Added conf_stdev switch

2 files changed, 6 insertions, 4 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 22768cc..4a34337 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -228,7 +228,7 @@ module OpenTox
           transformer = eval("OpenTox::Algorithm::Transform::#{params[:transform]["class"]}.new ([#{prediction}], #{params[:transform]["offset"]})")
           prediction = transformer.values[0]
           LOGGER.debug "Prediction is: '" + prediction.to_s + "'."
-          params[:conf_stdev] = "false" if params[:conf_stdev].nil?
+          params[:conf_stdev] = false if params[:conf_stdev].nil?
           confidence = get_confidence({:sims => sims, :acts => acts, :neighbors => params[:neighbors], :conf_stdev => params[:conf_stdev]})
           {:prediction => prediction, :confidence => confidence}
         rescue Exception => e
@@ -339,7 +339,7 @@ module OpenTox
           transformer = eval("OpenTox::Algorithm::Transform::#{params[:transform]["class"]}.new ([#{prediction}], #{params[:transform]["offset"]})")
           prediction = transformer.values[0]
           LOGGER.debug "Prediction is: '" + prediction.to_s + "'."
-          params[:conf_stdev] = "false" if params[:conf_stdev].nil?
+          params[:conf_stdev] = false if params[:conf_stdev].nil?
           confidence = get_confidence({:sims => sims, :acts => acts, :neighbors => params[:neighbors], :conf_stdev => params[:conf_stdev]})
           {:prediction => prediction, :confidence => confidence}
         rescue Exception => e
@@ -517,7 +517,7 @@ module OpenTox
       # @param[Hash] Required keys: :sims, :acts, :neighbors, :conf_stdev
       # @return[Float] Confidence
       def self.get_confidence(params)
-        if params[:conf_stdev] == "true"
+        if params[:conf_stdev]
           sim_median = Algorithm.median(params[:sims])
           if sim_median.nil?
             confidence = nil
diff --git a/lib/model.rb b/lib/model.rb
index fe7f895..0f1cc22 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -91,7 +91,7 @@ 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
+      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
 
       def initialize(uri=nil)
 
@@ -118,6 +118,7 @@ module OpenTox
         @min_sim = 0.3
         @prop_kernel = false
         @transform = { "class" => "NOP"  }
+        @conf_stdev = false
 
       end
 
@@ -223,6 +224,7 @@ module OpenTox
                                                           :prop_kernel => @prop_kernel,
                                                           :value_map => @value_map,
                                                           :nr_hits => @nr_hits,
+                                                          :conf_stdev => @conf_stdev,
                                                           :transform => @transform } ) ")
 
           value_feature_uri = File.join( @uri, "predicted", "value")