From baffedfc7543cfc8a90fc185fc91f2748ce94528 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 25 May 2011 10:24:13 +0200
Subject: Fixed add_neighbor

---
 lib/model.rb | 25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

(limited to 'lib/model.rb')

diff --git a/lib/model.rb b/lib/model.rb
index f5e0410..3d27706 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -338,28 +338,45 @@ module OpenTox
         @prediction_dataset
       end
 
+      # Calculate the propositionalization matrix aka instantiation matrix (0/1 entries for features)
+#      def get_prop_matrix
+#        matrix = Array.new
+#        begin 
+#        @neighbors.each do |n|
+#          row = []
+#          @features.each do |f|
+#            row << @fingerprints[n].include?(f) ? 0.0 : @p_values[f]
+#          end
+#          matrix << row
+#        end
+#        rescue Exception => e
+#          LOGGER.debug "get_prop_matrix failed with '" + $! + "'"
+#        end
+#        matrix
+#      end
+
       # Find neighbors and store them as object variable, access only a subset of compounds for that.
       def neighbors_balanced(s, l, start, offset)
         @compound_features = eval("#{@feature_calculation_algorithm}(@compound,@features)") if @feature_calculation_algorithm
         @neighbors = []
           [ l[start, offset ] , s ].flatten.each do |training_compound| # AM: access only a balanced subset
             training_features = @fingerprints[training_compound]
-            add_neighbor training_features
+            add_neighbor training_features, training_compound
         end
 
       end
 
-      # Find neighbors and store them as object variable.
+      # Find neighbors and store them as object variable, access all compounds for that.
       def neighbors
         @compound_features = eval("#{@feature_calculation_algorithm}(@compound,@features)") if @feature_calculation_algorithm
         @neighbors = []
         @fingerprints.each do |training_compound,training_features| # AM: access all compounds
-           add_neighbor training_features
+           add_neighbor training_features, training_compound
         end
       end
 
       # Adds a neighbor to @neighbors if it passes the similarity threshold.
-      def add_neighbor(training_features)
+      def add_neighbor(training_features, training_compound)
         sim = eval("#{@similarity_algorithm}(@compound_features,training_features,@p_values)")
         if sim > @min_sim
           @activities[training_compound].each do |act|
-- 
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