Uses of Class
com.milaboratory.core.sequence.Sequence

Packages that use Sequence

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.batch
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.blast
com.milaboratory.core.clustering
com.milaboratory.core.io.sequence.fasta
com.milaboratory.core.motif
com.milaboratory.core.mutations
com.milaboratory.core.mutations.generator
com.milaboratory.core.sequence
com.milaboratory.core.sequence.provider
com.milaboratory.core.tree

Uses of Sequence in com.milaboratory.core.alignment

Classes in com.milaboratory.core.alignment with type parameters of type Sequence

Modifier and Type	Class and Description
class	AbstractAlignmentScoring<S extends Sequence<S>> AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
class	AffineGapAlignmentScoring<S extends Sequence<S>> AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
class	Alignment<S extends Sequence<S>>
interface	AlignmentIterator<S extends Sequence<S>> Iterates over all positions in alignment
class	AlignmentIteratorForward<S extends Sequence<S>> Iterates over all positions in alignment
class	AlignmentIteratorReverse<S extends Sequence<S>> Iterates over all positions in alignment
interface	AlignmentScoring<S extends Sequence<S>> AlignmentScoring - interface which is to be implemented by any scoring system
class	BandedAlignerParameters<S extends Sequence<S>>
class	LinearGapAlignmentScoring<S extends Sequence<S>> LinearGapAlignmentScoring - scoring system which uses penalty for gap

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

Modifier and Type	Method and Description
static <S extends Sequence<S>> Alignment<S>	AlignerCustom.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>	Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2) Performs global alignment
static <S extends Sequence<S>> Alignment<S>	Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2)
static <S extends Sequence<S>> Alignment<S>	Aligner.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>	Aligner.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>	AlignerCustom.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>	AlignerCustom.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)
static <S extends Sequence<S>> Alignment<S>	Aligner.alignLocal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2) Performs local alignment
static <S extends Sequence<S>> Alignment<S>	Aligner.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>	Aligner.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>	Aligner.alignOnlySubstitutions(S from, S to)
static <S extends Sequence<S>> Alignment<S>	Aligner.alignOnlySubstitutions(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring)
static <S extends Sequence<S>> int	Aligner.alignOnlySubstitutions0(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring, MutationsBuilder<S> builder)
static <S extends Sequence<S>> MultiAlignmentHelper	MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings, Range subjectRange, Alignment<S>... alignments)
static <S extends Sequence<S>> MultiAlignmentHelper	MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings, Range subjectRange, S subject, Alignment<S>... alignments)
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>> S	AlignmentUtils.getAlignedSequence2Part(Alignment<S> alignment)
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment, AlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment, LinearGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment, AlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment, LinearGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static <S extends Sequence<S>> Alignment<S>	AlignmentUtils.shiftIndelsAtHomopolymers(Alignment<S> alignment) Shifts indels to the left at homopolymer regions
static <S extends Sequence<S>> String	AlignmentUtils.toStringSimple(S initialSequence, Mutations<S> mutations)

Uses of Sequence in com.milaboratory.core.alignment.batch

Classes in com.milaboratory.core.alignment.batch with type parameters of type Sequence

Modifier and Type	Class and Description
class	AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>
interface	AlignmentHit<S extends Sequence<S>,P>
class	AlignmentHitImpl<S extends Sequence<S>,P>
interface	BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>> Represents aligner that can align a sequence against a set of other sequences.
interface	BatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<S,P>> BatchAligner with self-managed database (user can directly add subject sequences before running alignment).
interface	BatchAlignerWithBaseWithFilter<S extends Sequence<S>,P,H extends AlignmentHit<S,P>>
interface	HasSequence<S extends Sequence<S>> Interface for objects which natively have a sequence as their distinctive property.
interface	PipedBatchAligner<S extends Sequence<S>,H extends AlignmentHit<? extends S,?>> Represents aligner that can align a sequence against a set of other sequences.
interface	PipedBatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<? extends S,? extends P>> PipedBatchAligner with self-managed database (user can directly add subject sequences before running alignment).
interface	SequenceExtractor<O,S extends Sequence<S>> Interface for class to extract sequences from objects
class	SimpleBatchAligner<S extends Sequence<S>,P> Simplest implementation of BatchAligner, which aligns target sequence with all subjects using classical (low performance) alignment algorithms.
class	SimpleBatchAlignerParameters<S extends Sequence<S>> Parameters of SimpleBatchAligner.
interface	WithBase<S extends Sequence<S>,P> Interface for aligners with self-managed database (user can directly add subject sequences before running alignment)

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

Methods in com.milaboratory.core.alignment.benchmark with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> S	ChallengeProvider.randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomDataGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
static <S extends Sequence<S>> S	ChallengeProvider.randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomGenerator r, int minLength, int maxLength, boolean basicLettersOnly)

Uses of Sequence in com.milaboratory.core.alignment.blast

Classes in com.milaboratory.core.alignment.blast with type parameters of type Sequence

Modifier and Type	Class and Description
class	BlastAligner<S extends Sequence<S>,P>
class	BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>>
class	BlastAlignerExt<S extends Sequence<S>>
class	BlastAlignerExtAbstract<S extends Sequence<S>,H extends BlastHitExt<S>> Blast aligner of query sequences with external (non-milib-managed) database of sequences.
class	BlastDB<S extends Sequence<S>>
class	BlastHit<S extends Sequence<S>,P>
class	BlastHitExt<S extends Sequence<S>>

Methods in com.milaboratory.core.alignment.blast with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> BlastDB	BlastDBBuilder.build(List<S> sequences)
static <S extends Sequence<S>> BlastDB	BlastDBBuilder.build(List<S> sequences, boolean buildIdIndex)
static <S extends Sequence<S>> BlastDB<S>	BlastDB.get(String name)

Uses of Sequence in com.milaboratory.core.clustering

Classes in com.milaboratory.core.clustering with type parameters of type Sequence

Modifier and Type	Class and Description
class	Clustering<T,S extends Sequence<S>>
interface	ClusteringStrategy<T,S extends Sequence<S>>
interface	SequenceExtractor<T,S extends Sequence>

Methods in com.milaboratory.core.clustering with type parameters of type Sequence

Modifier and Type	Method and Description
static <T,S extends Sequence<S>> List<Cluster<T>>	Clustering.performClustering(Collection<T> inputObjects, SequenceExtractor<T,S> sequenceExtractor, ClusteringStrategy<T,S> strategy)

Uses of Sequence in com.milaboratory.core.io.sequence.fasta

Classes in com.milaboratory.core.io.sequence.fasta with type parameters of type Sequence

Modifier and Type	Class and Description
class	FastaReader<S extends Sequence<S>> Reads amino acid or nucleotide sequence from FASTA formatted file
class	FastaRecord<S extends Sequence<S>> Represents single fasta record
class	FastaWriter<S extends Sequence<S>> Writer of FASTA files.
class	RandomAccessFastaReader<S extends Sequence<S>>

Uses of Sequence in com.milaboratory.core.motif

Classes in com.milaboratory.core.motif with type parameters of type Sequence

Modifier and Type	Class and Description
class	Motif<S extends Sequence<S>> Data structure for efficient exact and fuzzy matching/searching of sequences (wildcard-aware).
class	MotifBuilder<S extends Sequence<S>>

Methods in com.milaboratory.core.motif with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> Motif<S>	MotifUtils.twoSequenceMotif(S seq1, int offset1, S seq2, int offset2, int length)

Methods in com.milaboratory.core.motif with parameters of type Sequence

Modifier and Type	Method and Description
BitapMatcher	BitapPattern.exactMatcher(Sequence sequence, int from, int to)
int	BitapPattern.exactSearch(Sequence sequence)
int	BitapPattern.exactSearch(Sequence sequence, int from)
int	BitapPattern.exactSearch(Sequence sequence, int from, int to)
BitapMatcher	BitapPattern.substitutionAndIndelMatcherFirst(int maxNumberOfErrors, Sequence sequence) Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
BitapMatcher	BitapPattern.substitutionAndIndelMatcherFirst(int maxNumberOfErrors, Sequence sequence, int from, int to) Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.
BitapMatcher	BitapPattern.substitutionAndIndelMatcherLast(int maxNumberOfErrors, Sequence sequence) Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
BitapMatcher	BitapPattern.substitutionAndIndelMatcherLast(int maxNumberOfErrors, Sequence sequence, int from, int to) Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.
BitapMatcher	BitapPattern.substitutionOnlyMatcherFirst(int substitutions, Sequence sequence) Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
BitapMatcher	BitapPattern.substitutionOnlyMatcherFirst(int substitutions, Sequence sequence, int from, int to) Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.

Uses of Sequence in com.milaboratory.core.mutations

Classes in com.milaboratory.core.mutations with type parameters of type Sequence

Modifier and Type	Class and Description
class	Mutations<S extends Sequence<S>>
class	MutationsBuilder<S extends Sequence<S>>

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

Modifier and Type	Method and Description
<S extends Sequence<S>> Mutations<S>	MutationsCounter.build(Alphabet<S> alphabet, MutationsCounter.Filter filter)
static <S extends Sequence<S>> Mutations<S>	Mutations.decode(String string, Alphabet<S> alphabet)
static <S extends Sequence<S>> Mutations<S>	Mutations.empty(Alphabet<S> alphabet)
static <S extends Sequence> boolean	MutationsUtil.isCompatibleWithSequence(S sequence, int[] mutations)
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 Sequence

Modifier and Type	Method and Description
static void	MutationsUtil.shiftIndelsAtHomopolymers(Sequence seq1, int[] 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 void	MutationsUtil.shiftIndelsAtHomopolymers(Sequence seq1, int seq1From, int[] 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

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

Methods in com.milaboratory.core.mutations.generator with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> int	UniformMutationsGenerator.createUniformMutation(S sequence, org.apache.commons.math3.random.RandomGenerator generator)
static <S extends Sequence<S>> int	UniformMutationsGenerator.createUniformMutation(S sequence, org.apache.commons.math3.random.RandomGenerator generator, MutationType type)
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)

Uses of Sequence in com.milaboratory.core.sequence

Classes in com.milaboratory.core.sequence with type parameters of type Sequence

Modifier and Type	Class and Description
class	Alphabet<S extends Sequence<S>> Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
class	Sequence<S extends Sequence<S>> Parent class for all types of sequences.
interface	SequenceBuilder<S extends Sequence<S>> Interface for factory class for a certain type of sequence.
class	SequenceWithQuality<S extends Sequence<S>> A container of sequence and its quality.

Subclasses of Sequence in com.milaboratory.core.sequence

Modifier and Type	Class and Description
class	AminoAcidSequence Representation of amino acid sequences.
class	NucleotideSequence Representation of nucleotide sequence.

Methods in com.milaboratory.core.sequence with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> int	SequencesUtils.mismatchCount(S seq0, int seq0Offset, S seq1, int seq1Offset, int length) Calculates number of mismatches (comparing position by position) between two regions of one or two different sequences.
static <S extends Sequence<S>> S	SequencesUtils.wildcardsToRandomBasic(S sequence, long seed) Converts sequence with wildcards to a sequence without wildcards by converting wildcard letters to uniformly distributed letters from the set of letters allowed by the wildcard.

Uses of Sequence in com.milaboratory.core.sequence.provider

Classes in com.milaboratory.core.sequence.provider with type parameters of type Sequence

Modifier and Type	Class and Description
class	CachedSequenceProvider<S extends Sequence<S>>
interface	SequenceProvider<S extends Sequence<S>> Provides access to the sequence that may be too big to be loaded to the memory.
interface	SequenceProviderFactory<S extends Sequence<S>>
static class	SequenceProviderUtils.LazySequenceProvider<S extends Sequence<S>>

Methods in com.milaboratory.core.sequence.provider with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<S>> SequenceProvider<S>	SequenceProviderUtils.fromSequence(S sequence)
static <S extends Sequence<S>> SequenceProvider<S>	SequenceProviderUtils.lazyProvider(SequenceProviderFactory<S> factory)
static <S extends Sequence<S>> SequenceProvider<S>	SequenceProviderUtils.subProvider(SequenceProvider<S> provider, Range targetRange)

Uses of Sequence in com.milaboratory.core.tree

Classes in com.milaboratory.core.tree with type parameters of type Sequence

Modifier and Type	Interface and Description
interface	MutationGuide<S extends Sequence<S>>
class	NeighborhoodIterator<S extends Sequence<S>,O> Created by dbolotin on 25/06/14.
class	SequenceTreeMap<S extends Sequence<S>,O> Sequence tree map, with fast neighbours search.