bio-band 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bio-band.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-band"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["arrigonialberto86"]
-  s.date = "2013-07-27"
+  s.date = "2013-07-30"
   s.description = "Data mining and machine learning algorithms for JRuby "
   s.email = "arrigonialberto86@gmail.com"
   s.executables = ["bio-band"]
@@ -62,6 +62,8 @@ Gem::Specification.new do |s|
     "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/rules/rules.rb ",
+    "lib/bio-band/weka/classifiers/rules/rules_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",

data/features/step_definitions/weka_clustering.rb

@@ -27,4 +27,8 @@ end
 
 Then(/^I want to report result statistics$/) do
   puts @clustered
+end
+
+Then(/^I want to use Weka clustering cross\-validation$/) do
+  puts @clustered.validate
 end

data/features/weka_clustering.feature

@@ -10,5 +10,6 @@ Feature: Weka dataset clustering
     And I want to set K = "4" as K-means option
     And I want to perform clustering on the parsed dataset
     And I want to report result statistics 
+    And I want to use Weka clustering cross-validation
 
 

data/lib/bio-band/apache/stat/regression.rb

@@ -13,6 +13,7 @@ module Apache
         obj = SimpleRegression.new
         obj.addData(data)
         return obj
+        # add Jruby methods for regression analysis
       end
 
 

data/lib/bio-band/weka.rb

@@ -1,11 +1,12 @@
 require 'bio-band/weka/db/db'
-require 'bio-band/weka/filters/unsupervised/attribute/attribute.rb'
-require 'bio-band/weka/filters/unsupervised/instance/instance.rb'
-require 'bio-band/weka/filters/supervised/instance/instance.rb'
-require 'bio-band/weka/filters/supervised/attribute/attribute.rb'
-require 'bio-band/weka/classifiers/bayes/bayes.rb'
-require 'bio-band/weka/classifiers/evaluation.rb'
-require 'bio-band/weka/classifiers/functions/functions.rb'
-require 'bio-band/weka/classifiers/trees/trees.rb'
-require 'bio-band/weka/classifiers/lazy/lazy.rb'
-require 'bio-band/weka/clusterers/clusterers.rb'
+require 'bio-band/weka/filters/unsupervised/attribute/attribute'
+require 'bio-band/weka/filters/unsupervised/instance/instance'
+require 'bio-band/weka/filters/supervised/instance/instance'
+require 'bio-band/weka/filters/supervised/attribute/attribute'
+require 'bio-band/weka/classifiers/bayes/bayes'
+require 'bio-band/weka/classifiers/evaluation'
+require 'bio-band/weka/classifiers/functions/functions'
+require 'bio-band/weka/classifiers/trees/trees'
+require 'bio-band/weka/classifiers/lazy/lazy'
+require 'bio-band/weka/classifiers/rules/rules'
+require 'bio-band/weka/clusterers/clusterers'

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

@@ -1,12 +1,13 @@
 module Weka
 	module Classifier
 		java_import 'weka.classifiers.Evaluation'
+    java_import 'java.util.Random'
 
 		class Evaluation
 			def summary
 				puts toSummaryString
 			end
-
 		end
+    
 	end
 end

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

@@ -0,0 +1,32 @@
+$:.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"
+
+      class DecisionTable
+        include Rules_utils
+        class Base < DecisionTable
+          def initialize
+            super
+            init_rules
+          end
+        end
+      end
+
+      class DTNB
+        include Rules_utils
+        class Base < DTNB
+          def initialize
+            super
+            init_rules
+          end
+        end
+      end
+
+    end
+  end
+end

data/lib/bio-band/weka/classifiers/rules/rules_utils.rb

@@ -0,0 +1,45 @@
+#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"
+
+  def init_rules
+    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 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

@@ -5,6 +5,7 @@ module Weka
 	module Classifier
 		module Trees
       java_import 'weka.classifiers.trees.J48'
+      java_import 'weka.classifiers.trees.FT'
       java_import 'weka.classifiers.trees.RandomForest'
 
       class FT

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

@@ -5,6 +5,17 @@ module Weka
 	module Clusterer
     java_import 'weka.clusterers.SimpleKMeans'
     java_import 'weka.clusterers.FarthestFirst'
+    java_import 'weka.clusterers.EM'
+
+    class EM
+      include Clusterer_utils
+      class Base < EM
+        def initialize
+          super
+          init_clusterer
+        end
+      end
+    end
 
     class SimpleKMeans
       include Clusterer_utils

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

@@ -2,6 +2,7 @@
 #to inherit the following methods (instance and class methods)
 module Clusterer_utils
 	java_import "weka.core.Utils"
+	java_import "weka.clusterers.ClusterEvaluation"
 
 	def init_clusterer
     set_options(self.class.options) if self.class.options 
@@ -36,6 +37,14 @@ module Clusterer_utils
     get_capabilities.to_s
   end
 
+  # 'data' is an Instances class object
+ 	def validate
+ 		eval = ClusterEvaluation.new
+ 		eval.setClusterer(self)
+ 		eval.evaluateClusterer(self.class.data)
+ 		eval.clusterResultsToString
+ 	end 
+
 	#Class methods module
 	module ClassMethods
 		

metadata

@@ -2,14 +2,14 @@
 name: bio-band
 version: !ruby/object:Gem::Version
   prerelease:
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - arrigonialberto86
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2013-07-27 00:00:00.000000000 Z
+date: 2013-07-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -254,6 +254,8 @@ files:
 - 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/rules/rules.rb '
+- lib/bio-band/weka/classifiers/rules/rules_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