com.milaboratory.core.alignment

Class AlignmentUtils

java.lang.Object

com.milaboratory.core.alignment.AlignmentUtils

public final class AlignmentUtils
extends Object

Author:

Dmitry Bolotin, Stanislav Poslavsky

Method Summary

Methods

Modifier and Type	Method and Description
static <S extends Sequence<S>> int	calculateScore(S seq1, Mutations<S> mutations, AlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AffineGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, LinearGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> S	getAlignedSequence2Part(Alignment<S> alignment)
static <S extends Sequence<S>> Alignment<S>	shiftIndelsAtHomopolymers(Alignment<S> alignment) Shifts indels to the left at homopolymer regions
static <S extends Sequence<S>> String	toStringSimple(S initialSequence, Mutations<S> mutations)

Methods inherited from class java.lang.Object

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

Method Detail

calculateScore

public static <S extends Sequence<S>> int calculateScore(S seq1,
                                         Mutations<S> mutations,
                                         AlignmentScoring<S> scoring)

Calculates score of alignment

Type Parameters:

S - sequence type

Parameters:

seq1 - target sequence

mutations - mutations (alignment)

scoring - scoring

Returns:

score

calculateScore

public static <S extends Sequence<S>> int calculateScore(S seq1,
                                         Range seq1Range,
                                         Mutations<S> mutations,
                                         AlignmentScoring<S> scoring)

Calculates score of alignment

Type Parameters:

S - sequence type

Parameters:

seq1 - target sequence

seq1Range - aligned range

mutations - mutations (alignment)

scoring - scoring

Returns:

score

calculateScore

public static <S extends Sequence<S>> int calculateScore(S seq1,
                                         Range seq1Range,
                                         Mutations<S> mutations,
                                         LinearGapAlignmentScoring<S> scoring)

Calculates score of alignment

Type Parameters:

S - sequence type

Parameters:

seq1 - target sequence

seq1Range - aligned range

mutations - mutations (alignment)

scoring - scoring

Returns:

score

calculateScore

public static <S extends Sequence<S>> int calculateScore(S seq1,
                                         Range seq1Range,
                                         Mutations<S> mutations,
                                         AffineGapAlignmentScoring<S> scoring)

Calculates score of alignment

Type Parameters:

S - sequence type

Parameters:

seq1 - target sequence

seq1Range - aligned range

mutations - mutations (alignment)

scoring - scoring

Returns:

score

shiftIndelsAtHomopolymers

public static <S extends Sequence<S>> Alignment<S> shiftIndelsAtHomopolymers(Alignment<S> alignment)

Shifts indels to the left at homopolymer regions

toStringSimple

public static <S extends Sequence<S>> String toStringSimple(S initialSequence,
                                            Mutations<S> mutations)

getAlignedSequence2Part

public static <S extends Sequence<S>> S getAlignedSequence2Part(Alignment<S> alignment)