Index (MiLib 1.8.3 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Alanine byte representation
A - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Adenine byte representation
A_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Alanine wildcard
A_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Adenine byte representation
AABlastAligner - Class in com.milaboratory.core.alignment.blast
AABlastAligner() - Constructor for class com.milaboratory.core.alignment.blast.AABlastAligner
AABlastAligner(BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.AABlastAligner
AABlastAlignerExt - Class in com.milaboratory.core.alignment.blast
AABlastAlignerExt(BlastDB) - Constructor for class com.milaboratory.core.alignment.blast.AABlastAlignerExt
AABlastAlignerExt(BlastDB, BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.AABlastAlignerExt
AABlastHit - Class in com.milaboratory.core.alignment.blast
AABlastHit(Alignment<AminoAcidSequence>, P, BlastHit<AminoAcidSequence, ?>) - Constructor for class com.milaboratory.core.alignment.blast.AABlastHit
AABlastHit(Alignment<AminoAcidSequence>, P, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.AABlastHit
AABlastHitExt - Class in com.milaboratory.core.alignment.blast
AABlastHitExt(Alignment<AminoAcidSequence>, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.AABlastHitExt
aabs(int) - Static method in class com.milaboratory.core.alignment.Alignment
AbstractAlignmentScoring<S extends Sequence<S>> - Class in com.milaboratory.core.alignment: AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
AbstractAlignmentScoring(Alphabet<S>, SubstitutionMatrix) - Constructor for class com.milaboratory.core.alignment.AbstractAlignmentScoring: Abstract class constructor.
AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>> - Class in com.milaboratory.core.alignment.batch
AbstractBatchAligner() - Constructor for class com.milaboratory.core.alignment.batch.AbstractBatchAligner
AbstractKAlignerParameters - Interface in com.milaboratory.core.alignment.kaligner1
AbstractLongProcessReporter - Class in com.milaboratory.util
AbstractLongProcessReporter() - Constructor for class com.milaboratory.util.AbstractLongProcessReporter
AbstractLongProcessReporter(long, double) - Constructor for class com.milaboratory.util.AbstractLongProcessReporter
AbstractMultiReader<R extends SequenceRead> - Class in com.milaboratory.core.io.sequence: Created by dbolotin on 23/06/14.
AbstractMultiReader(SingleReader...) - Constructor for class com.milaboratory.core.io.sequence.AbstractMultiReader
AbstractRandomAccessReader<T> - Class in com.milaboratory.core.io.util: Abstract class that allows random access to some records written in file.
AbstractRandomAccessReader(FileIndex, RandomAccessFile) - Constructor for class com.milaboratory.core.io.util.AbstractRandomAccessReader
AbstractSeq<S extends AbstractSeq<S>> - Class in com.milaboratory.core.sequence
AbstractSeq() - Constructor for class com.milaboratory.core.sequence.AbstractSeq
AbstractSequenceReader<R extends SequenceRead> - Class in com.milaboratory.core.io.sequence
AbstractSequenceReader() - Constructor for class com.milaboratory.core.io.sequence.AbstractSequenceReader
accept(long, int, int, int[]) - Method in interface com.milaboratory.core.mutations.MutationsCounter.Filter
Action - Interface in com.milaboratory.cli: Created by dbolotin on 20/08/14.
ActionHelper - Interface in com.milaboratory.cli
ActionHelpProvider - Interface in com.milaboratory.cli
ActionParameters - Class in com.milaboratory.cli
ActionParameters() - Constructor for class com.milaboratory.cli.ActionParameters
ActionParametersParser - Interface in com.milaboratory.cli
ActionParametersWithOutput - Class in com.milaboratory.cli
ActionParametersWithOutput() - Constructor for class com.milaboratory.cli.ActionParametersWithOutput
actions - Variable in class com.milaboratory.cli.JCommanderBasedMain
add(Cluster<T>) - Method in class com.milaboratory.core.clustering.Cluster
add(E) - Method in class com.milaboratory.util.AtomicEnumHistogram
add(double) - Method in class com.milaboratory.util.AtomicHistogram
add(int) - Method in class com.milaboratory.util.IntArrayList
add(int, int) - Method in class com.milaboratory.util.IntArrayList
add(int[], int, int) - Method in class com.milaboratory.util.IntArrayList: Copies an array from the specified source array, beginning at the specified position.
add0(long, long) - Static method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
add1(long, long) - Static method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
add2(long, long) - Static method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
add3(long, long) - Static method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
addAll(int[]) - Method in class com.milaboratory.util.IntArrayList
addAll(IntArrayList) - Method in class com.milaboratory.util.IntArrayList
addAnnotationString(String, String) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
addArgumentsTo(List<String>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
addEnvVariablesTo(ProcessBuilder) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
addIndexPoint(long) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
addOneRead() - Method in class com.milaboratory.core.io.sequence.AbstractSequenceReader
addRecord(String, long) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
addReference(S, P) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAligner
addReference(S, P) - Method in interface com.milaboratory.core.alignment.batch.WithBase: Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries with).
addReference(S, P) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
addReference(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Adds new reference sequence to the base of this aligner and returns index assigned to it.
addReference(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Adds new reference sequence to the base of this mapper and returns index assigned to it.
addReference(NucleotideSequence, P) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner
addReference(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Adds new reference sequence to the base of this mapper and returns index assigned to it.
addReference(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Adds new reference sequence to the base of this mapper and returns index assigned to it.
addReference(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2: Adds new reference sequence to the base of this mapper and returns index assigned to it.
addReference(NucleotideSequence, P) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2
addReference(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Adds new reference sequence to the base of this mapper and returns index assigned to it.
addSubjectQuality(String, SequenceQuality) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
adjust(Mutations<?>, int) - Method in class com.milaboratory.core.mutations.MutationsCounter
adjust(Mutations<?>, MutationsEnumerator, int) - Method in class com.milaboratory.core.mutations.MutationsCounter
advance() - Method in interface com.milaboratory.core.alignment.AlignmentIterator: Advance iterator to the next position
advance() - Method in class com.milaboratory.core.alignment.AlignmentIteratorForward: Advance to the next alignment position
advance() - Method in class com.milaboratory.core.alignment.AlignmentIteratorReverse: Advance to the next alignment position
AffineGapAlignmentScoring<S extends Sequence<S>> - Class in com.milaboratory.core.alignment: AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
AffineGapAlignmentScoring(Alphabet<S>, SubstitutionMatrix, int, int) - Constructor for class com.milaboratory.core.alignment.AffineGapAlignmentScoring
AffineGapAlignmentScoring(Alphabet<S>, int[], int, int) - Constructor for class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Creates new AffineGapScoring
AffineGapAlignmentScoring(Alphabet<S>, int, int, int, int) - Constructor for class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Creates scoring with uniform match and mismatch scores
AffineGapAlignmentScoring.SerializationObject - Class in com.milaboratory.core.alignment
AffineGapAlignmentScoring.SerializationObject() - Constructor for class com.milaboratory.core.alignment.AffineGapAlignmentScoring.SerializationObject
AffineGapAlignmentScoring.SerializationObject(Alphabet, SubstitutionMatrix, int, int) - Constructor for class com.milaboratory.core.alignment.AffineGapAlignmentScoring.SerializationObject
afterCandidatesArrayDone(IntArrayList[]) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
afterTrimming(int, IntArrayList) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
afterUntangling(IntArrayList) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
aggregate(Range, CoverageCounter.Provider) - Method in class com.milaboratory.core.mutations.CoverageCounter
aggregate(Range, int) - Method in class com.milaboratory.core.mutations.CoverageCounter
aggregate(Alignment<?>, CoverageCounter.Provider) - Method in class com.milaboratory.core.mutations.MutationConsensusBuilder
aggregate(SequenceQuality) - Method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
aggregate(SequenceQuality) - Method in class com.milaboratory.core.sequence.quality.MaximalQualityAggregator
aggregate(SequenceQuality) - Method in class com.milaboratory.core.sequence.quality.MinimalQualityAggregator
aggregate(SequenceQuality) - Method in class com.milaboratory.core.sequence.quality.MiniMaxQualityAggregator
aggregate(SequenceQuality) - Method in interface com.milaboratory.core.sequence.quality.QualityAggregator
aggregate(SequenceQuality) - Method in class com.milaboratory.core.sequence.quality.SumQualityAggregator
align(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
align(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
align(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Classical Banded Alignment
align(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Classical Banded Alignment
align(S) - Method in class com.milaboratory.core.alignment.batch.AbstractBatchAligner
align(OutputPort<Q>, SequenceExtractor<Q, S>) - Method in class com.milaboratory.core.alignment.batch.AbstractBatchAligner
align(OutputPort<Q>) - Method in class com.milaboratory.core.alignment.batch.AbstractBatchAligner
align(S) - Method in interface com.milaboratory.core.alignment.batch.BatchAligner
align(S, int, int) - Method in interface com.milaboratory.core.alignment.batch.BatchAligner
align(S, int, int, BitArray) - Method in interface com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter
align(OutputPort<Q>, SequenceExtractor<Q, S>) - Method in interface com.milaboratory.core.alignment.batch.PipedBatchAligner: Starts processing of input sequences and returns pipe of results.
align(OutputPort<Q>) - Method in interface com.milaboratory.core.alignment.batch.PipedBatchAligner: Starts processing of input sequences and returns pipe of results.
align(S, int, int) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAligner
align(S) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAligner
align(OutputPort<Q>, SequenceExtractor<Q, S>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
align(OutputPort<Q>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
align(OutputPort<Q>, SequenceExtractor<Q, S>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
align(OutputPort<Q>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
align(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Performs a comprehensive alignment of a sequence.
align(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Performs a comprehensive alignment of a sequence.
align(NucleotideSequence, int, int, boolean, BitArray) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Performs a comprehensive alignment of a sequence.
align(NucleotideSequence, int, int, BitArray) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner
align(OutputPort<Q>, SequenceExtractor<Q, NucleotideSequence>) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner
align(OutputPort<Q>) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner
align(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Performs an alignment.
align(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Performs an alignment for a part of the target sequence.
align(NucleotideSequence, int, int, BitArray) - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Performs an alignment for a part of the target sequence.
align(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2
align(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2
align(NucleotideSequence, int, int, BitArray) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2
align(NucleotideSequence) - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Performs an alignment.
align(NucleotideSequence, int, int) - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Performs an alignment for a part of the target sequence.
align(NucleotideSequence, int, int, BitArray) - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Performs an alignment for a part of the target sequence.
align0(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, BandedAffineAligner.MatrixCache) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner: Classical Banded Alignment with affine gap scoring.
align0(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, CachedIntArray) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Classical Banded Alignment
alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S>, S, S, int, int, int, int, boolean, boolean, Alphabet<S>, AlignerCustom.AffineMatrixCache) - Static method in class com.milaboratory.core.alignment.AlignerCustom
Aligner - Class in com.milaboratory.core.alignment
AlignerCustom - Class in com.milaboratory.core.alignment: Collection of custom aligners
AlignerCustom() - Constructor for class com.milaboratory.core.alignment.AlignerCustom
AlignerCustom.AffineMatrixCache - Class in com.milaboratory.core.alignment
AlignerCustom.AffineMatrixCache() - Constructor for class com.milaboratory.core.alignment.AlignerCustom.AffineMatrixCache
AlignerCustom.LinearMatrixCache - Class in com.milaboratory.core.alignment
AlignerCustom.LinearMatrixCache() - Constructor for class com.milaboratory.core.alignment.AlignerCustom.LinearMatrixCache
AlignerCustom.Matrix - Class in com.milaboratory.core.alignment
AlignerCustom.Matrix(int[], int, int) - Constructor for class com.milaboratory.core.alignment.AlignerCustom.Matrix
AlignerCustom.MatrixCache - Interface in com.milaboratory.core.alignment
alignerTime - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
alignGlobal(AlignmentScoring<S>, S, S, int, int, int, int) - Static method in class com.milaboratory.core.alignment.Aligner
alignGlobal(AlignmentScoring<S>, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs global alignment
alignGlobal(AlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAligner: Classical Banded Alignment.
alignGlobalAffine(AffineGapAlignmentScoring<S>, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs global alignment using affine gap scoring system (different penalties exist for gap opening and gap extension)
alignGlobalLinear(LinearGapAlignmentScoring, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs global alignment using Linear scoring system (penalty exists only for gap)
alignLeftAdded(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Semi-semi-global alignment with artificially added letters.
alignLeftAdded0(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, CachedIntArray) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Semi-semi-global alignment with artificially added letters.
alignLinearSemiLocalLeft0(LinearGapAlignmentScoring<S>, S, S, int, int, int, int, boolean, boolean, Alphabet<S>, AlignerCustom.LinearMatrixCache) - Static method in class com.milaboratory.core.alignment.AlignerCustom: Align two sequences from left to right; left edges of both sequences considered to be already aligned.
alignLinearSemiLocalRight0(LinearGapAlignmentScoring<S>, S, S, int, int, int, int, boolean, boolean, Alphabet<S>, AlignerCustom.LinearMatrixCache) - Static method in class com.milaboratory.core.alignment.AlignerCustom
alignLocal(AlignmentScoring<S>, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs local alignment
alignLocalAffine(AffineGapAlignmentScoring<S>, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs local alignment using Affine gap scoring system (different penalties exist for gap opening and gap extension)
alignLocalLinear(LinearGapAlignmentScoring<S>, S, S) - Static method in class com.milaboratory.core.alignment.Aligner: Performs local alignment using Linear scoring system (penalty exists only for gap)
Alignment<S extends Sequence<S>> - Class in com.milaboratory.core.alignment
Alignment(S, Mutations<S>, float) - Constructor for class com.milaboratory.core.alignment.Alignment
Alignment(S, Mutations<S>, AlignmentScoring<S>) - Constructor for class com.milaboratory.core.alignment.Alignment
Alignment(S, Mutations<S>, Range, Range, AlignmentScoring<S>) - Constructor for class com.milaboratory.core.alignment.Alignment
Alignment(S, Mutations<S>, Range, Range, float) - Constructor for class com.milaboratory.core.alignment.Alignment
ALIGNMENT_SCORE_HIT_COMPARATOR - Static variable in class com.milaboratory.core.alignment.batch.BatchAlignmentUtil
AlignmentCache - Class in com.milaboratory.core.alignment: AlignmentCache - class which is providing cached array for BandedLinearAligner.
AlignmentHelper - Class in com.milaboratory.core.alignment
AlignmentHelper(String, String, int[], int[], BitArray) - Constructor for class com.milaboratory.core.alignment.AlignmentHelper
AlignmentHelper(String, String, int[], int[], BitArray, int) - Constructor for class com.milaboratory.core.alignment.AlignmentHelper
AlignmentHit<S extends Sequence<S>,P> - Interface in com.milaboratory.core.alignment.batch
AlignmentHitImpl<S extends Sequence<S>,P> - Class in com.milaboratory.core.alignment.batch
AlignmentHitImpl(Alignment<S>, P) - Constructor for class com.milaboratory.core.alignment.batch.AlignmentHitImpl
AlignmentIterator<S extends Sequence<S>> - Interface in com.milaboratory.core.alignment: Iterates over all positions in alignment
AlignmentIteratorForward<S extends Sequence<S>> - Class in com.milaboratory.core.alignment: Iterates over all positions in alignment
AlignmentIteratorForward(Mutations<S>, Range) - Constructor for class com.milaboratory.core.alignment.AlignmentIteratorForward: Create alignment iterator
AlignmentIteratorForward(Mutations<S>, Range, int) - Constructor for class com.milaboratory.core.alignment.AlignmentIteratorForward: Create alignment iterator
AlignmentIteratorReverse<S extends Sequence<S>> - Class in com.milaboratory.core.alignment: Iterates over all positions in alignment
AlignmentIteratorReverse(Mutations<S>, Range) - Constructor for class com.milaboratory.core.alignment.AlignmentIteratorReverse: Create alignment iterator
AlignmentIteratorReverse(Mutations<S>, Range, int) - Constructor for class com.milaboratory.core.alignment.AlignmentIteratorReverse: Create alignment iterator
AlignmentResult<H extends AlignmentHit<?,?>> - Interface in com.milaboratory.core.alignment.batch
AlignmentResultImpl<H extends AlignmentHit<?,?>> - Class in com.milaboratory.core.alignment.batch
AlignmentResultImpl() - Constructor for class com.milaboratory.core.alignment.batch.AlignmentResultImpl
AlignmentResultImpl(List<H>) - Constructor for class com.milaboratory.core.alignment.batch.AlignmentResultImpl
AlignmentScoring<S extends Sequence<S>> - Interface in com.milaboratory.core.alignment: AlignmentScoring - interface which is to be implemented by any scoring system
AlignmentSerializer - Class in com.milaboratory.core.io.binary
AlignmentSerializer() - Constructor for class com.milaboratory.core.io.binary.AlignmentSerializer
AlignmentTrimmer - Class in com.milaboratory.core.alignment
AlignmentTrimmer() - Constructor for class com.milaboratory.core.alignment.AlignmentTrimmer
AlignmentUtils - Class in com.milaboratory.core.alignment
alignOnlySubstitutions(S, S, int, int, int, int, AlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.Aligner
alignOnlySubstitutions(S, S) - Static method in class com.milaboratory.core.alignment.Aligner
alignOnlySubstitutions0(S, S, int, int, int, int, AlignmentScoring<S>, MutationsBuilder<S>) - Static method in class com.milaboratory.core.alignment.Aligner
alignPositions(MultiAlignmentHelper[]) - Static method in class com.milaboratory.core.alignment.MultiAlignmentHelper
alignRightAdded(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Semi-semi-global alignment with artificially added letters.
alignRightAdded0(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, CachedIntArray) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Semi-semi-global alignment with artificially added letters.
alignSemiLocalLeft(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
alignSemiLocalLeft(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
alignSemiLocalLeft0(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, CachedIntArray) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
alignSemiLocalRight(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
alignSemiLocalRight(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
alignSemiLocalRight0(LinearGapAlignmentScoring, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, CachedIntArray) - Static method in class com.milaboratory.core.alignment.BandedLinearAligner: Alignment which identifies what is the highly similar part of the both sequences.
allInitialClusters - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
allInitialRecordsCount - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
allowMutation(S, int, byte, byte) - Method in interface com.milaboratory.core.tree.MutationGuide
AllowNoArguments - Annotation Type in com.milaboratory.cli
allows(byte, int) - Method in class com.milaboratory.core.motif.Motif
allRemovedByTrimming - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
allRemovedByUntangling - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
allTrimming - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
allUntangledClusters - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
alphabet - Variable in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Link to alphabet
Alphabet<S extends Sequence<S>> - Class in com.milaboratory.core.sequence: Interface for sequence letters alphabet (amino acid, nucleotide, etc.).
ALPHABET - Static variable in class com.milaboratory.core.sequence.AminoAcidSequence: Amino acid alphabet
ALPHABET - Static variable in class com.milaboratory.core.sequence.NucleotideSequence: Nucleotide alphabet
alphabet - Variable in class com.milaboratory.core.tree.SequenceTreeMap
Alphabet.AlphabetSerialization - Class in com.milaboratory.core.sequence
Alphabet.AlphabetSerialization() - Constructor for class com.milaboratory.core.sequence.Alphabet.AlphabetSerialization
Alphabet.AlphabetSerialization(byte) - Constructor for class com.milaboratory.core.sequence.Alphabet.AlphabetSerialization
Alphabets - Class in com.milaboratory.core.sequence: Registry of all alphabets.
Alphabets.Deserializer - Class in com.milaboratory.core.sequence
Alphabets.Deserializer() - Constructor for class com.milaboratory.core.sequence.Alphabets.Deserializer
Alphabets.Serializer - Class in com.milaboratory.core.sequence
Alphabets.Serializer() - Constructor for class com.milaboratory.core.sequence.Alphabets.Serializer
AminoAcidAlphabet - Class in com.milaboratory.core.sequence: Amino acid alphabet with additional symbols.
aminoAcidPosition - Variable in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition: Position of amino acid in aa sequence
AminoAcidSequence - Class in com.milaboratory.core.sequence: Representation of amino acid sequences.
AminoAcidSequence(byte[]) - Constructor for class com.milaboratory.core.sequence.AminoAcidSequence: Creates sequence with specified data.
AminoAcidSequence(String) - Constructor for class com.milaboratory.core.sequence.AminoAcidSequence: Creates amino acid sequence from its string representation (case insensitive).
AminoAcidSequence.AminoAcidSequencePosition - Class in com.milaboratory.core.sequence: This class represents mapping of nucleotide sequence position onto translated amino acid sequence.
AminoAcidSequence.AminoAcidSequencePosition(int, int) - Constructor for class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
and(BitArray) - Method in class com.milaboratory.util.BitArray
append(Mutations<S>) - Method in class com.milaboratory.core.mutations.MutationsBuilder
append(MutationsBuilder<S>) - Method in class com.milaboratory.core.mutations.MutationsBuilder
append(Mutations<S>, int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
append(int[]) - Method in class com.milaboratory.core.mutations.MutationsBuilder
append(int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
append(byte) - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
append(S) - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
append(NSequenceWithQuality) - Method in class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
append(S) - Method in interface com.milaboratory.core.sequence.SeqBuilder: Appends seq.
append(byte) - Method in interface com.milaboratory.core.sequence.SequenceBuilder: Appends letter.
append(byte[]) - Method in interface com.milaboratory.core.sequence.SequenceBuilder: Appends letters array.
append(S) - Method in interface com.milaboratory.core.sequence.SequenceBuilder
appendDeletion(int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
appendDeletion(int, int, S) - Method in class com.milaboratory.core.mutations.MutationsBuilder
appendInsertion(int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
appendInsertion(int, S) - Method in class com.milaboratory.core.mutations.MutationsBuilder
appendNextRecord(long) - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Appends next record to this index builder and returns this.
appendSubstitution(int, int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
arguments - Variable in class com.milaboratory.cli.JCommanderBasedMain
ArrayIterator<T> - Class in com.milaboratory.util
ArrayIterator(T[]) - Constructor for class com.milaboratory.util.ArrayIterator
ArraySeqBuilder<S extends AbstractSeq<S>,B extends ArraySeqBuilder<S,B>> - Class in com.milaboratory.core.sequence
ArraysUtils - Class in com.milaboratory.util
asArray() - Method in class com.milaboratory.core.sequence.Sequence: Returns an array of bytes that encodes this sequence.
asArray() - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns an underlying array of bytes.
asRawRecordsPort() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader: Returns output port of raw records.
AtomicEnumHistogram<E extends Enum<E>> - Class in com.milaboratory.util
AtomicEnumHistogram(Class<E>) - Constructor for class com.milaboratory.util.AtomicEnumHistogram
AtomicEnumHistogram.SerializableResult - Class in com.milaboratory.util
AtomicEnumHistogram.SerializableResult(String[], long[]) - Constructor for class com.milaboratory.util.AtomicEnumHistogram.SerializableResult
AtomicHistogram - Class in com.milaboratory.util
AtomicHistogram(double[]) - Constructor for class com.milaboratory.util.AtomicHistogram
AtomicHistogram(int, int) - Constructor for class com.milaboratory.util.AtomicHistogram
AtomicHistogram(double, double, int) - Constructor for class com.milaboratory.util.AtomicHistogram
AtomicHistogram.SerializableResult - Class in com.milaboratory.util
AtomicHistogram.SerializableResult(double[], long, long[], double) - Constructor for class com.milaboratory.util.AtomicHistogram.SerializableResult
AverageQualityAggregator - Class in com.milaboratory.core.sequence.quality
AverageQualityAggregator(int) - Constructor for class com.milaboratory.core.sequence.quality.AverageQualityAggregator

B

B - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Aspartic acid or Asparagine (N or D) byte representation
B - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not A (B comes after A)
B_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Aspartic acid or Asparagine (N or D) wildcard
B_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not A (B comes after A)
BAD_QUALITY_VALUE - Static variable in class com.milaboratory.core.sequence.SequenceQuality: Default value of bad quality
BandedAffineAligner - Class in com.milaboratory.core.alignment
BandedAffineAligner.MatrixCache - Class in com.milaboratory.core.alignment
BandedAffineAligner.MatrixCache() - Constructor for class com.milaboratory.core.alignment.BandedAffineAligner.MatrixCache
BandedAligner - Class in com.milaboratory.core.alignment
BandedAligner() - Constructor for class com.milaboratory.core.alignment.BandedAligner
BandedAlignerParameters<S extends Sequence<S>> - Class in com.milaboratory.core.alignment
BandedAlignerParameters(AlignmentScoring<S>, int, int) - Constructor for class com.milaboratory.core.alignment.BandedAlignerParameters
BandedLinearAligner - Class in com.milaboratory.core.alignment
BandedMatrix - Class in com.milaboratory.core.alignment: BandedMatrix - class which used to store alignment matrix for BandedLinearAligner.
BandedMatrix(CachedIntArray, int, int, int) - Constructor for class com.milaboratory.core.alignment.BandedMatrix
BandedSemiLocalResult - Class in com.milaboratory.core.alignment: BandedSemiLocalResult - class which is result of BandedSemiLocal alignment.
BandedSemiLocalResult(int, int, int) - Constructor for class com.milaboratory.core.alignment.BandedSemiLocalResult: Creates new BandedSemiLocalResult
basicSize() - Method in class com.milaboratory.core.sequence.Alphabet: Gets number of letters in this alphabet without wildcard letters
basicSize() - Method in class com.milaboratory.core.sequence.Wildcard: Returns a number of basic letters that matches this wildcard.
BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>> - Interface in com.milaboratory.core.alignment.batch: Represents aligner that can align a sequence against a set of other sequences.
BatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<S,P>> - Interface in com.milaboratory.core.alignment.batch: BatchAligner with self-managed database (user can directly add subject sequences before running alignment).
BatchAlignerWithBaseParameters - Interface in com.milaboratory.core.alignment.batch
BatchAlignerWithBaseWithFilter<S extends Sequence<S>,P,H extends AlignmentHit<S,P>> - Interface in com.milaboratory.core.alignment.batch
BatchAlignmentUtil - Class in com.milaboratory.core.alignment.batch
BatchAlignmentUtil() - Constructor for class com.milaboratory.core.alignment.batch.BatchAlignmentUtil
beforeClose() - Method in class com.milaboratory.primitivio.PipeWriter
beforeClose() - Method in class com.milaboratory.primitivio.PWriter
belongsToAlphabet(Alphabet<?>, String) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Check if a sequence contains letters only from specified alphabet.
Benchmark<T extends BatchAlignerWithBaseParameters> - Class in com.milaboratory.core.alignment.benchmark
Benchmark(long) - Constructor for class com.milaboratory.core.alignment.benchmark.Benchmark
Benchmark(long, long) - Constructor for class com.milaboratory.core.alignment.benchmark.Benchmark
Benchmark.ExceptionData - Class in com.milaboratory.core.alignment.benchmark
Benchmark.ExceptionData(long, Throwable, NucleotideSequence[], NucleotideSequence, BenchmarkInput) - Constructor for class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
Benchmark.ExceptionListener - Interface in com.milaboratory.core.alignment.benchmark
BenchmarkInput<T extends BatchAlignerWithBaseParameters> - Class in com.milaboratory.core.alignment.benchmark: Created by dbolotin on 27/10/15.
BenchmarkInput(T, Challenge) - Constructor for class com.milaboratory.core.alignment.benchmark.BenchmarkInput
BenchmarkResults - Class in com.milaboratory.core.alignment.benchmark
BenchmarkResults(BenchmarkInput, KAligner2Statistics, long, int, int, int, int, int, int) - Constructor for class com.milaboratory.core.alignment.benchmark.BenchmarkResults
Bit2Array - Class in com.milaboratory.util
Bit2Array(int) - Constructor for class com.milaboratory.util.Bit2Array
BitapMatcher - Interface in com.milaboratory.core.motif
BitapMatcherFilter - Class in com.milaboratory.core.motif
BitapMatcherFilter(BitapMatcher) - Constructor for class com.milaboratory.core.motif.BitapMatcherFilter
BitapMatcherImpl - Class in com.milaboratory.core.motif
BitapMatcherImpl(int, int, int) - Constructor for class com.milaboratory.core.motif.BitapMatcherImpl
BitapPattern - Class in com.milaboratory.core.motif: Use Motif.getBitapPattern() to create bitap pattern.
BitArray - Class in com.milaboratory.util
BitArray(List<Boolean>) - Constructor for class com.milaboratory.util.BitArray
BitArray(boolean...) - Constructor for class com.milaboratory.util.BitArray
BitArray(int) - Constructor for class com.milaboratory.util.BitArray
bitCount() - Method in class com.milaboratory.util.BitArray
Blast - Class in com.milaboratory.core.alignment.blast: This class stores Blast path and manages interaction between JVM and binary blast commands.
Blast() - Constructor for class com.milaboratory.core.alignment.blast.Blast
BlastAligner<S extends Sequence<S>,P> - Class in com.milaboratory.core.alignment.blast
BlastAligner() - Constructor for class com.milaboratory.core.alignment.blast.BlastAligner
BlastAligner(BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.BlastAligner
BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>> - Class in com.milaboratory.core.alignment.blast
BlastAlignerAbstract() - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
BlastAlignerAbstract(BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
BlastAlignerExt<S extends Sequence<S>> - Class in com.milaboratory.core.alignment.blast
BlastAlignerExt(BlastDB) - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerExt
BlastAlignerExt(BlastDB, BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerExt
BlastAlignerExtAbstract<S extends Sequence<S>,H extends BlastHitExt<S>> - Class in com.milaboratory.core.alignment.blast: Blast aligner of query sequences with external (non-milib-managed) database of sequences.
BlastAlignerExtAbstract(BlastDB) - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
BlastAlignerExtAbstract(BlastDB, BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
BlastAlignerParameters - Class in com.milaboratory.core.alignment.blast
BlastAlignerParameters() - Constructor for class com.milaboratory.core.alignment.blast.BlastAlignerParameters
BlastDB<S extends Sequence<S>> - Class in com.milaboratory.core.alignment.blast
BlastDB(String, String, long, long, Alphabet<S>, List<String>, boolean) - Constructor for class com.milaboratory.core.alignment.blast.BlastDB
BlastDBBuilder - Class in com.milaboratory.core.alignment.blast
BlastDBBuilder() - Constructor for class com.milaboratory.core.alignment.blast.BlastDBBuilder
BlastHit<S extends Sequence<S>,P> - Class in com.milaboratory.core.alignment.blast
BlastHit(Alignment<S>, P, BlastHit<S, ?>) - Constructor for class com.milaboratory.core.alignment.blast.BlastHit
BlastHit(Alignment<S>, P, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.BlastHit
BlastHitExt<S extends Sequence<S>> - Class in com.milaboratory.core.alignment.blast
BlastHitExt(Alignment<S>, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.BlastHitExt
BLASTMatrix - Enum in com.milaboratory.core.alignment: BLASTMatrix - enum of available BLAST AminoAcid substitution matrices
BlastStrand - Enum in com.milaboratory.core.alignment.blast
BlastTask - Enum in com.milaboratory.core.alignment.blast
boundaries - Variable in class com.milaboratory.util.AtomicHistogram.SerializableResult
btopDecode(String, Alphabet) - Static method in class com.milaboratory.core.mutations.MutationsUtil: Decodes btop-encoded mutations.
build(List<S>) - Static method in class com.milaboratory.core.alignment.blast.BlastDBBuilder
build(List<S>, boolean) - Static method in class com.milaboratory.core.alignment.blast.BlastDBBuilder
build(MultiAlignmentHelper.Settings, Range, Alignment<S>...) - Static method in class com.milaboratory.core.alignment.MultiAlignmentHelper
build(MultiAlignmentHelper.Settings, Range, S, Alignment<S>...) - Static method in class com.milaboratory.core.alignment.MultiAlignmentHelper
build() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
build() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
build() - Method in class com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
build(Alphabet<S>, MutationsCounter.Filter) - Method in class com.milaboratory.core.mutations.MutationsCounter
build() - Method in class com.milaboratory.util.Sorter
byteSymbolToCode(byte) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet

C

C - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Cysteine byte representation
C - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Cytosine byte representation
C_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Cysteine wildcard
C_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Cytosine byte representation
CachedIntArray - Class in com.milaboratory.core.alignment: CachedIntArray - class which is used for storing alignment matrix.
CachedIntArray() - Constructor for class com.milaboratory.core.alignment.CachedIntArray
CachedSequenceProvider<S extends Sequence<S>> - Class in com.milaboratory.core.sequence.provider
CachedSequenceProvider(Alphabet<S>, SequenceProvider<S>) - Constructor for class com.milaboratory.core.sequence.provider.CachedSequenceProvider: Cached sequence provider wrapping specified sequence provider.
CachedSequenceProvider(Alphabet<S>, String) - Constructor for class com.milaboratory.core.sequence.provider.CachedSequenceProvider: Cached sequence provider without underlying sequence provider, with automatically inferred provider size.
CachedSequenceProvider(Alphabet<S>, int, String) - Constructor for class com.milaboratory.core.sequence.provider.CachedSequenceProvider: Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S>, int) - Constructor for class com.milaboratory.core.sequence.provider.CachedSequenceProvider: Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S>) - Constructor for class com.milaboratory.core.sequence.provider.CachedSequenceProvider: Cached sequence provider without underlying sequence provider, with automatically inferred provider size.
calculateAlignment() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
calculateAllAlignments() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Calculates alignments for all hits
calculateHit(int, IntArrayList, IntArrayList) - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Array list wrapper for KMapper2.calculateHit(int, int[], int, int, IntArrayList).
calculateInitialPartitioning(IntArrayList) - Method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
calculateInitialPartitioning(int[]) - Method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
calculateInitialPartitioning(int[], int, int) - Method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator: Accepts array with elements in the following format:
calculateScore(AlignmentScoring<S>) - Method in class com.milaboratory.core.alignment.Alignment: Calculates score for this alignment using another scoring.
calculateScore(S, Mutations<S>, AlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils: Calculates score of alignment
calculateScore(S, Range, Mutations<S>, AlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils: Calculates score of alignment
calculateScore(S, Range, Mutations<S>, LinearGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils: Calculates score of alignment
calculateScore(S, Range, Mutations<S>, AffineGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils: Calculates score of alignment
canAddToCluster(Cluster<T>, T, NeighborhoodIterator<S, T[]>) - Method in interface com.milaboratory.core.clustering.ClusteringStrategy
CanReportProgress - Interface in com.milaboratory.util
CanReportProgressAndStage - Interface in com.milaboratory.util
ceil() - Method in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
challenge - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkInput
Challenge - Class in com.milaboratory.core.alignment.benchmark
Challenge(NucleotideSequence[], List<KAlignerQuery>, ChallengeParameters, long) - Constructor for class com.milaboratory.core.alignment.benchmark.Challenge
ChallengeParameters - Class in com.milaboratory.core.alignment.benchmark: Created by dbolotin on 27/10/15.
ChallengeParameters(int, int, int, int, int, int, int, int, int, int, int, double, double, double, NucleotideMutationModel, int, int, AffineGapAlignmentScoring<NucleotideSequence>) - Constructor for class com.milaboratory.core.alignment.benchmark.ChallengeParameters
ChallengeProvider - Class in com.milaboratory.core.alignment.benchmark: Created by dbolotin on 27/10/15.
ChallengeProvider(ChallengeParameters, long) - Constructor for class com.milaboratory.core.alignment.benchmark.ChallengeProvider
changeOfTop1 - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
changeOfTop2 - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
chars(char, int) - Static method in class com.milaboratory.util.StringUtil
chechAlphabet(Alphabet<?>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
check(Mutations) - Static method in class com.milaboratory.core.mutations.MutationsUtil
check(int[]) - Static method in class com.milaboratory.core.mutations.MutationsUtil
clear(int) - Method in class com.milaboratory.util.BitArray
clear() - Method in class com.milaboratory.util.IntArrayList
clearAll() - Method in class com.milaboratory.util.BitArray
clone() - Method in class com.milaboratory.core.alignment.BandedAlignerParameters
clone() - Method in interface com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters
clone() - Method in interface com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
clone() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
clone() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
clone() - Method in class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
clone() - Method in interface com.milaboratory.core.mutations.generator.NucleotideMutationModel: Clones only parameters, the state is generated randomly.
clone() - Method in class com.milaboratory.core.mutations.MutationsBuilder
clone() - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
clone() - Method in class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
clone() - Method in interface com.milaboratory.core.sequence.SeqBuilder: Returns a deep copy of this builder
clone() - Method in interface com.milaboratory.core.sequence.SequenceBuilder
clone() - Method in class com.milaboratory.core.sequence.SequenceQualityBuilder
clone() - Method in class com.milaboratory.util.Bit2Array
clone() - Method in class com.milaboratory.util.BitArray
clone() - Method in class com.milaboratory.util.IntArrayList
close() - Method in class com.milaboratory.core.io.sequence.AbstractMultiReader
close() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader: Closes the reader
close() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
close() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper
close() - Method in class com.milaboratory.core.io.sequence.fasta.FastaWriter: Close writer.
close() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
close() - Method in class com.milaboratory.core.io.sequence.fastq.FastqRecordsReader: Closes the output port
close() - Method in class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
close() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
close() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
close() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
close() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Closes the output port
close() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
close() - Method in interface com.milaboratory.core.io.sequence.SequenceWriter: Closes this writer
close() - Method in class com.milaboratory.primitivio.PipeDataInputReader
close() - Method in class com.milaboratory.primitivio.PReader
close() - Method in class com.milaboratory.primitivio.PrimitivI
close() - Method in class com.milaboratory.primitivio.PrimitivO
close() - Method in class com.milaboratory.primitivio.PWriter
close() - Method in class com.milaboratory.util.CountingInputStream
close() - Method in interface com.milaboratory.util.LongProcess
closed - Variable in class com.milaboratory.primitivio.PReader
closed - Variable in class com.milaboratory.primitivio.PWriter
Cluster<T> - Class in com.milaboratory.core.clustering: Representation of single cluster.
Cluster(T) - Constructor for class com.milaboratory.core.clustering.Cluster
Cluster(T, Cluster<T>) - Constructor for class com.milaboratory.core.clustering.Cluster
Clustering<T,S extends Sequence<S>> - Class in com.milaboratory.core.clustering
Clustering(Collection<T>, SequenceExtractor<T, S>, ClusteringStrategy<T, S>) - Constructor for class com.milaboratory.core.clustering.Clustering
ClusteringStrategy<T,S extends Sequence<S>> - Interface in com.milaboratory.core.clustering
CMD_BLASTDBCMD - Static variable in class com.milaboratory.core.alignment.blast.Blast
CMD_BLASTN - Static variable in class com.milaboratory.core.alignment.blast.Blast
CMD_BLASTP - Static variable in class com.milaboratory.core.alignment.blast.Blast
CMD_MAKEBLASTDB - Static variable in class com.milaboratory.core.alignment.blast.Blast
codeAt(int) - Method in class com.milaboratory.core.sequence.Sequence: Returns letter code at specified position.
codeToSymbol(byte) - Method in class com.milaboratory.core.sequence.Alphabet: Gets a char symbol for an alphabet code of the letter
codeToWildcard(byte) - Method in class com.milaboratory.core.sequence.Alphabet: Returns wildcard defined by specified code (letter).
com.milaboratory.cli - package com.milaboratory.cli
com.milaboratory.core - package com.milaboratory.core
com.milaboratory.core.alignment - package com.milaboratory.core.alignment
com.milaboratory.core.alignment.batch - package com.milaboratory.core.alignment.batch
com.milaboratory.core.alignment.benchmark - package com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.blast - package com.milaboratory.core.alignment.blast
com.milaboratory.core.alignment.kaligner1 - package com.milaboratory.core.alignment.kaligner1
com.milaboratory.core.alignment.kaligner2 - package com.milaboratory.core.alignment.kaligner2
com.milaboratory.core.clustering - package com.milaboratory.core.clustering
com.milaboratory.core.io - package com.milaboratory.core.io
com.milaboratory.core.io.binary - package com.milaboratory.core.io.binary: Contains PrimitivIO (see com.milaboratory.primitivio) serializers for MiLib classes that don't need access to package only constructors and fields.
com.milaboratory.core.io.sequence - package com.milaboratory.core.io.sequence
com.milaboratory.core.io.sequence.fasta - package com.milaboratory.core.io.sequence.fasta
com.milaboratory.core.io.sequence.fastq - package com.milaboratory.core.io.sequence.fastq
com.milaboratory.core.io.util - package com.milaboratory.core.io.util
com.milaboratory.core.merger - package com.milaboratory.core.merger
com.milaboratory.core.motif - package com.milaboratory.core.motif
com.milaboratory.core.mutations - package com.milaboratory.core.mutations
com.milaboratory.core.mutations.generator - package com.milaboratory.core.mutations.generator
com.milaboratory.core.sequence - package com.milaboratory.core.sequence
com.milaboratory.core.sequence.provider - package com.milaboratory.core.sequence.provider
com.milaboratory.core.sequence.quality - package com.milaboratory.core.sequence.quality
com.milaboratory.core.tree - package com.milaboratory.core.tree
com.milaboratory.primitivio - package com.milaboratory.primitivio
com.milaboratory.primitivio.annotations - package com.milaboratory.primitivio.annotations
com.milaboratory.test - package com.milaboratory.test
com.milaboratory.util - package com.milaboratory.util
combineWith(Mutations<S>) - Method in class com.milaboratory.core.mutations.Mutations: Returns combined mutations array (this applied before other).
command() - Method in interface com.milaboratory.cli.Action
command - Variable in class com.milaboratory.cli.JCommanderBasedMain
COMPARATOR_BY_FROM - Static variable in class com.milaboratory.core.Range
compare(int, int) - Method in interface com.milaboratory.util.IntArrayList.IntComparator
compareTo(Range) - Method in class com.milaboratory.core.Range
compareTo(S) - Method in class com.milaboratory.core.sequence.Sequence
complementCode(byte) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet: Returns a complementary nucleotide code.
complementCode(Wildcard) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet: Returns a complementary nucleotide code.
complementWildcard(byte) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet: Returns a complementary wildcard object
complementWildcard(Wildcard) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet: Returns a complementary wildcard object
CompressionType - Enum in com.milaboratory.core.io
computeRawVarint32Size(int) - Static method in class com.milaboratory.core.io.util.IOUtil: Compute the number of bytes that would be needed to encode a varint.
computeRawVarint64Size(long) - Static method in class com.milaboratory.core.io.util.IOUtil: Compute the number of bytes that would be needed to encode a varint.
concat(Mutations<S>) - Method in class com.milaboratory.core.mutations.Mutations: Concatenates this and other
concatenate(S) - Method in class com.milaboratory.core.sequence.AbstractSeq
concatenate(NSequenceWithQuality) - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
concatenate(S) - Method in interface com.milaboratory.core.sequence.Seq: Returns a concatenation of this and other sequence (so this will be followed by other in the result).
concatenate(SequenceQuality...) - Method in class com.milaboratory.core.sequence.SequenceQuality
concatenate(S...) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Returns a concatenation of several sequences.
concatenate(int[], int...) - Static method in class com.milaboratory.util.ArraysUtils
concatenate(long[], long...) - Static method in class com.milaboratory.util.ArraysUtils
concatenate(T[], T...) - Static method in class com.milaboratory.util.ArraysUtils
constantDelta(int) - Static method in class com.milaboratory.core.mutations.CoverageCounter
construct(int, byte[]) - Static method in class com.milaboratory.util.Bit2Array
construct(byte[], int) - Static method in class com.milaboratory.util.BitArray
containIntersectingRanges(Range) - Method in class com.milaboratory.util.RangeMap
contains(int) - Method in class com.milaboratory.core.Range: Returns true if range contains provided position.
contains(Range) - Method in class com.milaboratory.core.Range: Returns true if range contains other range.
contains(int) - Method in class com.milaboratory.util.IntArrayList
containsBoundary(int) - Method in class com.milaboratory.core.Range
containStops() - Method in class com.milaboratory.core.sequence.AminoAcidSequence: Returns whether this sequence contains stop codons
containsWildcards(int, int) - Method in class com.milaboratory.core.sequence.NucleotideSequence: Returns true if sequence contains wildcards in specified region.
containsWildcards() - Method in class com.milaboratory.core.sequence.NucleotideSequence: Returns true if sequence contains wildcards.
containWildcards() - Method in class com.milaboratory.core.sequence.Sequence
convertAAPositionToNt(int, int, TranslationParameters) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence
convertAAPositionToNtFromCenter(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence
convertAAPositionToNtFromLeft(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence
convertAAPositionToNtFromRight(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence
convertBit2ArrayToNSequence(Bit2Array) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Used to read legacy file formats.
convertBoundariesToRelativePosition(int...) - Method in class com.milaboratory.core.Range
convertBoundaryToAbsolutePosition(int) - Method in class com.milaboratory.core.Range: Converts relative boundary position to absolute position
convertBoundaryToRelativePosition(int) - Method in class com.milaboratory.core.Range: Returns relative boundary position inside this range.
convertNSequenceToBit2Array(NucleotideSequence) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Used to write legacy file formats.
convertNtPositionToAA(int, int, TranslationParameters) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence
convertNtPositionToAAFromCenter(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Converts position from nucleotide to amino acid sequence if it was translated using AminoAcidSequence.translateFromCenter(NucleotideSequence).
convertNtPositionToAAFromLeft(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Converts position from nucleotide to amino acid sequence if it was translated using AminoAcidSequence.translateFromLeft(NucleotideSequence).
convertNtPositionToAAFromRight(int, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Converts position from nucleotide to amino acid sequence if it was translated using AminoAcidSequence.translateFromRight(NucleotideSequence).
convertPointsToRelativePosition(int...) - Method in class com.milaboratory.core.Range
convertPointToAbsolutePosition(int) - Method in class com.milaboratory.core.Range: Converts relative point position to absolute position
convertPointToRelativePosition(int) - Method in class com.milaboratory.core.Range: Returns relative point position inside this range.
convertToSeq1Position(int) - Method in class com.milaboratory.core.alignment.Alignment: Converts specified position from sequence2 coordinates to sequence1 coordinates.
convertToSeq1Position(int) - Method in class com.milaboratory.core.mutations.Mutations: Converts position from coordinates in seq2 (after mutation) to coordinates in seq1 (before mutation) using this alignment (mutations).
convertToSeq1Range(Range) - Method in class com.milaboratory.core.alignment.Alignment: Converts range in sequence2 to range in sequence1, or returns null if input range is not fully covered by alignment
convertToSeq2Position(int) - Method in class com.milaboratory.core.alignment.Alignment: Converts specified position from sequence1 coordinates to sequence2 coordinates.
convertToSeq2Position(int) - Method in class com.milaboratory.core.mutations.Mutations: Converts position from coordinates in seq1 (before mutation) to coordinates in seq2 (after mutation) using this alignment (mutations).
convertToSeq2Range(Range) - Method in class com.milaboratory.core.alignment.Alignment: Converts range in sequence1 to range in sequence2, or returns null if input range is not fully covered by alignment
copyFrom(Bit2Array, int, int, int) - Method in class com.milaboratory.util.Bit2Array
copyFrom(IntArrayList) - Method in class com.milaboratory.util.IntArrayList
count(int) - Method in class com.milaboratory.core.mutations.CoverageCounter
count(long) - Method in class com.milaboratory.util.CountingInputStream: Increments the counter of already read bytes.
countClusters(IntArrayList) - Static method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
countingInputStream - Variable in class com.milaboratory.primitivio.PReader
CountingInputStream - Class in com.milaboratory.util: Stream that tracks the number of bytes read.
CountingInputStream(InputStream) - Constructor for class com.milaboratory.util.CountingInputStream
countOf(MutationType) - Method in class com.milaboratory.core.mutations.Mutations
countOfIndels() - Method in class com.milaboratory.core.mutations.Mutations
CoverageCounter - Class in com.milaboratory.core.mutations
CoverageCounter(Range) - Constructor for class com.milaboratory.core.mutations.CoverageCounter
CoverageCounter(int, int) - Constructor for class com.milaboratory.core.mutations.CoverageCounter
CoverageCounter.Provider - Interface in com.milaboratory.core.mutations
coveredFraction - Variable in class com.milaboratory.util.AtomicHistogram.SerializableResult
create(QualityFormat, long, byte[], int, short, short, short, short, boolean) - Static method in class com.milaboratory.core.io.sequence.SingleReadLazy
create() - Method in interface com.milaboratory.core.sequence.provider.SequenceProviderFactory
create(int) - Method in enum com.milaboratory.core.sequence.quality.QualityAggregationType
create(QualityFormat, byte[], int, int, boolean) - Static method in class com.milaboratory.core.sequence.SequenceQuality: Factory method for the SequenceQualityPhred object.
create(QualityFormat, byte[], boolean) - Static method in class com.milaboratory.core.sequence.SequenceQuality: Factory method for the SequenceQualityPhred object.
create() - Method in interface com.milaboratory.util.Factory
createAligner() - Method in interface com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters
createAligner() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
createAligner() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
createAndDestroy() - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Creates FileIndex assembled by this builder.
createAndDestroy() - Method in class com.milaboratory.core.motif.MotifBuilder
createAndDestroy() - Method in class com.milaboratory.core.mutations.MutationsBuilder
createAndDestroy() - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
createAndDestroy() - Method in class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
createAndDestroy() - Method in interface com.milaboratory.core.sequence.SeqBuilder: Creates the sequence and destroys this builder.
createAndDestroy() - Method in interface com.milaboratory.core.sequence.SequenceBuilder
createBuilder() - Method in class com.milaboratory.core.sequence.Alphabet: Returns a sequence builder for corresponding sequence type.
createDeletion(int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createFilter(Filter) - Method in interface com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter
createFilter(Filter) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner
createFilter(Filter) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2
createFromParameters(KAlignerParameters) - Static method in class com.milaboratory.core.alignment.kaligner1.KMapper: Factory method to create KMapper using parametners specified in the KAlignerParameters object.
createFromParameters(KAlignerParameters2) - Static method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.
createFromParameters(KAlignerParameters2, KAligner2Statistics) - Static method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.
createHit(Alignment<AminoAcidSequence>, P, BlastHit<AminoAcidSequence, ?>) - Method in class com.milaboratory.core.alignment.blast.AABlastAligner
createHit(Alignment<AminoAcidSequence>, double, double, double, Range, String, String) - Method in class com.milaboratory.core.alignment.blast.AABlastAlignerExt
createHit(Alignment<S>, P, BlastHit<S, ?>) - Method in class com.milaboratory.core.alignment.blast.BlastAligner
createHit(Alignment<S>, P, BlastHit<S, ?>) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerAbstract
createHit(Alignment, double, double, double, Range, String, String) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerExt
createHit(Alignment<S>, double, double, double, Range, String, String) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
createHit(Alignment<NucleotideSequence>, P, BlastHit<NucleotideSequence, ?>) - Method in class com.milaboratory.core.alignment.blast.NBlastAligner
createHit(Alignment<NucleotideSequence>, double, double, double, Range, String, String) - Method in class com.milaboratory.core.alignment.blast.NBlastAlignerExt
createIfAbsent(S, Factory<O>) - Method in class com.milaboratory.core.tree.SequenceTreeMap
createIndex() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
createInputStream(InputStream) - Method in enum com.milaboratory.core.io.CompressionType
createInputStream(InputStream, int) - Method in enum com.milaboratory.core.io.CompressionType
createInsertion(int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createInstance() - Method in class com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1
createMutation(MutationType, int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createMutation(int, int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createMutation(MutationType, int, int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createMutation(int, int, int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createOutputStream(OutputStream) - Method in enum com.milaboratory.core.io.CompressionType
createOutputStream(OutputStream, int) - Method in enum com.milaboratory.core.io.CompressionType
createRead(long, QualityFormat) - Method in class com.milaboratory.core.io.sequence.fastq.FastqRecordsReader
createSerializer(Class<?>, SerializersManager) - Method in interface com.milaboratory.primitivio.DefaultSerializersProvider
createSerializer(Class<?>, SerializersManager) - Method in class com.milaboratory.primitivio.DefaultSerializersProviderImpl
createSubstitution(int, int, int) - Static method in class com.milaboratory.core.mutations.Mutation
createTargets(PairedRead) - Method in enum com.milaboratory.core.PairedEndReadsLayout
createTargets(SingleRead) - Method in enum com.milaboratory.core.PairedEndReadsLayout
createTargets(SequenceRead) - Method in enum com.milaboratory.core.PairedEndReadsLayout
createUniformMutation(S, RandomGenerator) - Static method in class com.milaboratory.core.mutations.generator.UniformMutationsGenerator
createUniformMutation(S, RandomGenerator, MutationType) - Static method in class com.milaboratory.core.mutations.generator.UniformMutationsGenerator
createUniformMutationAsObject(S, RandomGenerator) - Static method in class com.milaboratory.core.mutations.generator.UniformMutationsGenerator
createUniformMutationAsObject(S, RandomGenerator, MutationType) - Static method in class com.milaboratory.core.mutations.generator.UniformMutationsGenerator
cumulativeAAMutation - Variable in class com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
currentRecordNumber - Variable in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Current record number, i.e.
CustomSerializer - Annotation Type in com.milaboratory.primitivio.annotations
CustomSerializerImpl - Class in com.milaboratory.primitivio
CustomSerializerImpl(HashMap<Class<?>, CustomSerializerImpl.TypeInfo>) - Constructor for class com.milaboratory.primitivio.CustomSerializerImpl
CustomSerializerImpl.TypeInfo - Class in com.milaboratory.primitivio
CustomSerializerImpl.TypeInfo(byte, Serializer) - Constructor for class com.milaboratory.primitivio.CustomSerializerImpl.TypeInfo

D

D - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Aspartic Acid byte representation
D - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not C (D comes after C)
D_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Aspartic Acid wildcard
D_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not C (D comes after C)
db - Variable in class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
DECIMAL_FORMAT - Static variable in class com.milaboratory.test.Read
DECIMAL_FORMAT - Static variable in class com.milaboratory.util.TimeUtils
decode(String, Alphabet<S>) - Static method in class com.milaboratory.core.mutations.Mutations
decode(String, Alphabet) - Static method in class com.milaboratory.core.mutations.MutationsUtil: Decodes mutations encoded using format described in Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).
decodeAA(String) - Static method in class com.milaboratory.core.mutations.Mutations
decodeNuc(String) - Static method in class com.milaboratory.core.mutations.Mutations
decodeZigZag32(int) - Static method in class com.milaboratory.core.io.util.IOUtil: Decode a ZigZag-encoded 32-bit value.
decodeZigZag64(long) - Static method in class com.milaboratory.core.io.util.IOUtil: Decode a ZigZag-encoded 64-bit value.
DEFAULT_BUFFER_SIZE - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
DEFAULT_BUFFER_SIZE - Static variable in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
DEFAULT_BUFFER_SIZE - Static variable in class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
DEFAULT_INDEX_STEP - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Default index step = the most common HDD cluster size
DEFAULT_MAX_LENGTH - Static variable in class com.milaboratory.core.io.sequence.fasta.FastaWriter
DEFAULT_MAX_QUALITY_VALUE - Static variable in class com.milaboratory.core.merger.MergerParameters
DEFAULT_PENALTY - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
DEFAULT_QUALITY_FORMAT - Static variable in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: If FastqReader fails to guess file format, this value will be used by default.
DEFAULT_REPORTING_INTERVAL - Static variable in class com.milaboratory.util.AbstractLongProcessReporter: 1 second
DEFAULT_REPORTING_PROGRESS_DELTA - Static variable in class com.milaboratory.util.AbstractLongProcessReporter
DEFAULT_SETTINGS - Static variable in class com.milaboratory.core.alignment.MultiAlignmentHelper
DEFAULT_VALUE - Static variable in class com.milaboratory.core.alignment.BandedMatrix: Value of empty cell
DefaultSerializersProvider - Interface in com.milaboratory.primitivio
DefaultSerializersProviderImpl - Class in com.milaboratory.primitivio
DefaultSerializersProviderImpl() - Constructor for class com.milaboratory.primitivio.DefaultSerializersProviderImpl
DefaultSerializersProviderImpl.CustomEnumSerializer<E extends Enum<E>> - Class in com.milaboratory.primitivio: For Compatibility with previous format
DefaultSerializersProviderImpl.CustomEnumSerializer(Class<E>, E...) - Constructor for class com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer
delta(int) - Method in interface com.milaboratory.core.mutations.CoverageCounter.Provider
description - Variable in class com.milaboratory.core.io.sequence.fasta.FastaReader.RawFastaRecord
deserialize(JsonParser, DeserializationContext) - Method in class com.milaboratory.core.sequence.Alphabets.Deserializer
deserialize(JsonParser, DeserializationContext) - Method in class com.milaboratory.core.tree.TreeSearchParameters.Deserializer
detectCompressionType(File) - Static method in enum com.milaboratory.core.io.CompressionType
detectCompressionType(String) - Static method in enum com.milaboratory.core.io.CompressionType
DOT_MATCH_SETTINGS - Static variable in class com.milaboratory.core.alignment.MultiAlignmentHelper
DROPPED_CLUSTER - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
DUMMY_EXTRACTOR - Static variable in class com.milaboratory.core.alignment.batch.BatchAlignmentUtil

E

E - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamic Acid representation
E_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamic Acid wildcard
empty(Alphabet<S>) - Static method in class com.milaboratory.core.mutations.Mutations
EMPTY - Static variable in class com.milaboratory.core.sequence.AminoAcidSequence: Empty sequence
EMPTY - Static variable in class com.milaboratory.core.sequence.NSequenceWithQuality
EMPTY - Static variable in class com.milaboratory.core.sequence.NucleotideSequence: Empty instance
EMPTY - Static variable in class com.milaboratory.core.sequence.SequenceQuality
EMPTY_AMINO_ACID_MUTATIONS - Static variable in class com.milaboratory.core.mutations.Mutations: Identity mutations object for amino acid sequences.
EMPTY_NUCLEOTIDE_MUTATIONS - Static variable in class com.milaboratory.core.mutations.Mutations: Identity mutations object for nucleotide sequences.
enable() - Static method in class com.milaboratory.core.alignment.AlignmentCache: Enables CachedArray system
enclosingRange() - Method in class com.milaboratory.util.RangeMap: Return range enclosing all range-keys of this container.
encode(int, Alphabet) - Static method in class com.milaboratory.core.mutations.Mutation: Encodes single mutation in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
encode() - Method in class com.milaboratory.core.mutations.Mutations
encode(String) - Method in class com.milaboratory.core.mutations.Mutations
encode(int[], Alphabet) - Static method in class com.milaboratory.core.mutations.MutationsUtil: Encodes mutations in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
encode(int[], Alphabet, String) - Static method in class com.milaboratory.core.mutations.MutationsUtil: Encodes mutations in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
encode(int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Encodes current quality line with given offset.
encode(QualityFormat) - Method in class com.milaboratory.core.sequence.SequenceQuality: Encodes current quality line with given format.
encodeFixed(int, Alphabet) - Static method in class com.milaboratory.core.mutations.Mutation
encodeFixed() - Method in class com.milaboratory.core.mutations.Mutations
encodeFixed(int[], Alphabet) - Static method in class com.milaboratory.core.mutations.MutationsUtil
encodeTo(QualityFormat, byte[], int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Encodes current quality line with given offset.
encodeToString(int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Encodes current quality line with given offset.
encodeZigZag32(int) - Static method in class com.milaboratory.core.io.util.IOUtil: Encode a ZigZag-encoded 32-bit value.
encodeZigZag64(long) - Static method in class com.milaboratory.core.io.util.IOUtil: Encode a ZigZag-encoded 64-bit value.
ensureCapacity(int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
ensureCapacity(int) - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
ensureCapacity(int) - Method in class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
ensureCapacity(int) - Method in interface com.milaboratory.core.sequence.SeqBuilder: Ensures capacity of this builder.
ensureCapacity(int) - Method in interface com.milaboratory.core.sequence.SequenceBuilder
ensureCapacity(int) - Method in class com.milaboratory.util.IntArrayList
ensureEntry(Range) - Method in class com.milaboratory.core.sequence.provider.CachedSequenceProvider
ensureInternalCapacity(int) - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
entrySet() - Method in class com.milaboratory.core.sequence.provider.CachedSequenceProvider
entrySet() - Method in class com.milaboratory.util.RangeMap
equals(Object) - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
equals(Object) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
equals(Object) - Method in class com.milaboratory.core.alignment.Alignment
equals(Object) - Method in class com.milaboratory.core.alignment.BandedAlignerParameters
equals(Object) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
equals(Object) - Method in class com.milaboratory.core.alignment.kaligner1.KMappingHit
equals(Object) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
equals(Object) - Method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring
equals(Object) - Method in class com.milaboratory.core.clustering.Cluster
equals(Object) - Method in class com.milaboratory.core.io.sequence.fasta.FastaRecord
equals(Object) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
equals(Object) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord
equals(Object) - Method in class com.milaboratory.core.io.sequence.MultiRead
equals(Object) - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
equals(Object) - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
equals(Object) - Method in class com.milaboratory.core.merger.MergerParameters
equals(Object) - Method in class com.milaboratory.core.merger.PairedReadMergingResult
equals(Object) - Method in class com.milaboratory.core.motif.Motif
equals(Object) - Method in class com.milaboratory.core.mutations.Mutations
equals(Object) - Method in class com.milaboratory.core.Range
equals(Object) - Method in class com.milaboratory.core.sequence.Alphabet: Checks that in is the same object (this points to the same address as obj) All Alphabet implementations must be singletons.
equals(Object) - Method in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
equals(Object) - Method in class com.milaboratory.core.sequence.Sequence
equals(Object) - Method in class com.milaboratory.core.sequence.SequenceQuality
equals(Object) - Method in class com.milaboratory.core.sequence.SequenceWithQuality
equals(Object) - Method in class com.milaboratory.core.sequence.TranslationParameters
equals(Object) - Method in class com.milaboratory.core.tree.SequenceTreeMap.Node
equals(Object) - Method in class com.milaboratory.core.tree.TreeSearchParameters
equals(Object) - Method in class com.milaboratory.util.Bit2Array
equals(Object) - Method in class com.milaboratory.util.BitArray
equals(Object) - Method in class com.milaboratory.util.IntArrayList
exactMatcher(Sequence, int, int) - Method in class com.milaboratory.core.motif.BitapPattern
exactSearch(Sequence) - Method in class com.milaboratory.core.motif.BitapPattern
exactSearch(Sequence, int) - Method in class com.milaboratory.core.motif.BitapPattern
exactSearch(Sequence, int, int) - Method in class com.milaboratory.core.motif.BitapPattern
exception - Variable in class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
executionTime - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
expand(int) - Method in class com.milaboratory.core.Range
expand(int, int) - Method in class com.milaboratory.core.Range
expectedAlignment - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
extend(int) - Method in class com.milaboratory.util.Bit2Array
extract(O) - Method in interface com.milaboratory.core.alignment.batch.SequenceExtractor
extractAbsoluteMutationsForRange(Range) - Method in class com.milaboratory.core.mutations.Mutations: Extracts mutations for a range of positions in the original sequence.
extractAbsoluteMutationsForRange(int, int) - Method in class com.milaboratory.core.mutations.Mutations: Extracts mutations for a range of positions in the original sequence.
extractFilePosition(long) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Extracts file position part from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)
extractProgress(CountingOutputPort<?>, long) - Static method in class com.milaboratory.util.SmartProgressReporter
extractProgress(CountLimitingOutputPort<?>) - Static method in class com.milaboratory.util.SmartProgressReporter
extractRawDataArray(Bit2Array) - Static method in class com.milaboratory.util.Bit2Array
extractRawDataArray(BitArray) - Static method in class com.milaboratory.util.BitArray
extractRelativeMutationsForRange(Range) - Method in class com.milaboratory.core.mutations.Mutations: Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -range.from).
extractRelativeMutationsForRange(int, int) - Method in class com.milaboratory.core.mutations.Mutations: Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -from).
extractSkipLetters(long) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Extracts number of letters to skip from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)

F

F - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Phenylalanine byte representation
F_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Phenylalanine wildcard
Factory<T> - Interface in com.milaboratory.util
falsePositives - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
FastaReader<S extends Sequence<S>> - Class in com.milaboratory.core.io.sequence.fasta: Reads amino acid or nucleotide sequence from FASTA formatted file
FastaReader(InputStream, Alphabet<S>, long) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaReader: Creates reader from the specified input stream.
FastaReader(InputStream, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaReader: Creates reader for stream with unknown size.
FastaReader(String, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaReader: Creates FASTA reader for file
FastaReader(File, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaReader: Creates FASTA reader for file
FastaReader.RawFastaRecord - Class in com.milaboratory.core.io.sequence.fasta: Used internally
FastaRecord<S extends Sequence<S>> - Class in com.milaboratory.core.io.sequence.fasta: Represents single fasta record
FastaRecord(long, String, S) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaRecord: General constructor.
FastaSequenceReaderWrapper - Class in com.milaboratory.core.io.sequence.fasta: Converts FastaReader<NucleotideSequence> to SingleReader.
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence>) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence>, boolean) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
FastaSequenceWriterWrapper - Class in com.milaboratory.core.io.sequence.fasta
FastaSequenceWriterWrapper(String) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper
FastaWriter<S extends Sequence<S>> - Class in com.milaboratory.core.io.sequence.fasta: Writer of FASTA files.
FastaWriter(String) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaWriter: Creates FASTA writer
FastaWriter(File) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaWriter: Creates FASTA writer
FastaWriter(File, int) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaWriter: Creates FASTA writer
FastaWriter(OutputStream) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaWriter: Creates FASTA writer
FastaWriter(OutputStream, int) - Constructor for class com.milaboratory.core.io.sequence.fasta.FastaWriter: Creates FASTA writer
fastqParse(byte[], int, int, int, byte, long, boolean) - Static method in class com.milaboratory.core.sequence.UnsafeFactory
FastqRecordsReader - Class in com.milaboratory.core.io.sequence.fastq: High performance reader of FASTQ records.
FastqRecordsReader(boolean, RandomAccessFile, int, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.FastqRecordsReader: See main constructor for parameters.
FastqRecordsReader(boolean, InputStream, int, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.FastqRecordsReader: See main constructor for parameters.
file - Variable in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Random access file
FILE_POSITION_OFFSET - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Bit-shift that should be applied to encoded file position to get "file position" field.
fileIndex - Variable in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Index of file
FileIndex - Class in com.milaboratory.core.io.util: Index of file that contains sequential records.
FileIndexBuilder - Class in com.milaboratory.core.io.util: FileIndex builder.
FileIndexBuilder(long) - Constructor for class com.milaboratory.core.io.util.FileIndexBuilder: Creates index builder with specified step between records, i.e.
fillWildcardScores(int[], Alphabet<?>, byte...) - Static method in class com.milaboratory.core.alignment.ScoringUtils: Fills up scores for wildcards by averaging scores for all their matching scores combinations.
filteredHitsByAlignments - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
finalize() - Method in class com.milaboratory.core.alignment.blast.BlastDB
finalize() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2
findAllIntersecting(Range) - Method in class com.milaboratory.util.RangeMap
findAllIntersectingOrTouching(Range) - Method in class com.milaboratory.util.RangeMap
findContaining(Range) - Method in class com.milaboratory.util.RangeMap
findNext() - Method in interface com.milaboratory.core.motif.BitapMatcher
findNext() - Method in class com.milaboratory.core.motif.BitapMatcherFilter
findNext() - Method in class com.milaboratory.core.motif.BitapMatcherImpl
findSingleIntersection(Range) - Method in class com.milaboratory.util.RangeMap
firsMutationPosition() - Method in class com.milaboratory.core.mutations.Mutations
FIRST_RECORD_ID - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
firstMutationWithPosition(int) - Method in class com.milaboratory.core.mutations.Mutations
firstMutationWithPosition(int, int, int) - Method in class com.milaboratory.core.mutations.Mutations
floor() - Method in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
flush() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper
flush() - Method in class com.milaboratory.core.io.sequence.fasta.FastaWriter: Flush underlying stream.
flush() - Method in class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
flush() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
flush() - Method in interface com.milaboratory.core.io.sequence.SequenceWriter: Writes all buffers to the underlying stream
FNV_BASIS - Static variable in class com.milaboratory.util.HashFunctions: Fowler/Noll/Vo hash algorithms FNV_BASIS constant
FNV_PRIME_32 - Static variable in class com.milaboratory.util.HashFunctions: Fowler/Noll/Vo hash algorithms FNV_PRIME constant for 32 bit hash
FNV_PRIME_64 - Static variable in class com.milaboratory.util.HashFunctions: Fowler/Noll/Vo hash algorithms FNV_PRIME constant for 64 bit hash
force - Variable in class com.milaboratory.cli.ActionParametersWithOutput
forwardIterator() - Method in class com.milaboratory.core.alignment.Alignment: Returns alignment iterator.
FOUR_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
FOUR_MISMATCHES - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
FOUR_MISMATCHES_OR_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
FROM_OFFSET - Static variable in class com.milaboratory.core.mutations.Mutation
FromCenter - Static variable in class com.milaboratory.core.sequence.TranslationParameters
FromLeftWithIncompleteCodon - Static variable in class com.milaboratory.core.sequence.TranslationParameters
FromLeftWithoutIncompleteCodon - Static variable in class com.milaboratory.core.sequence.TranslationParameters
fromName(String) - Static method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
FromRightWithIncompleteCodon - Static variable in class com.milaboratory.core.sequence.TranslationParameters
FromRightWithoutIncompleteCodon - Static variable in class com.milaboratory.core.sequence.TranslationParameters
fromSequence(byte[], int, int) - Static method in class com.milaboratory.core.sequence.NucleotideSequence: Creates nucleotide sequence from specified byte array.
fromSequence(S) - Static method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils
fullVersion - Variable in class com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
fullVersion() - Method in class com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
fullVersionInfoCallback - Variable in class com.milaboratory.cli.JCommanderBasedMain
FVN32hash(byte[]) - Static method in class com.milaboratory.util.HashFunctions: Fowler-Noll-Vo 32 bit hash (FNV-1a) for bytes array.
FVN32hash(int) - Static method in class com.milaboratory.util.HashFunctions: Fowler-Noll-Vo 32 bit hash (FNV-1a) for integer key.
FVN64hash(byte[]) - Static method in class com.milaboratory.util.HashFunctions: Fowler-Noll-Vo 64 bit hash (FNV-1a) for bytes array.
FVN64hash(long) - Static method in class com.milaboratory.util.HashFunctions: Fowler-Noll-Vo 64 bit hash (FNV-1a) for long key.
FVN64to32hash(long) - Static method in class com.milaboratory.util.HashFunctions: Fowler-Noll-Vo 32 bit hash (FNV-1a) for long key.

G

G - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glycine byte representation
G - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Guanine byte representation
G_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glycine wildcard
G_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Guanine byte representation
generateDB(RandomDataGenerator, ChallengeParameters) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
generateMutation(int, int) - Method in class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
generateMutation(int, int) - Method in interface com.milaboratory.core.mutations.generator.NucleotideMutationModel
generateMutations(NucleotideSequence, NucleotideMutationModel, Range) - Static method in class com.milaboratory.core.mutations.generator.MutationsGenerator
generateMutations(NucleotideSequence, NucleotideMutationModel, int, int) - Static method in class com.milaboratory.core.mutations.generator.MutationsGenerator
generateMutations(NucleotideSequence, NucleotideMutationModel) - Static method in class com.milaboratory.core.mutations.generator.MutationsGenerator
GenericNucleotideMutationModel - Class in com.milaboratory.core.mutations.generator
GenericNucleotideMutationModel(SubstitutionModel, double, double) - Constructor for class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
GenericNucleotideMutationModel(SubstitutionModel, double, double, long) - Constructor for class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
GeneticCode - Class in com.milaboratory.core.sequence: Defines standard genetic code.
GeneticCode() - Constructor for class com.milaboratory.core.sequence.GeneticCode
get(int, int) - Method in class com.milaboratory.core.alignment.AlignerCustom.Matrix
get() - Static method in class com.milaboratory.core.alignment.AlignmentCache: Returns available CachedIntArray if AlignemntCache is on or creates new CachedIntArray otherwise
get(int, int) - Method in class com.milaboratory.core.alignment.BandedMatrix
get(String) - Static method in class com.milaboratory.core.alignment.blast.BlastDB
get(int) - Method in class com.milaboratory.core.alignment.CachedIntArray: Returns int[] array.
get(int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
get(int) - Method in interface com.milaboratory.core.sequence.MultiNSequenceWithQuality
get(int) - Method in class com.milaboratory.core.sequence.MultiNSequenceWithQualityImpl
get(int) - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
get(S) - Method in class com.milaboratory.core.tree.SequenceTreeMap
get(int) - Method in class com.milaboratory.util.Bit2Array
get(int) - Method in class com.milaboratory.util.BitArray
get(int) - Method in class com.milaboratory.util.IntArrayList
getAbsoluteMinClusterScore() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Returns minimal score for the cluster
getAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
getAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns minimal absolute score of a hit obtained by KAligner
getAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns minimal score
getAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns minimal absolute score of a hit obtained by KAligner
getAbsoluteMutations() - Method in class com.milaboratory.core.alignment.Alignment: Returns mutations in absolute (global) sequence1 coordinates.
getAbsoluteRangeFor(Range) - Method in class com.milaboratory.core.Range: Reverse operation for Range.getRelativeRangeOf(Range).
getAbsQueryPositionAt(int, int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getAbsSubjectPositionAt(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getActualPositionWidth() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getAffineGapPenalty(int) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns score value for a gap with length l
getAlignedSequence2Part(Alignment<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils
getAligner() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns link to aligner
getAlignment() - Method in interface com.milaboratory.core.alignment.batch.AlignmentHit
getAlignment() - Method in class com.milaboratory.core.alignment.batch.AlignmentHitImpl
getAlignment() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getAlignment() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
getAlignmentHelper() - Method in class com.milaboratory.core.alignment.Alignment: Returns alignment helper to simplify alignment output in conventional (BLAST) form.
getAlignmentStopPenalty() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
getAlignmentStopPenalty() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
getAll() - Static method in class com.milaboratory.core.sequence.Alphabets: Returns unmodifiable collection of all registered alphabets.
getAllWildcards() - Method in class com.milaboratory.core.sequence.Alphabet: Returns a collection of all wildcards defined for this.
getAlphabet() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Returns alphabet
getAlphabet() - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getAlphabet() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getAlphabet() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getAlphabet() - Method in class com.milaboratory.core.mutations.Mutations
getAlphabet() - Method in class com.milaboratory.core.sequence.AminoAcidSequence
getAlphabet() - Method in class com.milaboratory.core.sequence.NucleotideSequence
getAlphabet() - Method in class com.milaboratory.core.sequence.Sequence: Returns the alphabet corresponding to this type of sequence.
getAlphabetName() - Method in class com.milaboratory.core.sequence.Alphabet: Returns the human readable name of this alphabet.
getAminoAcid(NucleotideSequence, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Returns amino acid encoded by triplet starting from specified position (in terms of standard genetic code)
getAminoAcid(int) - Static method in class com.milaboratory.core.sequence.GeneticCode
getAminoAcidBLASTScoring(BLASTMatrix) - Static method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
getAminoAcidBLASTScoring(BLASTMatrix, int, int) - Static method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns AminoAcid BLAST scoring
getAminoAcidBLASTScoring(BLASTMatrix) - Static method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns standard amino acid BLAST scoring with #gapPenalty=5
getAminoAcidBLASTScoring(BLASTMatrix, int) - Static method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns standard amino acid BLAST scoring
getArrayReference(IntArrayList) - Static method in class com.milaboratory.util.IntArrayList
getAvailableNames() - Static method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns all available parameters presets
getAvailableRange() - Method in exception com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException
getAverageTiming() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getBadFraction() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getBasicMask() - Method in class com.milaboratory.core.sequence.Wildcard: Returns basicMask representation of the wildcard.
getBatchSize() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getBestHit() - Method in interface com.milaboratory.core.alignment.batch.AlignmentResult
getBestHit() - Method in class com.milaboratory.core.alignment.batch.AlignmentResultImpl
getBestHit() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns best hit (hit with highest alignment or mapper (if lazy alignment is used) score) or null if there is no hits in this result
getBestHit() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentResult2
getBitapPattern() - Method in class com.milaboratory.core.motif.Motif
getBits() - Method in class com.milaboratory.util.BitArray
getBitScore() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getBlastTask() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getBoundaries() - Method in class com.milaboratory.util.AtomicHistogram
getBranch() - Method in class com.milaboratory.util.VersionInfo
getBuilder() - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
getBuilder() - Method in interface com.milaboratory.core.sequence.Seq: Returns a builder for corresponding seq type.
getBuilder() - Method in class com.milaboratory.core.sequence.Sequence
getBuilder() - Method in class com.milaboratory.core.sequence.SequenceQuality
getByFirstLetterOfName(char) - Static method in class com.milaboratory.core.sequence.Alphabets: Searches for instance of Alphabet using first letter of it's name
getById(byte) - Static method in class com.milaboratory.core.sequence.Alphabets: Returns instance of Alphabet from its byte id.
getByName(String) - Static method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns parameters by specified preset name
getByName(String) - Static method in class com.milaboratory.core.sequence.Alphabets: Returns instance of Alphabet from its string name.
getBytesRead() - Method in class com.milaboratory.util.CountingInputStream: Returns the current number of bytes read from this stream.
getClusters() - Method in class com.milaboratory.core.clustering.Clustering
getCode() - Method in class com.milaboratory.core.sequence.Wildcard: Returns alphabet code.
getCode(int) - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getColumnDelta() - Method in class com.milaboratory.core.alignment.BandedMatrix
getCommandLineArguments() - Method in interface com.milaboratory.cli.ActionHelper
getCommandLineArguments() - Method in class com.milaboratory.cli.JCommanderBasedMain
getCoverageWeight(SequenceQuality, int) - Method in interface com.milaboratory.core.mutations.SequenceWeighter
getCoveredFraction() - Method in class com.milaboratory.util.AtomicHistogram
getCurrentAlignment() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getCurrentAlignment(LinearGapAlignmentScoring<S>) - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getCurrentBranchingSequence() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getCurrentMutation() - Method in interface com.milaboratory.core.alignment.AlignmentIterator: Current mutation or Mutation.NON_MUTATION if on match
getCurrentMutation() - Method in class com.milaboratory.core.alignment.AlignmentIteratorForward
getCurrentMutation() - Method in class com.milaboratory.core.alignment.AlignmentIteratorReverse
getCurrentMutations() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getCurrentRecordNumber() - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Returns the number of record that will be returned on AbstractRandomAccessReader.take()
getData() - Method in interface com.milaboratory.core.io.sequence.SingleRead
getData() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
getData() - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
getDB() - Method in class com.milaboratory.core.alignment.benchmark.Challenge
getDefaultPrintStream() - Method in interface com.milaboratory.cli.ActionHelper
getDefaultPrintStream() - Method in class com.milaboratory.cli.JCommanderBasedMain
getDeletionPenalty() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getDeletions() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getDescription() - Method in class com.milaboratory.core.io.sequence.fasta.FastaRecord: Returns description string (text that goes after ">")
getDescription() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord: Returns fasta record description line.
getDescription() - Method in interface com.milaboratory.core.io.sequence.SingleRead
getDescription() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
getDescription() - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
getDifferencesCombination(double, double[]) - Static method in class com.milaboratory.core.tree.PenaltyUtils
getDifferencesCombination(double, double[], int[]) - Static method in class com.milaboratory.core.tree.PenaltyUtils
getEmpiricalNucleotideMutationModel() - Static method in class com.milaboratory.core.mutations.generator.MutationModels
getEmpiricalNucleotideMutationModelWithNoise(RandomGenerator, double, double) - Static method in class com.milaboratory.core.mutations.generator.MutationModels
getEmpiricalNucleotideSubstitutionModel() - Static method in class com.milaboratory.core.mutations.generator.SubstitutionModels
getEmpiricalNucleotideSubstitutionModelWithNoise(RandomGenerator, double, double) - Static method in class com.milaboratory.core.mutations.generator.SubstitutionModels
getEmptySequence() - Method in class com.milaboratory.core.sequence.Alphabet: Returns empty sequence singleton
getEmptyValue(DeserializationContext) - Method in class com.milaboratory.core.sequence.Alphabets.Deserializer
getErrors() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getEValue() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getEValue() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getExecutionTime() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getExtraClusterScore() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2
getFalsePositiveFraction() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getFrame() - Method in class com.milaboratory.core.sequence.TranslationParameters
getFrom() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingHit
getFrom(int) - Static method in class com.milaboratory.core.mutations.Mutation
getFrom() - Method in class com.milaboratory.core.Range: Returns from value.
getFromAsCodeByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getFromAsSymbolByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getFromCLIName(String) - Static method in enum com.milaboratory.core.merger.QualityMergingAlgorithm
getFromLeft() - Method in class com.milaboratory.core.sequence.TranslationParameters
getFromSymbol(int, Alphabet) - Static method in class com.milaboratory.core.mutations.Mutation
getFullSourceId(int) - Method in class com.milaboratory.core.Target
getGapExtend() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getGapExtensionPenalty() - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns penalty value for extending gap
getGapOpen() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getGapOpenPenalty() - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns penalty value for opening gap
getGapPenalty() - Method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns penalty score for gap
getHead() - Method in class com.milaboratory.core.clustering.Cluster
getHist() - Method in class com.milaboratory.util.AtomicEnumHistogram
getHist() - Method in class com.milaboratory.util.AtomicHistogram
getHits() - Method in interface com.milaboratory.core.alignment.batch.AlignmentResult
getHits() - Method in class com.milaboratory.core.alignment.batch.AlignmentResultImpl
getHits() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns list of hits found in target sequence
getHits() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingResult
getHits() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentResult2
getHits() - Method in class com.milaboratory.core.alignment.kaligner2.KMappingResult2
getHitSequence() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getHost() - Method in class com.milaboratory.util.VersionInfo
getId() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getId() - Method in class com.milaboratory.core.io.sequence.fasta.FastaRecord: Returns serial id of fasta record (zero-based)
getId() - Method in class com.milaboratory.core.io.sequence.MultiRead
getId() - Method in interface com.milaboratory.core.io.sequence.SequenceRead
getId() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
getId() - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
getId() - Method in class com.milaboratory.core.sequence.Alphabet: Returns byte id of this alphabet
getIdentity() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getIdentityType() - Method in class com.milaboratory.core.merger.MergerParameters
getIdentityType() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getIdFasta(int) - Static method in class com.milaboratory.core.alignment.blast.BlastDBBuilder
getIdKey(int) - Static method in class com.milaboratory.core.alignment.blast.BlastDBBuilder
getIds() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord
getIndex() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getIndexStep() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
getInput() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getInsertionPenalty() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getInsertions() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getIntroducedDifferences() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getKMersHit() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getKValue() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns number of nucleotides in kMer (value of k)
getKValue() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2
getLabels() - Method in class com.milaboratory.util.AtomicEnumHistogram
getLast() - Method in class com.milaboratory.core.mutations.MutationsBuilder
getLastRecordNumber() - Method in class com.milaboratory.core.io.util.FileIndex: Returns the last record number indexed by this index.
getLength() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord: Returns record length in letters.
getLength() - Method in class com.milaboratory.core.mutations.MutationsEnumerator
getLengthDelta() - Method in class com.milaboratory.core.mutations.Mutations: Returns the difference between the length of initial sequence and length of mutated sequence.
getLettersCount() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getLine1() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the first line of formatted alignment (query sequence)
getLine1Compact() - Method in class com.milaboratory.core.alignment.AlignmentHelper
getLine2() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the second line of formatted alignment (alignment markup)
getLine3() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the third line of formatted alignment (subject sequence)
getLine3Compact() - Method in class com.milaboratory.core.alignment.AlignmentHelper
getLinePatterns() - Static method in class com.milaboratory.core.alignment.blast.BlastDB
getLinesCount() - Method in class com.milaboratory.util.NSequenceWithQualityPrintHelper
getLower() - Method in class com.milaboratory.core.Range: Returns lower (with least value) bound of this range.
getMapperAbsoluteMinClusterScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
getMapperAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
getMapperAbsoluteMinScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
getMapperExtraClusterScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
getMapperKMersPerPosition() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: If mapperKValue > 0, it is possible to map several seeds with holes in different places to the same position in target sequence.
getMapperKValue() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns kValue (length of kMers or seeds) used by KMapper
getMapperKValue() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
getMapperMatchScore() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns reward for successfully mapped seeds (used in KMapper)
getMapperMatchScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns reward for successfully mapped seeds (used in KMapper)
getMapperMaxClusterIndels() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
getMapperMaxClusters() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Max allowed clusters
getMapperMaxSeedsDistance() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns maximal distance between randomly chosen seeds during alignment in KMapper
getMapperMaxSeedsDistance() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns maximal distance between randomly chosen seeds during alignment in KMapper
getMapperMinSeedsDistance() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns minimal distance between randomly chosen seeds during alignment in KMapper
getMapperMinSeedsDistance() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns minimal distance between randomly chosen seeds during alignment in KMapper
getMapperMismatchPenalty() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns penalty score for not mapped seeds (used in KMapper)
getMapperMismatchScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns penalty score for not mapped seeds (used in KMapper)
getMapperNValue() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns kValue (length of kMers or seeds) used by KMapper
getMapperOffsetShiftPenalty() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns penalty for different offset between adjacent seeds (used in KMapper)
getMapperOffsetShiftScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns penalty for different offset between adjacent seeds (used in KMapper)
getMapperRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
getMapperRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
getMapperSlotCount() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
getMappingHit() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
getMappingResult() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns mapping result
getMarkup() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Get the alignment markup line
getMatchingCode(int) - Method in class com.milaboratory.core.sequence.Wildcard: Returns i-th code that this wildcard matches.
getMatrix() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getMatrix() - Method in enum com.milaboratory.core.alignment.BLASTMatrix
getMaxAdjacentIndels() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns maximal allowed number of insertions and deletions between 2 kMers
getMaxClusterDepth() - Method in interface com.milaboratory.core.clustering.ClusteringStrategy
getMaxDeletions() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getMaxDistance() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns maximal distance between kMer seed positions in target sequence
getMaxDistance() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Returns maximal distance between kMer seed positions in target sequence
getMaxErrors(int) - Method in class com.milaboratory.core.tree.TreeSearchParameters
getMaxHits() - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
getMaxHits() - Method in interface com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
getMaxHits() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns maximal number of hits stored by KAlignmentResult
getMaxHits() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns maximal number of hits stored by KAlignmentResult
getMaximalMatchScore() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
getMaximalMatchScore() - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getMaximalMismatchScore() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
getMaximalMismatchScore() - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getMaxIndels() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns maximal number of insertions and deletions
getMaxInsertions() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getMaxPenalty() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getMaxQuality() - Method in class com.milaboratory.core.merger.MergerParameters
getMaxSubstitutions() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getMaxValue() - Method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
getMetadata(String) - Method in class com.milaboratory.core.io.util.FileIndex: Returns a metadata record.
getMinAlignmentLength() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns minimal allowed alignment length
getMinDistance() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns minimal distance between kMer seed positions in target sequence
getMinDistance() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Returns minimal distance between kMer seed positions in target sequence
getMinimalIdentity() - Method in class com.milaboratory.core.merger.MergerParameters
getMinimalMatchScore() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
getMinimalMatchScore() - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getMinimalMismatchScore() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
getMinimalMismatchScore() - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getMinimalOverlap() - Method in class com.milaboratory.core.merger.MergerParameters
getMinValue() - Method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
getMismatched() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getMismatchedFraction() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getMismatches() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getMutatedRange() - Method in class com.milaboratory.core.mutations.Mutations
getMutation(int) - Method in class com.milaboratory.core.mutations.Mutations
getMutationsCount() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getMutationsPointer() - Method in interface com.milaboratory.core.alignment.AlignmentIterator: Points to current mutation or if currentMutation == Mutation.NON_MUTATION points to the next mutation.
getMutationsPointer() - Method in class com.milaboratory.core.alignment.AlignmentIteratorForward
getMutationsPointer() - Method in class com.milaboratory.core.alignment.AlignmentIteratorReverse
getMutationWeight(SequenceQuality, int, int, int[]) - Method in interface com.milaboratory.core.mutations.SequenceWeighter
getName() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getName() - Method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
getName() - Method in class com.milaboratory.util.VersionInfo
getNearestPosition(long) - Method in class com.milaboratory.core.io.util.FileIndex: Returns the nearest (from the left side, i.e.
getNearestRecordNumber(long) - Method in class com.milaboratory.core.io.util.FileIndex: Returns the record number, which is nearest (from the left side, i.e.
getNeighborhoodIterator(S, int, int, int, int) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNeighborhoodIterator(S, int, int, int, int, MutationGuide<S>) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNeighborhoodIterator(S, int, int, int) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNeighborhoodIterator(S, double, double[], int[], MutationGuide<S>) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNeighborhoodIterator(S, TreeSearchParameters) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNeighborhoodIterator(S, TreeSearchParameters, MutationGuide<S>) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNode(S) - Method in class com.milaboratory.core.tree.SequenceTreeMap
getNoHits() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getNoHitsFraction() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getNucleotideBLASTScoring() - Static method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns standard Nucleotide BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
getNucleotideBLASTScoring(int, int) - Static method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Returns Nucleotide BLAST scoring
getNucleotideBLASTScoring() - Static method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns standard Nucleotide BLAST scoring with #gapPenalty=5
getNucleotideBLASTScoring(int) - Static method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns standard Nucleotide BLAST scoring
getNullValue(DeserializationContext) - Method in class com.milaboratory.core.sequence.Alphabets.Deserializer
getNumAlignments() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getNumberOfErrors() - Method in interface com.milaboratory.core.motif.BitapMatcher
getNumberOfErrors() - Method in class com.milaboratory.core.motif.BitapMatcherFilter
getNumberOfErrors() - Method in class com.milaboratory.core.motif.BitapMatcherImpl
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.AbstractSequenceReader
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader: For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
getNumberOfReads() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
getNumberOfReads() - Method in interface com.milaboratory.core.io.sequence.SequenceReader: For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.
getNumThreads() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getNValue() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Returns number of nucleotides in kMer (value of k)
getObject() - Method in class com.milaboratory.core.tree.SequenceTreeMap.Node
getOffset() - Method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
getOffset() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getOffset() - Method in class com.milaboratory.core.mutations.MutationsEnumerator
getOptionValue() - Method in enum com.milaboratory.core.alignment.blast.BlastStrand
getOrCreate(byte) - Method in class com.milaboratory.core.tree.SequenceTreeMap.Node
getOriginalRead() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getOutputFiles() - Method in class com.milaboratory.cli.ActionParametersWithOutput
getOverlap() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getOverlappedSequence() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
getParams1NoGap(AffineGapAlignmentScoring<NucleotideSequence>, int, int, double) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
getParamsOneCluster(AffineGapAlignmentScoring<NucleotideSequence>, int, int, double) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
getParamsTwoClusters(AffineGapAlignmentScoring<NucleotideSequence>, int, int, double) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
getPartsLayout() - Method in class com.milaboratory.core.merger.MergerParameters
getPenalty() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getPenalty() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getPenalty(int) - Method in class com.milaboratory.core.tree.TreeSearchParameters
getPosition(int) - Static method in class com.milaboratory.core.mutations.Mutation
getPosition(int) - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getPositionByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getPossibleRelativeStrands() - Method in enum com.milaboratory.core.PairedEndReadsLayout: Determines possible relative (R1 relative to R2) strands.
getPreDefinedParameters() - Static method in class com.milaboratory.core.sequence.TranslationParameters
getProbability(int, int) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModel
getProbability(int, int) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
getProcessedGoodQueries() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getProcessedQueries() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getProgress() - Method in class com.milaboratory.core.clustering.Clustering
getProgress() - Method in class com.milaboratory.core.io.sequence.AbstractMultiReader
getProgress() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader
getProgress() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
getProgress() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
getProgress() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
getProgress() - Method in class com.milaboratory.primitivio.PReader
getProgress() - Method in interface com.milaboratory.util.CanReportProgress
getProgress() - Method in class com.milaboratory.util.ProgressAndStage
getProgressPeriod() - Method in class com.milaboratory.util.SmartProgressReporter
getProgressReporter(long) - Method in class com.milaboratory.util.CountingInputStream
getQuality() - Method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
getQuality() - Method in class com.milaboratory.core.sequence.quality.MaximalQualityAggregator
getQuality() - Method in class com.milaboratory.core.sequence.quality.MinimalQualityAggregator
getQuality() - Method in class com.milaboratory.core.sequence.quality.MiniMaxQualityAggregator
getQuality() - Method in interface com.milaboratory.core.sequence.quality.QualityAggregator
getQuality() - Method in class com.milaboratory.core.sequence.quality.SumQualityAggregator
getQuality() - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns quality.
getQualityFormat() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
getQualityLine(int) - Method in class com.milaboratory.util.NSequenceWithQualityPrintHelper
getQualityMergingAlgorithm() - Method in class com.milaboratory.core.merger.MergerParameters
getQuery() - Method in interface com.milaboratory.core.alignment.batch.PipedAlignmentResult
getQuery() - Method in class com.milaboratory.core.alignment.batch.PipedAlignmentResultImpl
getQuery() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResultP
getQueryFrom(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getQueryLeftTitle(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getQueryPositionAt(int, int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getQueryRightTitle(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getQueryTo(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getR1() - Method in class com.milaboratory.core.io.sequence.PairedRead
getR2() - Method in class com.milaboratory.core.io.sequence.PairedRead
getRange(int, int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
getRange(int, int, int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
getRange(int, int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getRange(int, int) - Method in class com.milaboratory.core.mutations.Mutations: Extracts sub mutations by from-to mutation indices.
getRange(Range) - Method in class com.milaboratory.core.sequence.AbstractSeq
getRange(int, int) - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
getRange(Range) - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
getRange(Range) - Method in class com.milaboratory.core.sequence.NucleotideSequence
getRange(Range) - Method in interface com.milaboratory.core.sequence.Seq: Returns a subsequence of this bounded by specified range.
getRange(int, int) - Method in interface com.milaboratory.core.sequence.Seq: Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).
getRange(int, int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns substring of current quality scores line.
getRange(Range) - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns substring of current quality scores line.
getRange(int, int) - Method in class com.milaboratory.util.Bit2Array
getRange(int, int) - Method in class com.milaboratory.util.BitArray
getRAWMutations() - Method in class com.milaboratory.core.mutations.Mutations
getRawTypeByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getRawTypeCode(int) - Static method in class com.milaboratory.core.mutations.Mutation: Returns: 0x20 for substitution, 0x40 for Deletion, 0x60 for insertion.
getRCStateOfTarget(int) - Method in class com.milaboratory.core.Target: true for RC, false for Direct
getRead(int) - Method in class com.milaboratory.core.io.sequence.MultiRead
getRead(int) - Method in interface com.milaboratory.core.io.sequence.SequenceRead
getRead(int) - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
getRead(int) - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
getReadIdOfTarget(int) - Method in class com.milaboratory.core.Target
getRecordById(String) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
getRecordByIdCheck(String) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
getRecordByIndex(int) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
getRecordPayload() - Method in interface com.milaboratory.core.alignment.batch.AlignmentHit
getRecordPayload() - Method in class com.milaboratory.core.alignment.batch.AlignmentHitImpl
getRecordPayload() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getRecordPayload() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
getRecordsCount() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getRecordSizeSummaryStatistics() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Method used internally.
getRecordSizeSummaryStatistics() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Method used internally.
getReference(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Returns sequence by its id (order number) in a base.
getReference(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2: Returns sequence by its id (order number) in a base.
getRegion(Range) - Method in class com.milaboratory.core.sequence.provider.CachedSequenceProvider
getRegion(Range) - Method in interface com.milaboratory.core.sequence.provider.SequenceProvider: Retrieves specified region of the sequence.
getRegion(Range) - Method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils.LazySequenceProvider
getRelativeMinScore() - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
getRelativeMinScore() - Method in interface com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
getRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns maximal ratio between best hit score and scores of other hits obtained by KAligner
getRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper: Returns maximal ratio between best hit score and other hits scores in returned result
getRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns maximal ratio between best hit score and scores of other hits obtained by KAligner
getRelativeMinScore() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2: Returns maximal ratio between best hit score and other hits scores in returned result
getRelativeMutations() - Method in class com.milaboratory.core.alignment.Alignment: Returns mutations in local coordinates, relative to sequence1range.
getRelativeRangeOf(Range) - Method in class com.milaboratory.core.Range
getResult() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
getReverseComplement() - Method in interface com.milaboratory.core.sequence.NSeq
getReverseComplement() - Method in class com.milaboratory.core.sequence.NSequenceWithQuality: Returns reverse complement sequence with reversed quality.
getReverseComplement() - Method in class com.milaboratory.core.sequence.NucleotideSequence: Returns reverse complement of this sequence.
getRevision() - Method in class com.milaboratory.util.VersionInfo
getReward() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
getRoot() - Method in class com.milaboratory.core.clustering.Cluster
getRowFactor() - Method in class com.milaboratory.core.alignment.BandedMatrix
getScore(byte, byte) - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Returns score value for specified alphabet letter codes
getScore() - Method in class com.milaboratory.core.alignment.Alignment: Return alignment score
getScore(byte, byte) - Method in interface com.milaboratory.core.alignment.AlignmentScoring
getScore() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getScoreErrorFraction() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getScoring() - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Returns scoring used for alignment.
getScoring() - Method in interface com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters
getScoring() - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
getScoring() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Returns scoring system used for building alignments
getScoring() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Returns scoring system used for building alignments
getSearchParameters() - Method in interface com.milaboratory.core.clustering.ClusteringStrategy
getSeedPosition(int) - Method in class com.milaboratory.core.alignment.kaligner1.KMappingResult
getSeedPosition(int) - Method in class com.milaboratory.core.alignment.kaligner2.KMappingResult2
getSeedsCount() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingResult
getSeedsCount() - Method in class com.milaboratory.core.alignment.kaligner2.KMappingResult2
getSeq1Position() - Method in interface com.milaboratory.core.alignment.AlignmentIterator: Points to current position in sequence1; if on insertion points to the next position after insertion point
getSeq1Position() - Method in class com.milaboratory.core.alignment.AlignmentIteratorForward
getSeq1Position() - Method in class com.milaboratory.core.alignment.AlignmentIteratorReverse
getSeq1String() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Get the aligned query sequence
getSeq2Position() - Method in interface com.milaboratory.core.alignment.AlignmentIterator: Points to current position in sequence2; if deletion points to the next position after deletion
getSeq2Position() - Method in class com.milaboratory.core.alignment.AlignmentIteratorForward
getSeq2Position() - Method in class com.milaboratory.core.alignment.AlignmentIteratorReverse
getSeq2String() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Get the aligned subject sequence
getSequence() - Method in interface com.milaboratory.core.alignment.batch.HasSequence
getSequence(T) - Method in interface com.milaboratory.core.clustering.SequenceExtractor
getSequence() - Method in class com.milaboratory.core.io.sequence.fasta.FastaRecord: Return sequence (main content of fasta record)
getSequence(int, Range) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getSequence(String, Range) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getSequence() - Method in class com.milaboratory.core.sequence.Sequence
getSequence() - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns sequence.
getSequence() - Method in class com.milaboratory.core.tree.SequenceTreeMap.NodeIterator
getSequence() - Method in class com.milaboratory.core.tree.SequenceTreeMap.NodeOp
getSequence() - Method in class com.milaboratory.core.tree.SequenceTreeMap.ValuesOp
getSequence1() - Method in class com.milaboratory.core.alignment.Alignment: Return initial sequence (upper sequence in alignment).
getSequence1PositionAt(int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
getSequence1Range() - Method in class com.milaboratory.core.alignment.Alignment: Returns aligned range of sequence1.
getSequence2PositionAt(int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
getSequence2Range() - Method in class com.milaboratory.core.alignment.Alignment: Returns aligned range of sequence2.
getSequenceLine(int) - Method in class com.milaboratory.util.NSequenceWithQualityPrintHelper
getSequenceProvider(int) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getSequenceProvider(String) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
getSerializableResult() - Method in class com.milaboratory.util.AtomicEnumHistogram
getSerializableResult() - Method in class com.milaboratory.util.AtomicHistogram
getSerializer(Class<T>) - Method in class com.milaboratory.primitivio.SerializersManager
getSerializer() - Method in class com.milaboratory.primitivio.TypeSerializationHelper
getSerializersManager() - Method in class com.milaboratory.primitivio.PrimitivI
getSerializersManager() - Method in class com.milaboratory.primitivio.PrimitivO
getSorted() - Method in class com.milaboratory.util.Sorter
getSortedDistinct(long[]) - Static method in class com.milaboratory.util.ArraysUtils: Sort array & return array with removed repetitive values.
getStage() - Method in interface com.milaboratory.util.CanReportProgressAndStage
getStage() - Method in class com.milaboratory.util.ProgressAndStage
getStartingRecordNumber() - Method in class com.milaboratory.core.io.util.FileIndex: Returns the first record number indexed by this index.
getStat() - Method in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
getState() - Method in class com.milaboratory.core.sequence.quality.AverageQualityAggregator
getStep() - Method in class com.milaboratory.core.io.util.FileIndex: Returns step of current index
getStopPenalty() - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Alignment score value in banded alignment matrix at which alignment terminates.
getSubjectFrom() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubjectId() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getSubjectLeftTitle() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubjectLength() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubjectPositionAt(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubjectRange() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getSubjectRightTitle() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubjectTitle() - Method in class com.milaboratory.core.alignment.blast.BlastHit
getSubjectTo() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
getSubSequence(int, int) - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns subsequence with its quality starting at from (inclusive) and ending at to (exclusive).
getSubSequence(Range) - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns subsequence with its quality with starting (inclusive) and ending (exclusive) points defined by range.
getSubstitutionPenalty() - Method in class com.milaboratory.core.tree.TreeSearchParameters
getSymbol() - Method in class com.milaboratory.core.sequence.Wildcard: Returns a wildcard letter.
getSymmetricMatrix(int, int, Alphabet<?>) - Static method in class com.milaboratory.core.alignment.ScoringUtils: Returns simple substitution matrix
getTarget() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns target sequence
getTargetFrom() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns position of first nucleotide of target sequence to be aligned
getTargetId() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
getTargetTo() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Returns position of last nucleotide of target sequence to be aligned
getTempDir() - Static method in class com.milaboratory.util.TempFileManager
getTempFile() - Static method in class com.milaboratory.util.TempFileManager
getTempFile(Path) - Static method in class com.milaboratory.util.TempFileManager
getThreadLocalRandom() - Static method in class com.milaboratory.util.RandomUtil
getThreadLocalRandomData() - Static method in class com.milaboratory.util.RandomUtil
getTimePeriod() - Method in class com.milaboratory.util.SmartProgressReporter
getTimestamp() - Method in class com.milaboratory.util.VersionInfo
getTitle() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getTitle() - Method in class com.milaboratory.core.alignment.blast.BlastHitExt
getTo() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingHit
getTo(int) - Static method in class com.milaboratory.core.mutations.Mutation
getTo() - Method in class com.milaboratory.core.Range: Returns to value.
getToAsCodeByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getToAsSymbolByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getToSymbol(int, Alphabet) - Static method in class com.milaboratory.core.mutations.Mutation
getTotalCountInHist() - Method in class com.milaboratory.util.AtomicHistogram
getTotalProcessed() - Method in class com.milaboratory.util.AtomicHistogram
getTotalSubstitutionProbability(int) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModel
getTriplet(NucleotideSequence, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Extracts int representation of triplet starting from specified position (see implementation for details).
getType(int) - Static method in class com.milaboratory.core.mutations.Mutation
getType() - Method in class com.milaboratory.core.mutations.MutationsEnumerator
getType(int) - Static method in enum com.milaboratory.core.mutations.MutationType: Returns MutationType.Substitution for 0, MutationType.Deletion for 1 and MutationType.Insertion for 2.
getType(int) - Method in class com.milaboratory.core.tree.NeighborhoodIterator
getTypeByIndex(int) - Method in class com.milaboratory.core.mutations.Mutations
getTypeFromRaw(int) - Static method in enum com.milaboratory.core.mutations.MutationType
getUniformlyDistributedBasicCode(long) - Method in class com.milaboratory.core.sequence.Wildcard: Returns uniformly distributed element (nucleotide or amino acid et cetera) corresponding to this wildcard.
getUniformNucleotideSubstitutionModel(double) - Static method in class com.milaboratory.core.mutations.generator.SubstitutionModels
getUniformQuality(byte, int) - Static method in class com.milaboratory.core.sequence.SequenceQuality: Creates a phred sequence quality containing only given values of quality.
getUpper() - Method in class com.milaboratory.core.Range: Returns upper (with biggest value) bound of this range.
getVersion() - Method in class com.milaboratory.util.VersionInfo
getVersionInfoForArtifact(String) - Static method in class com.milaboratory.util.VersionInfo
getVolumes() - Method in class com.milaboratory.core.alignment.blast.BlastDB
getWidth() - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Width of banded alignment matrix.
getWildcardForAnyLetter() - Method in class com.milaboratory.core.sequence.Alphabet: Returns wildcard for any letter (e.g.
getWordSize() - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
GlobalObjectMappers - Class in com.milaboratory.util: Created by dbolotin on 24.01.14.
GlobalObjectMappers() - Constructor for class com.milaboratory.util.GlobalObjectMappers
GlobalObjectMappers.DefaultPrettyPrinter1 - Class in com.milaboratory.util
GlobalObjectMappers.DefaultPrettyPrinter1() - Constructor for class com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1
GlobalObjectMappers.DefaultPrettyPrinter1(DefaultPrettyPrinter) - Constructor for class com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1
go(ActionHelper) - Method in interface com.milaboratory.cli.Action
GOOD_QUALITY_VALUE - Static variable in class com.milaboratory.core.sequence.SequenceQuality: Default value of good quality

H

H - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Histidine byte representation
H - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not G (H comes after G)
H_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Histidine wildcard
H_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not G (H comes after G)
handlesReference() - Method in class com.milaboratory.core.io.binary.AlignmentSerializer
handlesReference() - Method in class com.milaboratory.core.io.binary.RangeSerializer
handlesReference() - Method in class com.milaboratory.primitivio.CustomSerializerImpl
handlesReference() - Method in class com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer
handlesReference() - Method in class com.milaboratory.primitivio.JSONSerializer
handlesReference() - Method in interface com.milaboratory.primitivio.Serializer
hashCode() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring
hashCode() - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
hashCode() - Method in class com.milaboratory.core.alignment.Alignment
hashCode() - Method in class com.milaboratory.core.alignment.BandedAlignerParameters
hashCode() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
hashCode() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingHit
hashCode() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
hashCode() - Method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring
hashCode() - Method in class com.milaboratory.core.clustering.Cluster
hashCode() - Method in class com.milaboratory.core.io.sequence.fasta.FastaRecord
hashCode() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
hashCode() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord
hashCode() - Method in class com.milaboratory.core.io.sequence.MultiRead
hashCode() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
hashCode() - Method in class com.milaboratory.core.merger.MergerParameters
hashCode() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
hashCode() - Method in class com.milaboratory.core.motif.Motif
hashCode() - Method in class com.milaboratory.core.mutations.Mutations
hashCode() - Method in class com.milaboratory.core.Range
hashCode() - Method in class com.milaboratory.core.sequence.Alphabet: Returns "address in memory" (hash code as specified by Object.hashCode().
hashCode() - Method in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
hashCode() - Method in class com.milaboratory.core.sequence.Sequence
hashCode() - Method in class com.milaboratory.core.sequence.SequenceQuality
hashCode() - Method in class com.milaboratory.core.sequence.SequenceWithQuality
hashCode() - Method in class com.milaboratory.core.sequence.TranslationParameters
hashCode() - Method in class com.milaboratory.core.tree.SequenceTreeMap.Node
hashCode() - Method in class com.milaboratory.core.tree.TreeSearchParameters
hashCode() - Method in class com.milaboratory.util.Bit2Array
hashCode() - Method in class com.milaboratory.util.BitArray
hashCode() - Method in class com.milaboratory.util.IntArrayList
HashFunctions - Class in com.milaboratory.util: Hashing algorithms.
hasHits() - Method in interface com.milaboratory.core.alignment.batch.AlignmentResult
hasHits() - Method in class com.milaboratory.core.alignment.batch.AlignmentResultImpl
hasHits() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Checks if there are hits
hasHits() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignmentResult2
hasNext() - Method in class com.milaboratory.util.ArrayIterator
hasNext() - Method in class com.milaboratory.util.SingleIterator
hasSameDirection(Range) - Method in class com.milaboratory.core.Range: Returns true if two ranges has the same direction.
HasSequence<S extends Sequence<S>> - Interface in com.milaboratory.core.alignment.batch: Interface for objects which natively have a sequence as their distinctive property.
help - Variable in class com.milaboratory.cli.ActionParameters
help() - Method in class com.milaboratory.cli.ActionParameters
help - Variable in class com.milaboratory.cli.JCommanderBasedMain.MainParameters
help() - Method in class com.milaboratory.cli.JCommanderBasedMain.MainParameters
HiddenAction - Annotation Type in com.milaboratory.cli
hist - Variable in class com.milaboratory.util.AtomicEnumHistogram.SerializableResult
hist - Variable in class com.milaboratory.util.AtomicHistogram.SerializableResult
hitCalculationTime - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics

I

I - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Isoleucine byte representation
I_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Isoleucine wildcard
identity() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the identity of alignment, i.e.
identity(MergerParameters.IdentityType, NSequenceWithQuality, int, NSequenceWithQuality, int, int) - Static method in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
IGBLAST_NUCLEOTIDE_SCORING - Static variable in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Scoring as used in IgBlast for alignments of V genes
IGBLAST_NUCLEOTIDE_SCORING_THRESHOLD - Static variable in class com.milaboratory.core.alignment.AffineGapAlignmentScoring: Scoring threshold as used in IgBlast for alignments of V genes
IllegalFileFormatException - Exception in com.milaboratory.core.io.sequence
IllegalFileFormatException() - Constructor for exception com.milaboratory.core.io.sequence.IllegalFileFormatException
IllegalFileFormatException(String) - Constructor for exception com.milaboratory.core.io.sequence.IllegalFileFormatException
INCOMPLETE_CODON - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Incomplete codon byte representation
INCOMPLETE_CODON_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Incomplete codon wildcard
index(Path) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Index fasta file with automatic step selection or load previously created index
index(Path, boolean) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Index fasta file with automatic step selection or load previously created index
index(Path, boolean, LongProcessReporter) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Index fasta file with automatic step selection or load previously created index
index(Path, int, boolean) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Index fasta file or loads previously created index
index(Path, int, boolean, LongProcessReporter) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Index fasta file or loads previously created index
INDEX_SUFFIX - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
indexById(int) - Method in class com.milaboratory.core.alignment.kaligner2.KMappingHit2
indexOf(S) - Method in class com.milaboratory.core.sequence.Sequence: Tests whether this sequence contains subSequence and returns position of the first matched letter in this sequence or -1 if it does not contain subSequence.
indexOf(int) - Method in class com.milaboratory.util.IntArrayList
individualAAMutation - Variable in class com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
initialClusters(int, IntArrayList) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
input - Variable in class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
input - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
input - Variable in class com.milaboratory.primitivio.PReader
inputQueries - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
INSTANCE - Static variable in class com.milaboratory.util.LongProcessReporter.DefaultLongProcessReporter
IntArrayList - Class in com.milaboratory.util: Array list of primitive integers.
IntArrayList() - Constructor for class com.milaboratory.util.IntArrayList
IntArrayList(int) - Constructor for class com.milaboratory.util.IntArrayList
IntArrayList(int...) - Constructor for class com.milaboratory.util.IntArrayList
IntArrayList.IntComparator - Interface in com.milaboratory.util
IntCombinations - Class in com.milaboratory.util
IntCombinations(int, int) - Constructor for class com.milaboratory.util.IntCombinations
intersection(Range) - Method in class com.milaboratory.core.Range: Returns intersection range with other range.
intersectionWithTouch(Range) - Method in class com.milaboratory.core.Range: Returns intersection range with other range.
intersects(BitArray) - Method in class com.milaboratory.util.BitArray
intersectsWith(Range) - Method in class com.milaboratory.core.Range: Returns true if range intersects with other range.
intersectsWith(Wildcard) - Method in class com.milaboratory.core.sequence.Wildcard: Returns true if set of symbols represented by this wildcard intersects with set of symbols represented by otherWildcard.
intersectsWithOrTouches(Range) - Method in class com.milaboratory.core.Range: Returns true if range intersects with or touches other range.
inverse() - Method in class com.milaboratory.core.Range: Returns reversed range.
invert(S) - Method in class com.milaboratory.core.alignment.Alignment: Having sequence2 creates alignment from sequence2 to sequence1
invert() - Method in class com.milaboratory.core.mutations.Mutations: Inverts mutations, so that they reflect difference from seq2 to seq1.
IOUtil - Class in com.milaboratory.core.io.util: IOUtils contains methods for compact encoding of 32 and 64 bit integers.
IOUtil() - Constructor for class com.milaboratory.core.io.util.IOUtil
isBasic() - Method in class com.milaboratory.core.sequence.Wildcard: Returns true if and only if this wildcards has only one matching letter, so it represents definite letter and formally it is not a wildcard.
isClean() - Method in class com.milaboratory.util.BitArray: Returns false if some bits in array are set.
isCompatibleWith(S) - Method in class com.milaboratory.core.mutations.Mutations
isCompatibleWithSequence(S, int[]) - Static method in class com.milaboratory.core.mutations.MutationsUtil
isCurrentTop() - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.State
isDeletion(int) - Static method in class com.milaboratory.core.mutations.Mutation
isDetectStageChange() - Method in class com.milaboratory.util.SmartProgressReporter
isEmpty() - Method in class com.milaboratory.core.mutations.Mutations
isEmpty() - Method in class com.milaboratory.core.Range: Returns true if length() == 0.
isEmpty() - Method in class com.milaboratory.util.IntArrayList
isEmpty() - Method in class com.milaboratory.util.RangeMap
isFalse() - Method in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
isFinished() - Method in class com.milaboratory.core.clustering.Clustering
isFinished() - Method in class com.milaboratory.core.io.sequence.AbstractMultiReader
isFinished() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader
isFinished() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
isFinished() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
isFinished() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
isFinished() - Method in class com.milaboratory.primitivio.PReader
isFinished() - Method in interface com.milaboratory.util.CanReportProgress
isFinished() - Method in class com.milaboratory.util.ProgressAndStage
isFloatingLeftBound() - Method in interface com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
isFloatingLeftBound() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Checks if left bound of alignment is floating
isFloatingLeftBound() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Checks if left bound of alignment is floating
isFloatingRightBound() - Method in interface com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
isFloatingRightBound() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Checks if right bound of alignment is floating
isFloatingRightBound() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Checks if right bound of alignment is floating
isForceOverwrite() - Method in class com.milaboratory.cli.ActionParametersWithOutput
isGlobal() - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
isGreedy() - Method in class com.milaboratory.core.tree.TreeSearchParameters
isIncludeIncomplete() - Method in class com.milaboratory.core.sequence.TranslationParameters
isInDel(int) - Static method in class com.milaboratory.core.mutations.Mutation
isInitialized() - Method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils.LazySequenceProvider
isInsertion(int) - Static method in class com.milaboratory.core.mutations.Mutation
isOnRecord() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
isOverFragmented() - Method in class com.milaboratory.util.RangeMap
isPrintStackTrace() - Method in class com.milaboratory.cli.JCommanderBasedMain
isReference() - Method in class com.milaboratory.core.io.binary.AlignmentSerializer
isReference() - Method in class com.milaboratory.core.io.binary.RangeSerializer
isReference() - Method in class com.milaboratory.primitivio.CustomSerializerImpl
isReference() - Method in class com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer
isReference() - Method in class com.milaboratory.primitivio.JSONSerializer
isReference() - Method in interface com.milaboratory.primitivio.Serializer
isReverse() - Method in class com.milaboratory.core.Range: Returns true if this range is reversed.
isReversed() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
isSorted(int[]) - Static method in class com.milaboratory.core.mutations.MutationsUtil
isSubstitution(int) - Static method in class com.milaboratory.core.mutations.Mutation
isSuccessful() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
isWildcard(byte) - Method in class com.milaboratory.core.sequence.Alphabet: Returns true if this code represents wildcard symbol
it() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
iterator() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult
iterator() - Method in class com.milaboratory.core.io.sequence.MultiRead
iterator() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
iterator() - Method in class com.milaboratory.core.io.sequence.SingleReadLazy

J

J - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Leucine or Isoleucine (I or L) byte representation
J_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Leucine or Isoleucine (I or L) wildcard
JCommanderBasedMain - Class in com.milaboratory.cli
JCommanderBasedMain(String, Action...) - Constructor for class com.milaboratory.cli.JCommanderBasedMain
JCommanderBasedMain.MainParameters - Class in com.milaboratory.cli
JCommanderBasedMain.MainParameters() - Constructor for class com.milaboratory.cli.JCommanderBasedMain.MainParameters
JCommanderBasedMain.MainParametersWithVersion - Class in com.milaboratory.cli
JCommanderBasedMain.MainParametersWithVersion() - Constructor for class com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
JCommanderBasedMain.ProcessResult - Enum in com.milaboratory.cli
JenkinWang32shift(int) - Static method in class com.milaboratory.util.HashFunctions: Based on an original suggestion on Robert Jenkin's part in 1997 and Thomas Wang 2007 updates.
JenkinWang64shift(long) - Static method in class com.milaboratory.util.HashFunctions: Based on an original suggestion on Robert Jenkin's part in 1997 and Thomas Wang 2007 updates.
JSONSerializer - Class in com.milaboratory.primitivio
JSONSerializer(Class<?>) - Constructor for class com.milaboratory.primitivio.JSONSerializer

K

K - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Lysine byte representation
K - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Keto
K_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Lysine wildcard
K_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Keto
KAligner - Class in com.milaboratory.core.alignment.kaligner1: KAligner is a comprehensive aligner for nucleotide sequences.
KAligner(KAlignerParameters) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAligner: Creates new KAligner.
KAligner(KAlignerParameters, boolean) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAligner: Creates new KAligner.
KAligner2 - Class in com.milaboratory.core.alignment.kaligner2
KAligner2(KAlignerParameters2) - Constructor for class com.milaboratory.core.alignment.kaligner2.KAligner2
KAligner2(KAlignerParameters2, KAligner2Statistics) - Constructor for class com.milaboratory.core.alignment.kaligner2.KAligner2
KAligner2Statistics - Class in com.milaboratory.core.alignment.kaligner2
KAligner2Statistics() - Constructor for class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
KAligner2Statistics.ClusterTrimmingType - Enum in com.milaboratory.core.alignment.kaligner2
KAligner2Statistics.State - Class in com.milaboratory.core.alignment.kaligner2
KAligner2Statistics.State() - Constructor for class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.State
KAlignerParameters - Class in com.milaboratory.core.alignment.kaligner1
KAlignerParameters() - Constructor for class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
KAlignerParameters(int, boolean, boolean, float, float, float, float, float, int, int, int, int, int, float, float, int, LinearGapAlignmentScoring<NucleotideSequence>) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Creates new KAligner
KAlignerParameters2 - Class in com.milaboratory.core.alignment.kaligner2
KAlignerParameters2() - Constructor for class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
KAlignerParameters2(int, int, boolean, boolean, int, int, int, float, int, int, int, int, int, int, int, int, int, int, int, float, int, AffineGapAlignmentScoring) - Constructor for class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
KAlignerQuery - Class in com.milaboratory.core.alignment.benchmark
KAlignerQuery(int, List<Range>, List<Range>, List<Mutations<NucleotideSequence>>, NucleotideSequence, Alignment<NucleotideSequence>) - Constructor for class com.milaboratory.core.alignment.benchmark.KAlignerQuery
KAlignerQuery(NucleotideSequence) - Constructor for class com.milaboratory.core.alignment.benchmark.KAlignerQuery
kAlignerResult(KAlignmentResult2) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
KAlignmentHit - Class in com.milaboratory.core.alignment.kaligner1: KAlignmentHit - class which represents single hit for KAlignmentResult
KAlignmentHit(KAlignmentResult, int) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAlignmentHit: Creates new KAlignmentHit
KAlignmentHit2 - Class in com.milaboratory.core.alignment.kaligner2
KAlignmentHit2(KAlignmentResult2, int, Alignment<NucleotideSequence>, P) - Constructor for class com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
KAlignmentResult - Class in com.milaboratory.core.alignment.kaligner1: KAlignmentResult - class which is result of KAligner.align(com.milaboratory.core.sequence.NucleotideSequence), KAligner.align(com.milaboratory.core.sequence.NucleotideSequence, int, int), KAligner#align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean) methods.
KAlignmentResult(KAligner, KMappingResult, NucleotideSequence, int, int) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Creates new KAlignmentResult
KAlignmentResult2 - Class in com.milaboratory.core.alignment.kaligner2: Created by dbolotin on 26/10/15.
KAlignmentResult2(KMappingResult2, List<KAlignmentHit2>, NucleotideSequence, int, int) - Constructor for class com.milaboratory.core.alignment.kaligner2.KAlignmentResult2
KAlignmentResultP<P,Q> - Class in com.milaboratory.core.alignment.kaligner1: Piped version of KAlignmentResult.
KAlignmentResultP(Q, KAligner, KMappingResult, NucleotideSequence, int, int) - Constructor for class com.milaboratory.core.alignment.kaligner1.KAlignmentResultP
KMapper - Class in com.milaboratory.core.alignment.kaligner1: KMapper - class to perform fast alignment based only on matches between kMers of target and one of reference sequences.
KMapper(int, int, int, float, float, int, float, float, float, int, boolean, boolean) - Constructor for class com.milaboratory.core.alignment.kaligner1.KMapper: Creates new KMer mapper.
KMapper2 - Class in com.milaboratory.core.alignment.kaligner2: KMapper - class to perform fast alignment based only on matches between kMers of target and one of reference sequences.
KMapper2(int, int, int, int, int, int, int, float, int, int, int, int, int, int, int, boolean, boolean) - Constructor for class com.milaboratory.core.alignment.kaligner2.KMapper2: Creates new KMer mapper.
KMapper2(int, int, int, int, int, int, int, float, int, int, int, int, int, int, int, boolean, boolean, KAligner2Statistics) - Constructor for class com.milaboratory.core.alignment.kaligner2.KMapper2: Creates new KMer mapper.
KMappingHit - Class in com.milaboratory.core.alignment.kaligner1: KMappingHit - class which represents single hit for KMappingResult
KMappingHit(int, int, float, int, int) - Constructor for class com.milaboratory.core.alignment.kaligner1.KMappingHit: Creates new KMappingHit
KMappingHit2 - Class in com.milaboratory.core.alignment.kaligner2: KMappingHit - class which represents single hit for KMappingResult2
KMappingHit2(int, int[], int[], int) - Constructor for class com.milaboratory.core.alignment.kaligner2.KMappingHit2
KMappingResult - Class in com.milaboratory.core.alignment.kaligner1: KMappingResult - class which is result of KMapper#align(com.milaboratory.core.sequence.nucleotide.NucleotideSequence, int, int), KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) methods.
KMappingResult(IntArrayList, List<KMappingHit>) - Constructor for class com.milaboratory.core.alignment.kaligner1.KMappingResult: Creates new KMappingResult
KMappingResult2 - Class in com.milaboratory.core.alignment.kaligner2: KMappingResult - class which is result of KMapper#align(com.milaboratory.core.sequence.nucleotide.NucleotideSequence, int, int), KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) methods.
KMappingResult2(IntArrayList, List<KMappingHit2>) - Constructor for class com.milaboratory.core.alignment.kaligner2.KMappingResult2: Creates new KMappingResult
kMappingResults(KMappingResult2) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics

L

L - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Leucine byte representation
L_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Leucine wildcard
labels - Variable in class com.milaboratory.util.AtomicEnumHistogram.SerializableResult
last() - Method in class com.milaboratory.util.IntArrayList
LAST_INDEX - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
LAST_RECORD_ID - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
LAST_VALUE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
lastAccessibleRecordNumber() - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Returns the number of the last record that is indexed by this index builder.
lastMutationPosition() - Method in class com.milaboratory.core.mutations.Mutations
lazyProvider(SequenceProviderFactory<S>) - Static method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils
leftTrimAlignment(Alignment<S>, AlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from left side.
leftTrimAlignment(Alignment<S>, LinearGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from left side.
leftTrimAlignment(Alignment<S>, AffineGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from left side.
length() - Method in class com.milaboratory.core.Range: Returns the length of this range.
LETTER_MASK - Static variable in class com.milaboratory.core.mutations.Mutation
LinearGapAlignmentScoring<S extends Sequence<S>> - Class in com.milaboratory.core.alignment: LinearGapAlignmentScoring - scoring system which uses penalty for gap
LinearGapAlignmentScoring(Alphabet<S>, SubstitutionMatrix, int) - Constructor for class com.milaboratory.core.alignment.LinearGapAlignmentScoring
LinearGapAlignmentScoring(Alphabet<S>, int[], int) - Constructor for class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Creates new LinearGapAlignmentScoring
LinearGapAlignmentScoring(Alphabet<S>, int, int, int) - Constructor for class com.milaboratory.core.alignment.LinearGapAlignmentScoring: Returns scoring with uniform match and mismatch scores
LinearGapAlignmentScoring.SerializationObject - Class in com.milaboratory.core.alignment
LinearGapAlignmentScoring.SerializationObject() - Constructor for class com.milaboratory.core.alignment.LinearGapAlignmentScoring.SerializationObject
LinearGapAlignmentScoring.SerializationObject(Alphabet, SubstitutionMatrix, int) - Constructor for class com.milaboratory.core.alignment.LinearGapAlignmentScoring.SerializationObject
loadValueFrom(BitArray) - Method in class com.milaboratory.util.BitArray
log10ProbabilityOfErrorAt(int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Get the log10 of probability of error (e.g.
LongProcess - Interface in com.milaboratory.util
LongProcessReporter - Interface in com.milaboratory.util
LongProcessReporter.DefaultLongProcessReporter - Class in com.milaboratory.util
LongProcessReporter.DefaultLongProcessReporter() - Constructor for class com.milaboratory.util.LongProcessReporter.DefaultLongProcessReporter
lowerCaseMatch - Variable in class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
lowerCaseMismatch - Variable in class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings

M

M - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Methionine byte representation
M - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: aMino
M_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Methionine wildcard
M_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: aMino
MAGIC - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Magic integer written before serialized index
MAGIC - Static variable in class com.milaboratory.core.io.util.FileIndex: For serialization
main(String...) - Method in class com.milaboratory.cli.JCommanderBasedMain
main(String[]) - Static method in class com.milaboratory.test.Read
mapperTotalTime - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
mapping - Variable in class com.milaboratory.core.mutations.MutationsUtil.MutationsWitMapping
markMatchWithSpecialLetter - Variable in class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
markup - Variable in class com.milaboratory.core.alignment.AlignmentHelper
maskToWildcard(long) - Method in class com.milaboratory.core.sequence.Alphabet: Converts wildcard basicMask to Wildcard object.
match - Variable in class com.milaboratory.core.alignment.AlignmentHelper
MATCH_SCORE - Static variable in class com.milaboratory.core.merger.PairedReadMergingResult
matchChar - Variable in class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
matches(S, int) - Method in class com.milaboratory.core.motif.Motif
matches(byte) - Method in class com.milaboratory.core.sequence.Wildcard: Returns whether this wildcard contains specified element (nucleotide or amino acid etc.).
MAX_POSITION_VALUE - Static variable in class com.milaboratory.core.mutations.Mutation
MAX_QUALITY_VALUE - Static variable in class com.milaboratory.core.sequence.SequenceQuality: This value encoded with Phred+33 will giv 'z'.
MAX_RERUNS - Static variable in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
MAX_VALUE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
MaximalQualityAggregator - Class in com.milaboratory.core.sequence.quality
MaximalQualityAggregator(int) - Constructor for class com.milaboratory.core.sequence.quality.MaximalQualityAggregator
mean() - Method in class com.milaboratory.util.AtomicHistogram
meanValue() - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns average sequence quality value
merge(NSequenceWithQuality, NSequenceWithQuality) - Method in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
merge(NSequenceWithQuality, NSequenceWithQuality, PairedRead) - Method in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
MergerParameters - Class in com.milaboratory.core.merger
MergerParameters(QualityMergingAlgorithm, PairedEndReadsLayout, int, Integer, double, MergerParameters.IdentityType) - Constructor for class com.milaboratory.core.merger.MergerParameters
MergerParameters.IdentityType - Enum in com.milaboratory.core.merger
MIN_SCORE_VALUE - Static variable in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
MIN_VALUE - Static variable in class com.milaboratory.core.alignment.AlignerCustom
MIN_VALUE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
MinimalQualityAggregator - Class in com.milaboratory.core.sequence.quality
MinimalQualityAggregator(int) - Constructor for class com.milaboratory.core.sequence.quality.MinimalQualityAggregator
MiniMaxQualityAggregator - Class in com.milaboratory.core.sequence.quality
MiniMaxQualityAggregator(int) - Constructor for class com.milaboratory.core.sequence.quality.MiniMaxQualityAggregator
minValue() - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns the worst sequence quality value
MISMATCH_SCORE - Static variable in class com.milaboratory.core.merger.PairedReadMergingResult
mismatchCount(S, int, S, int, int) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Calculates number of mismatches (comparing position by position) between two regions of one or two different sequences.
mismatched - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
MismatchOnlyPairedReadMerger - Class in com.milaboratory.core.merger
MismatchOnlyPairedReadMerger(MergerParameters) - Constructor for class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger: Creates paired-end reads merger for Illumina (or other opposite reads) data.
MismatchOnlyPairedReadMerger(int, double, int, QualityMergingAlgorithm, PairedEndReadsLayout) - Constructor for class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger: Creates paired-end reads merger.
MismatchOnlyPairedReadMerger(int, double, MergerParameters.IdentityType, int, QualityMergingAlgorithm, PairedEndReadsLayout) - Constructor for class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger: Creates paired-end reads merger.
mix(int, int, int) - Static method in class com.milaboratory.util.HashFunctions: Robert Jenkins' 96 bit Mix Function.
Motif<S extends Sequence<S>> - Class in com.milaboratory.core.motif: Data structure for efficient exact and fuzzy matching/searching of sequences (wildcard-aware).
Motif(S) - Constructor for class com.milaboratory.core.motif.Motif: Creates motif from sequence.
MotifBuilder<S extends Sequence<S>> - Class in com.milaboratory.core.motif
MotifBuilder(Alphabet<S>, int) - Constructor for class com.milaboratory.core.motif.MotifBuilder
MotifUtils - Class in com.milaboratory.core.motif
MotifUtils() - Constructor for class com.milaboratory.core.motif.MotifUtils
move(int) - Method in class com.milaboratory.core.alignment.Alignment: Returns alignment with seq2range = seq2Range.move(offset), and everything else inherited from this alignment.
move(int, int) - Static method in class com.milaboratory.core.mutations.Mutation
move(int) - Method in class com.milaboratory.core.mutations.Mutations: Moves positions of mutations by specified offset
move(int) - Method in class com.milaboratory.core.Range: Returns range moved using provided offset (e.g.
MultiAlignmentHelper - Class in com.milaboratory.core.alignment
MultiAlignmentHelper.Settings - Class in com.milaboratory.core.alignment
MultiAlignmentHelper.Settings(boolean, boolean, boolean, char, char) - Constructor for class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
MultiNSequenceWithQuality - Interface in com.milaboratory.core.sequence
MultiNSequenceWithQualityImpl - Class in com.milaboratory.core.sequence
MultiNSequenceWithQualityImpl(NSequenceWithQuality...) - Constructor for class com.milaboratory.core.sequence.MultiNSequenceWithQualityImpl
multiplyProbabilities(double) - Method in class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
multiplyProbabilities(double) - Method in interface com.milaboratory.core.mutations.generator.NucleotideMutationModel
multiplyProbabilities(double) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModel
MultiRead - Class in com.milaboratory.core.io.sequence
MultiRead(SingleRead[]) - Constructor for class com.milaboratory.core.io.sequence.MultiRead
MultiReader - Class in com.milaboratory.core.io.sequence
MultiReader(SingleReader...) - Constructor for class com.milaboratory.core.io.sequence.MultiReader
MurmurHash2(byte[], int) - Static method in class com.milaboratory.util.HashFunctions: MurmurHash hash function for bytes array.
MurmurHash2(int, int) - Static method in class com.milaboratory.util.HashFunctions: MurmurHash hash function integer.
MurmurHash2(byte[]) - Static method in class com.milaboratory.util.HashFunctions: MurmurHash hash function for bytes array with default seed value equals 0x2f1a32b3.
MurmurHash2(int) - Static method in class com.milaboratory.util.HashFunctions: MurmurHash hash function integer with default seed value equals to 0x2f1a32b3.
mutate(S) - Method in class com.milaboratory.core.mutations.Mutations
mutate(NSequenceWithQuality, Mutations<NucleotideSequence>) - Static method in class com.milaboratory.core.mutations.MutationsUtil
Mutation - Class in com.milaboratory.core.mutations
MUTATION_POSITION_MASK - Static variable in class com.milaboratory.core.mutations.Mutation
MUTATION_TYPE_MASK - Static variable in class com.milaboratory.core.mutations.Mutation
MUTATION_TYPE_OFFSET - Static variable in class com.milaboratory.core.mutations.Mutation
MutationConsensusBuilder - Class in com.milaboratory.core.mutations
MutationConsensusBuilder(Range) - Constructor for class com.milaboratory.core.mutations.MutationConsensusBuilder
MutationGuide<S extends Sequence<S>> - Interface in com.milaboratory.core.tree
MutationModels - Class in com.milaboratory.core.mutations.generator
MutationModels() - Constructor for class com.milaboratory.core.mutations.generator.MutationModels
Mutations<S extends Sequence<S>> - Class in com.milaboratory.core.mutations
Mutations(Alphabet<S>, IntArrayList) - Constructor for class com.milaboratory.core.mutations.Mutations
Mutations(Alphabet<S>, String) - Constructor for class com.milaboratory.core.mutations.Mutations
Mutations(Alphabet<S>, int...) - Constructor for class com.milaboratory.core.mutations.Mutations
mutations - Variable in class com.milaboratory.core.mutations.MutationsUtil.MutationsWitMapping
MutationsBuilder<S extends Sequence<S>> - Class in com.milaboratory.core.mutations
MutationsBuilder(Alphabet<S>, boolean, int[], int) - Constructor for class com.milaboratory.core.mutations.MutationsBuilder
MutationsBuilder(Alphabet<S>) - Constructor for class com.milaboratory.core.mutations.MutationsBuilder
MutationsBuilder(Alphabet<S>, boolean) - Constructor for class com.milaboratory.core.mutations.MutationsBuilder
MutationsCounter - Class in com.milaboratory.core.mutations
MutationsCounter() - Constructor for class com.milaboratory.core.mutations.MutationsCounter
MutationsCounter.Filter - Interface in com.milaboratory.core.mutations
MutationsEnumerator - Class in com.milaboratory.core.mutations
MutationsEnumerator(Mutations) - Constructor for class com.milaboratory.core.mutations.MutationsEnumerator
MutationsGenerator - Class in com.milaboratory.core.mutations.generator
mutationsInTarget - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
MutationsUtil - Class in com.milaboratory.core.mutations
MutationsUtil.MutationNt2AADescriptor - Class in com.milaboratory.core.mutations
MutationsUtil.MutationNt2AADescriptor(int, int, int) - Constructor for class com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
MutationsUtil.MutationsWitMapping - Class in com.milaboratory.core.mutations
MutationsUtil.MutationsWitMapping(Mutations<AminoAcidSequence>, int[]) - Constructor for class com.milaboratory.core.mutations.MutationsUtil.MutationsWitMapping
MutationType - Enum in com.milaboratory.core.mutations

N

N - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Asparagine byte representation
N - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: any Nucleotide
N_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Asparagine wildcard
N_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: any Nucleotide
nanoTimeToString(long) - Static method in class com.milaboratory.util.TimeUtils
NBlastAligner - Class in com.milaboratory.core.alignment.blast
NBlastAligner() - Constructor for class com.milaboratory.core.alignment.blast.NBlastAligner
NBlastAligner(BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.NBlastAligner
NBlastAlignerExt - Class in com.milaboratory.core.alignment.blast
NBlastAlignerExt(BlastDB) - Constructor for class com.milaboratory.core.alignment.blast.NBlastAlignerExt
NBlastAlignerExt(BlastDB, BlastAlignerParameters) - Constructor for class com.milaboratory.core.alignment.blast.NBlastAlignerExt
NBlastHit - Class in com.milaboratory.core.alignment.blast
NBlastHit(Alignment<NucleotideSequence>, P, BlastHit<NucleotideSequence, ?>) - Constructor for class com.milaboratory.core.alignment.blast.NBlastHit
NBlastHit(Alignment<NucleotideSequence>, P, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.NBlastHit
NBlastHitExt - Class in com.milaboratory.core.alignment.blast
NBlastHitExt(Alignment<NucleotideSequence>, double, double, double, Range, String, String) - Constructor for class com.milaboratory.core.alignment.blast.NBlastHitExt
NeighborhoodIterator<S extends Sequence<S>,O> - Class in com.milaboratory.core.tree: Created by dbolotin on 25/06/14.
NeighborhoodIterator(S, TreeSearchParameters, MutationGuide, SequenceTreeMap.Node<O>) - Constructor for class com.milaboratory.core.tree.NeighborhoodIterator: Constrictor for root NeighborhoodIterator iterator.
next() - Method in class com.milaboratory.core.mutations.MutationsEnumerator
next() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
next() - Method in class com.milaboratory.core.tree.SequenceTreeMap.NodeIterator
next() - Method in class com.milaboratory.util.ArrayIterator
next() - Method in class com.milaboratory.util.SingleIterator
nextNode() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
nextQuery() - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
nextRecord(boolean) - Method in class com.milaboratory.core.io.sequence.fastq.FastqRecordsReader
nodeIterator() - Method in class com.milaboratory.core.tree.SequenceTreeMap
nodes() - Method in class com.milaboratory.core.tree.SequenceTreeMap
nodesOp() - Method in class com.milaboratory.core.tree.SequenceTreeMap
noHits - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
NON_MUTATION - Static variable in class com.milaboratory.core.mutations.Mutation
NON_MUTATION_1 - Static variable in class com.milaboratory.core.mutations.Mutation
NSeq<S extends NSeq<S>> - Interface in com.milaboratory.core.sequence
NSequenceWithQuality - Class in com.milaboratory.core.sequence: Container of nucleotide sequence with its quality.
NSequenceWithQuality(NucleotideSequence, SequenceQuality) - Constructor for class com.milaboratory.core.sequence.NSequenceWithQuality: Creates nucleotide sequence with its quality
NSequenceWithQuality(String, String) - Constructor for class com.milaboratory.core.sequence.NSequenceWithQuality
NSequenceWithQuality(String) - Constructor for class com.milaboratory.core.sequence.NSequenceWithQuality
NSequenceWithQuality(NucleotideSequence, byte) - Constructor for class com.milaboratory.core.sequence.NSequenceWithQuality
NSequenceWithQuality(NucleotideSequence) - Constructor for class com.milaboratory.core.sequence.NSequenceWithQuality
NSequenceWithQualityBuilder - Class in com.milaboratory.core.sequence: Created by poslavsky on 10/07/14.
NSequenceWithQualityBuilder() - Constructor for class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
NSequenceWithQualityPrintHelper - Class in com.milaboratory.util
NSequenceWithQualityPrintHelper(NSequenceWithQuality, int, int) - Constructor for class com.milaboratory.util.NSequenceWithQualityPrintHelper
nt2aa(NucleotideSequence, Mutations<NucleotideSequence>, TranslationParameters) - Static method in class com.milaboratory.core.mutations.MutationsUtil
nt2aa(NucleotideSequence, Mutations<NucleotideSequence>, TranslationParameters, int) - Static method in class com.milaboratory.core.mutations.MutationsUtil
nt2aaDetailed(NucleotideSequence, Mutations<NucleotideSequence>, TranslationParameters, int) - Static method in class com.milaboratory.core.mutations.MutationsUtil: Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
nt2aaWithMapping(NucleotideSequence, Mutations<NucleotideSequence>, TranslationParameters, int) - Static method in class com.milaboratory.core.mutations.MutationsUtil
nt2IndividualAA(NucleotideSequence, Mutations<NucleotideSequence>, TranslationParameters) - Static method in class com.milaboratory.core.mutations.MutationsUtil
NucleotideAlphabet - Class in com.milaboratory.core.sequence: An alphabet for nucleotide sequences.
NucleotideMutationModel - Interface in com.milaboratory.core.mutations.generator
NucleotideSequence - Class in com.milaboratory.core.sequence: Representation of nucleotide sequence.
NucleotideSequence(String) - Constructor for class com.milaboratory.core.sequence.NucleotideSequence: Creates nucleotide sequence from its string representation (e.g.
NucleotideSequence(char[]) - Constructor for class com.milaboratory.core.sequence.NucleotideSequence: Creates nucleotide sequence from char array of nucleotides (e.g.
NucleotideSequence(byte[]) - Constructor for class com.milaboratory.core.sequence.NucleotideSequence: Creates nucleotide sequence from specified Bit2Array (will be copied in constructor).
NULL - Static variable in interface com.milaboratory.util.LongProcessReporter: /dev/null
numberOfAlignmentsHits - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
numberOfClusters() - Method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
numberOfMappingHits - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
numberOfParts() - Method in class com.milaboratory.core.Target: 1 for SingleRead input or 2 for PairedRead input
numberOfReads() - Method in class com.milaboratory.core.io.sequence.MultiRead
numberOfReads() - Method in interface com.milaboratory.core.io.sequence.SequenceRead
numberOfReads() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
numberOfReads() - Method in class com.milaboratory.core.io.sequence.SingleReadLazy
numberOfSequences() - Method in interface com.milaboratory.core.sequence.MultiNSequenceWithQuality
numberOfSequences() - Method in class com.milaboratory.core.sequence.MultiNSequenceWithQualityImpl
numberOfSequences() - Method in class com.milaboratory.core.sequence.NSequenceWithQuality
numberOfStops() - Method in class com.milaboratory.core.sequence.AminoAcidSequence: Returns the number of stop codons that contained in this sequence

O

ObjectSerializer<O> - Interface in com.milaboratory.util: Created by dbolotin on 04/04/2017.
ObjectSerializer.PrimitivIOObjectSerializer<O> - Class in com.milaboratory.util: Implementation of ObjectSerializer for objects supporting PrimitivIO based serialization.
ObjectSerializer.PrimitivIOObjectSerializer(Class<O>) - Constructor for class com.milaboratory.util.ObjectSerializer.PrimitivIOObjectSerializer
offset - Variable in class com.milaboratory.core.alignment.AlignmentHelper
offsetById(int) - Method in class com.milaboratory.core.alignment.kaligner2.KMappingHit2
OffsetPacksAccumulator - Class in com.milaboratory.core.alignment.kaligner2
OffsetPacksAccumulator(int, int, int, int, int, int) - Constructor for class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
ONE_INDEL - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
ONE_LINE - Static variable in class com.milaboratory.util.GlobalObjectMappers
ONE_MISMATCH - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
ONE_MISMATCH_OR_INDEL - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
onException(Benchmark.ExceptionData) - Method in interface com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionListener
or(Motif<S>) - Method in class com.milaboratory.core.motif.Motif: Returns per-position or of two motifs.
or(BitArray) - Method in class com.milaboratory.util.BitArray
originalNtMutation - Variable in class com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
outOfRangeChar - Variable in class com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
output - Variable in class com.milaboratory.primitivio.PWriter
OUTPUT_RECORD_SIZE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
outputStream - Variable in class com.milaboratory.cli.JCommanderBasedMain
overlap(NSequenceWithQuality, NSequenceWithQuality, int) - Method in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
overrideMinimalIdentity(double) - Method in class com.milaboratory.core.merger.MergerParameters
overrideReadsLayout(PairedEndReadsLayout) - Method in class com.milaboratory.core.merger.MergerParameters

P

P - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Proline byte representation
P_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Proline wildcard
pabs(int) - Static method in class com.milaboratory.core.mutations.Mutations: Converts positions returned by Mutations.convertToSeq2Position(int) and Mutations.convertToSeq1Position(int) to a positive number by applying (-1 - x) transformation for negative input values.
PairedEndReadsLayout - Enum in com.milaboratory.core
PairedFastqReader - Class in com.milaboratory.core.io.sequence.fastq: Created by dbolotin on 23/06/14.
PairedFastqReader(File, File) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(String, String) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(File, File, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(String, String, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(File, File, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(String, String, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(File, File, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(String, String, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(File, File, QualityFormat, CompressionType, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(String, String, QualityFormat, CompressionType, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(InputStream, InputStream, QualityFormat, CompressionType, boolean, int, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(InputStream, InputStream) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(InputStream, InputStream, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(InputStream, InputStream, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqReader(SingleFastqReader, SingleFastqReader) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqReader
PairedFastqWriter - Class in com.milaboratory.core.io.sequence.fastq
PairedFastqWriter(File, File) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
PairedFastqWriter(String, String) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
PairedFastqWriter(String, String, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
PairedFastqWriter(SingleFastqWriter, SingleFastqWriter) - Constructor for class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
PairedRead - Class in com.milaboratory.core.io.sequence
PairedRead(SingleRead...) - Constructor for class com.milaboratory.core.io.sequence.PairedRead
PairedReader - Class in com.milaboratory.core.io.sequence: Created by dbolotin on 23/06/14.
PairedReader(SingleReader...) - Constructor for class com.milaboratory.core.io.sequence.PairedReader
PairedReadMergingResult - Class in com.milaboratory.core.merger
PairedReadMergingResult(PairedRead) - Constructor for class com.milaboratory.core.merger.PairedReadMergingResult: Constructor for failed merging result.
PairedReadMergingResult(PairedRead, NSequenceWithQuality, int, int, boolean, int, MergerParameters.IdentityType, double) - Constructor for class com.milaboratory.core.merger.PairedReadMergingResult: Constructor for successful merging result.
PairedSequenceWriter - Interface in com.milaboratory.core.io.sequence
parameters - Variable in class com.milaboratory.core.alignment.benchmark.Challenge
params() - Method in interface com.milaboratory.cli.Action
params - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkInput
parse(String) - Method in class com.milaboratory.core.sequence.Alphabet: Parses string representation of sequence.
parseParameters(String[]) - Method in interface com.milaboratory.cli.ActionParametersParser
ParserException - Exception in com.milaboratory.util: Created by dbolotin on 25/07/14.
ParserException() - Constructor for exception com.milaboratory.util.ParserException
ParserException(String) - Constructor for exception com.milaboratory.util.ParserException
ParseUtil - Class in com.milaboratory.util
ParseUtil.BracketsInfo - Class in com.milaboratory.util
ParseUtil.BracketsInfo(String) - Constructor for class com.milaboratory.util.ParseUtil.BracketsInfo
peek() - Method in class com.milaboratory.util.IntArrayList: Return last element leaving it in stack.
PenaltyUtils - Class in com.milaboratory.core.tree
PenaltyUtils() - Constructor for class com.milaboratory.core.tree.PenaltyUtils
performClustering() - Method in class com.milaboratory.core.clustering.Clustering
performClustering(Collection<T>, SequenceExtractor<T, S>, ClusteringStrategy<T, S>) - Static method in class com.milaboratory.core.clustering.Clustering
PipedAlignmentResult<H extends AlignmentHit<?,?>,Q> - Interface in com.milaboratory.core.alignment.batch
PipedAlignmentResultImpl<H extends AlignmentHit<?,?>,Q> - Class in com.milaboratory.core.alignment.batch
PipedAlignmentResultImpl(List<H>, Q) - Constructor for class com.milaboratory.core.alignment.batch.PipedAlignmentResultImpl
PipeDataInputReader<O> - Class in com.milaboratory.primitivio
PipeDataInputReader(Class<O>, PrimitivI) - Constructor for class com.milaboratory.primitivio.PipeDataInputReader
PipeDataInputReader(Class<O>, PrimitivI, long) - Constructor for class com.milaboratory.primitivio.PipeDataInputReader
PipedBatchAligner<S extends Sequence<S>,H extends AlignmentHit<? extends S,?>> - Interface in com.milaboratory.core.alignment.batch: Represents aligner that can align a sequence against a set of other sequences.
PipedBatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<? extends S,? extends P>> - Interface in com.milaboratory.core.alignment.batch: PipedBatchAligner with self-managed database (user can directly add subject sequences before running alignment).
PipeReader<O> - Class in com.milaboratory.primitivio
PipeReader(Class<? super O>, String) - Constructor for class com.milaboratory.primitivio.PipeReader
PipeReader(Class<? super O>, File) - Constructor for class com.milaboratory.primitivio.PipeReader
PipeReader(Class<? super O>, InputStream) - Constructor for class com.milaboratory.primitivio.PipeReader
PipeWriter<O> - Class in com.milaboratory.primitivio
PipeWriter(String) - Constructor for class com.milaboratory.primitivio.PipeWriter
PipeWriter(File) - Constructor for class com.milaboratory.primitivio.PipeWriter
PipeWriter(OutputStream) - Constructor for class com.milaboratory.primitivio.PipeWriter
pop() - Method in class com.milaboratory.util.IntArrayList: Removes the object at the top of this stack and returns that object as the value of this function.
POSITION_COMPARATOR - Static variable in class com.milaboratory.core.mutations.Mutation: Compares int mutations by their positions
POSITION_OFFSET - Static variable in class com.milaboratory.core.mutations.Mutation
positionInTarget(IntArrayList, int) - Static method in class com.milaboratory.core.alignment.kaligner2.KMapper2
positionInTriplet - Variable in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition: Position of particular nucleotide in triplet encoding amino acid at aminoAcidPosition.
possibleAlphabets(String) - Static method in class com.milaboratory.core.sequence.SequencesUtils: Returns a set of possible alphabets for a given string.
PReader - Class in com.milaboratory.primitivio
PReader(String) - Constructor for class com.milaboratory.primitivio.PReader
PReader(File) - Constructor for class com.milaboratory.primitivio.PReader
PReader(FileInputStream) - Constructor for class com.milaboratory.primitivio.PReader
PReader(InputStream) - Constructor for class com.milaboratory.primitivio.PReader
PReader(InputStream, long) - Constructor for class com.milaboratory.primitivio.PReader
PRETTY - Static variable in class com.milaboratory.util.GlobalObjectMappers
PrimitivI - Class in com.milaboratory.primitivio
PrimitivI(InputStream) - Constructor for class com.milaboratory.primitivio.PrimitivI
PrimitivI(DataInput) - Constructor for class com.milaboratory.primitivio.PrimitivI
PrimitivI(DataInput, SerializersManager) - Constructor for class com.milaboratory.primitivio.PrimitivI
PrimitivO - Class in com.milaboratory.primitivio
PrimitivO(OutputStream) - Constructor for class com.milaboratory.primitivio.PrimitivO
PrimitivO(DataOutput) - Constructor for class com.milaboratory.primitivio.PrimitivO
PrimitivO(DataOutput, SerializersManager) - Constructor for class com.milaboratory.primitivio.PrimitivO
printActionHelp(JCommander, Action) - Method in class com.milaboratory.cli.JCommanderBasedMain
printDefaultHelp() - Method in interface com.milaboratory.cli.ActionHelpProvider
printException(RuntimeException, JCommander, Action) - Method in class com.milaboratory.cli.JCommanderBasedMain
printGlobalHelp() - Method in class com.milaboratory.cli.JCommanderBasedMain
printHelp(StringBuilder) - Method in interface com.milaboratory.cli.ActionHelpProvider
printHelpOnError - Variable in class com.milaboratory.cli.JCommanderBasedMain
printHitAlignment(KAlignmentHit) - Static method in class com.milaboratory.core.alignment.kaligner1.KAlignmentHit
printStackTrace - Variable in class com.milaboratory.cli.JCommanderBasedMain
probabilityOfErrorAt(int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Get probability of error (e.g.
process(BenchmarkInput) - Method in class com.milaboratory.core.alignment.benchmark.Benchmark
process(PairedRead) - Method in class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
processAllChildren(TObjectProcedure<Cluster<T>>) - Method in class com.milaboratory.core.clustering.Cluster
processBuffer(String) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
processBuffer(byte[]) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
processBuffer(byte[], int, int) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
processedGoodQueries - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
processedQueries - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
ProcessException - Exception in com.milaboratory.cli: Created by dbolotin on 28/06/16.
ProcessException() - Constructor for exception com.milaboratory.cli.ProcessException
ProcessException(String) - Constructor for exception com.milaboratory.cli.ProcessException
ProgressAndStage - Class in com.milaboratory.util
ProgressAndStage(String) - Constructor for class com.milaboratory.util.ProgressAndStage
push(int) - Method in class com.milaboratory.util.IntArrayList: Alias for addAll(int) method.
put(S, O) - Method in class com.milaboratory.core.tree.SequenceTreeMap
put(O) - Method in class com.milaboratory.primitivio.PipeWriter
put(Range, T) - Method in class com.milaboratory.util.RangeMap
putKnownReference(Object) - Method in class com.milaboratory.primitivio.PrimitivI
putKnownReference(Object) - Method in class com.milaboratory.primitivio.PrimitivO
putMetadata(String, String) - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Puts metadata.
PWriter - Class in com.milaboratory.primitivio
PWriter(String) - Constructor for class com.milaboratory.primitivio.PWriter
PWriter(File) - Constructor for class com.milaboratory.primitivio.PWriter
PWriter(OutputStream) - Constructor for class com.milaboratory.primitivio.PWriter
PWriter(PrimitivO) - Constructor for class com.milaboratory.primitivio.PWriter

Q

Q - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamine byte representation
Q_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamine wildcard
QualityAggregationType - Enum in com.milaboratory.core.sequence.quality
QualityAggregator - Interface in com.milaboratory.core.sequence.quality
QualityFormat - Enum in com.milaboratory.core.io.sequence.fastq: A base class to store various sequencing quality formats.
QualityMergingAlgorithm - Enum in com.milaboratory.core.merger
queries - Variable in class com.milaboratory.core.alignment.benchmark.Challenge
queries() - Method in class com.milaboratory.core.alignment.benchmark.Challenge
query - Variable in class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
query - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
queryClusters - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
queryPosition(long) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord: Returns encoded position (positionInFile << 20) | (numberOfLettersToSkip).

R

R - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Arginine byte representation
R - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: puRine
R_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Arginine wildcard
R_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: puRine
RandomAccessFastaIndex - Class in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.IndexBuilder - Class in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.IndexBuilder() - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
RandomAccessFastaIndex.IndexBuilder(int) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
RandomAccessFastaIndex.IndexRecord - Class in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.IndexRecord(int, String, long, int) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord
RandomAccessFastaIndex.MultipleMatchingRecordsException - Exception in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.MultipleMatchingRecordsException(String) - Constructor for exception com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.MultipleMatchingRecordsException
RandomAccessFastaIndex.NoSuchRecordException - Exception in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.NoSuchRecordException(String) - Constructor for exception com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.NoSuchRecordException
RandomAccessFastaIndex.StreamIndexBuilder - Class in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaIndex.StreamIndexBuilder() - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
RandomAccessFastaIndex.StreamIndexBuilder(int) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
RandomAccessFastaIndex.StreamIndexBuilder(int, long) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
RandomAccessFastaIndex.StreamIndexBuilder(RandomAccessFastaIndex.IndexBuilder, long) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
RandomAccessFastaReader<S extends Sequence<S>> - Class in com.milaboratory.core.io.sequence.fasta
RandomAccessFastaReader(String, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastaReader(Path, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastaReader(String, Alphabet<S>, boolean) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastaReader(Path, Alphabet<S>, boolean) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastaReader(Path, RandomAccessFastaIndex, Alphabet<S>) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastaReader(SeekableByteChannel, RandomAccessFastaIndex, Alphabet<S>, int) - Constructor for class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
RandomAccessFastqReader - Class in com.milaboratory.core.io.sequence.fastq: FASTQ file reader with random access.
RandomAccessFastqReader(String, String) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader: Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(String, String, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader: Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(String, String, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader: Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(File, FileIndex, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader: Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(RandomAccessFile, FileIndex, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader: Creates reader of specified FASTQ file with specified index.
RandomAccessPairedFastqReader - Class in com.milaboratory.core.io.sequence.fastq: FASTQ file reader for paired reads with random access.
RandomAccessPairedFastqReader(String, String, String, String) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
RandomAccessPairedFastqReader(RandomAccessFile, FileIndex, RandomAccessFile, FileIndex) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
RandomAccessPairedFastqReader(String, String, String, String, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
RandomAccessPairedFastqReader(RandomAccessFile, FileIndex, RandomAccessFile, FileIndex, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
RandomAccessPairedFastqReader(RandomAccessFastqReader, RandomAccessFastqReader) - Constructor for class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
randomize(OutputPort<T>, RandomDataGenerator, int, ObjectSerializer<T>, File) - Static method in class com.milaboratory.util.Randomizer
Randomizer<T> - Class in com.milaboratory.util: Created by dbolotin on 04/04/2017.
randomSequence(Alphabet<S>, RandomDataGenerator, int, int, boolean) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
randomSequence(Alphabet<S>, RandomGenerator, int, int, boolean) - Static method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
RandomUtil - Class in com.milaboratory.util
Range - Class in com.milaboratory.core: This class represents a range of positions in a sequence (e.g.
Range(int, int, boolean) - Constructor for class com.milaboratory.core.Range
Range(int, int) - Constructor for class com.milaboratory.core.Range
RangeMap<T> - Class in com.milaboratory.util
RangeMap() - Constructor for class com.milaboratory.util.RangeMap
RangeMap.IntersectingRangesException - Exception in com.milaboratory.util
RangeMap.IntersectingRangesException() - Constructor for exception com.milaboratory.util.RangeMap.IntersectingRangesException
RangeMap.IntersectingRangesException(String) - Constructor for exception com.milaboratory.util.RangeMap.IntersectingRangesException
RangeSerializer - Class in com.milaboratory.core.io.binary
RangeSerializer() - Constructor for class com.milaboratory.core.io.binary.RangeSerializer
RAW_MUTATION_TYPE_DELETION - Static variable in class com.milaboratory.core.mutations.Mutation
RAW_MUTATION_TYPE_INSERTION - Static variable in class com.milaboratory.core.mutations.Mutation
RAW_MUTATION_TYPE_RESERVED - Static variable in class com.milaboratory.core.mutations.Mutation
RAW_MUTATION_TYPE_SUBSTITUTION - Static variable in class com.milaboratory.core.mutations.Mutation
rawType - Variable in enum com.milaboratory.core.mutations.MutationType
read(PrimitivI) - Method in class com.milaboratory.core.io.binary.AlignmentSerializer
read(PrimitivI) - Method in class com.milaboratory.core.io.binary.RangeSerializer
read(InputStream) - Static method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
read(String) - Static method in class com.milaboratory.core.io.util.FileIndex: Reads index from file.
read(File) - Static method in class com.milaboratory.core.io.util.FileIndex: Reads index from file.
read(InputStream) - Static method in class com.milaboratory.core.io.util.FileIndex: Reads index from input stream.
read(PrimitivI) - Method in class com.milaboratory.primitivio.CustomSerializerImpl
read(PrimitivI) - Method in class com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer
read(PrimitivI) - Method in class com.milaboratory.primitivio.JSONSerializer
read(PrimitivI) - Method in interface com.milaboratory.primitivio.Serializer
Read - Class in com.milaboratory.test
Read() - Constructor for class com.milaboratory.test.Read
read() - Method in class com.milaboratory.util.CountingInputStream
read(byte[]) - Method in class com.milaboratory.util.CountingInputStream
read(byte[], int, int) - Method in class com.milaboratory.util.CountingInputStream
read(InputStream) - Method in class com.milaboratory.util.ObjectSerializer.PrimitivIOObjectSerializer
read(InputStream) - Method in interface com.milaboratory.util.ObjectSerializer
readBoolean() - Method in class com.milaboratory.primitivio.PrimitivI
readByte() - Method in class com.milaboratory.primitivio.PrimitivI
readChar() - Method in class com.milaboratory.primitivio.PrimitivI
readDouble() - Method in class com.milaboratory.primitivio.PrimitivI
readEnumMap(PrimitivI, Class<K>, Class<V>) - Static method in class com.milaboratory.primitivio.Util
readFloat() - Method in class com.milaboratory.primitivio.PrimitivI
readFrom(DataInput) - Static method in class com.milaboratory.util.Bit2Array
readFully(byte[]) - Method in class com.milaboratory.primitivio.PrimitivI
readFully(byte[], int, int) - Method in class com.milaboratory.primitivio.PrimitivI
readInt() - Method in class com.milaboratory.primitivio.PrimitivI
readLine() - Method in class com.milaboratory.primitivio.PrimitivI
readList(Class<O>, String) - Static method in class com.milaboratory.primitivio.Util
readList(Class<O>, File) - Static method in class com.milaboratory.primitivio.Util
readList(Class<O>, InputStream) - Static method in class com.milaboratory.primitivio.Util
readList(Class<O>, PrimitivI) - Static method in class com.milaboratory.primitivio.Util
readLong() - Method in class com.milaboratory.primitivio.PrimitivI
readMap(PrimitivI, Class<K>, Class<V>) - Static method in class com.milaboratory.primitivio.Util
readObject(Class<T>) - Method in class com.milaboratory.primitivio.PrimitivI
readRawVarint32(InputStream, int) - Static method in class com.milaboratory.core.io.util.IOUtil: Read a raw Varint from the stream.
readRawVarint64(InputStream, long) - Static method in class com.milaboratory.core.io.util.IOUtil: Read a raw Varint from the stream.
readReference(Object) - Method in class com.milaboratory.primitivio.PrimitivI
readsCounter - Variable in class com.milaboratory.core.io.sequence.AbstractSequenceReader
readShort() - Method in class com.milaboratory.primitivio.PrimitivI
readToEnd() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
readUnsignedByte() - Method in class com.milaboratory.primitivio.PrimitivI
readUnsignedShort() - Method in class com.milaboratory.primitivio.PrimitivI
readUTF() - Method in class com.milaboratory.primitivio.PrimitivI
readVarInt() - Method in class com.milaboratory.primitivio.PrimitivI
readVarIntZigZag() - Method in class com.milaboratory.primitivio.PrimitivI
readVarLong() - Method in class com.milaboratory.primitivio.PrimitivI
readVarLongZigZag() - Method in class com.milaboratory.primitivio.PrimitivI
RECORD_SIZE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
refresh() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Refresh alignments of all hits
reg(Action) - Method in class com.milaboratory.cli.JCommanderBasedMain
register(Alphabet) - Static method in class com.milaboratory.core.sequence.Alphabets: Register new alphabet
registerCustomSerializer(Class<?>, Serializer<?>) - Method in class com.milaboratory.primitivio.SerializersManager
release() - Static method in class com.milaboratory.core.alignment.AlignmentCache: Release CacheIntArray
remove(S) - Method in class com.milaboratory.core.tree.SequenceTreeMap
remove() - Method in class com.milaboratory.util.ArrayIterator
remove(Range) - Method in class com.milaboratory.util.RangeMap
remove() - Method in class com.milaboratory.util.SingleIterator
removeLast() - Method in class com.milaboratory.core.mutations.MutationsBuilder
removeMutationsInRange(Range) - Method in class com.milaboratory.core.mutations.Mutations: See Mutations.removeMutationsInRange(int, int).
removeMutationsInRange(int, int) - Method in class com.milaboratory.core.mutations.Mutations: Removes mutations for a range of positions in the original sequence and performs shift of corresponding positions of mutations.
removeMutationsInRanges(Range...) - Method in class com.milaboratory.core.mutations.Mutations: See Mutations.removeMutationsInRange(int, int).
removeVersionInfoCallback() - Method in class com.milaboratory.cli.JCommanderBasedMain: Removes -v / --version option callbacks, and removes option by itself.
replaceAll(int, int) - Method in class com.milaboratory.util.IntArrayList
replaceFirst(int, int) - Method in class com.milaboratory.util.IntArrayList
report(long, String, double) - Method in class com.milaboratory.util.AbstractLongProcessReporter
reportStatus(double) - Method in interface com.milaboratory.util.LongProcess
rerun - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
reRunBecauseOfMicroTangling() - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
reseed(long) - Method in class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
reseed(long) - Method in interface com.milaboratory.core.mutations.generator.NucleotideMutationModel
reseedThreadLocal() - Static method in class com.milaboratory.util.RandomUtil
reseedThreadLocal(long) - Static method in class com.milaboratory.util.RandomUtil
reset() - Method in class com.milaboratory.util.IntCombinations
resetBufferOnSeek() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
resetBufferOnSeek() - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader
retriveSequenceById(String) - Method in class com.milaboratory.core.alignment.blast.BlastDB
reverse() - Method in class com.milaboratory.core.Range: Return reversed range.
reverse() - Method in class com.milaboratory.core.sequence.SequenceQuality: Gets quality values in reverse order
reverse(int[], int, int) - Static method in class com.milaboratory.util.ArraysUtils
reverse(int[]) - Static method in class com.milaboratory.util.ArraysUtils
reverse(byte[]) - Static method in class com.milaboratory.util.ArraysUtils
reverse() - Method in class com.milaboratory.util.IntArrayList
reverse(int, int) - Method in class com.milaboratory.util.IntArrayList
reversedProvider(SequenceProvider<NucleotideSequence>) - Static method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils
reverseIterator() - Method in class com.milaboratory.core.alignment.Alignment: Returns reverse alignment iterator.
reverseRange(int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
rightTrimAlignment(Alignment<S>, AlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from right side.
rightTrimAlignment(Alignment<S>, LinearGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from right side.
rightTrimAlignment(Alignment<S>, AffineGapAlignmentScoring<S>) - Static method in class com.milaboratory.core.alignment.AlignmentTrimmer: Try increase total alignment score by partially (or fully) trimming it from right side.
root - Variable in class com.milaboratory.core.tree.SequenceTreeMap
run() - Method in class com.milaboratory.util.SmartProgressReporter

S

S - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Serine byte representation
S - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Strong
S_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Serine wildcard
S_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Strong
sample(RandomGenerator, int) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModel
sampleAsMutation(RandomGenerator, int, int) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModel
score - Variable in class com.milaboratory.core.alignment.BandedSemiLocalResult: Score
SCORE - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
score() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
scoreError - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
ScoringUtils - Class in com.milaboratory.core.alignment: ScoringUtils - class which contains some useful helpers used in scoring systems
seed - Variable in class com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
seed - Variable in class com.milaboratory.core.alignment.benchmark.Challenge
seed(long) - Static method in class com.milaboratory.util.TempFileManager
SEED_NOT_FOUND_OFFSET - Static variable in class com.milaboratory.core.alignment.kaligner1.KMapper
SEED_NOT_FOUND_OFFSET - Static variable in class com.milaboratory.core.alignment.kaligner2.KMapper2
seedExtractionTime - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
seekToRecord(long) - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
seekToRecord(long) - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Sets the file-pointer offset, measured from the beginning of this file, at which the next record occurs.
semiGlobalLeft(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiGlobalLeft0(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, BandedAffineAligner.MatrixCache) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiGlobalRight(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiGlobalRight0(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, BandedAffineAligner.MatrixCache) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalLeft0(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, BandedAffineAligner.MatrixCache) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
semiLocalRight0(AffineGapAlignmentScoring<NucleotideSequence>, NucleotideSequence, NucleotideSequence, int, int, int, int, int, MutationsBuilder<NucleotideSequence>, BandedAffineAligner.MatrixCache) - Static method in class com.milaboratory.core.alignment.BandedAffineAligner
Seq<S extends Seq<S>> - Interface in com.milaboratory.core.sequence: Common interface for all objects representing sequence-like objects like (parent of all subtypes of Sequence; SequenceQuality; SequenceWithQuality)
seq1Position - Variable in class com.milaboratory.core.alignment.AlignmentHelper
seq1String - Variable in class com.milaboratory.core.alignment.AlignmentHelper
seq2Position - Variable in class com.milaboratory.core.alignment.AlignmentHelper
seq2String - Variable in class com.milaboratory.core.alignment.AlignmentHelper
SeqBuilder<S extends Seq<S>> - Interface in com.milaboratory.core.sequence: Interface for classes that build seq objects.
sequence - Variable in class com.milaboratory.core.io.sequence.fasta.FastaReader.RawFastaRecord
Sequence<S extends Sequence<S>> - Class in com.milaboratory.core.sequence: Parent class for all types of sequences.
Sequence() - Constructor for class com.milaboratory.core.sequence.Sequence
sequence1Stop - Variable in class com.milaboratory.core.alignment.BandedSemiLocalResult: Positions at which alignment terminates.
sequence2Stop - Variable in class com.milaboratory.core.alignment.BandedSemiLocalResult: Positions at which alignment terminates.
SequenceBuilder<S extends Sequence<S>> - Interface in com.milaboratory.core.sequence: Interface for factory class for a certain type of sequence.
SequenceExtractor<O,S extends Sequence<S>> - Interface in com.milaboratory.core.alignment.batch: Interface for class to extract sequences from objects
SequenceExtractor<T,S extends Sequence> - Interface in com.milaboratory.core.clustering
SequenceProvider<S extends Sequence<S>> - Interface in com.milaboratory.core.sequence.provider: Provides access to the sequence that may be too big to be loaded to the memory.
SequenceProviderFactory<S extends Sequence<S>> - Interface in com.milaboratory.core.sequence.provider
SequenceProviderIndexOutOfBoundsException - Exception in com.milaboratory.core.sequence.provider
SequenceProviderIndexOutOfBoundsException(Range) - Constructor for exception com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException
SequenceProviderUtils - Class in com.milaboratory.core.sequence.provider
SequenceProviderUtils.LazySequenceProvider<S extends Sequence<S>> - Class in com.milaboratory.core.sequence.provider
SequenceProviderUtils.LazySequenceProvider(SequenceProviderFactory<S>) - Constructor for class com.milaboratory.core.sequence.provider.SequenceProviderUtils.LazySequenceProvider
SequenceQuality - Class in com.milaboratory.core.sequence: Representation of nucleotide sequence quality based on phred quality scores.
SequenceQuality(String) - Constructor for class com.milaboratory.core.sequence.SequenceQuality: Creates a phred sequence quality from a Sanger formatted quality string (33 based).
SequenceQuality(String, int) - Constructor for class com.milaboratory.core.sequence.SequenceQuality: Creates a phred sequence quality from a string formatted with corresponding offset.
SequenceQuality(String, QualityFormat) - Constructor for class com.milaboratory.core.sequence.SequenceQuality: Creates a phred sequence quality from a string formatted with corresponding offset.
SequenceQuality(byte[]) - Constructor for class com.milaboratory.core.sequence.SequenceQuality: Creates quality object from raw quality score values.
SequenceQualityBuilder - Class in com.milaboratory.core.sequence: Created by poslavsky on 09/07/14.
SequenceQualityBuilder() - Constructor for class com.milaboratory.core.sequence.SequenceQualityBuilder
SequenceQualityBuilder(byte[], int) - Constructor for class com.milaboratory.core.sequence.SequenceQualityBuilder
SequenceRead - Interface in com.milaboratory.core.io.sequence
SequenceReader<S extends SequenceRead> - Interface in com.milaboratory.core.io.sequence: If this reader has some system resources associated with it (like opened file or network streams) implement OutputPortCloseable interface along with this interface.
SequenceReaderCloseable<S extends SequenceRead> - Interface in com.milaboratory.core.io.sequence: Created by dbolotin on 18/07/14.
SequenceReadUtil - Class in com.milaboratory.core.io.sequence
SequencesUtils - Class in com.milaboratory.core.sequence: Utility methods for sequences.
SequencesUtils() - Constructor for class com.milaboratory.core.sequence.SequencesUtils
SequenceTreeMap<S extends Sequence<S>,O> - Class in com.milaboratory.core.tree: Sequence tree map, with fast neighbours search.
SequenceTreeMap(Alphabet<S>) - Constructor for class com.milaboratory.core.tree.SequenceTreeMap: Creates a tree map for specified Alphabet.
SequenceTreeMap.Node<O> - Class in com.milaboratory.core.tree
SequenceTreeMap.Node(int) - Constructor for class com.milaboratory.core.tree.SequenceTreeMap.Node
SequenceTreeMap.NodeIterator - Class in com.milaboratory.core.tree
SequenceTreeMap.NodeIterator(SequenceTreeMap.Node<O>) - Constructor for class com.milaboratory.core.tree.SequenceTreeMap.NodeIterator
SequenceTreeMap.NodeOp - Class in com.milaboratory.core.tree
SequenceTreeMap.NodeOp(SequenceTreeMap.Node<O>) - Constructor for class com.milaboratory.core.tree.SequenceTreeMap.NodeOp
SequenceTreeMap.ValuesOp - Class in com.milaboratory.core.tree
SequenceTreeMap.ValuesOp(SequenceTreeMap.Node<O>) - Constructor for class com.milaboratory.core.tree.SequenceTreeMap.ValuesOp
SequenceWeighter - Interface in com.milaboratory.core.mutations
SequenceWithQuality<S extends Sequence<S>> - Class in com.milaboratory.core.sequence: A container of sequence and its quality.
SequenceWithQuality(S, SequenceQuality) - Constructor for class com.milaboratory.core.sequence.SequenceWithQuality: Creates sequence with quality from specified values.
SequenceWriter<R extends SequenceRead> - Interface in com.milaboratory.core.io.sequence: Common class for sequence writers.
Serializable - Annotation Type in com.milaboratory.primitivio.annotations
serialize(Alphabet, JsonGenerator, SerializerProvider) - Method in class com.milaboratory.core.sequence.Alphabets.Serializer
serialize(TreeSearchParameters, JsonGenerator, SerializerProvider) - Method in class com.milaboratory.core.tree.TreeSearchParameters.Serializer
Serializer<T> - Interface in com.milaboratory.primitivio
SerializersManager - Class in com.milaboratory.primitivio
SerializersManager() - Constructor for class com.milaboratory.primitivio.SerializersManager
set(int, int, int) - Method in class com.milaboratory.core.alignment.AlignerCustom.Matrix
set(int, int, int) - Method in class com.milaboratory.core.alignment.BandedMatrix
set(int, int) - Method in class com.milaboratory.core.mutations.MutationsBuilder
set(int, byte) - Method in interface com.milaboratory.core.sequence.SequenceBuilder: Sets letter at the specified position.
set(int, int) - Method in class com.milaboratory.util.Bit2Array
set(int) - Method in class com.milaboratory.util.BitArray
set(int, boolean) - Method in class com.milaboratory.util.BitArray
set(BitArray) - Method in class com.milaboratory.util.BitArray
set(int, int) - Method in class com.milaboratory.util.IntArrayList
setAbsoluteMinScore(float) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
setAbsoluteMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets minimal absolute score of a hit obtained by KAligner
setAbsoluteMinScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets minimal absolute score of a hit obtained by KAligner
setAlignmentStopPenalty(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
setAlignmentStopPenalty(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
setAll() - Method in class com.milaboratory.util.BitArray
setAllowedLetter(int, byte) - Method in class com.milaboratory.core.motif.MotifBuilder
setBatchSize(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setBlastPath(String) - Static method in class com.milaboratory.core.alignment.blast.Blast: Sets the blast path (e.g.
setBlastTask(BlastTask) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setConcurrentBlastProcessCount(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerAbstract: Sets the number of concurrent BLAST processes to serve a single alignment session (single BlastAlignerAbstract.align(OutputPort) or BlastAlignerAbstract.align(OutputPort, SequenceExtractor method invocation).
setConcurrentBlastProcessCount(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract: Sets the number of concurrent BLAST processes to serve a single alignment session (single BlastAlignerExtAbstract.align(OutputPort) or BlastAlignerExtAbstract.align(OutputPort, SequenceExtractor method invocation).
setDetectStageChange(boolean) - Method in class com.milaboratory.util.SmartProgressReporter
setEValue(double) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setExceptionListener(Benchmark.ExceptionListener) - Method in class com.milaboratory.core.alignment.benchmark.Benchmark
setFinished(boolean) - Method in class com.milaboratory.util.ProgressAndStage
setFloatingLeftBound(boolean) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets left left bound of alignment
setFloatingLeftBound(boolean) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets left left bound of alignment
setFloatingRightBound(boolean) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets right left bound of alignment
setFloatingRightBound(boolean) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets right left bound of alignment
setGapExtend(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setGapExtensionScore(int) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
setGapOpen(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setGapOpenScore(int) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
setGlobal(boolean) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
setGlobalInitialSeed(long) - Static method in class com.milaboratory.util.RandomUtil
setLastRecordLength(long) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
setMapperAbsoluteMinClusterScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
setMapperAbsoluteMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
setMapperAbsoluteMinScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
setMapperExtraClusterScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
setMapperKMersPerPosition(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: If mapperKValue > 0, it is possible to map several seeds with holes in different places to the same position in target sequence.
setMapperKValue(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets kValue (length of kMers or seeds) used by KMapper
setMapperKValue(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
setMapperMatchScore(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets for successfully mapped seeds (used in KMapper)
setMapperMatchScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets for successfully mapped seeds (used in KMapper)
setMapperMaxClusterIndels(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
setMapperMaxClusters(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Max allowed clusters
setMapperMaxSeedsDistance(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets maximal distance between randomly chosen seeds during alignment in KMapper
setMapperMaxSeedsDistance(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets maximal distance between randomly chosen seeds during alignment in KMapper
setMapperMinSeedsDistance(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets minimal distance between randomly chosen seeds during alignment in KMapper
setMapperMinSeedsDistance(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets minimal distance between randomly chosen seeds during alignment in KMapper
setMapperMismatchPenalty(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets penalty score for not mapped seed
setMapperMismatchScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets penalty score for not mapped seed
setMapperNValue(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets kValue (length of kMers or seeds) used by KMapper
setMapperOffsetShiftPenalty(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets penalty for different offset between adjacent seeds (used in KMapper),
setMapperOffsetShiftScore(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets penalty for different offset between adjacent seeds (used in KMapper),
setMapperRelativeMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
setMapperRelativeMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
setMapperSlotCount(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
setMatchScore(int) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
setMatchScore(Alphabet<?>, int[], int) - Static method in class com.milaboratory.core.alignment.ScoringUtils
setMatrix(String) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setMaxAdjacentIndels(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets maximal allowed number of insertions and deletions between 2 kMers
setMaxHits(int) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
setMaxHits(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets maximal number of hits stored by KAlignmentResult
setMaxHits(int) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets maximal number of hits stored by KAlignmentResult
setMinAlignmentLength(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets minimal allowed alignment length
setMinimalPositionWidth(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
setMismatchScore(int) - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
setMismatchScore(Alphabet<?>, int[], int) - Static method in class com.milaboratory.core.alignment.ScoringUtils
setNumAlignments(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setNumThreads(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setObject(O) - Method in class com.milaboratory.core.tree.SequenceTreeMap.Node
setOutputStream(PrintStream) - Method in class com.milaboratory.cli.JCommanderBasedMain
setPenalty(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setPrefix(String) - Static method in class com.milaboratory.util.TempFileManager
setPrintStackTrace(boolean) - Method in class com.milaboratory.cli.JCommanderBasedMain
setProbability(int, int, double) - Method in class com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
setProgress(double) - Method in class com.milaboratory.util.ProgressAndStage
setProgressPeriod(double) - Method in class com.milaboratory.util.SmartProgressReporter
setQueryCount(int) - Method in class com.milaboratory.core.alignment.benchmark.ChallengeParameters
setQueryLeftTitle(int, String) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
setQueryRightTitle(int, String) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
setReadId(long, SequenceRead) - Static method in class com.milaboratory.core.io.sequence.SequenceReadUtil
setRegion(Range, S) - Method in class com.milaboratory.core.sequence.provider.CachedSequenceProvider
setRelativeMinScore(float) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
setRelativeMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets maximal ratio between best hit score and scores of other hits obtained by KAligner
setRelativeMinScore(float) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets maximal ratio between best hit score and scores of other hits obtained by KAligner
setReward(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
setScoring(AlignmentScoring<S>) - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Sets scoring used for alignment.
setScoring(AlignmentScoring<S>) - Method in class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
setScoring(LinearGapAlignmentScoring) - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters: Sets scoring system used for building alignments
setScoring(AffineGapAlignmentScoring<NucleotideSequence>) - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2: Sets scoring system used for building alignments
setStage(String) - Method in class com.milaboratory.util.ProgressAndStage
setStartingRecordNumber(long) - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Sets the starting record number to a specified one.
setStartingRecordPosition(long) - Method in class com.milaboratory.core.io.util.FileIndexBuilder: Sets the starting record to a specified pointer (in bytes).
setStopPenalty(int) - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Sets alignment score value in banded alignment matrix at which alignment terminates.
setSubjectLeftTitle(String) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
setSubjectRightTitle(String) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
setThreadCount(int) - Method in class com.milaboratory.core.alignment.kaligner1.KAligner: Sets number of threads to be used in piped processing.

0 -> Runtime.getRuntime().availableProcessors()
1 -> process in the same thread as take() method call
2...
setTimePeriod(double) - Method in class com.milaboratory.util.SmartProgressReporter
setTotalSize(long) - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
setTotalSize(long) - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
setVersionInfoCallback(Runnable) - Method in class com.milaboratory.cli.JCommanderBasedMain: Enables -v / --version parameter.
setVersionInfoCallback(Runnable, Runnable) - Method in class com.milaboratory.cli.JCommanderBasedMain: Enables -v / --version parameter.
setWidth(int) - Method in class com.milaboratory.core.alignment.BandedAlignerParameters: Sets width of banded alignment matrix.
setWordSize(int) - Method in class com.milaboratory.core.alignment.blast.BlastAlignerParameters
shiftIndelsAtHomopolymers(Alignment<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils: Shifts indels to the left at homopolymer regions
shiftIndelsAtHomopolymers(S, Mutations<S>) - Static method in class com.milaboratory.core.mutations.MutationsUtil: 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
shiftIndelsAtHomopolymers(S, int, Mutations<S>) - Static method in class com.milaboratory.core.mutations.MutationsUtil: 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
shiftIndelsAtHomopolymers(Sequence, int[]) - Static method in class com.milaboratory.core.mutations.MutationsUtil: 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
shiftIndelsAtHomopolymers(Sequence, int, int[]) - Static method in class com.milaboratory.core.mutations.MutationsUtil: 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
shortVersion - Variable in class com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
shortVersion() - Method in class com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
shortVersionInfoCallback - Variable in class com.milaboratory.cli.JCommanderBasedMain
sig() - Method in class com.milaboratory.core.Range: Return +1 if this range is normal and -1 if it is reversed
similarity() - Method in class com.milaboratory.core.alignment.Alignment: Returns number of matches divided by sum of number of matches and mismatches.
SimpleBatchAligner<S extends Sequence<S>,P> - Class in com.milaboratory.core.alignment.batch: Simplest implementation of BatchAligner, which aligns target sequence with all subjects using classical (low performance) alignment algorithms.
SimpleBatchAligner(SimpleBatchAlignerParameters<S>) - Constructor for class com.milaboratory.core.alignment.batch.SimpleBatchAligner
SimpleBatchAlignerParameters<S extends Sequence<S>> - Class in com.milaboratory.core.alignment.batch: Parameters of SimpleBatchAligner.
SimpleBatchAlignerParameters(int, float, float, boolean, AlignmentScoring<S>) - Constructor for class com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
SingleFastqIndexer - Class in com.milaboratory.core.io.sequence.fastq
SingleFastqIndexer(SingleFastqReader, long) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
SingleFastqReader - Class in com.milaboratory.core.io.sequence.fastq
SingleFastqReader(String, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream, QualityFormat, CompressionType, boolean, int, boolean, boolean) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqReader: Creates a SingleFastqReader stream from a FASTQ files with single-end read data
SingleFastqWriter - Class in com.milaboratory.core.io.sequence.fastq
SingleFastqWriter(String) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(File) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(OutputStream) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(File, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(String, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(OutputStream, QualityFormat, CompressionType) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleFastqWriter(OutputStream, QualityFormat, CompressionType, int) - Constructor for class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
SingleIterator<T> - Class in com.milaboratory.util: Iterator over one single element.
SingleIterator(T) - Constructor for class com.milaboratory.util.SingleIterator
SingleRead - Interface in com.milaboratory.core.io.sequence: Single read
SingleReader - Interface in com.milaboratory.core.io.sequence
SingleReadImpl - Class in com.milaboratory.core.io.sequence
SingleReadImpl(long, NSequenceWithQuality, String) - Constructor for class com.milaboratory.core.io.sequence.SingleReadImpl
SingleReadLazy - Class in com.milaboratory.core.io.sequence
SingleSequenceWriter - Interface in com.milaboratory.core.io.sequence
size() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the size of aligned region
size() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
size() - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
size() - Method in class com.milaboratory.core.motif.Motif
size() - Method in class com.milaboratory.core.mutations.Mutations
size() - Method in class com.milaboratory.core.mutations.MutationsBuilder
size() - Method in class com.milaboratory.core.sequence.Alphabet: Gets number of letters in this alphabet including wildcard letters
size() - Method in class com.milaboratory.core.sequence.ArraySeqBuilder
size() - Method in class com.milaboratory.core.sequence.NSequenceWithQualityBuilder
size() - Method in class com.milaboratory.core.sequence.provider.CachedSequenceProvider
size() - Method in interface com.milaboratory.core.sequence.provider.SequenceProvider: Returns the length of the sequence this object represents.
size() - Method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils.LazySequenceProvider
size() - Method in interface com.milaboratory.core.sequence.Seq: Returns size of this sequence
size() - Method in interface com.milaboratory.core.sequence.SeqBuilder: Size of sequence being created.
size() - Method in class com.milaboratory.core.sequence.SequenceQuality: Returns size of quality array
size() - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns the size of this sequence and quality (sequence and quality has same sizes).
size() - Method in class com.milaboratory.core.sequence.Wildcard: Returns a number of letters (including wildcards) that matches this wildcard.
size() - Method in class com.milaboratory.util.Bit2Array
size() - Method in class com.milaboratory.util.BitArray
size() - Method in class com.milaboratory.util.IntArrayList
skip() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
skip() - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader
SKIP_MASK - Static variable in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex: Bit mask for encoded file position.
skipBytes(int) - Method in class com.milaboratory.primitivio.PrimitivI
SmartProgressReporter - Class in com.milaboratory.util
SmartProgressReporter(CanReportProgressAndStage, PrintStream) - Constructor for class com.milaboratory.util.SmartProgressReporter
SmartProgressReporter(CanReportProgressAndStage) - Constructor for class com.milaboratory.util.SmartProgressReporter
SmartProgressReporter(String, CanReportProgress) - Constructor for class com.milaboratory.util.SmartProgressReporter
SmartProgressReporter(String, CanReportProgress, PrintStream) - Constructor for class com.milaboratory.util.SmartProgressReporter
sort() - Method in class com.milaboratory.util.IntArrayList
sort(OutputPort<T>, Comparator<T>, int, Class<T>, File) - Static method in class com.milaboratory.util.Sorter: Sort objects supporting PrimitivIO serialization.
sort(OutputPort<T>, Comparator<T>, int, ObjectSerializer<T>, File) - Static method in class com.milaboratory.util.Sorter
sortAccordingToMapperScores() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignmentResult: Sorts hits according to KMappingHit alignment score
Sorter<T> - Class in com.milaboratory.util: Created by poslavsky on 28/02/2017.
Sorter(OutputPort<T>, Comparator<T>, int, ObjectSerializer<T>, File) - Constructor for class com.milaboratory.util.Sorter
spaces(int) - Static method in class com.milaboratory.util.StringUtil
split(int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
split(int, int) - Method in class com.milaboratory.core.alignment.AlignmentHelper
split(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
split(int, boolean) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
splitWithBrackets(String, char, String) - Static method in class com.milaboratory.util.ParseUtil
splitWithBrackets(String, char, ParseUtil.BracketsInfo) - Static method in class com.milaboratory.util.ParseUtil
stableSort(IntArrayList.IntComparator) - Method in class com.milaboratory.util.IntArrayList
start(String) - Method in class com.milaboratory.util.AbstractLongProcessReporter
start(String) - Method in interface com.milaboratory.util.LongProcessReporter
startProgressReport(SmartProgressReporter) - Static method in class com.milaboratory.util.SmartProgressReporter
startProgressReport(CanReportProgressAndStage, PrintStream) - Static method in class com.milaboratory.util.SmartProgressReporter
startProgressReport(CanReportProgressAndStage) - Static method in class com.milaboratory.util.SmartProgressReporter
startProgressReport(String, CanReportProgress) - Static method in class com.milaboratory.util.SmartProgressReporter
startProgressReport(String, CanReportProgress, PrintStream) - Static method in class com.milaboratory.util.SmartProgressReporter
stat - Variable in class com.milaboratory.core.alignment.benchmark.BenchmarkResults
stderrReporter() - Static method in class com.milaboratory.util.AbstractLongProcessReporter
STOP - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Stop codon byte representation
STOP_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Stop codon wildcard
STRETCH_INDEX_MARK - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
STRETCH_INDEX_MASK - Static variable in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
StringUtil - Class in com.milaboratory.util
subjectToAlignmentPosition(int) - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
subProvider(SequenceProvider<S>, Range) - Static method in class com.milaboratory.core.sequence.provider.SequenceProviderUtils
subsMatrix - Variable in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Stores information about how the object was created.
subsMatrixActual - Variable in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Actual substitution matrix
substitutionAndIndelMatcherFirst(int, Sequence) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
substitutionAndIndelMatcherFirst(int, Sequence, int, int) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.
substitutionAndIndelMatcherLast(int, Sequence) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
substitutionAndIndelMatcherLast(int, Sequence, int, int) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.
SubstitutionModel - Class in com.milaboratory.core.mutations.generator
SubstitutionModel(double[]) - Constructor for class com.milaboratory.core.mutations.generator.SubstitutionModel
SubstitutionModelBuilder - Class in com.milaboratory.core.mutations.generator
SubstitutionModelBuilder(Alphabet) - Constructor for class com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
SubstitutionModelBuilder(int) - Constructor for class com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
SubstitutionModels - Class in com.milaboratory.core.mutations.generator
substitutionOnlyMatcherFirst(int, Sequence) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a whole sequence.
substitutionOnlyMatcherFirst(int, Sequence, int, int) - Method in class com.milaboratory.core.motif.BitapPattern: Returns a BitapMatcher preforming a fuzzy search in a subsequence of sequence.
SumQualityAggregator - Class in com.milaboratory.core.sequence.quality
SumQualityAggregator(int, byte) - Constructor for class com.milaboratory.core.sequence.quality.SumQualityAggregator
symbolAt(int) - Method in class com.milaboratory.core.sequence.Sequence: Returns a character representation of element at specified position.
symbolByteFromCode(byte) - Static method in class com.milaboratory.core.sequence.NucleotideAlphabet: Returns UTF-8 character corresponding to specified byte-code.
symbolToCode(char) - Method in class com.milaboratory.core.sequence.Alphabet: Gets the binary code representing given symbol (case insensitive) or -1 if there is no such symbol in this alphabet
symbolToCode(char) - Method in class com.milaboratory.core.sequence.AminoAcidAlphabet
symbolToCodeWithException(char) - Method in class com.milaboratory.core.sequence.Alphabet: Gets the binary code corresponding to given symbol (case insensitive) or throws IllegalArgumentException if there is no such symbol in this alphabet
symbolToWildcard(char) - Method in class com.milaboratory.core.sequence.Alphabet: Returns a wildcard object for specified letter.

T

T - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Threonine byte representation
T - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Thymine byte representation
T_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Threonine wildcard
T_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Thymine byte representation
take() - Method in class com.milaboratory.core.alignment.benchmark.ChallengeProvider
take() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader: Return next FASTA record or null if end of stream is reached.
take() - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
take() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
take(long) - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
take(long) - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
take() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
take() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
take() - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqReader
take() - Method in class com.milaboratory.core.io.sequence.MultiReader
take() - Method in class com.milaboratory.core.io.sequence.PairedReader
take(long) - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Returns the specified record or null if recordNumber is greater than actual number of records in file.
take() - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader: Returns the next record or null if no more records exist.
take() - Method in class com.milaboratory.core.tree.SequenceTreeMap.NodeOp
take() - Method in class com.milaboratory.core.tree.SequenceTreeMap.ValuesOp
take() - Method in class com.milaboratory.primitivio.PipeDataInputReader
take() - Method in class com.milaboratory.primitivio.PipeReader
take() - Method in class com.milaboratory.util.IntCombinations
take0() - Method in class com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
take0() - Method in class com.milaboratory.core.io.util.AbstractRandomAccessReader
takeRawRecord() - Method in class com.milaboratory.core.io.sequence.fasta.FastaReader: Return next raw FASTA record or null if end of stream is reached.
takeReads() - Method in class com.milaboratory.core.io.sequence.AbstractMultiReader
Target - Class in com.milaboratory.core
targetClusters - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
targetId - Variable in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
targets - Variable in class com.milaboratory.core.Target
TempFileManager - Class in com.milaboratory.util
TempFileManager() - Constructor for class com.milaboratory.util.TempFileManager
threads - Variable in class com.milaboratory.core.alignment.batch.AbstractBatchAligner: 0 -> Runtime.getRuntime().availableProcessors() 1 -> process in the same thread as take() method call 2...
THREE_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
THREE_MISMATCHES - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
THREE_MISMATCHES_OR_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
time(long) - Static method in class com.milaboratory.test.Read
TimeUtils - Class in com.milaboratory.util
TimeUtils() - Constructor for class com.milaboratory.util.TimeUtils
toArray() - Method in class com.milaboratory.util.IntArrayList
toByteArray() - Method in class com.milaboratory.util.Bit2Array
toCompactString() - Method in class com.milaboratory.core.alignment.Alignment
toCompactString() - Method in class com.milaboratory.core.alignment.AlignmentHelper: Gets the alignment string in contact format (no markup line, mismatches shown by lower-case characters)
toList() - Method in class com.milaboratory.core.tree.NeighborhoodIterator
toMap() - Method in class com.milaboratory.core.tree.SequenceTreeMap
toMotif() - Method in class com.milaboratory.core.sequence.Sequence: Converts sequnce to motif data structure efficient for exact and fuzzy wildcard-aware matching and searching of sequences.
toOneLine(Object) - Static method in class com.milaboratory.util.GlobalObjectMappers
topInitialClusters - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
topInitialRecordsCount - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
topRemovedByTrimming - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
topRemovedByUntangling - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
toPrettyString() - Method in class com.milaboratory.core.sequence.SequenceWithQuality: Returns a pretty string representation of this.
topTrimming - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
topUntangledClusters - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
toString() - Method in class com.milaboratory.core.alignment.Alignment
toString() - Method in class com.milaboratory.core.alignment.AlignmentHelper
toString() - Method in class com.milaboratory.core.alignment.BandedMatrix
toString() - Method in class com.milaboratory.core.alignment.batch.AlignmentResultImpl
toString() - Method in class com.milaboratory.core.alignment.batch.PipedAlignmentResultImpl
toString() - Method in class com.milaboratory.core.alignment.benchmark.KAlignerQuery
toString() - Method in class com.milaboratory.core.alignment.blast.BlastHit
toString() - Method in class com.milaboratory.core.alignment.kaligner1.KAlignerParameters
toString() - Method in class com.milaboratory.core.alignment.kaligner1.KMapper
toString() - Method in class com.milaboratory.core.alignment.kaligner1.KMappingHit
toString() - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
toString() - Method in class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
toString() - Method in class com.milaboratory.core.alignment.kaligner2.KMapper2
toString() - Method in class com.milaboratory.core.alignment.kaligner2.KMappingHit2
toString() - Method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
toString(IntArrayList, IntArrayList, int[]) - Static method in class com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
toString() - Method in class com.milaboratory.core.alignment.MultiAlignmentHelper
toString() - Method in class com.milaboratory.core.clustering.Cluster
toString() - Method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat
toString() - Method in class com.milaboratory.core.io.sequence.PairedRead
toString() - Method in class com.milaboratory.core.io.sequence.SingleReadImpl
toString() - Method in class com.milaboratory.core.merger.PairedReadMergingResult
toString(Alphabet, int) - Static method in class com.milaboratory.core.mutations.Mutation
toString() - Method in class com.milaboratory.core.mutations.Mutations
toString() - Method in class com.milaboratory.core.mutations.MutationsBuilder
toString() - Method in class com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
toString() - Method in class com.milaboratory.core.Range
toString() - Method in class com.milaboratory.core.sequence.Alphabet: Convert alphabet to a readable string.
toString() - Method in class com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
toString() - Method in class com.milaboratory.core.sequence.Sequence
toString() - Method in class com.milaboratory.core.sequence.SequenceQuality
toString() - Method in class com.milaboratory.core.sequence.SequenceWithQuality
toString() - Method in class com.milaboratory.core.sequence.TranslationParameters
toString() - Method in class com.milaboratory.util.AtomicEnumHistogram
toString() - Method in class com.milaboratory.util.AtomicHistogram
toString() - Method in class com.milaboratory.util.BitArray
toString() - Method in class com.milaboratory.util.IntArrayList
toString() - Method in class com.milaboratory.util.NSequenceWithQualityPrintHelper
toString() - Method in class com.milaboratory.util.VersionInfo
toStringSimple(S, Mutations<S>) - Static method in class com.milaboratory.core.alignment.AlignmentUtils
toStringWithSeq2Quality(SequenceQuality) - Method in class com.milaboratory.core.alignment.AlignmentHelper
total - Variable in class com.milaboratory.util.AtomicHistogram.SerializableResult
totalCount() - Method in class com.milaboratory.core.clustering.Cluster
totalSize - Variable in class com.milaboratory.primitivio.PReader
totalTime - Variable in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
translate(NucleotideSequence, int) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Translate sequence in one of frames (-1, -2, -3 frames are not implemented, use NucleotideSequence.getReverseComplement()) discarding all incomplete codons on both boundaries.
translate(NucleotideSequence) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Translates sequence having length divisible by 3, starting from first nucleotide.
translate(NucleotideSequence, TranslationParameters) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Use one of specialized method instead: AminoAcidSequence.translateFromLeft(NucleotideSequence) AminoAcidSequence.translateFromRight(NucleotideSequence) AminoAcidSequence.translateFromCenter(NucleotideSequence)
translate(byte[], int, NucleotideSequence, int, int) - Static method in class com.milaboratory.core.sequence.GeneticCode
translateFromCenter(NucleotideSequence) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Translates sequence from both sides, so the first nucleotide of the first triplet matches first nucleotide of the sequence, and last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.
translateFromLeft(NucleotideSequence) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Translates sequence from the left side, so the first nucleotide of the first triplet matches first nucleotide of the sequence.
translateFromRight(NucleotideSequence) - Static method in class com.milaboratory.core.sequence.AminoAcidSequence: Translates sequence from the right side, so the last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.
TranslationParameters - Class in com.milaboratory.core.sequence
traverseToTheEnd(SequenceTreeMap.Node<O>, int) - Method in class com.milaboratory.core.tree.NeighborhoodIterator
TreeSearchParameters - Class in com.milaboratory.core.tree
TreeSearchParameters(int[], double[], double) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters(int[], double[], double, boolean) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters(int, int, int) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters: Parameters to search with limited number of each mutation type.
TreeSearchParameters(int, int, int, boolean) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters: Parameters to search with limited number of each mutation type.
TreeSearchParameters(int, int, int, int, boolean) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters(int, int, int, int) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters(int, int, int, double, double, double, double, boolean) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters(int, int, int, double, double, double, double) - Constructor for class com.milaboratory.core.tree.TreeSearchParameters
TreeSearchParameters.Deserializer - Class in com.milaboratory.core.tree
TreeSearchParameters.Deserializer() - Constructor for class com.milaboratory.core.tree.TreeSearchParameters.Deserializer
TreeSearchParameters.Serializer - Class in com.milaboratory.core.tree
TreeSearchParameters.Serializer() - Constructor for class com.milaboratory.core.tree.TreeSearchParameters.Serializer
trimmingEvent(KAligner2Statistics.ClusterTrimmingType) - Method in class com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
tryMerge(Range) - Method in class com.milaboratory.core.Range: Returns union range with other range.
TWO_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
TWO_MISMATCHES - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
TWO_MISMATCHES_OR_INDELS - Static variable in class com.milaboratory.core.tree.TreeSearchParameters
twoSequenceMotif(S, int, S, int, int) - Static method in class com.milaboratory.core.motif.MotifUtils
TypeSerializationHelper - Class in com.milaboratory.primitivio
TypeSerializationHelper(Serializer) - Constructor for class com.milaboratory.primitivio.TypeSerializationHelper

U

uniformBasicMatchScore() - Method in class com.milaboratory.core.alignment.AbstractAlignmentScoring: Returns @code{true} if @code{getScore(i, i)} returns the same score for all basic letters values of @code{i}.
UniformMutationsGenerator - Class in com.milaboratory.core.mutations.generator
UniformMutationsGenerator() - Constructor for class com.milaboratory.core.mutations.generator.UniformMutationsGenerator
UnsafeFactory - Class in com.milaboratory.core.sequence: Don't use this class.
Util - Class in com.milaboratory.primitivio

V

V - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Valine byte representation
V - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not T (V comes after T and U)
V_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Valine wildcard
V_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: not T (V comes after T and U)
validate() - Method in class com.milaboratory.cli.ActionParameters
validate() - Method in class com.milaboratory.cli.ActionParametersWithOutput
value(int) - Method in class com.milaboratory.core.sequence.SequenceQuality: Get the raw sequence quality value (in binary format) at given sequence point
valueOf(String) - Static method in enum com.milaboratory.cli.JCommanderBasedMain.ProcessResult: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.alignment.blast.BlastStrand: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.alignment.blast.BlastTask: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.alignment.BLASTMatrix: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.ClusterTrimmingType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.io.CompressionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.merger.MergerParameters.IdentityType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.merger.QualityMergingAlgorithm: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.mutations.MutationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.PairedEndReadsLayout: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.milaboratory.core.sequence.quality.QualityAggregationType: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.milaboratory.cli.JCommanderBasedMain.ProcessResult: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.alignment.blast.BlastStrand: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.alignment.blast.BlastTask: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.alignment.BLASTMatrix: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.ClusterTrimmingType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.io.CompressionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.io.sequence.fastq.QualityFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.merger.MergerParameters.IdentityType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.merger.QualityMergingAlgorithm: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.mutations.MutationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.PairedEndReadsLayout: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.milaboratory.core.sequence.quality.QualityAggregationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class com.milaboratory.core.tree.SequenceTreeMap
valuesOp() - Method in class com.milaboratory.core.tree.SequenceTreeMap
VersionInfo - Class in com.milaboratory.util
VersionInfo(String, String, String, String, String, Date) - Constructor for class com.milaboratory.util.VersionInfo

W

W - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Tryptophan byte representation
W - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Weak
W_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Tryptophan wildcard
W_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: Weak
Wang32shiftmult(int) - Static method in class com.milaboratory.util.HashFunctions: This method uses a combination of bit shifts and integer multiplication to hash the input key.
Wang64to32shift(long) - Static method in class com.milaboratory.util.HashFunctions: Hashing long to int.
Wildcard - Class in com.milaboratory.core.sequence: Representation of a wildcard symbol.
wildcardsToRandomBasic(S, long) - Static method in class com.milaboratory.core.sequence.SequencesUtils: 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.
WithBase<S extends Sequence<S>,P> - Interface in com.milaboratory.core.alignment.batch: Interface for aligners with self-managed database (user can directly add subject sequences before running alignment)
withIncompleteCodon(int) - Static method in class com.milaboratory.core.sequence.TranslationParameters: E.g.
without(Range) - Method in class com.milaboratory.core.Range: Subtract provided range and return list of ranges contained in current range and not intersecting with other range.
withoutIncompleteCodon(int) - Static method in class com.milaboratory.core.sequence.TranslationParameters: E.g.
write(PrimitivO, Alignment) - Method in class com.milaboratory.core.io.binary.AlignmentSerializer
write(PrimitivO, Range) - Method in class com.milaboratory.core.io.binary.RangeSerializer
write(SingleRead) - Method in class com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper
write(FastaRecord<S>) - Method in class com.milaboratory.core.io.sequence.fasta.FastaWriter
write(String, S) - Method in class com.milaboratory.core.io.sequence.fasta.FastaWriter
write(OutputStream) - Method in class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
write(PairedRead) - Method in class com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
write(SingleRead) - Method in class com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
write(R) - Method in interface com.milaboratory.core.io.sequence.SequenceWriter: Writes corresponding subtype of SequenceRead
write(String) - Method in class com.milaboratory.core.io.util.FileIndex: Writes this index to specified file.
write(File) - Method in class com.milaboratory.core.io.util.FileIndex: Writes this index to specified file.
write(OutputStream) - Method in class com.milaboratory.core.io.util.FileIndex: Writes this index to specified output stream.
write(PrimitivO, Object) - Method in class com.milaboratory.primitivio.CustomSerializerImpl
write(PrimitivO, Object) - Method in class com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer
write(PrimitivO, Object) - Method in class com.milaboratory.primitivio.JSONSerializer
write(int) - Method in class com.milaboratory.primitivio.PrimitivO
write(byte[]) - Method in class com.milaboratory.primitivio.PrimitivO
write(byte[], int, int) - Method in class com.milaboratory.primitivio.PrimitivO
write(PrimitivO, T) - Method in interface com.milaboratory.primitivio.Serializer
write(Collection<O>, OutputStream) - Method in class com.milaboratory.util.ObjectSerializer.PrimitivIOObjectSerializer
write(Collection<O>, OutputStream) - Method in interface com.milaboratory.util.ObjectSerializer: Implementation may close stream.
writeBoolean(boolean) - Method in class com.milaboratory.primitivio.PrimitivO
writeByte(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeBytes(String) - Method in class com.milaboratory.primitivio.PrimitivO
writeChar(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeChars(String) - Method in class com.milaboratory.primitivio.PrimitivO
writeDouble(double) - Method in class com.milaboratory.primitivio.PrimitivO
writeFloat(float) - Method in class com.milaboratory.primitivio.PrimitivO
writeInt(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeList(List<?>, String) - Static method in class com.milaboratory.primitivio.Util
writeList(List<?>, File) - Static method in class com.milaboratory.primitivio.Util
writeList(List<?>, OutputStream) - Static method in class com.milaboratory.primitivio.Util
writeList(List<?>, PrimitivO) - Static method in class com.milaboratory.primitivio.Util
writeLong(long) - Method in class com.milaboratory.primitivio.PrimitivO
writeMap(Map<K, V>, PrimitivO) - Static method in class com.milaboratory.primitivio.Util
writeObject(Object, Class<?>) - Method in class com.milaboratory.primitivio.PrimitivO
writeObject(Object) - Method in class com.milaboratory.primitivio.PrimitivO
writeObjectFieldValueSeparator(JsonGenerator) - Method in class com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1
writeRawVarint32(OutputStream, int) - Static method in class com.milaboratory.core.io.util.IOUtil: Encode and write a varint.
writeRawVarint64(OutputStream, long) - Static method in class com.milaboratory.core.io.util.IOUtil: Encode and write a varint.
writeReference(Object) - Method in class com.milaboratory.primitivio.PrimitivO
writeReplace() - Method in class com.milaboratory.core.alignment.AffineGapAlignmentScoring
writeReplace() - Method in class com.milaboratory.core.alignment.LinearGapAlignmentScoring
writeReplace() - Method in class com.milaboratory.core.sequence.Alphabet
writeShort(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeTo(DataOutput) - Method in class com.milaboratory.util.Bit2Array
writeUTF(String) - Method in class com.milaboratory.primitivio.PrimitivO
writeVarInt(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeVarIntZigZag(int) - Method in class com.milaboratory.primitivio.PrimitivO
writeVarLong(long) - Method in class com.milaboratory.primitivio.PrimitivO
writeVarLongZigZag(long) - Method in class com.milaboratory.primitivio.PrimitivO
WrongQualityFormat - Exception in com.milaboratory.core.io.sequence.fastq
WrongQualityFormat() - Constructor for exception com.milaboratory.core.io.sequence.fastq.WrongQualityFormat
WrongQualityFormat(String) - Constructor for exception com.milaboratory.core.io.sequence.fastq.WrongQualityFormat

X

X - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Any amino acid byte representation
X_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Any amino acid wildcard
xor(BitArray) - Method in class com.milaboratory.util.BitArray

Y

Y - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Tyrosine byte representation
Y - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: pYrimidine
Y_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Tyrosine wildcard
Y_WILDCARD - Static variable in class com.milaboratory.core.sequence.NucleotideAlphabet: pYrimidine

Z

Z - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamine or Glutamic acid (E or Q) byte representation
Z_WILDCARD - Static variable in class com.milaboratory.core.sequence.AminoAcidAlphabet: Glutamine or Glutamic acid (E or Q) wildcard
zigZagDecodeInt(int) - Static method in class com.milaboratory.primitivio.Util
zigZagDecodeLong(long) - Static method in class com.milaboratory.primitivio.Util
zigZagEncodeInt(int) - Static method in class com.milaboratory.primitivio.Util
zigZagEncodeLong(long) - Static method in class com.milaboratory.primitivio.Util

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