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-rw-r--r--lib/model.rb15
1 files changed, 8 insertions, 7 deletions
diff --git a/lib/model.rb b/lib/model.rb
index 98433d0..227d4d3 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -74,14 +74,8 @@ module OpenTox
neighbors = []
compounds.each_with_index do |compound,c|
t = Time.new
- database_activities = training_dataset.values(compound,prediction_feature)
- if use_database_values and database_activities and !database_activities.empty?
- database_activities = database_activities.first if database_activities.size == 1
- predictions << {:compound => compound, :value => database_activities, :confidence => "measured", :warning => "Compound #{compound.smiles} occurs in training dataset with activity '#{database_activities}'."}
- next
- end
- neighbors = compound.send(neighbor_algorithm, neighbor_algorithm_parameters)
+ neighbors = compound.send(neighbor_algorithm, neighbor_algorithm_parameters)
# add activities
# TODO: improve efficiency, takes 3 times longer than previous version
neighbors.collect! do |n|
@@ -90,6 +84,13 @@ module OpenTox
acts.empty? ? nil : n << acts
end
neighbors.compact! # remove neighbors without training activities
+
+ database_activities = training_dataset.values(compound,prediction_feature)
+ if use_database_values and database_activities and !database_activities.empty?
+ database_activities = database_activities.first if database_activities.size == 1
+ predictions << {:compound => compound, :value => database_activities, :confidence => "measured", :warning => "Compound #{compound.smiles} occurs in training dataset with activity '#{database_activities}'."}
+ next
+ end
predictions << Algorithm.run(prediction_algorithm, compound, {:neighbors => neighbors,:training_dataset_size => training_dataset.data_entries.size})
=begin
# TODO scaled dataset for physchem