com.milaboratory.core.alignment

Class BandedSemiLocalResult

java.lang.Object

com.milaboratory.core.alignment.BandedSemiLocalResult

All Implemented Interfaces:

Serializable

public final class BandedSemiLocalResult
extends Object
implements Serializable

BandedSemiLocalResult - class which is result of BandedSemiLocal alignment.

BandedSemiLocal alignment - alignment where part of second sequence is aligned either to left part of to right part of first sequence.

"Banded alignment" means that sequences to be aligned are very similar and number of mutations is very low.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
int	score Score
int	sequence1Stop Positions at which alignment terminates.
int	sequence2Stop Positions at which alignment terminates.

Constructor Summary

Constructors

Constructor and Description
BandedSemiLocalResult(int sequence1Stop, int sequence2Stop, int score) Creates new BandedSemiLocalResult

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

sequence1Stop

public final int sequence1Stop

Positions at which alignment terminates.

If BandedSemiLocalLeft alignment was performed, second sequence is aligned to the left part of first sequence. If BandedSemiLocalRight alignment was performed, second sequence is aligned to the right part of first sequence.

sequence2Stop

public final int sequence2Stop

Positions at which alignment terminates.

If BandedSemiLocalLeft alignment was performed, second sequence is aligned to the left part of first sequence. If BandedSemiLocalRight alignment was performed, second sequence is aligned to the right part of first sequence.

score

public final int score

Score

Constructor Detail

BandedSemiLocalResult

public BandedSemiLocalResult(int sequence1Stop,
                     int sequence2Stop,
                     int score)

Creates new BandedSemiLocalResult

Parameters:

sequence1Stop - position at which alignment of first sequence terminates (inclusive)

sequence2Stop - position at which alignment of second sequence terminates (inclusive)