Merge branch 'reg_min_max' into development

3 files changed, 13 insertions, 2 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 9a5ff01..0ba6a83 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -330,6 +330,7 @@ module OpenTox
           prediction = mlr( {:n_prop => props[0], :q_prop => props[1], :sims => sims, :acts => acts} )
           transformer = eval("OpenTox::Algorithm::Transform::#{params[:transform]["class"]}.new ([#{prediction}], #{params[:transform]["offset"]})")
           prediction = transformer.values[0]
+          prediction = nil if prediction.infinite? || params[:prediction_min_max][1] < prediction || params[:prediction_min_max][0] > prediction  
           LOGGER.debug "Prediction is: '" + prediction.to_s + "'."
           params[:conf_stdev] = false if params[:conf_stdev].nil?
           confidence = get_confidence({:sims => sims, :acts => acts, :neighbors => params[:neighbors], :conf_stdev => params[:conf_stdev]})
@@ -441,6 +442,7 @@ module OpenTox
           prediction = props.nil? ? local_svm(acts, sims, "nu-svr", params) : local_svm_prop(props, acts, "nu-svr")
           transformer = eval("OpenTox::Algorithm::Transform::#{params[:transform]["class"]}.new ([#{prediction}], #{params[:transform]["offset"]})")
           prediction = transformer.values[0]
+          prediction = nil if prediction.infinite? || params[:prediction_min_max][1] < prediction || params[:prediction_min_max][0] > prediction  
           LOGGER.debug "Prediction is: '" + prediction.to_s + "'."
           params[:conf_stdev] = false if params[:conf_stdev].nil?
           confidence = get_confidence({:sims => sims, :acts => acts, :neighbors => params[:neighbors], :conf_stdev => params[:conf_stdev]})
diff --git a/lib/model.rb b/lib/model.rb
index 26c42a5..ff0ce0e 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -102,7 +102,7 @@ module OpenTox
       include Algorithm
       include Model
 
-      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel, :value_map, :nr_hits, :transform, :conf_stdev
+      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel, :value_map, :nr_hits, :transform, :conf_stdev, :prediction_min_max
 
       def initialize(uri=nil)
 
@@ -120,6 +120,7 @@ module OpenTox
         @p_values = {}
         @fingerprints = {}
         @value_map = {}
+        @prediction_min_max = [] 
 
         @feature_calculation_algorithm = "Substructure.match"
         @similarity_algorithm = "Similarity.tanimoto"
@@ -224,6 +225,13 @@ module OpenTox
           } )
         end
 
+        if OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type == "regression"
+          all_activities = [] 
+          all_activities = @activities.values.flatten.collect! { |i| i.to_f }
+          @prediction_min_max[0] = (all_activities.to_scale.min/2)
+          @prediction_min_max[1] = (all_activities.to_scale.max*2)
+        end
+
         unless database_activity(subjectid) # adds database activity to @prediction_dataset
 
           neighbors
@@ -237,6 +245,7 @@ module OpenTox
                                                           :value_map => @value_map,
                                                           :nr_hits => @nr_hits,
                                                           :conf_stdev => @conf_stdev,
+                                                          :prediction_min_max => @prediction_min_max,
                                                           :transform => @transform } ) ")
 
           value_feature_uri = File.join( @uri, "predicted", "value")
diff --git a/lib/serializer.rb b/lib/serializer.rb
index 03dcf1f..d53f7fb 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -192,7 +192,7 @@ module OpenTox
         @object[metadata[OT.featureDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] }
         @object[metadata[OT.trainingDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] }
         @object[metadata[OT.dependentVariables]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] }
-        metadata[OT.predictedVariables].each{|feature| @object[feature] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] }}
+        metadata[OT.predictedVariables].each{|feature| @object[feature] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }]}} unless metadata[OT.predictedVariables].nil?
         # TODO: add algorithms from parameters
         @object["http://ot-dev.in-silico.ch/algorithm/fminer/bbrc"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] }
         @object["http://ot-dev.in-silico.ch/algorithm/fminer/last"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] }