Ordered addition of entries to fminer

1 files changed, 26 insertions, 10 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index b921b9c..64fa508 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -75,10 +75,26 @@ module OpenTox
         end
       end
 
-      def add_fminer_data(fminer_instance, value_map)
+      def add_fminer_data(fminer_instance, value_map, prepare_backend=true)
+
+
+        # detect nr duplicates per compound
+        compound_sizes = {}
+        @training_dataset.compounds.each do |compound|
+          entries=@training_dataset.data_entries[compound]
+          entries.each do |feature, values|
+            compound_sizes[compound] || compound_sizes[compound] = []
+            compound_sizes[compound] << values.size
+          end
+          compound_sizes[compound].uniq!
+          raise "Inappropriate data for fminer" if compound_sizes[compound].size > 1
+          compound_sizes[compound] = compound_sizes[compound][0] # integer instead of array
+        end
 
         id = 1 # fminer start id is not 0
-        @training_dataset.data_entries.each do |compound,entry| #order of compounds does not influence result
+
+        @training_dataset.compounds.each do |compound|
+          entry=@training_dataset.data_entries[compound]
           begin
             smiles = OpenTox::Compound.smiles(compound.to_s)
           rescue
@@ -92,29 +108,29 @@ module OpenTox
 
           entry.each do |feature,values|
             if feature == @prediction_feature.uri
-              values.each do |value|
-                if value.nil? 
+              (0...compound_sizes[compound]).each { |i|
+                if values[i].nil? 
                   LOGGER.warn "No #{feature} activity for #{compound.to_s}."
                 else
                   if @prediction_feature.feature_type == "classification"
-                    activity= value_map.invert[value].to_i # activities are mapped to 1..n
+                    activity= value_map.invert[values[i]].to_i # activities are mapped to 1..n
                     @db_class_sizes[activity-1].nil? ? @db_class_sizes[activity-1]=1 : @db_class_sizes[activity-1]+=1 # AM effect
                   elsif @prediction_feature.feature_type == "regression"
-                    activity= value.to_f 
+                    activity= values[i].to_f 
                   end
                   begin
-                    fminer_instance.AddCompound(smiles,id)
-                    fminer_instance.AddActivity(activity, id)
+                    fminer_instance.AddCompound(smiles,id) if prepare_backend
+                    fminer_instance.AddActivity(activity, id) if prepare_backend
                     @all_activities[id]=activity # DV: insert global information
                     @compounds[id] = compound
                     @smi[id] = smiles
                     id += 1
                   rescue Exception => e
-                    LOGGER.warn "Could not add " + smiles + "\t" + value.to_s + " to fminer"
+                    LOGGER.warn "Could not add " + smiles + "\t" + values[i].to_s + " to fminer"
                     LOGGER.warn e.backtrace
                   end
                 end
-              end
+              }
             end
           end
         end