From dce530c27024faf332f60c1ae0bc67f797336add Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 7 Nov 2011 12:57:22 +0100
Subject: Init to numeric branch

---
 last-utils |  2 +-
 lazar.rb   | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 libfminer  |  2 +-
 3 files changed, 58 insertions(+), 3 deletions(-)

diff --git a/last-utils b/last-utils
index 04bd1b7..8c02f7e 160000
--- a/last-utils
+++ b/last-utils
@@ -1 +1 @@
-Subproject commit 04bd1b73f54bb7422d3c08bb5a81bc02af04f6ff
+Subproject commit 8c02f7e71450cac6d8c5d7d34ecb620046b4ea46
diff --git a/lazar.rb b/lazar.rb
index 9750a56..98734e4 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -63,6 +63,10 @@ post '/lazar/?' do
 		lazar = OpenTox::Model::Lazar.new
     lazar.min_sim = params[:min_sim].to_f if params[:min_sim]
     
+
+
+
+    # AM: Manage endpoint related variables.
     if prediction_feature.feature_type == "classification"
       @training_classes = training_activities.accept_values(prediction_feature.uri).sort
       @training_classes.each_with_index { |c,i|
@@ -82,9 +86,23 @@ post '/lazar/?' do
     end
     params[:nr_hits] = "true" if lazar.nr_hits
 
+
+
+
+
+
     task.progress 10
 
-		if params[:feature_dataset_uri]
+
+
+
+    # 
+    # AM: features
+    # 
+    #
+
+    # READ OR CREATE
+    if params[:feature_dataset_uri]
       feature_dataset_uri = params[:feature_dataset_uri]
       training_features = OpenTox::Dataset.new(feature_dataset_uri)
       case training_features.feature_type(@subjectid)
@@ -109,6 +127,9 @@ post '/lazar/?' do
       training_features = OpenTox::Dataset.new(feature_dataset_uri)
     end
 
+
+
+    # WRITE IN MODEL
     training_features.load_all(@subjectid)
 		raise OpenTox::NotFoundError.new "Dataset #{feature_dataset_uri} not found." if training_features.nil?
 
@@ -119,6 +140,8 @@ post '/lazar/?' do
     training_features.data_entries.each do |compound,entry|
       lazar.fingerprints[compound] = {} unless lazar.fingerprints[compound]
       entry.keys.each do |feature|
+
+        # CASE 1: Substructure
         if lazar.feature_calculation_algorithm == "Substructure.match"
           if training_features.features[feature]
             smarts = training_features.features[feature][OT.smarts]
@@ -134,6 +157,8 @@ post '/lazar/?' do
               lazar.effects[smarts] = training_features.features[feature][OT.effect]
             end
           end
+
+        # CASE 2: Others
         else
           case training_features.feature_type(@subjectid)
           when "classification"
@@ -159,6 +184,15 @@ post '/lazar/?' do
     end
     task.progress 80
 
+
+
+
+    # 
+    # AM: SETTINGS
+    # 
+    # 
+    # 
+
     # AM: allow settings override by user
     lazar.prediction_algorithm = "Neighbors.#{params[:prediction_algorithm]}" unless params[:prediction_algorithm].nil?
     if prediction_feature.feature_type == "regression" 
@@ -169,6 +203,19 @@ post '/lazar/?' do
     lazar.conf_stdev = false
     lazar.conf_stdev = true if params[:conf_stdev] == "true"
 
+
+
+
+
+
+
+
+    # 
+    # AM TRANSFORMATIONS
+    # 
+    # 
+    # 
+
     # AM: Feed Data using Transformations
     if prediction_feature.feature_type == "regression"
       transformed_acts = []
@@ -200,6 +247,14 @@ post '/lazar/?' do
     end
     task.progress 90
 
+
+
+    # 
+    # AM: Metadata
+    # 
+    # 
+    # 
+
     lazar.metadata[DC.title] = "lazar model for #{URI.decode(File.basename(prediction_feature.uri))}"
     lazar.metadata[OT.dependentVariables] = prediction_feature.uri
     lazar.metadata[OT.trainingDataset] = dataset_uri
diff --git a/libfminer b/libfminer
index 07679a6..17932e8 160000
--- a/libfminer
+++ b/libfminer
@@ -1 +1 @@
-Subproject commit 07679a625a7acad864fd3abd80654a1a0a61e690
+Subproject commit 17932e809c35c93374ed3d5fd19a313325c35b41
-- 
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