From 47140182b4b40573ecf199122e3687f885c5381d Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 17 Jul 2013 14:50:35 +0200
Subject: uri objects fixed in ntriples serialsiation

---
 lib/neighbors.rb | 1 -
 lib/transform.rb | 4 ----
 2 files changed, 5 deletions(-)

diff --git a/lib/neighbors.rb b/lib/neighbors.rb
index 285afa8..c77325a 100644
--- a/lib/neighbors.rb
+++ b/lib/neighbors.rb
@@ -69,7 +69,6 @@ module OpenTox
       # @param [Hash] params Keys `:props, :activities, :sims, :min_train_performance` are required
       # @return [Numeric] A prediction value.
       def self.local_svm_regression(params)
-        puts "SVM"
 
         confidence = 0.0
         prediction = nil
diff --git a/lib/transform.rb b/lib/transform.rb
index 752f448..cb4fc87 100644
--- a/lib/transform.rb
+++ b/lib/transform.rb
@@ -242,7 +242,6 @@ 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/)
@@ -277,16 +276,13 @@ 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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