| 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
|
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<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>> |
Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs global alignment
|
static <S extends Sequence<S>> |
Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2) |
static <S extends Sequence<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>> |
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>> |
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>> |
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>> |
Aligner.alignLocal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs local alignment
|
static <S extends Sequence<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>> |
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>> |
Aligner.alignOnlySubstitutions(S from,
S to) |
static <S extends Sequence<S>> |
Aligner.alignOnlySubstitutions(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring) |
static <S extends Sequence<S>> |
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.build(MultiAlignmentHelper.Settings settings,
Range subjectRange,
Alignment<S>... alignments) |
static <S extends Sequence<S>> |
MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings,
Range subjectRange,
S subject,
Alignment<S>... alignments) |
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AffineGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
LinearGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.getAlignedSequence2Part(Alignment<S> alignment) |
static <S extends Sequence<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>> |
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>> |
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>> |
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>> |
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>> |
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>> |
AlignmentUtils.shiftIndelsAtHomopolymers(Alignment<S> alignment)
Shifts indels to the left at homopolymer regions
|
static <S extends Sequence<S>> |
AlignmentUtils.toStringSimple(S initialSequence,
Mutations<S> mutations) |
| 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)
|
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
ChallengeProvider.randomSequence(Alphabet<S> alphabet,
org.apache.commons.math3.random.RandomDataGenerator r,
int minLength,
int maxLength,
boolean basicLettersOnly) |
static <S extends Sequence<S>> |
ChallengeProvider.randomSequence(Alphabet<S> alphabet,
org.apache.commons.math3.random.RandomGenerator r,
int minLength,
int maxLength,
boolean basicLettersOnly) |
| 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>> |
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
BlastDBBuilder.build(List<S> sequences) |
static <S extends Sequence<S>> |
BlastDBBuilder.build(List<S> sequences,
boolean buildIdIndex) |
static <S extends Sequence<S>> |
BlastDB.get(String name) |
| 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> |
| Modifier and Type | Method and Description |
|---|---|
static <T,S extends Sequence<S>> |
Clustering.performClustering(Collection<T> inputObjects,
SequenceExtractor<T,S> sequenceExtractor,
ClusteringStrategy<T,S> strategy) |
| 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>> |
| 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>> |
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
MotifUtils.twoSequenceMotif(S seq1,
int offset1,
S seq2,
int offset2,
int length) |
| 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. |
| Modifier and Type | Class and Description |
|---|---|
class |
Mutations<S extends Sequence<S>> |
class |
MutationsBuilder<S extends Sequence<S>> |
| Modifier and Type | Method and Description |
|---|---|
<S extends Sequence<S>> |
MutationsCounter.build(Alphabet<S> alphabet,
MutationsCounter.Filter filter) |
static <S extends Sequence<S>> |
Mutations.decode(String string,
Alphabet<S> alphabet) |
static <S extends Sequence<S>> |
Mutations.empty(Alphabet<S> alphabet) |
static <S extends Sequence> |
MutationsUtil.isCompatibleWithSequence(S sequence,
int[] mutations) |
static <S extends Sequence<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>> |
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
|
| 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
|
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutation(S sequence,
org.apache.commons.math3.random.RandomGenerator generator) |
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutation(S sequence,
org.apache.commons.math3.random.RandomGenerator generator,
MutationType type) |
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutationAsObject(S sequence,
org.apache.commons.math3.random.RandomGenerator generator) |
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutationAsObject(S sequence,
org.apache.commons.math3.random.RandomGenerator generator,
MutationType type) |
| 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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AminoAcidSequence
Representation of amino acid sequences.
|
class |
NucleotideSequence
Representation of nucleotide sequence.
|
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
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>> |
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.
|
| 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>> |
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
SequenceProviderUtils.fromSequence(S sequence) |
static <S extends Sequence<S>> |
SequenceProviderUtils.lazyProvider(SequenceProviderFactory<S> factory) |
static <S extends Sequence<S>> |
SequenceProviderUtils.subProvider(SequenceProvider<S> provider,
Range targetRange) |
| 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.
|
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