Clusterer
+    java_import 'weka.clusterers.SimpleKMeans'
+    java_import 'weka.clusterers.FarthestFirst'
+
+    class SimpleKMeans
+      include Clusterer_utils
+      class Base < SimpleKMeans
+        def initialize
+          super
+          set_options(self.class.options) if self.class.options 
+          buildClusterer(self.class.data)
+        end
+      end
+    end
+
+    class FarthestFirst
+      include Clusterer_utils
+      class Base < FarthestFirst
+        def initialize
+          super
+          set_options(self.class.options) if self.class.options 
+          buildClusterer(self.class.data)
+        end
+      end
+    end
+
+	end
+end

data/lib/bio-band/weka/clusterers/clusterers_utils.rb

@@ -0,0 +1,49 @@
+#This module is used by the classes from the Clusterer module 
+#to inherit the following methods (instance and class methods)
+module Clusterer_utils
+	java_import "weka.core.Utils"
+
+	#Instance methods list
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  def set_options(options)
+  	options_inst = Utils.splitOptions(options)
+		setOptions(options_inst)
+  end
+
+	def list_options
+    options = ''
+		listOptions.each {|key| options="#{options}\n#{key.synopsis} #{key.description}"}
+    options
+	end
+
+	def description
+    globalInfo
+	end
+
+  def get_centroids 
+    getClusterCentroids
+  end
+
+  def list_capabilities
+    get_capabilities.to_s
+  end
+
+	#Class methods module
+	module ClassMethods
+		
+		def self.classifier_attr_accessor(*args)
+	    args.each do |arg|
+	      #Here's the getter
+	      self.class_eval("def #{arg};@#{arg};end")
+	      #Here's the setter
+	      self.class_eval("def set_#{arg}(val);@#{arg}=val;end")
+	  	end
+  	end
+
+		classifier_attr_accessor :options,:data
+
+	end
+end