procope.methods.scores
Class SocioAffinityCalculator

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

public class SocioAffinityCalculator
extends ScoresCalculator

Calculates socio affinity scores according to

Gavin et al.
Proteome survey reveals modularity of the yeast cell machinery.
Nature, 2006, 440, 631-636

For more information about this scoring method please check out the online manual.

Author:
Jan Krumsiek

Constructor Summary
SocioAffinityCalculator(PurificationData data)
          Creates a new socio affinity scores calculator based on a given purification data set.
 
Method Summary
 Set<Integer> getProteins()
          Returns all proteins of the purification data set used in this scores calculator
 float getScore(int protA, int protB)
          Calculates the socio affinity score for two given proteins based on the purification data set provided in the constructor.
 
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

SocioAffinityCalculator

public SocioAffinityCalculator(PurificationData data)
Creates a new socio affinity scores calculator based on a given purification data set.

Parameters:
data - purification data set used for scores calculation
Method Detail

getScore

public float getScore(int protA,
                      int protB)
Calculates the socio affinity score for two given proteins based on the purification data set provided in the constructor.

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

getProteins

public Set<Integer> getProteins()
Returns all proteins of the purification data set used in this scores calculator

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