From 606858c0f840c5311ce57dcad7e1ede69d494a1b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 12 Jul 2013 18:13:11 +0200
Subject: value type identification/conversion fixed

---
 lib/lazar.rb      | 2 +-
 lib/similarity.rb | 4 ++--
 lib/transform.rb  | 4 ++++
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/lazar.rb b/lib/lazar.rb
index f88c695..f849a48 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -149,7 +149,7 @@ module OpenTox
             # AM: transform to cosine space
             @min_sim = (@min_sim.to_f*2.0-1.0).to_s if @similarity_algorithm =~ /cosine/
             @training_activities = @training_dataset.data_entries.collect{|entry|
-              act = entry[prediction_feature_pos]
+              act = entry[prediction_feature_pos] if entry
               @prediction_feature.feature_type=="classification" ? @prediction_feature.value_map.invert[act] : act
             }
 
diff --git a/lib/similarity.rb b/lib/similarity.rb
index cdac4b8..5f02577 100644
--- a/lib/similarity.rb
+++ b/lib/similarity.rb
@@ -20,8 +20,8 @@ module OpenTox
         size = [ a.size, b.size ].min
         $logger.warn "fingerprints don't have equal size" if a.size != b.size
         (0...size).each { |idx|
-          common_p_sum += [ a[idx], b[idx] ].min
-          all_p_sum += [ a[idx], b[idx] ].max
+          common_p_sum += [ a[idx].to_f, b[idx].to_f ].min
+          all_p_sum += [ a[idx].to_f, b[idx].to_f ].max
         }
         (all_p_sum > 0.0) ? (common_p_sum/all_p_sum) : 0.0
       end
diff --git a/lib/transform.rb b/lib/transform.rb
index cb4fc87..752f448 100644
--- a/lib/transform.rb
+++ b/lib/transform.rb
@@ -242,6 +242,7 @@ module OpenTox
         # Transforms the model
         def transform
           get_matrices # creates @n_prop, @q_prop, @activities from ordered fingerprints
+          puts "MATRIX"
           @ids = (0..((@n_prop.length)-1)).to_a # surviving compounds; become neighbors
 
           if (@model.similarity_algorithm =~ /cosine/)
@@ -276,13 +277,16 @@ module OpenTox
             @q_prop = svd.transform(gsl_q_prop).row(0).to_a
             $logger.debug "S: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}"
           else
+            puts "CONVERT NILS"
             convert_nils # convert nil cells (for tanimoto); leave @n_props, @q_props, @ids untouched
           end
 
           # neighbor calculation
           @ids = [] # surviving compounds become neighbors
           @sims = [] # calculated by neighbor routine
+            puts "NEIGHBORS"
           neighbors
+            puts "NEIGHBORS FINISHED"
           n_prop_tmp = []; @ids.each { |idx| n_prop_tmp << @n_prop[idx] }; @n_prop = n_prop_tmp # select neighbors from matrix
           acts_tmp = []; @ids.each { |idx| acts_tmp << @activities[idx] }; @activities = acts_tmp
 
-- 
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