From f13763a8505ad997739b65d7cfcd804411ff9c77 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Thu, 26 May 2011 10:56:31 +0200
Subject: unify access to classification feature domain, replace methode
 feature_values with accept_values

---
 lib/dataset.rb | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

(limited to 'lib')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 4dc4296..fc7c263 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -167,16 +167,13 @@ module OpenTox
       @features
     end
 
-    def feature_classes(feature, subjectid=nil)
-      if Feature.find(feature, subjectid).feature_type == "classification"
-        classes = []
-        @data_entries.each do |c,e|
-          e[feature].each { |v| classes << v.to_s }
-        end
-        classes.uniq.sort
-      else
-        nil
-      end
+    # returns the accept_values of a feature, i.e. the classification domain / all possible feature values 
+    # @param [String] feature the URI of the feature
+    # @return [Array] return array with strings, nil if value is not set (e.g. when feature is numeric)
+    def accept_values(feature)
+      accept_values = features[feature][OT.acceptValue]
+      accept_values.sort if accept_values
+      accept_values
     end
 
     # Detect feature type(s) in the dataset
-- 
cgit v1.2.3


From f507227fd4efff3c8b32b2a8c8f2860af2546e3b Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 26 May 2011 13:11:32 +0200
Subject: Hotfix: Switch to balanced mode.

---
 lib/model.rb | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/model.rb b/lib/model.rb
index 139aed8..14471cc 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -176,11 +176,15 @@ module OpenTox
 
         return @prediction_dataset if database_activity(subjectid)
 
-
-       if metadata[RDF.type] == [OTA.ClassificationLazySingleTarget]
+        load_metadata(subjectid)
+        case OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type
+        when "classification"
           # AM: Balancing, see http://www.maunz.de/wordpress/opentox/2011/balanced-lazar
           l = Array.new # larger 
           s = Array.new # smaller fraction
+
+          raise "no fingerprints in model" if @fingerprints.size==0
+
           @fingerprints.each do |training_compound,training_features|
             @activities[training_compound].each do |act|
               case act.to_s
@@ -231,6 +235,7 @@ module OpenTox
           ### END AM balanced predictions
 
         else # regression case: no balancing
+          LOGGER.info "LAZAR: Unbalanced."
           neighbors
           prediction = eval("#{@prediction_algorithm}(@neighbors,{:similarity_algorithm => @similarity_algorithm, :p_values => @p_values})")
         end
-- 
cgit v1.2.3