All Classes
AABlastAligner
AABlastAlignerExt
AABlastHit
AABlastHitExt
AbstractAlignmentScoring
AbstractBatchAligner
AbstractKAlignerParameters
AbstractLongProcessReporter
AbstractMultiReader
AbstractRandomAccessReader
AbstractSeq
AbstractSequenceReader
Action
ActionHelper
ActionHelpProvider
ActionParameters
ActionParametersParser
ActionParametersWithOutput
AffineGapAlignmentScoring
AffineGapAlignmentScoring.SerializationObject
Aligner
AlignerCustom
AlignerCustom.AffineMatrixCache
AlignerCustom.LinearMatrixCache
AlignerCustom.Matrix
AlignerCustom.MatrixCache
Alignment
AlignmentCache
AlignmentHelper
AlignmentHit
AlignmentHitImpl
AlignmentIterator
AlignmentIteratorForward
AlignmentIteratorReverse
AlignmentResult
AlignmentResultImpl
AlignmentScoring
AlignmentSerializer
AlignmentTrimmer
AlignmentUtils
AllowNoArguments
Alphabet
Alphabet.AlphabetSerialization
Alphabets
Alphabets.Deserializer
Alphabets.Serializer
AminoAcidAlphabet
AminoAcidSequence
AminoAcidSequence.AminoAcidSequencePosition
ArrayIterator
ArraySeqBuilder
ArraysUtils
AtomicEnumHistogram
AtomicEnumHistogram.SerializableResult
AtomicHistogram
AtomicHistogram.SerializableResult
AverageQualityAggregator
BandedAffineAligner
BandedAffineAligner.MatrixCache
BandedAligner
BandedAlignerParameters
BandedLinearAligner
BandedMatrix
BandedSemiLocalResult
BatchAligner
BatchAlignerWithBase
BatchAlignerWithBaseParameters
BatchAlignerWithBaseWithFilter
BatchAlignmentUtil
Benchmark
Benchmark.ExceptionData
Benchmark.ExceptionListener
BenchmarkInput
BenchmarkResults
Bit2Array
BitapMatcher
BitapMatcherFilter
BitapMatcherImpl
BitapPattern
BitArray
Blast
BlastAligner
BlastAlignerAbstract
BlastAlignerExt
BlastAlignerExtAbstract
BlastAlignerParameters
BlastDB
BlastDBBuilder
BlastHit
BlastHitExt
BLASTMatrix
BlastStrand
BlastTask
CachedIntArray
CachedSequenceProvider
CanReportProgress
CanReportProgressAndStage
Challenge
ChallengeParameters
ChallengeProvider
Cluster
Clustering
ClusteringStrategy
CompressionType
CountingInputStream
CoverageCounter
CoverageCounter.Provider
CustomSerializer
CustomSerializerImpl
CustomSerializerImpl.TypeInfo
DefaultSerializersProvider
DefaultSerializersProviderImpl
DefaultSerializersProviderImpl.CustomEnumSerializer
Factory
FastaReader
FastaReader.RawFastaRecord
FastaRecord
FastaSequenceReaderWrapper
FastaSequenceWriterWrapper
FastaWriter
FastqRecordsReader
FileIndex
FileIndexBuilder
GenericNucleotideMutationModel
GeneticCode
GlobalObjectMappers
GlobalObjectMappers.DefaultPrettyPrinter1
HashFunctions
HasSequence
HiddenAction
IllegalFileFormatException
IntArrayList
IntArrayList.IntComparator
IntCombinations
IOUtil
JCommanderBasedMain
JCommanderBasedMain.MainParameters
JCommanderBasedMain.MainParametersWithVersion
JCommanderBasedMain.ProcessResult
JSONSerializer
KAligner
KAligner2
KAligner2Statistics
KAligner2Statistics.ClusterTrimmingType
KAligner2Statistics.State
KAlignerParameters
KAlignerParameters2
KAlignerQuery
KAlignmentHit
KAlignmentHit2
KAlignmentResult
KAlignmentResult2
KAlignmentResultP
KMapper
KMapper2
KMappingHit
KMappingHit2
KMappingResult
KMappingResult2
LinearGapAlignmentScoring
LinearGapAlignmentScoring.SerializationObject
LongProcess
LongProcessReporter
LongProcessReporter.DefaultLongProcessReporter
MaximalQualityAggregator
MergerParameters
MergerParameters.IdentityType
MinimalQualityAggregator
MiniMaxQualityAggregator
MismatchOnlyPairedReadMerger
Motif
MotifBuilder
MotifUtils
MultiAlignmentHelper
MultiAlignmentHelper.Settings
MultiNSequenceWithQuality
MultiNSequenceWithQualityImpl
MultiRead
MultiReader
Mutation
MutationConsensusBuilder
MutationGuide
MutationModels
Mutations
MutationsBuilder
MutationsCounter
MutationsCounter.Filter
MutationsEnumerator
MutationsGenerator
MutationsUtil
MutationsUtil.MutationNt2AADescriptor
MutationsUtil.MutationsWitMapping
MutationType
NBlastAligner
NBlastAlignerExt
NBlastHit
NBlastHitExt
NeighborhoodIterator
NSeq
NSequenceWithQuality
NSequenceWithQualityBuilder
NSequenceWithQualityPrintHelper
NucleotideAlphabet
NucleotideMutationModel
NucleotideSequence
ObjectSerializer
ObjectSerializer.PrimitivIOObjectSerializer
OffsetPacksAccumulator
PairedEndReadsLayout
PairedFastqReader
PairedFastqWriter
PairedRead
PairedReader
PairedReadMergingResult
PairedSequenceWriter
ParserException
ParseUtil
ParseUtil.BracketsInfo
PenaltyUtils
PipedAlignmentResult
PipedAlignmentResultImpl
PipeDataInputReader
PipedBatchAligner
PipedBatchAlignerWithBase
PipeReader
PipeWriter
PReader
PrimitivI
PrimitivO
ProcessException
ProgressAndStage
PWriter
QualityAggregationType
QualityAggregator
QualityFormat
QualityMergingAlgorithm
RandomAccessFastaIndex
RandomAccessFastaIndex.IndexBuilder
RandomAccessFastaIndex.MultipleMatchingRecordsException
RandomAccessFastaIndex.NoSuchRecordException
RandomAccessFastaIndex.StreamIndexBuilder
RandomAccessFastaReader
RandomAccessFastqReader
RandomAccessPairedFastqReader
Randomizer
RandomUtil
Range
RangeMap
RangeMap.IntersectingRangesException
RangeSerializer
Read
ScoringUtils
Seq
SeqBuilder
Sequence
SequenceBuilder
SequenceExtractor
SequenceExtractor
SequenceProvider
SequenceProviderFactory
SequenceProviderIndexOutOfBoundsException
SequenceProviderUtils
SequenceProviderUtils.LazySequenceProvider
SequenceQuality
SequenceQualityBuilder
SequenceRead
SequenceReader
SequenceReaderCloseable
SequenceReadUtil
SequencesUtils
SequenceTreeMap
SequenceTreeMap.Node
SequenceWeighter
SequenceWithQuality
SequenceWriter
Serializable
Serializer
SerializersManager
SimpleBatchAligner
SimpleBatchAlignerParameters
SingleFastqIndexer
SingleFastqReader
SingleFastqWriter
SingleIterator
SingleRead
SingleReader
SingleReadImpl
SingleReadLazy
SingleSequenceWriter
SmartProgressReporter
Sorter
StringUtil
SubstitutionModel
SubstitutionModelBuilder
SubstitutionModels
SumQualityAggregator
Target
TempFileManager
TimeUtils
TranslationParameters
TreeSearchParameters
TreeSearchParameters.Deserializer
TreeSearchParameters.Serializer
TypeSerializationHelper
UniformMutationsGenerator
UnsafeFactory
Util
VersionInfo
Wildcard
WithBase
WrongQualityFormat