methods.interologs
Class AlignmentInterologScorer
java.lang.Object
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
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 |
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 usedscoring
- use sequence identity or similarity
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 1target1
- target protein 1source2
- source protein 2target2
- target protein 2
- Returns:
- score for the new interolog