bio-band 0.1.2 → 0.1.3

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

@@ -2,7 +2,7 @@
 #to inherit the following methods (instance and class methods)
 module Bayes_utils
 
-	java_import "weka.core.Utils"
+  java_import "weka.core.Utils"
 
   def init_classifier
     set_options(self.class.options) if self.class.options 
@@ -10,39 +10,59 @@ module Bayes_utils
     buildClassifier(self.class.data)
   end
 
-	#Instance methods list
+  def init_instance_classifier(&block)
+    self.instance_eval(&block)
+    @dataset.setClassIndex(@class_index)
+    build_classifier(@dataset)
+  end
+
+  def set_data(data)
+    @dataset = data 
+  end
+
+  def set_class_index(class_index)
+    @class_index = class_index 
+  end
+
+  #Instance methods list
   def self.included(base)
     base.extend(ClassMethods)
   end
 
   def set_options(options)
-  	options_inst = Utils.splitOptions(options)
-		setOptions(options_inst)
+    options_inst = Utils.splitOptions(options)
+    setOptions(options_inst)
   end
 
-	def list_options
-		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
-	end
+  def list_options
+    listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
+  end
 
-	def description
-    puts globalInfo
-	end
+  def description
+    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
+  def cross_validate(fold)
+    eval = Weka::Classifier::Evaluation.new self.class.data
+    eval.crossValidateModel(self.class.ancestors[2].new, self.class.data, fold.to_java(:int), Random.new(1))
+    eval.summary
+  end
 
-		classifier_attr_accessor :options,:data,:class_index
+  #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
 
-	end
+    classifier_attr_accessor :options,:data,:class_index
+
+  end
 end
 
 

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

@@ -5,7 +5,7 @@ module Weka
 
 		class Evaluation
 			def summary
-				puts toSummaryString
+				toSummaryString
 			end
 		end
     

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

@@ -5,13 +5,168 @@ module Weka
 	module Classifier
 		module Functions
       java_import 'weka.classifiers.functions.LinearRegression'
+      java_import 'weka.classifiers.functions.PLSClassifier'
+      java_import 'weka.classifiers.functions.RBFNetwork'
+      java_import 'weka.classifiers.functions.GaussianProcesses'
+      java_import 'weka.classifiers.functions.LeastMedSq'
+      java_import 'weka.classifiers.functions.LibSVM'
+      java_import 'weka.classifiers.functions.SMO'
+      java_import 'weka.classifiers.functions.SMOreg'
+      java_import 'weka.classifiers.functions.SPegasos'
+      java_import 'weka.classifiers.functions.VotedPerceptron'
+      java_import 'weka.classifiers.functions.Winnow'
+
+
+      class LeastMedSq
+        include Functions_utils
+        class Base < LeastMedSq
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class LibSVM
+        include Functions_utils
+        class Base < LibSVM
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
 
       class LinearRegression
         include Functions_utils
         class Base < LinearRegression
-          def initialize
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class PLSClassifier
+        include Functions_utils
+        class Base < PLSClassifier
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class RBFNetwork
+        include Functions_utils
+        class Base < RBFNetwork
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class SMO
+        include Functions_utils
+        class Base < SMO
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class SMOreg
+        include Functions_utils
+        class Base < SMOreg
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class SPegasos
+        include Functions_utils
+        class Base < SPegasos
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end 
+
+      class GaussianProcesses
+        include Functions_utils
+        class Base < GaussianProcesses
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class VotedPerceptron
+        include Functions_utils
+        class Base < VotedPerceptron
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class Winnow
+        include Functions_utils
+        class Base < Winnow
+          def initialize(&block)
             super
-            init_function
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
           end
         end
       end

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

@@ -1,7 +1,7 @@
 #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"
+  java_import "weka.core.Utils"
 
   def init_function
     set_options(self.class.options) if self.class.options 
@@ -9,37 +9,57 @@ module Functions_utils
     buildClassifier(self.class.data)
   end
 
-	#Instance methods list
+  #Instance methods list
   def self.included(base)
     base.extend(ClassMethods)
   end
 
+  def init_instance_classifier(&block)
+    self.instance_eval(&block)
+    @dataset.setClassIndex(@class_index)
+    build_classifier(@dataset)
+  end
+
+  def set_data(data)
+    @dataset = data 
+  end
+
+  def set_class_index(class_index)
+    @class_index = class_index 
+  end
+
   def set_options(options)
-  	options_inst = Utils.splitOptions(options)
-		setOptions(options_inst)
+    options_inst = Utils.splitOptions(options)
+    setOptions(options_inst)
   end
 
-	def list_options
-		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
-	end
+  def list_options
+    listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
+  end
 
-	def description
+  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
+
+  def cross_validate(fold)
+    eval = Weka::Classifier::Evaluation.new self.class.data
+    eval.crossValidateModel(self.class.ancestors[2].new, self.class.data, fold.to_java(:int), Random.new(1))
+    eval.summary
+  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

@@ -6,16 +6,81 @@ module Weka
 		module Lazy
 
       java_import 'weka.classifiers.lazy.KStar' 
+      java_import 'weka.classifiers.lazy.LWL' 
+      java_import 'weka.classifiers.lazy.LBR'
+      java_import 'weka.classifiers.lazy.IB1'
+      java_import 'weka.classifiers.lazy.IBk'
 
 			class KStar
 				include Lazy_utils
 				class Base < KStar
-					def initialize
-						super
-            init_lazy
-					end
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
 				end
 			end
+
+      class LWL
+        include Lazy_utils
+        class Base < LWL
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class LBR
+        include Lazy_utils
+        class Base < LBR
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class IB1
+        include Lazy_utils
+        class Base < IB1
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class IBk
+        include Lazy_utils
+        class Base < IBk
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
     end
   end
 end

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

@@ -1,45 +1,65 @@
 #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"
+  java_import "weka.core.Utils"
 
   def init_lazy
-  	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)
+    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
 
-	#Instance methods list
+  #Instance methods list
   def self.included(base)
     base.extend(ClassMethods)
   end
 
+  def init_instance_classifier(&block)
+    self.instance_eval(&block)
+    @dataset.setClassIndex(@class_index)
+    build_classifier(@dataset)
+  end
+
+  def set_data(data)
+    @dataset = data 
+  end
+
+  def set_class_index(class_index)
+    @class_index = class_index 
+  end
+
   def set_options(options)
-  	options_inst = Utils.splitOptions(options)
-		setOptions(options_inst)
+    options_inst = Utils.splitOptions(options)
+    setOptions(options_inst)
   end
 
-	def list_options
-		listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
-	end
+  def list_options
+    listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
+  end
 
-	def description
+  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
+
+  def cross_validate(fold)
+    eval = Weka::Classifier::Evaluation.new self.class.data
+    eval.crossValidateModel(self.class.ancestors[2].new, self.class.data, fold.to_java(:int), Random.new(1))
+    eval.summary
+  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