Hierarchy For All Packages

Package Hierarchies:

• demo,
• org.biojava.nbio.core.alignment,
• org.biojava.nbio.core.alignment.matrices,
• org.biojava.nbio.core.alignment.template,
• org.biojava.nbio.core.exceptions,
• org.biojava.nbio.core.search.io,
• org.biojava.nbio.core.search.io.blast,
• org.biojava.nbio.core.sequence,
• org.biojava.nbio.core.sequence.compound,
• org.biojava.nbio.core.sequence.edits,
• org.biojava.nbio.core.sequence.features,
• org.biojava.nbio.core.sequence.io,
• org.biojava.nbio.core.sequence.io.embl,
• org.biojava.nbio.core.sequence.io.template,
• org.biojava.nbio.core.sequence.io.util,
• org.biojava.nbio.core.sequence.loader,
• org.biojava.nbio.core.sequence.location,
• org.biojava.nbio.core.sequence.location.template,
• org.biojava.nbio.core.sequence.reference,
• org.biojava.nbio.core.sequence.storage,
• org.biojava.nbio.core.sequence.template,
• org.biojava.nbio.core.sequence.transcription,
• org.biojava.nbio.core.sequence.views,
• org.biojava.nbio.core.util

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.core.alignment.matrices.AAindexFactory
  • org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
  • org.biojava.nbio.core.sequence.io.ABITrace
  • org.biojava.nbio.core.sequence.template.AbstractCompound (implements org.biojava.nbio.core.sequence.template.Compound)
    • org.biojava.nbio.core.sequence.compound.AminoAcidCompound (implements java.io.Serializable)
    • org.biojava.nbio.core.sequence.compound.CodonCompound
    • org.biojava.nbio.core.sequence.compound.NucleotideCompound (implements org.biojava.nbio.core.sequence.template.ComplementCompound)
  • org.biojava.nbio.core.sequence.template.AbstractCompoundSet<C> (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
    • org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet<C>
      • org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
      • org.biojava.nbio.core.sequence.compound.DNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
      • org.biojava.nbio.core.sequence.compound.RNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
  • org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<F,T> (implements org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>)
    • org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
    • org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
  • org.biojava.nbio.core.sequence.features.AbstractFeature<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
    • org.biojava.nbio.core.sequence.features.QualityFeature<S,C>
    • org.biojava.nbio.core.sequence.features.QuantityFeature<S,C>
    • org.biojava.nbio.core.sequence.features.TextFeature<S,C>
  • org.biojava.nbio.core.sequence.location.template.AbstractLocation (implements org.biojava.nbio.core.sequence.location.template.Location, java.io.Serializable)
    • org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
    • org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
    • org.biojava.nbio.core.sequence.location.SimpleLocation
      • org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
      • org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
      • org.biojava.nbio.core.sequence.location.SequenceLocation<S,C>
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.biojava.nbio.core.util.SoftHashMap<K,V>
  • org.biojava.nbio.core.sequence.reference.AbstractReference (implements org.biojava.nbio.core.sequence.reference.ReferenceInterface)
    • org.biojava.nbio.core.sequence.reference.GenbankReference
  • org.biojava.nbio.core.sequence.template.AbstractSequence<C> (implements org.biojava.nbio.core.sequence.template.Sequence<C>)
    • org.biojava.nbio.core.sequence.BasicSequence<C>
    • org.biojava.nbio.core.sequence.DNASequence
      • org.biojava.nbio.core.sequence.CDSSequence
      • org.biojava.nbio.core.sequence.ChromosomeSequence
      • org.biojava.nbio.core.sequence.ExonSequence
      • org.biojava.nbio.core.sequence.GeneSequence
      • org.biojava.nbio.core.sequence.IntronSequence
      • org.biojava.nbio.core.sequence.StartCodonSequence
      • org.biojava.nbio.core.sequence.StopCodonSequence
      • org.biojava.nbio.core.sequence.TranscriptSequence
    • org.biojava.nbio.core.sequence.ProteinSequence
    • org.biojava.nbio.core.sequence.RNASequence
  • org.biojava.nbio.core.sequence.AccessionID
  • org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>, java.io.Serializable)
  • org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.SequenceReader<C>)
    • org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.sequence.storage.BitSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava.nbio.core.sequence.storage.FourBitSequenceReader<C>
    • org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader<C>
  • org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
    • org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>
    • org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>
  • org.biojava.nbio.core.search.io.blast.BlastHitBuilder
  • org.biojava.nbio.core.search.io.blast.BlastHspBuilder
  • org.biojava.nbio.core.search.io.blast.BlastResultBuilder
  • org.biojava.nbio.core.search.io.blast.BlastTabularParser (implements org.biojava.nbio.core.search.io.ResultFactory)
  • org.biojava.nbio.core.search.io.blast.BlastXMLParser (implements org.biojava.nbio.core.search.io.ResultFactory)
  • org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound (implements org.biojava.nbio.core.sequence.template.Compound)
  • org.biojava.nbio.core.sequence.CDSComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.biojava.nbio.core.sequence.io.util.ClasspathResource
  • org.biojava.nbio.core.util.ConcurrencyTools
  • org.biojava.nbio.core.util.CRC64Checksum (implements java.util.zip.Checksum)
  • org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider (implements org.biojava.nbio.core.alignment.matrices.AAIndexProvider)
  • demo.DemoSixFrameTranslation
  • org.biojava.nbio.core.sequence.io.DNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C> (implements org.biojava.nbio.core.sequence.edits.Edit<C>)
    • org.biojava.nbio.core.sequence.edits.Edit.Delete<C>
    • org.biojava.nbio.core.sequence.edits.Edit.Insert<C>
    • org.biojava.nbio.core.sequence.edits.Edit.Substitute<C>
  • org.biojava.nbio.core.sequence.io.embl.EmblId
  • org.biojava.nbio.core.sequence.io.embl.EmblReader
  • org.biojava.nbio.core.sequence.io.embl.EmblRecord
  • org.biojava.nbio.core.sequence.io.embl.EmblReference
  • org.biojava.nbio.core.util.Equals
  • org.biojava.nbio.core.sequence.ExonComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.biojava.nbio.core.sequence.io.FastaGeneWriter
  • org.biojava.nbio.core.sequence.io.FastaReader<S,C>
  • org.biojava.nbio.core.sequence.io.FastaReaderHelper
  • org.biojava.nbio.core.sequence.io.FastaSequenceParser (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
  • org.biojava.nbio.core.sequence.io.FastaWriter<S,C>
  • org.biojava.nbio.core.sequence.io.FastaWriterHelper
  • org.biojava.nbio.core.util.FileDownloadUtils
  • org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.util.FlatFileCache
  • org.biojava.nbio.core.sequence.io.GenbankReader<S,C>
  • org.biojava.nbio.core.sequence.io.GenbankReaderHelper
  • org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
  • org.biojava.nbio.core.sequence.io.GenbankWriter<S,C>
  • org.biojava.nbio.core.sequence.io.GenbankWriterHelper
  • org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S,C>
    • org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>)
  • org.biojava.nbio.core.util.Hashcoder
  • org.biojava.nbio.core.search.io.Hit (implements java.lang.Iterable<T>)
  • org.biojava.nbio.core.search.io.Hsp<S,C>
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.biojava.nbio.core.util.UncompressInputStream
  • org.biojava.nbio.core.util.InputStreamProvider
  • org.biojava.nbio.core.sequence.location.InsdcLocations
  • org.biojava.nbio.core.sequence.location.InsdcParser
  • org.biojava.nbio.core.sequence.io.util.IOUtils
  • org.biojava.nbio.core.sequence.io.IUPACParser
  • org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable (implements org.biojava.nbio.core.sequence.transcription.Table)
  • org.biojava.nbio.core.sequence.storage.JoiningSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.sequence.location.template.Location.Tools
  • org.biojava.nbio.core.sequence.location.LocationHelper
  • org.biojava.nbio.core.exceptions.Messages
  • org.biojava.nbio.core.sequence.MultipleSequenceAlignment<S,C> (implements org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>)
  • demo.ParseFastaFileDemo
  • org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.core.util.PrettyXMLWriter (implements org.biojava.nbio.core.util.XMLWriter)
  • org.biojava.nbio.core.sequence.io.ProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
    • org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
  • org.biojava.nbio.core.sequence.features.Qualifier
    • org.biojava.nbio.core.sequence.features.DBReferenceInfo
      • org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
  • org.biojava.nbio.core.search.io.Result (implements java.lang.Iterable<T>)
    • org.biojava.nbio.core.search.io.blast.BlastResult
  • org.biojava.nbio.core.sequence.io.RNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix (implements org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
  • org.biojava.nbio.core.search.io.SearchIO (implements java.lang.Iterable<T>)
  • org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper<C>
  • org.biojava.nbio.core.sequence.SequenceComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.sequence.template.SequenceMixin
  • org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator<C> (implements java.util.Iterator<E>)
  • org.biojava.nbio.core.sequence.SequenceOptimizationHints
  • org.biojava.nbio.core.sequence.template.SequenceProxyView<C> (implements org.biojava.nbio.core.sequence.template.SequenceView<C>)
    • org.biojava.nbio.core.sequence.views.ComplementSequenceView<C>
    • org.biojava.nbio.core.sequence.views.ReversedSequenceView<C>
    • org.biojava.nbio.core.sequence.views.RnaSequenceView (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.util.SequenceTools
  • org.biojava.nbio.core.alignment.SimpleAlignedSequence<S,C> (implements org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>, java.io.Serializable)
  • org.biojava.nbio.core.sequence.location.SimplePoint (implements org.biojava.nbio.core.sequence.location.template.Point, java.io.Serializable)
    • org.biojava.nbio.core.sequence.location.FuzzyPoint
  • org.biojava.nbio.core.alignment.SimpleProfile<S,C> (implements org.biojava.nbio.core.alignment.template.Profile<S,C>, java.io.Serializable)
    • org.biojava.nbio.core.alignment.SimpleProfilePair<S,C> (implements org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.core.alignment.SimpleSequencePair<S,C> (implements org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix<C> (implements java.io.Serializable, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
  • org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.util.SingleLinkageClusterer
  • org.biojava.nbio.core.util.StringManipulationHelper
  • org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeatureRetriever<C>, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface)
  • org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper (implements java.io.Serializable)
  • org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
  • org.biojava.nbio.core.sequence.transcription.Table.Codon (implements org.biojava.nbio.core.sequence.template.Compound)
  • org.biojava.nbio.core.sequence.TaxonomyID
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.biojava.nbio.core.exceptions.CompoundNotFoundException
      • java.lang.RuntimeException
        • org.biojava.nbio.core.exceptions.ParserException
        • org.biojava.nbio.core.exceptions.TranslationException
  • org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
  • org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
  • org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface, org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.sequence.views.WindowedSequence<C> (implements java.lang.Iterable<T>)
  • org.biojava.nbio.core.util.XMLHelper

Interface Hierarchy

• org.biojava.nbio.core.alignment.matrices.AAIndexProvider
• org.biojava.nbio.core.sequence.template.Accessioned
  • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.location.template.Location)
  • org.biojava.nbio.core.sequence.location.template.Location (also extends java.lang.Iterable<T>)
    • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
    • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.sequence.template.SequenceReader<C>
      • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceView<C>
• java.lang.Comparable<T>
  • org.biojava.nbio.core.sequence.location.template.Point
• org.biojava.nbio.core.sequence.template.Compound
  • org.biojava.nbio.core.sequence.template.ComplementCompound
• org.biojava.nbio.core.sequence.template.CompoundSet<C>
• org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>
• org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
• org.biojava.nbio.core.sequence.edits.Edit<C>
• org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>
• org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>
• org.biojava.nbio.core.sequence.features.FeatureRetriever<C>
• org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
• org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>
• org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor
• java.lang.Iterable<T>
  • org.biojava.nbio.core.sequence.location.template.Location (also extends org.biojava.nbio.core.sequence.template.Accessioned)
    • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  • org.biojava.nbio.core.alignment.template.Profile<S,C>
    • org.biojava.nbio.core.alignment.template.MutableProfile<S,C>
      • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
      • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
    • org.biojava.nbio.core.alignment.template.ProfilePair<S,C>
      • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
    • org.biojava.nbio.core.alignment.template.ProfileView<S,C>
    • org.biojava.nbio.core.alignment.template.SequencePair<S,C>
      • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends org.biojava.nbio.core.sequence.template.Accessioned)
    • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.sequence.template.SequenceReader<C>
      • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceView<C>
• org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>
• org.biojava.nbio.core.sequence.location.template.Point.Resolver<T>
• org.biojava.nbio.core.sequence.reference.ReferenceInterface
• org.biojava.nbio.core.search.io.ResultFactory
• org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>
• org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>
• org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
• org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>
• org.biojava.nbio.core.sequence.transcription.Table
• org.biojava.nbio.core.util.XMLWriter

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
    • org.biojava.nbio.core.alignment.template.AlignedSequence.Step
    • org.biojava.nbio.core.sequence.DataSource
    • org.biojava.nbio.core.sequence.DNASequence.DNAType
    • org.biojava.nbio.core.sequence.transcription.Frame
    • org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
    • org.biojava.nbio.core.alignment.template.Profile.StringFormat
    • org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
    • org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
    • org.biojava.nbio.core.sequence.Strand