methods.interologs
Class AlignmentInterologScorer

java.lang.Object
  extended by methods.interologs.AlignmentInterologScorer
All Implemented Interfaces:
InterologScorer

public class AlignmentInterologScorer
extends Object
implements InterologScorer

Implements interolog scoring using similarity or identity from pairwise sequence alignments of the homologs. The actual interolog score is calculated as the geometric mean of the alignment measure of both source/target alignments.

Requires a SequenceAligner which contains all involved protein sequences.

Author:
Jan Krumsiek
See Also:
InterologsCalculator

Nested Class Summary
static class AlignmentInterologScorer.AlignmentScoring
          Defines the alignment measure which will be used
 
Constructor Summary
AlignmentInterologScorer(SequenceAligner aligner, AlignmentInterologScorer.AlignmentScoring scoring)
          Creates a new alignment length interolog scorer.
 
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

AlignmentInterologScorer

public AlignmentInterologScorer(SequenceAligner aligner,
                                AlignmentInterologScorer.AlignmentScoring scoring)
Creates a new alignment length interolog scorer.

Parameters:
aligner - the sequence aligner used for calculating pairwise alignments from which the identity or similarity information will be used
scoring - use sequence identity or similarity
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