public final class BandedLinearAligner extends Object
| Modifier and Type | Method and Description |
|---|---|
static Alignment<NucleotideSequence> |
align(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width)
Classical Banded Alignment
|
static Alignment<NucleotideSequence> |
align(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width)
Classical Banded Alignment
|
static float |
align0(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
CachedIntArray cachedArray)
Classical Banded Alignment
|
static Alignment<NucleotideSequence> |
alignLeftAdded(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width)
Semi-semi-global alignment with artificially added letters.
|
static BandedSemiLocalResult |
alignLeftAdded0(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
CachedIntArray cachedArray)
Semi-semi-global alignment with artificially added letters.
|
static Alignment<NucleotideSequence> |
alignRightAdded(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width)
Semi-semi-global alignment with artificially added letters.
|
static BandedSemiLocalResult |
alignRightAdded0(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
CachedIntArray cachedArray)
Semi-semi-global alignment with artificially added letters.
|
static Alignment<NucleotideSequence> |
alignSemiLocalLeft(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static Alignment<NucleotideSequence> |
alignSemiLocalLeft(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static BandedSemiLocalResult |
alignSemiLocalLeft0(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty,
MutationsBuilder<NucleotideSequence> mutations,
CachedIntArray cachedArray)
Alignment which identifies what is the highly similar part of the both sequences.
|
static Alignment<NucleotideSequence> |
alignSemiLocalRight(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static Alignment<NucleotideSequence> |
alignSemiLocalRight(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static BandedSemiLocalResult |
alignSemiLocalRight0(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty,
MutationsBuilder<NucleotideSequence> mutations,
CachedIntArray cachedArray)
Alignment which identifies what is the highly similar part of the both sequences.
|
public static float align0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray)
Both sequences must be highly similar
Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence)
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be alignedwidth - width of banded alignment matrix. In other terms max allowed number of indelsmutations - mutations array where all mutations will be keptcachedArray - cached (created once) array to be used in BandedMatrix, which is compact alignment
scoring matrixpublic static BandedSemiLocalResult alignRightAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray)
Alignment where second sequence is aligned to the right part of first sequence.
Whole second sequence must be highly similar to the first sequence
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be aligned including artificially added lettersaddedNucleotides1 - number of artificially added letters to the first sequenceoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned including artificially added lettersaddedNucleotides2 - number of artificially added letters to the second sequencewidth - width of banded alignment matrix. In other terms max allowed number of indelsmutations - mutations array where all mutations will be keptcachedArray - cached (created once) array to be used in BandedMatrix, which is compact
alignment scoring matrixpublic static BandedSemiLocalResult alignLeftAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray)
Alignment where second sequence is aligned to the left part of first sequence.
Whole second sequence must be highly similar to the first sequence, except last width letters, which
are to be checked whether they can improve alignment or not.
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedaddedNucleotides1 - number of artificially added letters to the first sequence;
must be 0 if seq1 is a pattern to match and seq2 is target sequence
where we search the patternoffset2 - offset in second sequencelength2 - length of second sequence's part to be alignedaddedNucleotides2 - number of artificially added letters to the second sequence;
if seq2 is target sequence where we search the pattern, this parameter must be equal
to maximum allowed number of indels (same as width parameter)width - width of banded alignment matrix. In other terms max allowed number of indelsmutations - mutations array where all mutations will be keptcachedArray - cached (created once) array to be used in BandedMatrix, which is compact
alignment scoring matrixpublic static BandedSemiLocalResult alignSemiLocalLeft0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray)
Alignment is done in the way that beginning of second sequences is aligned to beginning of first sequence.
Alignment terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only left part of second sequence is to be aligned
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned@param widthstopPenalty - alignment score value in banded alignment matrix at which alignment terminatesmutations - array where all mutations will be keptcachedArray - cached (created once) array to be used in BandedMatrix, which is compact alignment
scoring matrixpublic static BandedSemiLocalResult alignSemiLocalRight0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray)
Alignment is done in the way that end of second sequence is aligned to end of first sequence.
Alignment
terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only right part of second sequence is to be aligned.
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned@param widthstopPenalty - alignment score value in banded alignment matrix at which alignment terminatesmutations - array where all mutations will be keptcachedArray - cached (created once) array to be used in BandedMatrix, which is compact alignment
scoring matrixpublic static Alignment<NucleotideSequence> align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
Both sequences must be highly similar
Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence)
scoring - scoring systemseq1 - first sequenceseq2 - second sequencewidth - width of banded alignment matrix. In other terms max allowed number of indelspublic static Alignment<NucleotideSequence> align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
Both sequences must be highly similar
Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence)
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be alignedwidth - width of banded alignment matrix. In other terms max allowed number of indelspublic static Alignment<NucleotideSequence> alignLeftAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
Alignment where second sequence is aligned to the left part of first sequence.
Whole second sequence must be highly similar to the first sequence, except last width letters, which
are to be checked whether they can improve alignment or not.
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedaddedNucleotides1 - number of artificially added letters to the first sequenceoffset2 - offset in second sequencelength2 - length of second sequence's part to be alignedaddedNucleotides2 - number of artificially added letters to the second sequencewidth - width of banded alignment matrix. In other terms max allowed number of indelspublic static Alignment<NucleotideSequence> alignRightAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
Alignment where second sequence is aligned to the right part of first sequence.
Whole second sequence must be highly similar to the first sequence
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be aligned including artificially added lettersaddedNucleotides1 - number of artificially added letters to the first sequenceoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned including artificially added lettersaddedNucleotides2 - number of artificially added letters to the second sequencewidth - width of banded alignment matrix. In other terms max allowed number of indelspublic static Alignment<NucleotideSequence> alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty)
Alignment is done in the way that beginning of second sequences is aligned to beginning of first sequence.
Alignment terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only left part of second sequence is to be aligned
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned@param widthstopPenalty - alignment score value in banded alignment matrix at which alignment terminatespublic static Alignment<NucleotideSequence> alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty)
Alignment is done in the way that beginning of second sequences is aligned to beginning of first sequence.
Alignment terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only left part of second sequence is to be aligned
scoring - scoring systemseq1 - first sequenceseq2 - second sequencestopPenalty - alignment score value in banded alignment matrix at which alignment terminatespublic static Alignment<NucleotideSequence> alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty)
Alignment is done in the way that end of second sequence is aligned to end of first sequence.
Alignment
terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only right part of second sequence is to be aligned.
scoring - scoring systemseq1 - first sequenceseq2 - second sequenceoffset1 - offset in first sequencelength1 - length of first sequence's part to be alignedoffset2 - offset in second sequencelength2 - length of second sequence's part to be aligned@param widthstopPenalty - alignment score value in banded alignment matrix at which alignment terminatespublic static Alignment<NucleotideSequence> alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty)
Alignment is done in the way that end of second sequence is aligned to end of first sequence.
Alignment
terminates when score in banded alignment matrix reaches stopPenalty value.
In other words, only right part of second sequence is to be aligned.
scoring - scoring systemseq1 - first sequenceseq2 - second sequencestopPenalty - alignment score value in banded alignment matrix at which alignment terminatesCopyright © 2018. All rights reserved.