procope.evaluation.complexquality.go
Class TermSimilaritiesSchlicker

java.lang.Object
  extended by procope.evaluation.complexquality.go.TermSimilaritiesSchlicker
All Implemented Interfaces:
TermSimilarities

public class TermSimilaritiesSchlicker
extends Object
implements TermSimilarities

Implements the calculation of similarities between two GO terms as described in

Schlicker, A.; Domingues, F. S.; Rahnenführer, J. & Lengauer, T.
A new measure for functional similarity of gene products based on Gene Ontology.
BMC Bioinformatics, 2006, 7, 302
Pubmed: 16776819

Author:
Jan Krumsiek

Nested Class Summary
static class TermSimilaritiesSchlicker.TermSimilarityMeasure
          The similarity to be used.
 
Constructor Summary
TermSimilaritiesSchlicker(GONetwork gonet, GOAnnotations annotations, TermSimilaritiesSchlicker.TermSimilarityMeasure similarityMeasure, boolean caching)
          Creates a new term similarity calculator.
 
Method Summary
 float calculateSimilarity(String term1ID, String term2ID)
          Calculates the similarity of two given GO terms.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

TermSimilaritiesSchlicker

public TermSimilaritiesSchlicker(GONetwork gonet,
                                 GOAnnotations annotations,
                                 TermSimilaritiesSchlicker.TermSimilarityMeasure similarityMeasure,
                                 boolean caching)
Creates a new term similarity calculator.

Parameters:
gonet - the go network on which similarities will be calculated
annotations - the annotations needed for term frequency calculation
similarityMeasure - the similarity measure to be used
caching - enables or disables the caching of similarity scores to avoid multiple calculation of the same scores
Method Detail

calculateSimilarity

public float calculateSimilarity(String term1ID,
                                 String term2ID)
Calculates the similarity of two given GO terms. If both terms are the root term of the respective network, this method will return 0.

Specified by:
calculateSimilarity in interface TermSimilarities
Parameters:
term1ID - ID of the first term
term2ID - ID of the second term
Returns:
similarity value for the two given terms