procope.evaluation.complexquality.go
Class FunctionalSimilaritiesSchlicker

java.lang.Object
  procope.methods.scores.ScoresCalculator
      procope.evaluation.complexquality.go.FunctionalSimilarities
          procope.evaluation.complexquality.go.FunctionalSimilaritiesSchlicker

All Implemented Interfaces:

ProteinSet

public class FunctionalSimilaritiesSchlicker
extends FunctionalSimilarities

Implements the calculation of functional similarites between proteins 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

FunctionalSimilaritiesSchlicker.FunctionalSimilarityMeasure Functional semilarity measure.

Constructor Summary

FunctionalSimilaritiesSchlicker(GONetwork gonet, GOAnnotations annotations, TermSimilarities termSim, FunctionalSimilaritiesSchlicker.FunctionalSimilarityMeasure funSim)
Creates a new functional similarity score calculator.

Method Summary

Set<Integer>	getProteins() Returns the set of proteins contained in the annotations used in this scores calculator.
float	getScore(int protein1, int protein2) Calculates the functional similarity of two given proteins.

Methods inherited from class procope.methods.scores.ScoresCalculator

getScore

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FunctionalSimilaritiesSchlicker

public FunctionalSimilaritiesSchlicker(GONetwork gonet,
                                       GOAnnotations annotations,
                                       TermSimilarities termSim,
                                       FunctionalSimilaritiesSchlicker.FunctionalSimilarityMeasure funSim)

Creates a new functional similarity score calculator.

Parameters:

gonet - GO network to be used

annotations - annotations to be used

termSim - term similarity calculator

funSim - functional similarity measure

Method Detail

getScore

public float getScore(int protein1,
                      int protein2)

Calculates the functional similarity of two given proteins.

Specified by:

getScore in class FunctionalSimilarities

Parameters:

protein1 - first protein

protein2 - second protein

Returns:

functional similarity score or 0 if at least one of the proteins has no annotated GO terms

getProteins

public Set<Integer> getProteins()

Returns the set of proteins contained in the annotations used in this scores calculator.

Specified by:

getProteins in interface ProteinSet

Specified by:

getProteins in class ScoresCalculator

Returns:

a set of internal IDs