make yard documentation full yard 0.8.6.1 compatible

1 files changed, 66 insertions, 66 deletions

diff --git a/lib/validation.rb b/lib/validation.rb
index c4f6868..cb73ce6 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -2,7 +2,7 @@ require "yaml"
 
 module OldOpenTox
   attr_accessor :metadata, :uri
-  
+
   def initialize(uri=nil)
     @metadata = {}
     self.uri = uri if uri
@@ -13,17 +13,17 @@ module OldOpenTox
     yaml = OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"})
     @metadata = YAML.load(yaml)
   end
-  
+
   def delete (subjectid=nil)
     OpenTox::RestClientWrapper.delete(@uri.to_s,nil,{:subjectid => subjectid})
   end
 end
 
 module OpenTox
-  
+
   class Validation
     include OldOpenTox
-    
+
     # find validation, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -33,10 +33,10 @@ module OpenTox
       val.load_metadata( subjectid )
       val
     end
-    
+
     # returns a filtered list of validation uris
-    # @param [Hash,optional] params, validation-params to filter the uris (could be model, training_dataset, ..)  
-    # @return [Array]    
+    # @param params [Hash,optional] validation-params to filter the uris (could be model, training_dataset, ..)
+    # @return [Array]
     def self.list( params={} )
       filter_string = ""
       params.each do |k,v|
@@ -46,7 +46,7 @@ module OpenTox
       end
       (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string).split("\n"))
     end
-    
+
     # creates a training test split validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1))
     # @param [String,optional] subjectid
@@ -58,7 +58,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # creates a training test validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,training_dataset_uri,prediction_feature,test_dataset_uri,optional:algorithm_params)
     # @param [String,optional] subjectid
@@ -70,7 +70,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # creates a bootstrapping validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,random_seed(1))
     # @param [String,optional] subjectid
@@ -82,7 +82,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # looks for report for this validation, creates a report if no report is found
     # @param [String,optional] subjectid
     # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
@@ -92,20 +92,20 @@ module OpenTox
       @report = ValidationReport.create(@uri, {}, subjectid, waiting_task) unless @report
       @report.uri
     end
-    
+
     # creates a validation object from crossvaldiation statistics, raise error if not found
     # (as crossvaldiation statistics are returned as an average valdidation over all folds)
-    # @param [String] crossvalidation uri
+    # @param crossvalidation_uri [String] crossvalidation uri
     # @param [String,optional] subjectid
     # @return [OpenTox::Validation]
     def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
       find( File.join(crossvalidation_uri, 'statistics'),subjectid )
     end
-    
+
     # returns confusion matrix as array, predicted values are in rows
     # example:
     # [[nil,"active","moderate","inactive"],["active",1,3,99],["moderate",4,2,8],["inactive",3,8,6]]
-    # -> 99 inactive compounds have been predicted as active 
+    # -> 99 inactive compounds have been predicted as active
     def confusion_matrix
       raise "no classification statistics, probably a regression valdiation" unless @metadata[RDF::OT.classificationStatistics]
       matrix =  @metadata[RDF::OT.classificationStatistics][RDF::OT.confusionMatrix][RDF::OT.confusionMatrixCell]
@@ -124,38 +124,38 @@ module OpenTox
       end
       table
     end
-    
+
     # returns probability-distribution for a given prediction
     # it takes all predictions into account that have a confidence value that is >= confidence and that have the same predicted value
     # (minimum 12 predictions with the hightest confidence are selected (even if the confidence is lower than the given param)
-    # 
-    # @param [Float] confidence value (between 0 and 1)
-    # @param [String] predicted value
-    # @param [String,optional] subjectid
+    #
+    # @param confidence [Float] confidence value (between 0 and 1)
+    # @param prediction [String] predicted value
+    # @param subjectid [String,optional]
     # @return [Hash] see example
     #
     # Example 1:
-    # validation.probabilities(0.3,"active")
-    # -> {:min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05}}
+    #   validation.probabilities(0.3,"active")
+    #   -> { :min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05 } }
     # there have been 20 "active" predictions with confidence >= 0.3, 70 percent of them beeing correct
     #
     # Example 2:
-    # validation.probabilities(0.8,"active")
-    # -> {:min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0}}
+    #  validation.probabilities(0.8,"active")
+    #  -> { :min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0 } }
     # the given confidence value was to high (i.e. <12 predictions with confidence value >= 0.8)
     # the top 12 "active" predictions have a min_confidence of 0.45, 90 percent of them beeing correct
-    # 
+    #
     def probabilities( confidence, prediction, subjectid=nil )
       YAML.load(OpenTox::RestClientWrapper.get(@uri+"/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
         {:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
   end
-  
+
   class Crossvalidation
     include OldOpenTox
 
     attr_reader :report
-    
+
     # find crossvalidation, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -165,10 +165,10 @@ module OpenTox
       cv.load_metadata( subjectid )
       cv
     end
-    
+
     # returns a filtered list of crossvalidation uris
-    # @param [Hash,optional] params, crossvalidation-params to filter the uris (could be algorithm, dataset, ..)  
-    # @return [Array]    
+    # @param params [Hash,optional] crossvalidation-params to filter the uris (could be algorithm, dataset, ..)
+    # @return [Array]
     def self.list( params={} )
       filter_string = ""
       params.each do |k,v|
@@ -201,29 +201,29 @@ module OpenTox
       @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report
       @report.uri
     end
-    
+
     # loads metadata via yaml from crossvalidation object
     # fields (like for example the validations) can be acces via validation.metadata[RDF::OT.validation]
     def load_metadata( subjectid=nil )
       @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
-    
+
     # returns a Validation object containing the statistics of the crossavlidation
     def statistics( subjectid=nil )
       Validation.from_cv_statistics( @uri, subjectid )
     end
-    
+
     # documentation see OpenTox::Validation.probabilities
     def probabilities( confidence, prediction, subjectid=nil )
       YAML.load(OpenTox::RestClientWrapper.get(@uri+"/statistics/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
         {:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
-    
+
   end
-  
+
   class ValidationReport
     include OldOpenTox
-    
+
     # finds ValidationReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -234,23 +234,23 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds ValidationReport for a particular validation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param validation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::ValidationReport] nil if no report found
     def self.find_for_validation( validation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/validation?validation="+validation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : ValidationReport.new(uris[-1])
     end
-    
+
     # creates a validation report via validation
-    # @param [String] validation uri 
-    # @param [Hash] params addiditonal possible 
+    # @param validation_uri [String] validation uri
+    # @param params [Hash] params addiditonal possible
     #               (min_confidence, params={}, min_num_predictions, max_num_predictions)
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::ValidationReport]
     def self.create( validation_uri, params={}, subjectid=nil, waiting_task=nil )
       params = {} if params==nil
@@ -262,12 +262,12 @@ module OpenTox
       uri = wait_for_task(uri)
       ValidationReport.new(uri)
     end
-    
+
   end
 
   class CrossvalidationReport
     include OldOpenTox
-    
+
     # finds CrossvalidationReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -278,21 +278,21 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds CrossvalidationReport for a particular crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::CrossvalidationReport] nil if no report found
     def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/crossvalidation?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
     end
-    
+
     # creates a crossvalidation report via crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::CrossvalidationReport]
     def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
       uri = RestClientWrapper.post(File.join($validation[:uri],"/report/crossvalidation"),
@@ -301,11 +301,11 @@ module OpenTox
       CrossvalidationReport.new(uri)
     end
   end
-  
-  
+
+
   class AlgorithmComparisonReport
     include OldOpenTox
-    
+
     # finds AlgorithmComparisonReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -316,23 +316,23 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds AlgorithmComparisonReport for a particular crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::AlgorithmComparisonReport] nil if no report found
     def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1])
     end
-    
+
     # creates a algorithm comparison report via crossvalidation uris
-    # @param [Hash] crossvalidation uri_hash, see example 
-    # @param [Hash] params addiditonal possible 
+    # @param crossvalidation_uri_hash [Hash] crossvalidation uri_hash, see example
+    # @param params [Hash] params addiditonal possible
     #               (ttest_significance, ttest_attributes, min_confidence, min_num_predictions, max_num_predictions)
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::AlgorithmComparisonReport]
     # example for hash:
     # { :lazar-bbrc => [ http://host/validation/crossvalidation/x1, http://host/validation/crossvalidation/x2 ],
@@ -355,7 +355,7 @@ module OpenTox
       uri = wait_for_task(uri)
       AlgorithmComparisonReport.new(uri)
     end
-  end  
-  
+  end
+
 end