procope.methods.interologs.blast
Class BlastBBHAlignmentLengthConstraint
java.lang.Object
procope.methods.interologs.blast.BlastBBHAlignmentLengthConstraint
- All Implemented Interfaces:
- BlastBBHConstraints
public class BlastBBHAlignmentLengthConstraint
- extends Object
- implements BlastBBHConstraints
Ensures that BBHs are only accepted if their BLAST alignment covers a
minimum fraction of both aligned protein sequences. Requires access to the
sequence data of all involved proteins to determine their length.
- Author:
- Jan Krumsiek
Method Summary |
boolean |
acceptBBH(int protein1,
int protein2,
BlastHit forwardHit,
BlastHit backwardHit)
Accepts a BBH if the give minimum fraction of both protein sequences is
covered by the BLAST alignment. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BlastBBHAlignmentLengthConstraint
public BlastBBHAlignmentLengthConstraint(Sequences sequencePool,
float minAlign)
- Create new alignment length object.
- Parameters:
sequencePool
- The sequence pool which contains all involved sequences.
Needed for sequence length determination.minAlign
- fraction of both aligned protein sequences which have to
be covered by the alignment in order for the BBH to be accepted
acceptBBH
public boolean acceptBBH(int protein1,
int protein2,
BlastHit forwardHit,
BlastHit backwardHit)
- Accepts a BBH if the give minimum fraction of both protein sequences is
covered by the BLAST alignment.
- Specified by:
acceptBBH
in interface BlastBBHConstraints
- Parameters:
protein1
- first protein of the BBHprotein2
- second protein of the BBHforwardHit
- first BLAST hit leading to that BBHbackwardHit
- second BLAST hit leading to that BBH
- Returns:
- whether the BBH is accepted or not