methods.scores
Class HartCalculator

java.lang.Object
  extended by methods.scores.HartCalculator
All Implemented Interfaces:
ProteinSet, ScoresCalculator

public class HartCalculator
extends Object
implements ScoresCalculator

Calculates protein-protein interaction scores from purification data according to

Hart, G. T.; Lee, I. & Marcotte, E. R.
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.
BMC Bioinformatics, 2007, 8, 23

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


Constructor Summary
HartCalculator(Collection<PurificationData> datasets)
          Creates a new scores calculator from a list of purification data sets.
HartCalculator(PurificationData dataset)
          Creates a new scores calculator from a given purification data set.
HartCalculator(PurificationData[] datasets)
          Creates a new scores calculator from an array of purification data sets.
 
Method Summary
 Set<Integer> getProteins()
          Returns all proteins of the purification data set used in this scores calculator
 float getScore(int prot1, int prot2)
          Calculates the score of the given protein.
static void main(String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

HartCalculator

public HartCalculator(PurificationData dataset)
Creates a new scores calculator from a given purification data set.

Parameters:
dataset - purification dataset to be used

HartCalculator

public HartCalculator(Collection<PurificationData> datasets)
Creates a new scores calculator from a list of purification data sets.

Parameters:
datasets - purfication datasets to be used

HartCalculator

public HartCalculator(PurificationData[] datasets)
Creates a new scores calculator from an array of purification data sets.

Parameters:
datasets - purfication datasets to be used
Method Detail

getScore

public float getScore(int prot1,
                      int prot2)
Calculates the score of the given protein.

Specified by:
getScore in interface ScoresCalculator
Parameters:
prot1 - first protein
prot2 - 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 interface ScoresCalculator
Returns:
a set of internal IDs

main

public static void main(String[] args)
                 throws IOException
Throws:
IOException