procope.methods.scores
Class ScoresCalculator

java.lang.Object
  extended by procope.methods.scores.ScoresCalculator
All Implemented Interfaces:
ProteinSet
Direct Known Subclasses:
DiceCoefficients, DummyScores, FunctionalSimilarities, HartCalculator, PECalculator, SocioAffinityCalculator

public abstract class ScoresCalculator
extends Object
implements ProteinSet

Extended by all classes which calculate interaction scores between proteins based on experimental or other data.

Author:
Jan Krumsiek

Constructor Summary
ScoresCalculator()
           
 
Method Summary
abstract  Set<Integer> getProteins()
          Returns the set of proteins involved in this scores calculator.
abstract  float getScore(int protein1, int protein2)
          Returns the interaction score for two given proteins.
 float getScore(String protein1, String protein2)
          Returns the interaction score for two given proteins provided as String identifiers.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ScoresCalculator

public ScoresCalculator()
Method Detail

getScore

public abstract float getScore(int protein1,
                               int protein2)
Returns the interaction score for two given proteins.

Parameters:
protein1 - first protein
protein2 - second protein
Returns:
interaction score of the two proteins

getScore

public float getScore(String protein1,
                      String protein2)
Returns the interaction score for two given proteins provided as String identifiers. Does not have be overridden, the implementation in the abstract class automatically uses the ProteinManager to get internal IDs for the given proteins.

Parameters:
protein1 - string identifier of first protein
protein2 - string identifier of second protein
Returns:
interaction score of the two proteins
See Also:
ProteinManager

getProteins

public abstract Set<Integer> getProteins()
Returns the set of proteins involved in this scores calculator.

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