bio-band 0.1.0 → 0.1.1

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bio-band.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-band"
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["arrigonialberto86"]
-  s.date = "2013-07-25"
+  s.date = "2013-07-27"
   s.description = "Data mining and machine learning algorithms for JRuby "
   s.email = "arrigonialberto86@gmail.com"
   s.executables = ["bio-band"]
@@ -44,7 +44,9 @@ Gem::Specification.new do |s|
     "features/weka_pipeline.feature",
     "lib/bio-band.rb",
     "lib/bio-band/apache.rb",
+    "lib/bio-band/apache/stat/correlation.rb",
     "lib/bio-band/apache/stat/inference.rb",
+    "lib/bio-band/apache/stat/regression.rb",
     "lib/bio-band/core.rb",
     "lib/bio-band/core/parser/parser.rb",
     "lib/bio-band/core/type/apache_matrices.rb",

data/features/support/env.rb

@@ -1,3 +1,3 @@
 $LOAD_PATH << File.expand_path('../../../lib', __FILE__)
 $LOAD_PATH << File.expand_path('../../../resources/', __FILE__)
-require 'ruby_mining'
+require 'bio-band'

data/lib/bio-band/apache.rb

@@ -1 +1,2 @@
 require 'bio-band/apache/stat/inference.rb'
+require 'bio-band/apache/stat/correlation.rb'

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

@@ -0,0 +1,42 @@
+require 'java'
+
+module Apache
+  module Stat
+  	module Correlation
+
+      java_import "org.apache.commons.math3.stat.correlation.Covariance"
+      java_import "org.apache.commons.math3.stat.correlation.PearsonsCorrelation"
+      java_import "org.apache.commons.math3.stat.correlation.SpearmansCorrelation"
+
+      # Calculate covariance between two Numeric arrays
+      # * *Args*    :
+      #   - +Array1+ -> must be a RubyArray.
+      #   - +Array2+ -> must be a RubyArray.
+      def self.covariance(array_1,array_2)
+        obj = Covariance.new
+        result = obj.covariance(array_1.to_java(:double),array_2.to_java(:double))
+        result
+      end
+
+      # Calculate Pearson correlation between two Numeric arrays
+      # * *Args*    :
+      #   - +Array1+ -> must be a RubyArray.
+      #   - +Array2+ -> must be a RubyArray.
+      def self.pearson_correlation(array_1,array_2)
+        obj = PearsonsCorrelation.new
+        result = obj.correlation(array_1.to_java(:double),array_2.to_java(:double))
+        result
+      end
+
+      # Calculate Spearman correlation between two Numeric arrays
+      # * *Args*    :
+      #   - +Array1+ -> must be a RubyArray.
+      #   - +Array2+ -> must be a RubyArray.
+      def self.spearman_correlation(array_1,array_2)
+        obj = SpearmansCorrelation.new
+        result = obj.correlation(array_1.to_java(:double),array_2.to_java(:double))
+        result
+      end
+  	end
+  end
+end

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

@@ -0,0 +1,21 @@
+require 'java'
+
+module Apache
+  module Stat
+  	module Regression
+      java_import "org.apache.commons.math3.stat.regression.SimpleRegression"
+
+      # Create a simple regression model on the input data 
+      # * *Args*    :
+      #   - +vector+ -> must be a multidimensional array
+      def self.simple_regression(vector)
+        data = Core::Utils.bidimensional_to_double vector
+        obj = SimpleRegression.new
+        obj.addData(data)
+        return obj
+      end
+
+
+  	end
+  end
+end

data/lib/bio-band/weka.rb

@@ -1,11 +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'
+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'

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

@@ -15,9 +15,7 @@ module Weka
 				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)
+            init_classifier
 					end
 				end
 			end
@@ -27,9 +25,7 @@ module Weka
 				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)
+            init_classifier
 					end
 				end
 			end
@@ -39,9 +35,7 @@ module Weka
 				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)
+            init_classifier
 					end
 				end
 			end
@@ -51,9 +45,7 @@ module Weka
 				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)
+            init_classifier
 					end
 				end
 			end
@@ -63,9 +55,7 @@ module Weka
 				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)
+            init_classifier
 					end
 				end
 			end

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

@@ -1,8 +1,15 @@
 #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"
 
+  def init_classifier
+    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)

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

@@ -11,9 +11,7 @@ module Weka
         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)
+            init_function
           end
         end
       end

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

@@ -3,6 +3,12 @@
 module Functions_utils
 	java_import "weka.core.Utils"
 
+  def init_function
+    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)

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

@@ -12,9 +12,7 @@ module Weka
 				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)
+            init_lazy
 					end
 				end
 			end

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

@@ -3,6 +3,12 @@
 module Lazy_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)
+  end
+
 	#Instance methods list
   def self.included(base)
     base.extend(ClassMethods)

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

@@ -12,9 +12,7 @@ module Weka
         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)
+            init_tree
           end
         end
       end
@@ -24,9 +22,7 @@ module Weka
         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)
+            init_tree
           end
         end
       end
@@ -36,9 +32,7 @@ module Weka
         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)
+            init_tree
           end
         end
       end

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

@@ -3,6 +3,12 @@
 module Trees_utils
 	java_import "weka.core.Utils"
 
+  def init_tree
+    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)

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

@@ -11,8 +11,7 @@ module Weka
       class Base < SimpleKMeans
         def initialize
           super
-          set_options(self.class.options) if self.class.options 
-          buildClusterer(self.class.data)
+          init_clusterer
         end
       end
     end
@@ -22,8 +21,7 @@ module Weka
       class Base < FarthestFirst
         def initialize
           super
-          set_options(self.class.options) if self.class.options 
-          buildClusterer(self.class.data)
+          init_clusterer
         end
       end
     end

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

@@ -3,6 +3,11 @@
 module Clusterer_utils
 	java_import "weka.core.Utils"
 
+	def init_clusterer
+    set_options(self.class.options) if self.class.options 
+    buildClusterer(self.class.data)
+	end
+
 	#Instance methods list
   def self.included(base)
     base.extend(ClassMethods)

metadata

@@ -2,14 +2,14 @@
 name: bio-band
 version: !ruby/object:Gem::Version
   prerelease:
-  version: 0.1.0
+  version: 0.1.1
 platform: ruby
 authors:
 - arrigonialberto86
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2013-07-25 00:00:00.000000000 Z
+date: 2013-07-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -236,7 +236,9 @@ files:
 - features/weka_pipeline.feature
 - lib/bio-band.rb
 - lib/bio-band/apache.rb
+- lib/bio-band/apache/stat/correlation.rb
 - lib/bio-band/apache/stat/inference.rb
+- lib/bio-band/apache/stat/regression.rb
 - lib/bio-band/core.rb
 - lib/bio-band/core/parser/parser.rb
 - lib/bio-band/core/type/apache_matrices.rb