com.milaboratory.core.alignment

Class Aligner

java.lang.Object

com.milaboratory.core.alignment.Aligner

public final class Aligner
extends Object

Method Summary

Methods

Modifier and Type	Method and Description
static <S extends Sequence<S>> Alignment<S>	alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2) Performs global alignment
static <S extends Sequence<S>> Alignment<S>	alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2)
static <S extends Sequence<S>> Alignment<S>	alignGlobalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2) Performs global alignment using affine gap scoring system (different penalties exist for gap opening and gap extension)
static <S extends Sequence<S>> Alignment<S>	alignGlobalLinear(LinearGapAlignmentScoring scoring, S seq1, S seq2) Performs global alignment using Linear scoring system (penalty exists only for gap)
static <S extends Sequence<S>> Alignment<S>	alignLocal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2) Performs local alignment
static <S extends Sequence<S>> Alignment<S>	alignLocalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2) Performs local alignment using Affine gap scoring system (different penalties exist for gap opening and gap extension)
static <S extends Sequence<S>> Alignment<S>	alignLocalLinear(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2) Performs local alignment using Linear scoring system (penalty exists only for gap)
static <S extends Sequence<S>> Alignment<S>	alignOnlySubstitutions(S from, S to)
static <S extends Sequence<S>> Alignment<S>	alignOnlySubstitutions(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring)
static <S extends Sequence<S>> int	alignOnlySubstitutions0(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring, MutationsBuilder<S> builder)

Methods inherited from class java.lang.Object

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

Method Detail

alignOnlySubstitutions0

public static <S extends Sequence<S>> int alignOnlySubstitutions0(S seq1,
                                                  S seq2,
                                                  int seq1From,
                                                  int seq1Length,
                                                  int seq2From,
                                                  int seq2Length,
                                                  AlignmentScoring<S> scoring,
                                                  MutationsBuilder<S> builder)

alignOnlySubstitutions

public static <S extends Sequence<S>> Alignment<S> alignOnlySubstitutions(S seq1,
                                                          S seq2,
                                                          int seq1From,
                                                          int seq1Length,
                                                          int seq2From,
                                                          int seq2Length,
                                                          AlignmentScoring<S> scoring)

alignOnlySubstitutions

public static <S extends Sequence<S>> Alignment<S> alignOnlySubstitutions(S from,
                                                          S to)

alignGlobal

public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring,
                                               S seq1,
                                               S seq2,
                                               int offset1,
                                               int length1,
                                               int offset2,
                                               int length2)

alignGlobal

public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring,
                                               S seq1,
                                               S seq2)

Performs global alignment

Parameters:

alignmentScoring - scoring system

seq1 - first sequence

seq2 - second sequence

Returns:

array of mutations

alignGlobalLinear

public static <S extends Sequence<S>> Alignment<S> alignGlobalLinear(LinearGapAlignmentScoring scoring,
                                                     S seq1,
                                                     S seq2)

Performs global alignment using Linear scoring system (penalty exists only for gap)

Parameters:

scoring - linear scoring system

seq1 - first sequence

seq2 - second sequence

Returns:

array of mutations

alignGlobalAffine

public static <S extends Sequence<S>> Alignment<S> alignGlobalAffine(AffineGapAlignmentScoring<S> scoring,
                                                     S seq1,
                                                     S seq2)

Performs global alignment using affine gap scoring system (different penalties exist for gap opening and gap extension)

Parameters:

scoring - affine gap scoring system

seq1 - first sequence

seq2 - second sequence

Returns:

array of mutations

alignLocal

public static <S extends Sequence<S>> Alignment<S> alignLocal(AlignmentScoring<S> alignmentScoring,
                                              S seq1,
                                              S seq2)

Performs local alignment

Parameters:

alignmentScoring - scoring system

seq1 - first sequence

seq2 - second sequence

Returns:

result of alignment with information about alignment positions in both sequences and array of mutations

alignLocalLinear

public static <S extends Sequence<S>> Alignment<S> alignLocalLinear(LinearGapAlignmentScoring<S> scoring,
                                                    S seq1,
                                                    S seq2)

Performs local alignment using Linear scoring system (penalty exists only for gap)

Parameters:

seq1 - first sequence

seq2 - second sequence

Returns:

result of alignment with information about alignment positions in both sequences and array of mutations

alignLocalAffine

public static <S extends Sequence<S>> Alignment<S> alignLocalAffine(AffineGapAlignmentScoring<S> scoring,
                                                    S seq1,
                                                    S seq2)

Performs local alignment using Affine gap scoring system (different penalties exist for gap opening and gap extension)

Parameters:

seq1 - first sequence

seq2 - second sequence

Returns:

result of alignment with information about alignment positions in both sequences and array of mutations