procope.methods.interologs
Class EvalueInterologScorer

java.lang.Object
  procope.methods.interologs.EvalueInterologScorer

All Implemented Interfaces:

InterologScorer

public class EvalueInterologScorer
extends Object
implements InterologScorer

Implements interolog scoring using the geometric mean of the two BLAST evalues involved in a transferred protein interaction (when transferred using bidirectional best hits from BLAST).

Author:

Jan Krumsiek

See Also:

InterologsCalculator

Constructor Summary

EvalueInterologScorer(BlastHits forward, BlastHits backward)
Creates a new e-value interolog scorer from the given BLAST results.

Method Summary

float

getInterologScore(int source1, int target1, int source2, int target2) Calculates the score of a new interolog based on the source proteins (the nodes of the original interaction) and the target proteins (the nodes of the transferred interaction).

Methods inherited from class java.lang.Object

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

Constructor Detail

EvalueInterologScorer

public EvalueInterologScorer(BlastHits forward,
                             BlastHits backward)

Creates a new e-value interolog scorer from the given BLAST results.

Parameters:

forward - this is the result of the BLAST run where the organsim which is donating interactions (the source organism) was the query

backward - this is the result of the BLAST run where the organsim which is receiving interactions (the target organism) was the query

Method Detail

getInterologScore

public float getInterologScore(int source1,
                               int target1,
                               int source2,
                               int target2)

Description copied from interface: InterologScorer

Calculates the score of a new interolog based on the source proteins (the nodes of the original interaction) and the target proteins (the nodes of the transferred interaction).

Specified by:

getInterologScore in interface InterologScorer

Parameters:

source1 - source protein 1

target1 - target protein 1

source2 - source protein 2

target2 - target protein 2

Returns:

score for the new interolog