com.milaboratory.core.alignment

Class AlignmentTrimmer

java.lang.Object

com.milaboratory.core.alignment.AlignmentTrimmer

public class AlignmentTrimmer
extends Object

Constructor Summary

Constructors

Constructor and Description
AlignmentTrimmer()

Method Summary

Methods

Modifier and Type	Method and Description
static <S extends Sequence<S>> Alignment<S>	leftTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	leftTrimAlignment(Alignment<S> alignment, AlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	leftTrimAlignment(Alignment<S> alignment, LinearGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	rightTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static <S extends Sequence<S>> Alignment<S>	rightTrimAlignment(Alignment<S> alignment, AlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static <S extends Sequence<S>> Alignment<S>	rightTrimAlignment(Alignment<S> alignment, LinearGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentTrimmer

public AlignmentTrimmer()

Method Detail

leftTrimAlignment

public static <S extends Sequence<S>> Alignment<S> leftTrimAlignment(Alignment<S> alignment,
                                                     AlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from left side. If score can't be increased the same alignment will be returned.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment

leftTrimAlignment

public static <S extends Sequence<S>> Alignment<S> leftTrimAlignment(Alignment<S> alignment,
                                                     LinearGapAlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from left side. If score can't be increased the same alignment will be returned. LinearGapAlignmentScoring case.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment

leftTrimAlignment

public static <S extends Sequence<S>> Alignment<S> leftTrimAlignment(Alignment<S> alignment,
                                                     AffineGapAlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from left side. If score can't be increased the same alignment will be returned. AffineGapAlignmentScoring case.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment

rightTrimAlignment

public static <S extends Sequence<S>> Alignment<S> rightTrimAlignment(Alignment<S> alignment,
                                                      AlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from right side. If score can't be increased the same alignment will be returned.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment

rightTrimAlignment

public static <S extends Sequence<S>> Alignment<S> rightTrimAlignment(Alignment<S> alignment,
                                                      LinearGapAlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from right side. If score can't be increased the same alignment will be returned. LinearGapAlignmentScoring case.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment

rightTrimAlignment

public static <S extends Sequence<S>> Alignment<S> rightTrimAlignment(Alignment<S> alignment,
                                                      AffineGapAlignmentScoring<S> scoring)

Try increase total alignment score by partially (or fully) trimming it from right side. If score can't be increased the same alignment will be returned. LinearGapAlignmentScoring case.

Parameters:

alignment - input alignment

scoring - scoring

Returns:

resulting alignment