procope.evaluation.complexquality.go
Class TermSimilaritiesSchlicker
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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 calculatedannotations
- the annotations needed for term frequency calculationsimilarityMeasure
- the similarity measure to be usedcaching
- enables or disables the caching of similarity scores to
avoid multiple calculation of the same scores
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 termterm2ID
- ID of the second term
- Returns:
- similarity value for the two given terms