bio-band 0.1.2 → 0.1.3

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

@@ -0,0 +1,190 @@
+$:.unshift File.dirname(__FILE__)
+require 'mi_utils'
+
+module Weka
+	module Classifier
+		module Mi
+      java_import 'weka.classifiers.mi.CitationKNN'
+      java_import 'weka.classifiers.mi.MDD'
+      java_import 'weka.classifiers.mi.MIBoost'
+      java_import 'weka.classifiers.mi.MIDD'
+      java_import 'weka.classifiers.mi.MIEMDD'
+      java_import 'weka.classifiers.mi.MILR'
+      java_import 'weka.classifiers.mi.MINND'
+      java_import 'weka.classifiers.mi.MIOptimalBall'
+      java_import 'weka.classifiers.mi.MISMO'
+      java_import 'weka.classifiers.mi.MISVM'
+      java_import 'weka.classifiers.mi.MIWrapper'
+      java_import 'weka.classifiers.mi.SimpleMI'
+
+      class CitationKNN
+        include Mi_utils
+        class Base < CitationKNN
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MIEMDD
+        include Mi_utils
+        class Base < MIEMDD
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MILR
+        include Mi_utils
+        class Base < MILR
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MINND
+        include Mi_utils
+        class Base < MINND
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MIOptimalBall
+        include Mi_utils
+        class Base < MIOptimalBall
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MISMO
+        include Mi_utils
+        class Base < MISMO
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MISVM
+        include Mi_utils
+        class Base < MISVM
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MIWrapper
+        include Mi_utils
+        class Base < MIWrapper
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MDD
+        include Mi_utils
+        class Base < MDD
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MIBoost
+        include Mi_utils
+        class Base < MIBoost
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class MIDD
+        include Mi_utils
+        class Base < MIDD
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class SimpleMI
+        include Mi_utils
+        class Base < SimpleMI
+          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/mi/mi_utils.rb

@@ -0,0 +1,65 @@
+#This module is used by the 'mi' classifiers from 'mi.rb' 
+#to inherit the following methods (instance and class methods)
+module Mi_utils
+  java_import "weka.core.Utils"
+
+  def init_mi
+    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
+  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)
+  end
+
+  def list_options
+    listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+  end
+
+  def description
+    puts globalInfo
+  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/rules/rules.rb

@@ -0,0 +1,190 @@
+$:.unshift File.dirname(__FILE__)
+require 'rules_utils'
+
+module Weka
+  module Classifier
+    module Rules
+      java_import "weka.classifiers.rules.DecisionTable" 
+      java_import "weka.classifiers.rules.DTNB"
+      java_import "weka.classifiers.rules.JRip"
+      java_import "weka.classifiers.rules.M5Rules"
+      java_import "weka.classifiers.rules.NNge"
+      java_import "weka.classifiers.rules.OneR"
+      java_import "weka.classifiers.rules.PART"
+      java_import "weka.classifiers.rules.Prism"
+      java_import "weka.classifiers.rules.Ridor"
+      java_import "weka.classifiers.rules.Rule"
+      java_import "weka.classifiers.rules.RuleStats"
+      java_import "weka.classifiers.rules.ZeroR"
+
+      class DecisionTable
+        include Rules_utils
+        class Base < DecisionTable
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class DTNB
+        include Rules_utils
+        class Base < DTNB
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class JRip
+        include Rules_utils
+        class Base < JRip
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class M5Rules
+        include Rules_utils
+        class Base < M5Rules
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class NNge
+        include Rules_utils
+        class Base < NNge
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class OneR
+        include Rules_utils
+        class Base < OneR
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class PART
+        include Rules_utils
+        class Base < PART
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class Prism
+        include Rules_utils
+        class Base < Prism
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class Ridor
+        include Rules_utils
+        class Base < Ridor
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class Rule
+        include Rules_utils
+        class Base < Rule
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class RuleStats
+        include Rules_utils
+        class Base < RuleStats
+          def initialize(&block)
+            super
+            if block_given?
+              init_instance_classifier(&block)
+            else
+              init_classifier  
+            end
+          end
+        end
+      end
+
+      class ZeroR
+        include Rules_utils
+        class Base < ZeroR
+          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/rules/rules_utils.rb

@@ -1,7 +1,7 @@
 #This module is used by the 'rules' classifiers from 'rules.rb' 
 #to inherit the following methods (instance and class methods)
 module Rules_utils
-	java_import "weka.core.Utils"
+  java_import "weka.core.Utils"
 
   def init_rules
     set_options(self.class.options) if self.class.options 
@@ -9,37 +9,57 @@ module Rules_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