com.milaboratory.core.alignment

Class BandedAffineAligner

java.lang.Object

com.milaboratory.core.alignment.BandedAffineAligner

public class BandedAffineAligner
extends Object

Author:

Dmitry Bolotin, Stanislav Poslavsky

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BandedAffineAligner.MatrixCache

Method Summary

Methods

Modifier and Type	Method and Description
static Alignment<NucleotideSequence>	align(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	align(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static int	align0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache) Classical Banded Alignment with affine gap scoring.
static Alignment<NucleotideSequence>	semiGlobalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
static BandedSemiLocalResult	semiGlobalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	semiGlobalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
static BandedSemiLocalResult	semiGlobalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static BandedSemiLocalResult	semiLocalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static BandedSemiLocalResult	semiLocalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)

Methods inherited from class java.lang.Object

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

Method Detail

align0

public static int align0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
         NucleotideSequence seq1,
         NucleotideSequence seq2,
         int offset1,
         int length1,
         int offset2,
         int length2,
         int width,
         MutationsBuilder<NucleotideSequence> mutations,
         BandedAffineAligner.MatrixCache cache)

Classical Banded Alignment with affine gap scoring. Both sequences must be highly similar. Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence).

Parameters:

scoring - scoring system

seq1 - first sequence

seq2 - second sequence

offset1 - offset in first sequence

length1 - length of first sequence's part to be aligned

offset2 - offset in second sequence

length2 - length of second sequence's part to be aligned

width - width of banded alignment matrix. In other terms max allowed number of indels

mutations - mutations array where all mutations will be kept

cache - matrix cache

semiLocalRight0

public static BandedSemiLocalResult semiLocalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                    NucleotideSequence seq1,
                                    NucleotideSequence seq2,
                                    int offset1,
                                    int length1,
                                    int offset2,
                                    int length2,
                                    int width,
                                    MutationsBuilder<NucleotideSequence> mutations,
                                    BandedAffineAligner.MatrixCache cache)

semiLocalLeft0

public static BandedSemiLocalResult semiLocalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                   NucleotideSequence seq1,
                                   NucleotideSequence seq2,
                                   int offset1,
                                   int length1,
                                   int offset2,
                                   int length2,
                                   int width,
                                   MutationsBuilder<NucleotideSequence> mutations,
                                   BandedAffineAligner.MatrixCache cache)

semiGlobalRight0

public static BandedSemiLocalResult semiGlobalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                     NucleotideSequence seq1,
                                     NucleotideSequence seq2,
                                     int offset1,
                                     int length1,
                                     int addedNucleotides1,
                                     int offset2,
                                     int length2,
                                     int addedNucleotides2,
                                     int width,
                                     MutationsBuilder<NucleotideSequence> mutations,
                                     BandedAffineAligner.MatrixCache cache)

semiGlobalLeft0

public static BandedSemiLocalResult semiGlobalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                    NucleotideSequence seq1,
                                    NucleotideSequence seq2,
                                    int offset1,
                                    int length1,
                                    int addedNucleotides1,
                                    int offset2,
                                    int length2,
                                    int addedNucleotides2,
                                    int width,
                                    MutationsBuilder<NucleotideSequence> mutations,
                                    BandedAffineAligner.MatrixCache cache)

align

public static Alignment<NucleotideSequence> align(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                  NucleotideSequence seq1,
                                  NucleotideSequence seq2,
                                  int offset1,
                                  int length1,
                                  int offset2,
                                  int length2,
                                  int width)

align

public static Alignment<NucleotideSequence> align(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                  NucleotideSequence seq1,
                                  NucleotideSequence seq2,
                                  int width)

semiLocalRight

public static Alignment<NucleotideSequence> semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                           NucleotideSequence seq1,
                                           NucleotideSequence seq2,
                                           int offset1,
                                           int length1,
                                           int offset2,
                                           int length2,
                                           int width)

semiLocalRight

public static Alignment<NucleotideSequence> semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                           NucleotideSequence seq1,
                                           NucleotideSequence seq2,
                                           int width)

semiLocalLeft

public static Alignment<NucleotideSequence> semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                          NucleotideSequence seq1,
                                          NucleotideSequence seq2,
                                          int offset1,
                                          int length1,
                                          int offset2,
                                          int length2,
                                          int width)

semiLocalLeft

public static Alignment<NucleotideSequence> semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                          NucleotideSequence seq1,
                                          NucleotideSequence seq2,
                                          int width)

semiGlobalRight

public static Alignment<NucleotideSequence> semiGlobalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                            NucleotideSequence seq1,
                                            NucleotideSequence seq2,
                                            int offset1,
                                            int length1,
                                            int addedNucleotides1,
                                            int offset2,
                                            int length2,
                                            int addedNucleotides2,
                                            int width)

semiGlobalLeft

public static Alignment<NucleotideSequence> semiGlobalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                           NucleotideSequence seq1,
                                           NucleotideSequence seq2,
                                           int offset1,
                                           int length1,
                                           int addedNucleotides1,
                                           int offset2,
                                           int length2,
                                           int addedNucleotides2,
                                           int width)