Comments

18 files changed, 113 insertions, 48 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 86cf472..1a26322 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,11 +1,13 @@
-# algorithm.rb
-# Algorithm library
-# Author: Andreas Maunz
+=begin
+* Name: algorithm.rb
+* Description: General algorithms
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Algorithm
 
-
     # Minimum Frequency
     # @param [Integer] per-mil value
     # return [Integer] min-frequency
diff --git a/lib/algorithm/feature_values.rb b/lib/algorithm/feature_values.rb
index 284fae1..f08dea8 100644
--- a/lib/algorithm/feature_values.rb
+++ b/lib/algorithm/feature_values.rb
@@ -1,6 +1,9 @@
-# feature_values.rb
-# Feature Value library
-# Author: Andreas Maunz
+=begin
+* Name: feature_values.rb
+* Description: Feature value calculation
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Algorithm
diff --git a/lib/algorithm/fminer.rb b/lib/algorithm/fminer.rb
index d190fc0..19fa6aa 100644
--- a/lib/algorithm/fminer.rb
+++ b/lib/algorithm/fminer.rb
@@ -1,6 +1,9 @@
-# fminer.rb
-# Fminer library
-# Author: Andreas Maunz
+=begin
+* Name: fminer.rb
+* Description: Fminer library 
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Algorithm
diff --git a/lib/algorithm/neighbors.rb b/lib/algorithm/neighbors.rb
index 0001608..1ea6c25 100644
--- a/lib/algorithm/neighbors.rb
+++ b/lib/algorithm/neighbors.rb
@@ -1,6 +1,9 @@
-# neighbors.rb
-# Neighbor library
-# Author: Andreas Maunz
+=begin
+* Name: neighbors.rb
+* Description: Prediction algorithms library
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Algorithm
diff --git a/lib/algorithm/similarity.rb b/lib/algorithm/similarity.rb
index 9bd54e5..22b4c28 100644
--- a/lib/algorithm/similarity.rb
+++ b/lib/algorithm/similarity.rb
@@ -1,3 +1,10 @@
+=begin
+* Name: similarity.rb
+* Description: Similarity algorithms
+* Author: Andreas Maunz <andreas@maunz.de
+* Date: 10/2012
+=end
+
 module OpenTox
   class Algorithm
 
diff --git a/lib/algorithm/transform.rb b/lib/algorithm/transform.rb
index 6a615a5..afc76f9 100644
--- a/lib/algorithm/transform.rb
+++ b/lib/algorithm/transform.rb
@@ -1,6 +1,9 @@
-# transform.rb
-# Transformer library
-# Author: Andreas Maunz
+=begin
+* Name: transform.rb
+* Description: Transformation algorithms
+* Author: Andreas Maunz <andreas@maunz.de
+* Date: 10/2012
+=end
 
 module OpenTox
   class Algorithm
diff --git a/lib/dataset.rb b/lib/dataset.rb
index f1c7cf8..e7588ae 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -1,9 +1,11 @@
-# dataset.rb
-# Dataset library
-# Author: Andreas Maunz
+=begin
+* Name: dataset.rb
+* Description: Dataset algorithms
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
-
   class Dataset
 
     # Find database activities and calculate a consens
@@ -23,11 +25,8 @@ module OpenTox
       else
         nil
       end
-
     end
 
   end
-
 end
 
-
diff --git a/lib/model.rb b/lib/model.rb
index 3982509..76c5963 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,6 +1,9 @@
-# lazar.rb
-# Lazar model library
-# Author: Andreas Maunz
+=begin
+* Name: lazar.rb
+* Description: Lazar model representation
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
 
diff --git a/lib/utils/diag.rb b/lib/utils/diag.rb
index b2af8c6..fd37945 100644
--- a/lib/utils/diag.rb
+++ b/lib/utils/diag.rb
@@ -1,3 +1,10 @@
+=begin
+* Name: diag.rb
+* Description: Diagnostic tools
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
 # Print a diagnostic message
 def uri_list 
   puts "My load path is:\n#{$LOAD_PATH.join("\n")} \nI have loaded #{$LOADED_FEATURES.size} objects.\n\n"
diff --git a/lib/utils/html.rb b/lib/utils/html.rb
index aa4fe25..0392a1d 100644
--- a/lib/utils/html.rb
+++ b/lib/utils/html.rb
@@ -1,5 +1,12 @@
 #OT_LOGO = File.join(CONFIG[:services]["opentox-validation"],"resources/ot-logo.png")
 
+=begin
+* Name: html.rb
+* Description: Tools to provide html output
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
 # AM: needed since this gem has a nested directory structure
 require 'sinatra/url_for'
 
diff --git a/lib/utils/shims/dataset.rb b/lib/utils/shims/dataset.rb
index 62b9bf5..75948e0 100644
--- a/lib/utils/shims/dataset.rb
+++ b/lib/utils/shims/dataset.rb
@@ -1,5 +1,9 @@
-# Shims for translation to the new architecture (TM).
-# Author: Andreas Maunz, 2012
+=begin
+* Name: dataset.rb
+* Description: Dataset shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
 
diff --git a/lib/utils/shims/feature.rb b/lib/utils/shims/feature.rb
index df39829..297748b 100644
--- a/lib/utils/shims/feature.rb
+++ b/lib/utils/shims/feature.rb
@@ -1,5 +1,9 @@
-# Shims for translation to the new architecture (TM).
-# Author: Andreas Maunz, 2012
+=begin
+* Name: feature.rb
+* Description: Feature shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
 
diff --git a/lib/utils/shims/opentox.rb b/lib/utils/shims/opentox.rb
index cf48747..c10d535 100644
--- a/lib/utils/shims/opentox.rb
+++ b/lib/utils/shims/opentox.rb
@@ -1,5 +1,9 @@
-# Shims for translation to the new architecture (TM).
-# Author: Andreas Maunz, 2012
+=begin
+* Name: opentox.rb
+* Description: Architecture shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 # This avoids having to prefix everything with "RDF::" (e.g. "RDF::DC").
 # So that we can use our old code mostly as is.
@@ -37,7 +41,7 @@ module OpenTox
     
     # Search a model for a given parameter
     # @param[String] The parameter title
-    # @return[Object] The parameter value, or nil
+    # @return[Object] The parameter value
     def find_parameter_value(title)
       build_parameter_positions
       res = @parameters[@parameter_positions[title]][OT.paramValue.to_s] if @parameter_positions[title]
diff --git a/lib/utils/shims/task.rb b/lib/utils/shims/task.rb
index 3e19315..cb73e72 100644
--- a/lib/utils/shims/task.rb
+++ b/lib/utils/shims/task.rb
@@ -1,5 +1,10 @@
-# Shims for translation to the new architecture (TM).
-# Author: Andreas Maunz, 2012
+=begin
+* Name: task.rb
+* Description: Task shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
 
 module OpenTox
 
diff --git a/webapp/fminer.rb b/webapp/fminer.rb
index 20052e2..c6a100d 100644
--- a/webapp/fminer.rb
+++ b/webapp/fminer.rb
@@ -1,6 +1,9 @@
-# fminer.rb
-# Substructural descriptors
-# Author: Andreas Maunz
+=begin
+* Name: fminer.rb
+* Description: Subgraph descriptor calculation 
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 ENV['FMINER_SMARTS'] = 'true'
 ENV['FMINER_NO_AROMATIC'] = 'true'
diff --git a/webapp/fs.rb b/webapp/fs.rb
index 76a3af3..670885f 100644
--- a/webapp/fs.rb
+++ b/webapp/fs.rb
@@ -1,6 +1,9 @@
-# fs.rb
-# Feature selection
-# Author: Andreas Maunz
+=begin
+* Name: fs.rb
+* Description: feature selection
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Application < Service
diff --git a/webapp/lazar.rb b/webapp/lazar.rb
index 5e1c4df..fd2b489 100644
--- a/webapp/lazar.rb
+++ b/webapp/lazar.rb
@@ -1,7 +1,9 @@
-# lazar.rb
-# Lazar service
-# Author: Andreas Maunz
-
+=begin
+* Name: lazar.rb
+* Description: Lazar
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 $lazar_params = [ 
   "training_dataset_uri", 
diff --git a/webapp/sinatra.rb b/webapp/sinatra.rb
index bc05a25..d40633f 100644
--- a/webapp/sinatra.rb
+++ b/webapp/sinatra.rb
@@ -1,6 +1,9 @@
-# sinatra.rb
-# Common service
-# Author: Andreas Maunz
+=begin
+* Name: sinatra.rb
+* Description: Helper code for sinatra
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
 
 module OpenTox
   class Application < Service