Hierarchy For All Packages

Package Hierarchies:

• com.milaboratory.cli,
• com.milaboratory.core,
• com.milaboratory.core.alignment,
• com.milaboratory.core.alignment.batch,
• com.milaboratory.core.alignment.benchmark,
• com.milaboratory.core.alignment.blast,
• com.milaboratory.core.alignment.kaligner1,
• com.milaboratory.core.alignment.kaligner2,
• com.milaboratory.core.clustering,
• com.milaboratory.core.io,
• com.milaboratory.core.io.binary,
• com.milaboratory.core.io.sequence,
• com.milaboratory.core.io.sequence.fasta,
• com.milaboratory.core.io.sequence.fastq,
• com.milaboratory.core.io.util,
• com.milaboratory.core.merger,
• com.milaboratory.core.motif,
• com.milaboratory.core.mutations,
• com.milaboratory.core.mutations.generator,
• com.milaboratory.core.sequence,
• com.milaboratory.core.sequence.provider,
• com.milaboratory.core.sequence.quality,
• com.milaboratory.core.tree,
• com.milaboratory.primitivio,
• com.milaboratory.primitivio.annotations,
• com.milaboratory.test,
• com.milaboratory.util

Class Hierarchy

• java.lang.Object
  • com.milaboratory.core.alignment.AbstractAlignmentScoring<S> (implements com.milaboratory.core.alignment.AlignmentScoring<S>)
    • com.milaboratory.core.alignment.AffineGapAlignmentScoring<S> (implements java.io.Serializable)
    • com.milaboratory.core.alignment.LinearGapAlignmentScoring<S> (implements java.io.Serializable)
  • com.milaboratory.core.alignment.batch.AbstractBatchAligner<S,H> (implements com.milaboratory.core.alignment.batch.BatchAligner<S,H>, com.milaboratory.core.alignment.batch.PipedBatchAligner<S,H>)
    • com.milaboratory.core.alignment.batch.SimpleBatchAligner<S,P> (implements com.milaboratory.core.alignment.batch.BatchAlignerWithBase<S,P,H>)
  • com.milaboratory.util.AbstractLongProcessReporter (implements com.milaboratory.util.LongProcessReporter)
  • com.milaboratory.core.io.util.AbstractRandomAccessReader<T> (implements cc.redberry.pipe.OutputPort<T>)
    • com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader (implements java.lang.AutoCloseable, com.milaboratory.core.io.sequence.SingleReader)
  • com.milaboratory.core.sequence.AbstractSeq<S> (implements com.milaboratory.core.sequence.Seq<S>)
    • com.milaboratory.core.sequence.Sequence<S> (implements java.lang.Comparable<T>, com.milaboratory.core.alignment.batch.HasSequence<S>)
      • com.milaboratory.core.sequence.AminoAcidSequence
      • com.milaboratory.core.sequence.NucleotideSequence (implements com.milaboratory.core.sequence.NSeq<S>, java.io.Serializable)
    • com.milaboratory.core.sequence.SequenceQuality (implements java.io.Serializable)
  • com.milaboratory.core.io.sequence.AbstractSequenceReader<R> (implements com.milaboratory.core.io.sequence.SequenceReader<S>)
    • com.milaboratory.core.io.sequence.AbstractMultiReader<R> (implements com.milaboratory.util.CanReportProgress, com.milaboratory.core.io.sequence.SequenceReader<S>, com.milaboratory.core.io.sequence.SequenceReaderCloseable<S>)
      • com.milaboratory.core.io.sequence.MultiReader
      • com.milaboratory.core.io.sequence.PairedReader
        • com.milaboratory.core.io.sequence.fastq.PairedFastqReader
  • com.milaboratory.cli.ActionParameters
    • com.milaboratory.cli.ActionParametersWithOutput
  • com.milaboratory.core.alignment.AffineGapAlignmentScoring.SerializationObject (implements java.io.Serializable)
  • com.milaboratory.core.alignment.Aligner
  • com.milaboratory.core.alignment.AlignerCustom
  • com.milaboratory.core.alignment.AlignerCustom.AffineMatrixCache (implements com.milaboratory.core.alignment.AlignerCustom.MatrixCache)
  • com.milaboratory.core.alignment.AlignerCustom.LinearMatrixCache (implements com.milaboratory.core.alignment.AlignerCustom.MatrixCache)
  • com.milaboratory.core.alignment.AlignerCustom.Matrix
  • com.milaboratory.core.alignment.Alignment<S> (implements java.io.Serializable)
  • com.milaboratory.core.alignment.AlignmentCache
  • com.milaboratory.core.alignment.AlignmentHelper (implements java.io.Serializable)
  • com.milaboratory.core.alignment.batch.AlignmentHitImpl<S,P> (implements com.milaboratory.core.alignment.batch.AlignmentHit<S,P>)
    • com.milaboratory.core.alignment.blast.BlastHit<S,P>
      • com.milaboratory.core.alignment.blast.AABlastHit<P>
      • com.milaboratory.core.alignment.blast.BlastHitExt<S>
        • com.milaboratory.core.alignment.blast.AABlastHitExt
        • com.milaboratory.core.alignment.blast.NBlastHitExt
      • com.milaboratory.core.alignment.blast.NBlastHit<P>
  • com.milaboratory.core.alignment.AlignmentIteratorForward<S> (implements com.milaboratory.core.alignment.AlignmentIterator<S>)
  • com.milaboratory.core.alignment.AlignmentIteratorReverse<S> (implements com.milaboratory.core.alignment.AlignmentIterator<S>)
  • com.milaboratory.core.alignment.batch.AlignmentResultImpl<H> (implements com.milaboratory.core.alignment.batch.AlignmentResult<H>)
    • com.milaboratory.core.alignment.batch.PipedAlignmentResultImpl<H,Q> (implements com.milaboratory.core.alignment.batch.PipedAlignmentResult<H,Q>)
  • com.milaboratory.core.io.binary.AlignmentSerializer (implements com.milaboratory.primitivio.Serializer<T>)
  • com.milaboratory.core.alignment.AlignmentTrimmer
  • com.milaboratory.core.alignment.AlignmentUtils
  • com.milaboratory.core.sequence.Alphabet<S> (implements java.io.Serializable)
    • com.milaboratory.core.sequence.AminoAcidAlphabet
    • com.milaboratory.core.sequence.NucleotideAlphabet
  • com.milaboratory.core.sequence.Alphabet.AlphabetSerialization (implements java.io.Serializable)
  • com.milaboratory.core.sequence.Alphabets
  • com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition
  • com.milaboratory.util.ArrayIterator<T> (implements java.util.Iterator<E>)
  • com.milaboratory.core.sequence.ArraySeqBuilder<S,B> (implements com.milaboratory.core.sequence.SeqBuilder<S>)
    • com.milaboratory.core.sequence.SequenceQualityBuilder
  • com.milaboratory.util.ArraysUtils
  • com.milaboratory.util.AtomicEnumHistogram<E>
  • com.milaboratory.util.AtomicEnumHistogram.SerializableResult
  • com.milaboratory.util.AtomicHistogram
  • com.milaboratory.util.AtomicHistogram.SerializableResult
  • com.milaboratory.core.sequence.quality.AverageQualityAggregator (implements com.milaboratory.core.sequence.quality.QualityAggregator)
  • com.milaboratory.core.alignment.BandedAffineAligner
  • com.milaboratory.core.alignment.BandedAffineAligner.MatrixCache
  • com.milaboratory.core.alignment.BandedAligner
  • com.milaboratory.core.alignment.BandedAlignerParameters<S> (implements java.io.Serializable)
  • com.milaboratory.core.alignment.BandedLinearAligner
  • com.milaboratory.core.alignment.BandedMatrix (implements java.io.Serializable)
  • com.milaboratory.core.alignment.BandedSemiLocalResult (implements java.io.Serializable)
  • com.milaboratory.core.alignment.batch.BatchAlignmentUtil
  • com.milaboratory.core.alignment.benchmark.Benchmark<T> (implements cc.redberry.pipe.Processor<InputT,OutputT>)
  • com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionData
  • com.milaboratory.core.alignment.benchmark.BenchmarkInput<T>
  • com.milaboratory.core.alignment.benchmark.BenchmarkResults
  • com.milaboratory.util.Bit2Array (implements java.io.Serializable)
  • com.milaboratory.core.motif.BitapMatcherFilter (implements com.milaboratory.core.motif.BitapMatcher, java.io.Serializable)
  • com.milaboratory.core.motif.BitapMatcherImpl (implements com.milaboratory.core.motif.BitapMatcher, java.io.Serializable)
  • com.milaboratory.core.motif.BitapPattern (implements java.io.Serializable)
  • com.milaboratory.util.BitArray (implements java.io.Serializable)
  • com.milaboratory.core.alignment.blast.Blast
  • com.milaboratory.core.alignment.blast.BlastAlignerAbstract<S,P,H> (implements com.milaboratory.core.alignment.batch.PipedBatchAlignerWithBase<S,P,H>)
    • com.milaboratory.core.alignment.blast.AABlastAligner<P>
    • com.milaboratory.core.alignment.blast.BlastAligner<S,P>
    • com.milaboratory.core.alignment.blast.NBlastAligner<P>
  • com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract<S,H> (implements com.milaboratory.core.alignment.batch.PipedBatchAligner<S,H>)
    • com.milaboratory.core.alignment.blast.AABlastAlignerExt
    • com.milaboratory.core.alignment.blast.BlastAlignerExt<S>
    • com.milaboratory.core.alignment.blast.NBlastAlignerExt
  • com.milaboratory.core.alignment.blast.BlastAlignerParameters
  • com.milaboratory.core.alignment.blast.BlastDB<S>
  • com.milaboratory.core.alignment.blast.BlastDBBuilder
  • com.milaboratory.core.alignment.CachedIntArray (implements java.io.Serializable)
  • com.milaboratory.core.sequence.provider.CachedSequenceProvider<S> (implements com.milaboratory.core.sequence.provider.SequenceProvider<S>)
  • com.milaboratory.core.alignment.benchmark.Challenge
  • com.milaboratory.core.alignment.benchmark.ChallengeParameters
  • com.milaboratory.core.alignment.benchmark.ChallengeProvider (implements cc.redberry.pipe.OutputPort<T>)
  • com.milaboratory.core.clustering.Cluster<T> (implements java.io.Serializable)
  • com.milaboratory.core.clustering.Clustering<T,S> (implements com.milaboratory.util.CanReportProgress)
  • com.milaboratory.core.mutations.CoverageCounter
  • com.milaboratory.primitivio.CustomSerializerImpl (implements com.milaboratory.primitivio.Serializer<T>)
  • com.milaboratory.primitivio.CustomSerializerImpl.TypeInfo
  • cc.redberry.pipe.CUtils.OPIterator<T> (implements java.util.Iterator<E>)
    • com.milaboratory.core.tree.SequenceTreeMap.NodeIterator (implements java.io.Serializable)
  • com.fasterxml.jackson.core.util.DefaultPrettyPrinter (implements com.fasterxml.jackson.core.util.Instantiatable<T>, com.fasterxml.jackson.core.PrettyPrinter, java.io.Serializable)
    • com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1
  • com.milaboratory.primitivio.DefaultSerializersProviderImpl (implements com.milaboratory.primitivio.DefaultSerializersProvider)
  • com.milaboratory.primitivio.DefaultSerializersProviderImpl.CustomEnumSerializer<E> (implements com.milaboratory.primitivio.Serializer<T>)
  • com.milaboratory.core.io.sequence.fasta.FastaReader<S> (implements java.lang.AutoCloseable, com.milaboratory.util.CanReportProgress, cc.redberry.pipe.OutputPortCloseable<T>)
  • com.milaboratory.core.io.sequence.fasta.FastaReader.RawFastaRecord
  • com.milaboratory.core.io.sequence.fasta.FastaRecord<S>
  • com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper (implements com.milaboratory.util.CanReportProgress, com.milaboratory.core.io.sequence.SingleReader)
  • com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper (implements com.milaboratory.core.io.sequence.SingleSequenceWriter)
  • com.milaboratory.core.io.sequence.fasta.FastaWriter<S> (implements java.lang.AutoCloseable)
  • com.milaboratory.core.io.sequence.fastq.FastqRecordsReader (implements java.lang.AutoCloseable)
  • com.milaboratory.core.io.util.FileIndex
  • com.milaboratory.core.io.util.FileIndexBuilder
  • com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel (implements com.milaboratory.core.mutations.generator.NucleotideMutationModel, java.io.Serializable)
  • com.milaboratory.core.sequence.GeneticCode
  • com.milaboratory.util.GlobalObjectMappers
  • com.milaboratory.util.HashFunctions
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • com.milaboratory.util.CountingInputStream
  • com.milaboratory.util.IntArrayList (implements java.io.Serializable)
  • com.milaboratory.util.IntCombinations (implements cc.redberry.pipe.OutputPort<T>)
  • com.milaboratory.core.io.util.IOUtil
  • com.milaboratory.cli.JCommanderBasedMain (implements com.milaboratory.cli.ActionHelper)
  • com.milaboratory.cli.JCommanderBasedMain.MainParameters
    • com.milaboratory.cli.JCommanderBasedMain.MainParametersWithVersion
  • com.fasterxml.jackson.databind.JsonDeserializer<T>
    • com.milaboratory.core.sequence.Alphabets.Deserializer
    • com.milaboratory.core.tree.TreeSearchParameters.Deserializer
  • com.fasterxml.jackson.databind.JsonSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable)
    • com.milaboratory.core.sequence.Alphabets.Serializer
    • com.milaboratory.core.tree.TreeSearchParameters.Serializer
  • com.milaboratory.primitivio.JSONSerializer (implements com.milaboratory.primitivio.Serializer<T>)
  • com.milaboratory.core.alignment.kaligner1.KAligner<P> (implements com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>, com.milaboratory.core.alignment.batch.PipedBatchAlignerWithBase<S,P,H>, java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KAligner2<P> (implements com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>)
  • com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
  • com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.State
  • com.milaboratory.core.alignment.kaligner1.KAlignerParameters (implements com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters, java.lang.Cloneable, java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KAlignerParameters2 (implements com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters, java.lang.Cloneable, java.io.Serializable)
  • com.milaboratory.core.alignment.benchmark.KAlignerQuery
  • com.milaboratory.core.alignment.kaligner1.KAlignmentHit<P> (implements com.milaboratory.core.alignment.batch.AlignmentHit<S,P>, java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KAlignmentHit2<P> (implements com.milaboratory.core.alignment.batch.AlignmentHit<S,P>)
  • com.milaboratory.core.alignment.kaligner1.KAlignmentResult<P> (implements com.milaboratory.core.alignment.batch.AlignmentResult<H>, java.lang.Iterable<T>, java.io.Serializable)
    • com.milaboratory.core.alignment.kaligner1.KAlignmentResultP<P,Q> (implements com.milaboratory.core.alignment.batch.PipedAlignmentResult<H,Q>)
  • com.milaboratory.core.alignment.kaligner2.KAlignmentResult2<P> (implements com.milaboratory.core.alignment.batch.AlignmentResult<H>)
  • com.milaboratory.core.alignment.kaligner1.KMapper (implements java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KMapper2 (implements java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner1.KMappingHit (implements java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KMappingHit2 (implements java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner1.KMappingResult (implements java.io.Serializable)
  • com.milaboratory.core.alignment.kaligner2.KMappingResult2 (implements java.io.Serializable)
  • com.milaboratory.core.alignment.LinearGapAlignmentScoring.SerializationObject (implements java.io.Serializable)
  • com.milaboratory.util.LongProcessReporter.DefaultLongProcessReporter
  • com.milaboratory.core.sequence.quality.MaximalQualityAggregator (implements com.milaboratory.core.sequence.quality.QualityAggregator)
  • com.milaboratory.core.merger.MergerParameters (implements java.io.Serializable)
  • com.milaboratory.core.sequence.quality.MinimalQualityAggregator (implements com.milaboratory.core.sequence.quality.QualityAggregator)
  • com.milaboratory.core.sequence.quality.MiniMaxQualityAggregator (implements com.milaboratory.core.sequence.quality.QualityAggregator)
  • com.milaboratory.core.merger.MismatchOnlyPairedReadMerger (implements cc.redberry.pipe.Processor<InputT,OutputT>, java.io.Serializable)
  • com.milaboratory.core.motif.Motif<S> (implements java.io.Serializable)
  • com.milaboratory.core.motif.MotifBuilder<S>
  • com.milaboratory.core.motif.MotifUtils
  • com.milaboratory.core.alignment.MultiAlignmentHelper
  • com.milaboratory.core.alignment.MultiAlignmentHelper.Settings
  • com.milaboratory.core.sequence.MultiNSequenceWithQualityImpl (implements com.milaboratory.core.sequence.MultiNSequenceWithQuality)
  • com.milaboratory.core.io.sequence.MultiRead (implements com.milaboratory.core.io.sequence.SequenceRead, java.io.Serializable)
    • com.milaboratory.core.io.sequence.PairedRead
  • com.milaboratory.core.mutations.Mutation
  • com.milaboratory.core.mutations.MutationConsensusBuilder
  • com.milaboratory.core.mutations.generator.MutationModels
  • com.milaboratory.core.mutations.Mutations<S> (implements java.io.Serializable)
  • com.milaboratory.core.mutations.MutationsBuilder<S>
  • com.milaboratory.core.mutations.MutationsCounter
  • com.milaboratory.core.mutations.MutationsEnumerator
  • com.milaboratory.core.mutations.generator.MutationsGenerator
  • com.milaboratory.core.mutations.MutationsUtil
  • com.milaboratory.core.mutations.MutationsUtil.MutationNt2AADescriptor
  • com.milaboratory.core.mutations.MutationsUtil.MutationsWitMapping
  • com.milaboratory.core.tree.NeighborhoodIterator<S,O>
  • com.milaboratory.core.sequence.NSequenceWithQualityBuilder (implements com.milaboratory.core.sequence.SeqBuilder<S>)
  • com.milaboratory.util.NSequenceWithQualityPrintHelper
  • com.milaboratory.util.ObjectSerializer.PrimitivIOObjectSerializer<O> (implements com.milaboratory.util.ObjectSerializer<O>)
  • com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
  • com.milaboratory.core.io.sequence.fastq.PairedFastqWriter (implements com.milaboratory.core.io.sequence.PairedSequenceWriter)
  • com.milaboratory.core.merger.PairedReadMergingResult (implements java.io.Serializable)
  • com.milaboratory.util.ParseUtil
  • com.milaboratory.util.ParseUtil.BracketsInfo
  • com.milaboratory.core.tree.PenaltyUtils
  • com.milaboratory.primitivio.PipeDataInputReader<O> (implements cc.redberry.pipe.OutputPortCloseable<T>)
  • com.milaboratory.primitivio.PReader (implements java.lang.AutoCloseable, com.milaboratory.util.CanReportProgress)
    • com.milaboratory.primitivio.PipeReader<O> (implements cc.redberry.pipe.OutputPortCloseable<T>)
  • com.milaboratory.primitivio.PrimitivI (implements java.lang.AutoCloseable, java.io.DataInput)
  • com.milaboratory.primitivio.PrimitivO (implements java.lang.AutoCloseable, java.io.DataOutput)
  • com.milaboratory.util.ProgressAndStage (implements com.milaboratory.util.CanReportProgressAndStage)
  • com.milaboratory.primitivio.PWriter (implements java.lang.AutoCloseable)
    • com.milaboratory.primitivio.PipeWriter<O> (implements java.lang.AutoCloseable, cc.redberry.pipe.InputPort<T>)
  • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
  • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexBuilder
  • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord
  • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.StreamIndexBuilder
  • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader<S> (implements java.lang.AutoCloseable)
  • com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader (implements java.lang.AutoCloseable, com.milaboratory.core.io.sequence.SequenceReader<S>)
  • com.milaboratory.util.Randomizer<T>
  • com.milaboratory.util.RandomUtil
  • com.milaboratory.core.Range (implements java.lang.Comparable<T>, java.io.Serializable)
  • com.milaboratory.util.RangeMap<T> (implements java.io.Serializable)
  • com.milaboratory.core.io.binary.RangeSerializer (implements com.milaboratory.primitivio.Serializer<T>)
  • com.milaboratory.test.Read
  • com.milaboratory.core.alignment.ScoringUtils
  • com.milaboratory.core.sequence.provider.SequenceProviderUtils
  • com.milaboratory.core.sequence.provider.SequenceProviderUtils.LazySequenceProvider<S> (implements com.milaboratory.core.sequence.provider.SequenceProvider<S>)
  • com.milaboratory.core.io.sequence.SequenceReadUtil
  • com.milaboratory.core.sequence.SequencesUtils
  • com.milaboratory.core.tree.SequenceTreeMap<S,O> (implements java.io.Serializable)
  • com.milaboratory.core.tree.SequenceTreeMap.Node<O> (implements java.io.Serializable)
  • com.milaboratory.core.tree.SequenceTreeMap.NodeOp (implements cc.redberry.pipe.OutputPort<T>, java.io.Serializable)
  • com.milaboratory.core.tree.SequenceTreeMap.ValuesOp (implements cc.redberry.pipe.OutputPort<T>, java.io.Serializable)
  • com.milaboratory.core.sequence.SequenceWithQuality<S> (implements java.io.Serializable)
    • com.milaboratory.core.sequence.NSequenceWithQuality (implements com.milaboratory.core.sequence.MultiNSequenceWithQuality, com.milaboratory.core.sequence.NSeq<S>)
  • com.milaboratory.primitivio.SerializersManager
  • com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters<S>
  • com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer (implements com.milaboratory.util.CanReportProgress, cc.redberry.pipe.OutputPortCloseable<T>, com.milaboratory.core.io.sequence.SingleReader)
  • com.milaboratory.core.io.sequence.fastq.SingleFastqReader (implements com.milaboratory.util.CanReportProgress, com.milaboratory.core.io.sequence.SequenceReaderCloseable<S>, com.milaboratory.core.io.sequence.SingleReader)
  • com.milaboratory.core.io.sequence.fastq.SingleFastqWriter (implements com.milaboratory.core.io.sequence.SingleSequenceWriter)
  • com.milaboratory.util.SingleIterator<T> (implements java.util.Iterator<E>)
  • com.milaboratory.core.io.sequence.SingleReadImpl (implements com.milaboratory.core.io.sequence.SingleRead)
  • com.milaboratory.core.io.sequence.SingleReadLazy (implements com.milaboratory.core.io.sequence.SingleRead)
  • com.milaboratory.util.SmartProgressReporter (implements java.lang.Runnable)
  • com.milaboratory.util.Sorter<T>
  • com.milaboratory.util.StringUtil
  • com.milaboratory.core.mutations.generator.SubstitutionModel (implements java.io.Serializable)
  • com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
  • com.milaboratory.core.mutations.generator.SubstitutionModels
  • com.milaboratory.core.sequence.quality.SumQualityAggregator (implements com.milaboratory.core.sequence.quality.QualityAggregator)
  • com.milaboratory.core.Target
  • com.milaboratory.util.TempFileManager
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • java.lang.IllegalArgumentException
          • com.milaboratory.util.RangeMap.IntersectingRangesException
        • com.milaboratory.core.io.sequence.IllegalFileFormatException
          • com.milaboratory.core.io.sequence.fastq.WrongQualityFormat
        • java.lang.IndexOutOfBoundsException
          • com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException
        • com.milaboratory.util.ParserException
        • com.milaboratory.cli.ProcessException
        • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.MultipleMatchingRecordsException
        • com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.NoSuchRecordException
  • com.milaboratory.util.TimeUtils
  • com.milaboratory.core.sequence.TranslationParameters
  • com.milaboratory.core.tree.TreeSearchParameters (implements java.io.Serializable)
  • com.milaboratory.primitivio.TypeSerializationHelper
  • com.milaboratory.core.mutations.generator.UniformMutationsGenerator
  • com.milaboratory.core.sequence.UnsafeFactory
  • com.milaboratory.primitivio.Util
  • com.milaboratory.util.VersionInfo
  • com.milaboratory.core.sequence.Wildcard

Interface Hierarchy

• com.milaboratory.cli.Action
• com.milaboratory.cli.ActionHelper
• com.milaboratory.cli.ActionHelpProvider
• com.milaboratory.cli.ActionParametersParser
• com.milaboratory.core.alignment.AlignerCustom.MatrixCache
• com.milaboratory.core.alignment.batch.AlignmentHit<S,P>
• com.milaboratory.core.alignment.AlignmentIterator<S>
• com.milaboratory.core.alignment.batch.AlignmentResult<H>
  • com.milaboratory.core.alignment.batch.PipedAlignmentResult<H,Q>
• java.lang.AutoCloseable
  • com.milaboratory.util.LongProcess
  • cc.redberry.pipe.OutputPortCloseable<T> (also extends cc.redberry.pipe.OutputPort<T>)
    • com.milaboratory.core.io.sequence.SequenceReaderCloseable<S> (also extends com.milaboratory.core.io.sequence.SequenceReader<S>)
      • com.milaboratory.core.io.sequence.SingleReader
    • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.PairedSequenceWriter
  • com.milaboratory.core.io.sequence.SequenceReaderCloseable<S> (also extends cc.redberry.pipe.OutputPortCloseable<T>, com.milaboratory.core.io.sequence.SequenceReader<S>)
    • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.SequenceWriter<R>
    • com.milaboratory.core.io.sequence.PairedSequenceWriter
    • com.milaboratory.core.io.sequence.SingleSequenceWriter
  • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.SingleSequenceWriter
• com.milaboratory.core.alignment.batch.BatchAligner<S,H>
  • com.milaboratory.core.alignment.batch.BatchAlignerWithBase<S,P,H> (also extends com.milaboratory.core.alignment.batch.WithBase<S,P>)
    • com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>
  • com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>
• com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters
  • com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
• com.milaboratory.core.alignment.benchmark.Benchmark.ExceptionListener
• com.milaboratory.util.CanReportProgress
  • com.milaboratory.util.CanReportProgressAndStage
• java.util.Comparator<T>
  • com.milaboratory.core.clustering.ClusteringStrategy<T,S> (also extends java.io.Serializable)
• com.milaboratory.core.mutations.CoverageCounter.Provider
• com.milaboratory.primitivio.DefaultSerializersProvider
• com.milaboratory.util.Factory<T>
• com.milaboratory.core.alignment.batch.HasSequence<S>
• com.milaboratory.util.IntArrayList.IntComparator
• java.lang.Iterable<T>
  • com.milaboratory.core.io.sequence.SequenceRead
    • com.milaboratory.core.io.sequence.SingleRead (also extends java.io.Serializable)
  • com.milaboratory.core.io.sequence.SingleRead (also extends com.milaboratory.core.io.sequence.SequenceRead, java.io.Serializable)
• com.milaboratory.util.LongProcessReporter
• com.milaboratory.core.sequence.MultiNSequenceWithQuality
• com.milaboratory.core.tree.MutationGuide<S>
• com.milaboratory.core.mutations.MutationsCounter.Filter
• com.milaboratory.util.ObjectSerializer<O>
• cc.redberry.pipe.OutputPort<T>
  • cc.redberry.pipe.OutputPortCloseable<T> (also extends java.lang.AutoCloseable)
    • com.milaboratory.core.io.sequence.SequenceReaderCloseable<S> (also extends com.milaboratory.core.io.sequence.SequenceReader<S>)
      • com.milaboratory.core.io.sequence.SingleReader
    • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.SequenceReader<S>
    • com.milaboratory.core.io.sequence.SequenceReaderCloseable<S> (also extends cc.redberry.pipe.OutputPortCloseable<T>)
      • com.milaboratory.core.io.sequence.SingleReader
    • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.SequenceReaderCloseable<S> (also extends cc.redberry.pipe.OutputPortCloseable<T>, com.milaboratory.core.io.sequence.SequenceReader<S>)
    • com.milaboratory.core.io.sequence.SingleReader
  • com.milaboratory.core.io.sequence.SingleReader
• com.milaboratory.core.alignment.batch.PipedBatchAligner<S,H>
  • com.milaboratory.core.alignment.batch.PipedBatchAlignerWithBase<S,P,H> (also extends com.milaboratory.core.alignment.batch.WithBase<S,P>)
• com.milaboratory.core.sequence.quality.QualityAggregator
• com.milaboratory.core.sequence.Seq<S>
  • com.milaboratory.core.sequence.NSeq<S>
• com.milaboratory.core.sequence.SeqBuilder<S>
  • com.milaboratory.core.sequence.SequenceBuilder<S>
• com.milaboratory.core.alignment.batch.SequenceExtractor<O,S>
• com.milaboratory.core.sequence.provider.SequenceProvider<S>
• com.milaboratory.core.sequence.provider.SequenceProviderFactory<S>
• com.milaboratory.core.mutations.SequenceWeighter
• java.io.Serializable
  • com.milaboratory.core.alignment.AlignmentScoring<S>
  • com.milaboratory.core.motif.BitapMatcher
  • com.milaboratory.core.clustering.ClusteringStrategy<T,S> (also extends java.util.Comparator<T>)
  • com.milaboratory.core.mutations.generator.NucleotideMutationModel
  • com.milaboratory.core.clustering.SequenceExtractor<T,S>
  • com.milaboratory.core.io.sequence.SingleRead (also extends com.milaboratory.core.io.sequence.SequenceRead)
• com.milaboratory.primitivio.Serializer<T>
• com.milaboratory.core.alignment.batch.WithBase<S,P>
  • com.milaboratory.core.alignment.batch.BatchAlignerWithBase<S,P,H> (also extends com.milaboratory.core.alignment.batch.BatchAligner<S,H>)
    • com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>
  • com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter<S,P,H>
  • com.milaboratory.core.alignment.batch.PipedBatchAlignerWithBase<S,P,H> (also extends com.milaboratory.core.alignment.batch.PipedBatchAligner<S,H>)

Annotation Type Hierarchy

• com.milaboratory.cli.HiddenAction (implements java.lang.annotation.Annotation)
• com.milaboratory.cli.AllowNoArguments (implements java.lang.annotation.Annotation)
• com.milaboratory.primitivio.annotations.Serializable (implements java.lang.annotation.Annotation)
• com.milaboratory.primitivio.annotations.CustomSerializer (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.milaboratory.cli.JCommanderBasedMain.ProcessResult
    • com.milaboratory.core.alignment.BLASTMatrix (implements java.io.Serializable)
    • com.milaboratory.core.alignment.blast.BlastTask
    • com.milaboratory.core.alignment.blast.BlastStrand
    • com.milaboratory.core.alignment.kaligner2.KAligner2Statistics.ClusterTrimmingType
    • com.milaboratory.core.io.CompressionType
    • com.milaboratory.core.io.sequence.fastq.QualityFormat
    • com.milaboratory.core.merger.QualityMergingAlgorithm
    • com.milaboratory.core.merger.MergerParameters.IdentityType
    • com.milaboratory.core.mutations.MutationType
    • com.milaboratory.core.PairedEndReadsLayout (implements java.io.Serializable)
    • com.milaboratory.core.sequence.quality.QualityAggregationType