Uses of Class
com.milaboratory.core.mutations.Mutations

Packages that use Mutations

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.mutations
com.milaboratory.core.mutations.generator
com.milaboratory.core.tree

Uses of Mutations in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment that return Mutations

Modifier and Type	Method and Description
Mutations<S>	Alignment.getAbsoluteMutations() Returns mutations in absolute (global) sequence1 coordinates.
Mutations<S>	Alignment.getRelativeMutations() Returns mutations in local coordinates, relative to sequence1range.

Methods in com.milaboratory.core.alignment with parameters of type Mutations

Modifier and Type	Method and Description
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Mutations<S> mutations, AlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AffineGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, LinearGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> String	AlignmentUtils.toStringSimple(S initialSequence, Mutations<S> mutations)

Constructors in com.milaboratory.core.alignment with parameters of type Mutations

Constructor and Description
Alignment(S sequence1, Mutations<S> mutations, AlignmentScoring<S> scoring)
Alignment(S sequence1, Mutations<S> mutations, float score)
Alignment(S sequence1, Mutations<S> mutations, Range sequence1Range, Range sequence2Range, AlignmentScoring<S> scoring)
Alignment(S sequence1, Mutations<S> mutations, Range sequence1Range, Range sequence2Range, float score)
AlignmentIteratorForward(Mutations<S> mutations, Range seq1Range) Create alignment iterator
AlignmentIteratorForward(Mutations<S> mutations, Range seq1Range, int seq2Position) Create alignment iterator
AlignmentIteratorReverse(Mutations<S> mutations, Range seq1Range) Create alignment iterator
AlignmentIteratorReverse(Mutations<S> mutations, Range seq1Range, int seq2Position) Create alignment iterator

Uses of Mutations in com.milaboratory.core.alignment.benchmark

Fields in com.milaboratory.core.alignment.benchmark with type parameters of type Mutations

Modifier and Type	Field and Description
List<Mutations<NucleotideSequence>>	KAlignerQuery.mutationsInTarget

Constructor parameters in com.milaboratory.core.alignment.benchmark with type arguments of type Mutations

Constructor and Description
KAlignerQuery(int targetId, List<Range> queryClusters, List<Range> targetClusters, List<Mutations<NucleotideSequence>> mutationsInTarget, NucleotideSequence query, Alignment<NucleotideSequence> expectedAlignment)

Uses of Mutations in com.milaboratory.core.mutations

Fields in com.milaboratory.core.mutations declared as Mutations

Modifier and Type	Field and Description
static Mutations<AminoAcidSequence>	Mutations.EMPTY_AMINO_ACID_MUTATIONS Identity mutations object for amino acid sequences.
static Mutations<NucleotideSequence>	Mutations.EMPTY_NUCLEOTIDE_MUTATIONS Identity mutations object for nucleotide sequences.
Mutations<AminoAcidSequence>	MutationsUtil.MutationsWitMapping.mutations

Methods in com.milaboratory.core.mutations that return Mutations

Modifier and Type	Method and Description
<S extends Sequence<S>> Mutations<S>	MutationsCounter.build(Alphabet<S> alphabet, MutationsCounter.Filter filter)
Mutations<S>	Mutations.combineWith(Mutations<S> other) Returns combined mutations array (this applied before other).
Mutations<S>	Mutations.concat(Mutations<S> other) Concatenates this and other
Mutations<S>	MutationsBuilder.createAndDestroy()
static <S extends Sequence<S>> Mutations<S>	Mutations.decode(String string, Alphabet<S> alphabet)
static Mutations<AminoAcidSequence>	Mutations.decodeAA(String string)
static Mutations<NucleotideSequence>	Mutations.decodeNuc(String string)
static <S extends Sequence<S>> Mutations<S>	Mutations.empty(Alphabet<S> alphabet)
Mutations<S>	Mutations.extractAbsoluteMutationsForRange(int from, int to) Extracts mutations for a range of positions in the original sequence.
Mutations<S>	Mutations.extractAbsoluteMutationsForRange(Range range) Extracts mutations for a range of positions in the original sequence.
Mutations<S>	Mutations.extractRelativeMutationsForRange(int from, int to) Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -from).
Mutations<S>	Mutations.extractRelativeMutationsForRange(Range range) Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -range.from).
Mutations<S>	Mutations.getRange(int from, int to) Extracts sub mutations by from-to mutation indices.
Mutations<S>	Mutations.invert() Inverts mutations, so that they reflect difference from seq2 to seq1.
Mutations<S>	Mutations.move(int offset) Moves positions of mutations by specified offset
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
Mutations<S>	Mutations.removeMutationsInRange(int from, int to) Removes mutations for a range of positions in the original sequence and performs shift of corresponding positions of mutations.
Mutations<S>	Mutations.removeMutationsInRange(Range range) See removeMutationsInRange(int, int).
Mutations<S>	Mutations.removeMutationsInRanges(Range... ranges) See removeMutationsInRange(int, int).
static <S extends Sequence<S>> Mutations<S>	MutationsUtil.shiftIndelsAtHomopolymers(S seq1, int seq1From, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
static <S extends Sequence<S>> Mutations<S>	MutationsUtil.shiftIndelsAtHomopolymers(S seq1, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Methods in com.milaboratory.core.mutations with parameters of type Mutations

Modifier and Type	Method and Description
void	MutationsCounter.adjust(Mutations<?> mutations, int delta)
void	MutationsCounter.adjust(Mutations<?> mutations, MutationsEnumerator enumerator, int delta)
MutationsBuilder<S>	MutationsBuilder.append(Mutations<S> other)
MutationsBuilder<S>	MutationsBuilder.append(Mutations<S> other, int otherFrom, int length)
static boolean	MutationsUtil.check(Mutations mutations)
Mutations<S>	Mutations.combineWith(Mutations<S> other) Returns combined mutations array (this applied before other).
Mutations<S>	Mutations.concat(Mutations<S> other) Concatenates this and other
static NSequenceWithQuality	MutationsUtil.mutate(NSequenceWithQuality seq, Mutations<NucleotideSequence> mutations)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static MutationsUtil.MutationNt2AADescriptor[]	MutationsUtil.nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets) Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
static MutationsUtil.MutationsWitMapping	MutationsUtil.nt2aaWithMapping(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static int[]	MutationsUtil.nt2IndividualAA(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static <S extends Sequence<S>> Mutations<S>	MutationsUtil.shiftIndelsAtHomopolymers(S seq1, int seq1From, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
static <S extends Sequence<S>> Mutations<S>	MutationsUtil.shiftIndelsAtHomopolymers(S seq1, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Constructors in com.milaboratory.core.mutations with parameters of type Mutations

Constructor and Description
MutationsEnumerator(Mutations mutations)
MutationsUtil.MutationsWitMapping(Mutations<AminoAcidSequence> mutations, int[] mapping)

Uses of Mutations in com.milaboratory.core.mutations.generator

Methods in com.milaboratory.core.mutations.generator that return Mutations

Modifier and Type	Method and Description
static <S extends Sequence<S>> Mutations<S>	UniformMutationsGenerator.createUniformMutationAsObject(S sequence, org.apache.commons.math3.random.RandomGenerator generator)
static <S extends Sequence<S>> Mutations<S>	UniformMutationsGenerator.createUniformMutationAsObject(S sequence, org.apache.commons.math3.random.RandomGenerator generator, MutationType type)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, int from, int to)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, Range range)

Uses of Mutations in com.milaboratory.core.tree

Methods in com.milaboratory.core.tree that return Mutations

Modifier and Type	Method and Description
Mutations<S>	NeighborhoodIterator.getCurrentMutations()