com.milaboratory.core.alignment

Class AlignerCustom

java.lang.Object

com.milaboratory.core.alignment.AlignerCustom

public class AlignerCustom
extends Object

Collection of custom aligners

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AlignerCustom.AffineMatrixCache
static class	AlignerCustom.LinearMatrixCache
static class	AlignerCustom.Matrix
static interface	AlignerCustom.MatrixCache

Field Summary

Fields

Modifier and Type	Field and Description
static int	MIN_VALUE

Constructor Summary

Constructors

Constructor and Description
AlignerCustom()

Method Summary

Methods

Modifier and Type	Method and Description
static <S extends Sequence<S>> Alignment<S>	alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.AffineMatrixCache cache)
static <S extends Sequence<S>> Alignment<S>	alignLinearSemiLocalLeft0(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.LinearMatrixCache cache) Align two sequences from left to right; left edges of both sequences considered to be already aligned.
static <S extends Sequence<S>> Alignment<S>	alignLinearSemiLocalRight0(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.LinearMatrixCache cache)

Methods inherited from class java.lang.Object

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

Field Detail

MIN_VALUE

public static final int MIN_VALUE

See Also:

Constant Field Values

Constructor Detail

AlignerCustom

public AlignerCustom()

Method Detail

alignLinearSemiLocalLeft0

public static <S extends Sequence<S>> Alignment<S> alignLinearSemiLocalLeft0(LinearGapAlignmentScoring<S> scoring,
                                                             S seq1,
                                                             S seq2,
                                                             int offset1,
                                                             int length1,
                                                             int offset2,
                                                             int length2,
                                                             boolean boundSeq1,
                                                             boolean boundSeq2,
                                                             Alphabet<S> alphabet,
                                                             AlignerCustom.LinearMatrixCache cache)

Align two sequences from left to right; left edges of both sequences considered to be already aligned. Aligner optimize total alignment scoring using dynamic programing approach. Alignment is global in respect to seq1 if boundSeq1 = true. Alignment is global in respect to seq2 if boundSeq2 = true. This algorithm becomes pure Needleman–Wunsch algorithm if both boundSeq1 = true and boundSeq2 = true.

Type Parameters:

S - sequence type

Parameters:

scoring - alignment scoring

seq1 - first sequence (seq1)

seq2 - second sequence (seq2)

offset1 - position of first nucleotide to align in seq1 (this position is considered to be already aligned by the algorithm)

length1 - number of letters in seq1 to align (if boundSeq1 = true all length1 letters will be aligned, if boundSeq1 = false at most this many letters will be aligned)

offset2 - position of first nucleotide to align in seq2 (this position is considered to be already aligned by the algorithm)

length2 - number of letters in seq2 to align (if boundSeq2 = true all length2 letters will be aligned, if boundSeq2 = false at most this many letters will be aligned)

boundSeq1 - determines whether to build global (true) or local (false) alignment in respect to seq1

boundSeq2 - determines whether to build global (true) or local (false) alignment in respect to seq2

alphabet - alphabet of the sequences

cache - matrix cache

Returns:

alignment

alignLinearSemiLocalRight0

public static <S extends Sequence<S>> Alignment<S> alignLinearSemiLocalRight0(LinearGapAlignmentScoring<S> scoring,
                                                              S seq1,
                                                              S seq2,
                                                              int offset1,
                                                              int length1,
                                                              int offset2,
                                                              int length2,
                                                              boolean boundSeq1,
                                                              boolean boundSeq2,
                                                              Alphabet<S> alphabet,
                                                              AlignerCustom.LinearMatrixCache cache)

alignAffineSemiLocalLeft0

public static <S extends Sequence<S>> Alignment<S> alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S> scoring,
                                                             S seq1,
                                                             S seq2,
                                                             int offset1,
                                                             int length1,
                                                             int offset2,
                                                             int length2,
                                                             boolean boundSeq1,
                                                             boolean boundSeq2,
                                                             Alphabet<S> alphabet,
                                                             AlignerCustom.AffineMatrixCache cache)