bio-band 0.1.2 → 0.1.3

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

@@ -7,6 +7,32 @@ module Weka
       java_import 'weka.classifiers.trees.J48'
       java_import 'weka.classifiers.trees.FT'
       java_import 'weka.classifiers.trees.RandomForest'
+      java_import 'weka.classifiers.trees.BFTree'
+      java_import 'weka.classifiers.trees.J48graft'
+      java_import 'weka.classifiers.trees.LADTree'
+      java_import 'weka.classifiers.trees.LMT'
+      java_import 'weka.classifiers.trees.M5P'
+      java_import 'weka.classifiers.trees.RandomTree'
+
+      class ADTree
+        include Trees_utils
+        class Base < ADTree
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
+
+      class BFTree
+        include Trees_utils
+        class Base < BFTree
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
 
       class FT
         include Trees_utils
@@ -28,6 +54,36 @@ module Weka
         end
       end
 
+      class J48graft
+        include Trees_utils
+        class Base < J48graft
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
+
+      class LMT
+        include Trees_utils
+        class Base < LMT
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
+
+      class M5P
+        include Trees_utils
+        class Base < M5P
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
+
       class RandomForest
         include Trees_utils
         class Base < RandomForest
@@ -38,6 +94,16 @@ module Weka
         end
       end
 
+      class RandomTree
+        include Trees_utils
+        class Base < RandomTree
+          def initialize
+            super
+            init_tree
+          end
+        end
+      end
+
 		end
   end
 end

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

@@ -1,7 +1,7 @@
-#This module is used by the 'trees' classifiers from 'trees.rb' 
-#to inherit the following methods (instance and class methods)
+# 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"
+  java_import "weka.core.Utils"
 
   def init_tree
     set_options(self.class.options) if self.class.options 
@@ -9,39 +9,59 @@ module Trees_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.each {|key| puts "#{key.synopsis} #{key.description}"}
+  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/clusterers/clusterers.rb

@@ -6,6 +6,19 @@ module Weka
     java_import 'weka.clusterers.SimpleKMeans'
     java_import 'weka.clusterers.FarthestFirst'
     java_import 'weka.clusterers.EM'
+    java_import 'weka.clusterers.XMeans'
+    java_import 'weka.clusterers.HierarchicalClusterer'
+    java_import 'weka.clusterers.Cobweb'     
+
+    class Cobweb
+      include Clusterer_utils
+      class Base < Cobweb
+        def initialize
+          super
+          init_clusterer
+        end
+      end
+    end
 
     class EM
       include Clusterer_utils
@@ -17,6 +30,17 @@ module Weka
       end
     end
 
+    class HierarchicalClusterer
+      include Clusterer_utils
+      class Base < HierarchicalClusterer
+        def initialize
+          super
+          init_clusterer
+        end
+      end
+    end
+
+
     class SimpleKMeans
       include Clusterer_utils
       class Base < SimpleKMeans
@@ -37,5 +61,15 @@ module Weka
       end
     end
 
+    class XMeans
+      include Clusterer_utils
+      class Base < XMeans
+        def initialize
+          super
+          init_clusterer
+        end
+      end
+    end
+
 	end
 end

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

@@ -20,9 +20,7 @@ module Clusterer_utils
   end
 
 	def list_options
-    options = ''
-		listOptions.each {|key| options="#{options}\n#{key.synopsis} #{key.description}"}
-    options
+		listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
 	end
 
 	def description
@@ -38,7 +36,7 @@ module Clusterer_utils
   end
 
   # 'data' is an Instances class object
- 	def validate
+ 	def evaluate
  		eval = ClusterEvaluation.new
  		eval.setClusterer(self)
  		eval.evaluateClusterer(self.class.data)

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

@@ -1,74 +1,74 @@
 require 'java'
 
 module Weka
-	module Db
-		java_import 'weka.core.Instances'
-		java_import 'weka.core.converters.DatabaseLoader'
-		java_import 'weka.core.converters.DatabaseSaver'
+  module Db
+    java_import 'weka.core.Instances'
+    java_import 'weka.core.converters.DatabaseLoader'
+    java_import 'weka.core.converters.DatabaseSaver'
 
-		# Query data from a MySQL database
-		# * *Args*    :
-      	#   - +db_url+ -> The database URL
-      	#   - +user+ -> User name
-      	#   - +psw+ -> Password
-      	#   - +quey+ -> A query to submit
-		def Db.query_mysql(db_url,user,psw,query)
-			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
-				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
-					f.each_line do |line|
-						out.write line
-					end
-				end
-			end
-		    loader = DatabaseLoader.new
-			loader.setSource(db_url,user,psw)
-			loader.setQuery(query)
-			data = loader.getDataSet
-			return data
-		end
+    # Query data from a MySQL database
+    # * *Args*    :
+        #   - +db_url+ -> The database URL
+        #   - +user+ -> User name
+        #   - +psw+ -> Password
+        #   - +quey+ -> A query to submit
+    def Db.query_mysql(db_url,user,psw,query)
+      open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+        open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
+          f.each_line do |line|
+            out.write line
+          end
+        end
+      end
+        loader = DatabaseLoader.new
+      loader.setSource(db_url,user,psw)
+      loader.setQuery(query)
+      data = loader.getDataSet
+      return data
+    end
 
-		# Query data from a PostgreSQL database
-		# * *Args*    :
-      	#   - +db_url+ -> The database URL
-      	#   - +user+ -> User name
-      	#   - +psw+ -> Password
-      	#   - +quey+ -> A query to submit
-		def Db.query_postgresql(db_url,user,psw,query)
-			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
-				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_postgresql'),'r') do |f|
-					f.each_line do |line|
-						out.write line
-					end
-				end
-			end
-		    loader = DatabaseLoader.new
-			loader.setSource(db_url,user,psw)
-			loader.setQuery(query)
-			data = loader.getDataSet
-			return data
-		end
+    # Query data from a PostgreSQL database
+    # * *Args*    :
+        #   - +db_url+ -> The database URL
+        #   - +user+ -> User name
+        #   - +psw+ -> Password
+        #   - +quey+ -> A query to submit
+    def Db.query_postgresql(db_url,user,psw,query)
+      open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+        open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_postgresql'),'r') do |f|
+          f.each_line do |line|
+            out.write line
+          end
+        end
+      end
+        loader = DatabaseLoader.new
+      loader.setSource(db_url,user,psw)
+      loader.setQuery(query)
+      data = loader.getDataSet
+      return data
+    end
 
-		# Save an Instances class object to a Mysql database
-		# * *Args*    :
-      	#   - +db_url+ -> The database URL
-      	#   - +user+ -> User name
-      	#   - +psw+ -> Password
-      	#   - +data+ -> An Instances class object 
-      	#   - +table+ -> The destination table in the database     	
-		def Db.save_to_mysql(db_url,user,psw,data,table)
-			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
-				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
-					f.each_line do |line|
-						out.write line
-					end
-				end
-			end
-			saver = DatabaseSaver.new
-			saver.setDestination(db_url,user,psw)
-			saver.setTableName(table)
-			saver.setRelationForTableName(false)
-			saver.setInstances(data)
-			saver.writeBatch
-		end
-	end
+    # Save an Instances class object to a Mysql database
+    # * *Args*    :
+        #   - +db_url+ -> The database URL
+        #   - +user+ -> User name
+        #   - +psw+ -> Password
+        #   - +data+ -> An Instances class object 
+        #   - +table+ -> The destination table in the database      
+    def Db.save_to_mysql(db_url,user,psw,data,table)
+      open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+        open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
+          f.each_line do |line|
+            out.write line
+          end
+        end
+      end
+      saver = DatabaseSaver.new
+      saver.setDestination(db_url,user,psw)
+      saver.setTableName(table)
+      saver.setRelationForTableName(false)
+      saver.setInstances(data)
+      saver.writeBatch
+    end
+  end
 end

data/lib/bio-band/weka/filters/supervised/attribute/attribute.rb

@@ -8,16 +8,46 @@ module Weka
   		module Attribute
   			java_import "weka.core.Utils"
   			java_import "weka.filters.Filter"
+
+        java_import "weka.filters.supervised.attribute.AddClassification"
+        java_import "weka.filters.supervised.attribute.ClassOrder"
    			java_import "weka.filters.supervised.attribute.AttributeSelection"
+        java_import "weka.filters.supervised.attribute.NominalToBinary"
+        java_import "weka.filters.supervised.attribute.PLSFilter"
         java_import "weka.filters.supervised.attribute.Discretize"
 
+        class AddClassification  
+          include Supervised_Util
+        end
+
    			class AttributeSelection
           include Supervised_Util
-   			end
+          java_alias :evaluator, :setEvaluator, [Java::Weka.attributeSelection.ASEvaluation]
+          java_alias :search, :setSearch, [Java::Weka.attributeSelection.ASSearch]
+  			end
+
+        class ClassOrder
+          include Supervised_Util
+        end
 
         class Discretize  
           include Supervised_Util
         end
+
+        class NominalToBinary  
+          include Supervised_Util
+        end
+
+        class PLSFilter  
+          include Supervised_Util
+        end
+
+        Weka::Filter::Supervised::Attribute::AttributeSelection.__persistent__ = true
+        Weka::Filter::Supervised::Attribute::Discretize.__persistent__ = true
+        Weka::Filter::Supervised::Attribute::AddClassification.__persistent__ = true
+        Weka::Filter::Supervised::Attribute::ClassOrder.__persistent__ = true
+        Weka::Filter::Supervised::Attribute::NominalToBinary.__persistent__ = true
+        Weka::Filter::Supervised::Attribute::PLSFilter.__persistent__ = true
   			
   		end
   	end

data/lib/bio-band/weka/filters/supervised/supervised_utils.rb

@@ -1,32 +1,34 @@
 module Supervised_Util
-	java_import "weka.core.Utils"
-	java_import "weka.filters.Filter"
-
-	#Instance methods list
-	def filter_options
-		begin
-			listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
-		rescue
-			puts  "Sorry, list option is available for this filter"
-		end
-	end
-
-	def set_filter_options(options_string)
-		options = Utils.splitOptions(options_string)
-		setOptions(options)
-	end
-
-	def set_data(instances)
-		setInputFormat(instances)
-		@input = instances
-	end
-
-	def description
-    begin; puts globalInfo; rescue; NoMethodError; puts "Sorry, no description available for this filter"; end
-	end
-
-	def use
-		Filter.useFilter(@input,self)
-	end
-
-end
+  java_import "weka.core.Utils"
+  java_import "weka.filters.Filter"
+
+  #Instance methods list
+  def options_list
+    listOptions.map {|key| "#{key.synopsis} #{key.description}"}.join("\n")
+  end
+
+  def filter_options(options_string)
+    options = Utils.splitOptions(options_string)
+    setOptions(options)
+  end
+
+  def data(instances)
+    setInputFormat(instances)
+    @input = instances
+  end
+
+  def description
+    globalInfo
+  end
+
+  def use
+    Filter.useFilter(@input,self)
+  end
+
+  def set(&block)
+    self.instance_eval(&block)
+  end
+
+end
+
+