com.milaboratory.core.alignment

Class BandedAlignerParameters<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.alignment.BandedAlignerParameters<S>

All Implemented Interfaces:

Serializable

public final class BandedAlignerParameters<S extends Sequence<S>>
extends Object
implements Serializable

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
BandedAlignerParameters(AlignmentScoring<S> scoring, int width, int stopPenalty)

Method Summary

Methods

Modifier and Type	Method and Description
BandedAlignerParameters<S>	clone()
boolean	equals(Object o)
AlignmentScoring<S>	getScoring() Returns scoring used for alignment.
int	getStopPenalty() Alignment score value in banded alignment matrix at which alignment terminates.
int	getWidth() Width of banded alignment matrix.
int	hashCode()
BandedAlignerParameters	setScoring(AlignmentScoring<S> scoring) Sets scoring used for alignment.
BandedAlignerParameters	setStopPenalty(int stopPenalty) Sets alignment score value in banded alignment matrix at which alignment terminates.
BandedAlignerParameters	setWidth(int width) Sets width of banded alignment matrix.

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BandedAlignerParameters

public BandedAlignerParameters(AlignmentScoring<S> scoring,
                       int width,
                       int stopPenalty)

Method Detail

getScoring

public AlignmentScoring<S> getScoring()

Returns scoring used for alignment.

setScoring

public BandedAlignerParameters setScoring(AlignmentScoring<S> scoring)

Sets scoring used for alignment.

getWidth

public int getWidth()

Width of banded alignment matrix. This value affects maximal possible number of indels.

setWidth

public BandedAlignerParameters setWidth(int width)

Sets width of banded alignment matrix. This value is connected to max allowed number of indels.

getStopPenalty

public int getStopPenalty()

Alignment score value in banded alignment matrix at which alignment terminates.

setStopPenalty

public BandedAlignerParameters setStopPenalty(int stopPenalty)

Sets alignment score value in banded alignment matrix at which alignment terminates.

clone

public BandedAlignerParameters<S> clone()

Overrides:

clone in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object