procope.methods.scores
Class DiceCoefficients

java.lang.Object
  extended by procope.methods.scores.ScoresCalculator
      extended by procope.methods.scores.DiceCoefficients
All Implemented Interfaces:
ProteinSet

public class DiceCoefficients
extends ScoresCalculator

Provides an efficient implementation of "Dice coefficients", a protein protein affinity measure derived from purification datasets according to

Zhang et al.
From pull-down data to protein interaction networks and complexes with biological relevance.
Bioinformatics, 2008, 24, 979-986

Author:
Jan Krumsiek

Constructor Summary
DiceCoefficients(PurificationData data)
          Creates a new Dice coefficients calculator
 
Method Summary
 Set<Integer> getProteins()
          Returns the proteins involved in the purification data set for this Dice coefficients calculator
 float getScore(int protein1, int protein2)
          Returns the Dice coefficient for two given proteins, returns 0 if the protein indices are out of range or if protein1==protein2
 
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

DiceCoefficients

public DiceCoefficients(PurificationData data)
Creates a new Dice coefficients calculator

Parameters:
data - purification dataset to be used
Method Detail

getProteins

public Set<Integer> getProteins()
Returns the proteins involved in the purification data set for this Dice coefficients calculator

Specified by:
getProteins in interface ProteinSet
Specified by:
getProteins in class ScoresCalculator
Returns:
a set of internal IDs

getScore

public float getScore(int protein1,
                      int protein2)
Returns the Dice coefficient for two given proteins, returns 0 if the protein indices are out of range or if protein1==protein2

Specified by:
getScore in class ScoresCalculator
Parameters:
protein1 - first protein
protein2 - second protein
Returns:
interaction score of the two proteins