nimbus 0.3 → 0.4

data/lib/nimbus.rb

@@ -1,13 +1,13 @@
 require 'yaml'
 require 'optparse'
-require 'nimbus/exceptions'
-require 'nimbus/training_set'
-require 'nimbus/configuration'
-require 'nimbus/loss_functions'
-require 'nimbus/individual'
-require 'nimbus/tree'
-require 'nimbus/forest'
-require 'nimbus/application'
+require './lib/nimbus/exceptions'
+require './lib/nimbus/training_set'
+require './lib/nimbus/configuration'
+require './lib/nimbus/loss_functions'
+require './lib/nimbus/individual'
+require './lib/nimbus/tree'
+require './lib/nimbus/forest'
+require './lib/nimbus/application'
 
 module Nimbus
   

data/lib/nimbus/application.rb

@@ -25,7 +25,7 @@ module Nimbus
       nimbus_exception_handling do
         if @config.do_training && @config.load_training_data
           forest = ::Nimbus::Forest.new @config
-          forest.grow if @config.do_training && @config.load_training_data
+          forest.grow
           output_random_forest_file(forest)
           output_training_file_predictions(forest)
         end
@@ -37,7 +37,7 @@ module Nimbus
       @config ||= ::Nimbus::Configuration.new
     end
     
-    # Provide exception handling for the given block.
+    # Provides the default exception handling for the given block.
     def nimbus_exception_handling
       begin
         yield
@@ -55,7 +55,7 @@ module Nimbus
       end
     end
     
-    # Display the error message that caused the exception.
+    # Display an error message that caused a exception.
     def display_error_message(ex)
       Nimbus.error_message "* Nimbus encountered an error! The random forest was not generated *"
       Nimbus.error_message "#{ex.class}: #{ex.message}"

data/lib/nimbus/configuration.rb

@@ -98,7 +98,7 @@ module Nimbus
         @tree_max_branches    = user_config_params['forest']['max_branches'].to_i  if user_config_params['forest']['max_branches']
         @tree_node_min_size   = user_config_params['forest']['node_min_size'].to_i if user_config_params['forest']['node_min_size']
       end
-      
+
       check_configuration
       log_configuration
     end
@@ -110,6 +110,8 @@ module Nimbus
           next if line.strip == ''
           data_feno, data_id, *snp_list = line.strip.split
           raise Nimbus::InputFileError, "Individual ##{data_id} from training set has no value for all #{@tree_SNP_total_count} SNPs" unless snp_list.size == @tree_SNP_total_count
+          raise Nimbus::InputFileError, "There are individuals with no ID, please check data in training file." unless (!data_id.nil? && data_id.strip != '')
+          raise Nimbus::InputFileError, "Individual ##{data_id} has no fenotype value, please check data in training file." unless (!data_feno.nil? && data_feno.strip != '')
           @training_set.individuals[data_id.to_i] = Nimbus::Individual.new(data_id.to_i, data_feno.to_f, snp_list.map{|snp| snp.to_i})
           @training_set.ids_fenotypes[data_id.to_i] = data_feno.to_f
         end

data/lib/nimbus/forest.rb

@@ -40,7 +40,7 @@ module Nimbus
     end
     
     def bag
-      @bag ||= (1..@options.training_set.individuals.size).to_a
+      @bag ||= @options.training_set.all_ids
     end
     
     def acumulate_predictions(preds)

data/lib/nimbus/training_set.rb

@@ -7,6 +7,11 @@ module Nimbus
       @individuals   = individuals
       @ids_fenotypes = ids_fenotypes
     end
+    
+    def all_ids
+      @all_ids ||= @ids_fenotypes.keys
+      @all_ids
+    end
   end
   
 end

metadata

@@ -2,7 +2,7 @@
 name: nimbus
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: "0.3"
+  version: "0.4"
 platform: ruby
 authors: 
 - "Juanjo Baz\xC3\xA1n"
@@ -11,7 +11,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-19 00:00:00 Z
+date: 2011-08-20 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rspec