Hierarchy For Package com.biomatters.geneious.publicapi.documents.sequence

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk<T> (implements com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.AbstractPluginDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
    • com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument, com.biomatters.geneious.publicapi.documents.sequence.PairedReads, com.biomatters.geneious.publicapi.documents.PluginDocument.SizeRequiredToLoadIntoMemoryProvider, com.biomatters.geneious.publicapi.documents.Renamable, com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible, com.biomatters.geneious.publicapi.documents.XMLSerializableWithProgress)
  • com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence (implements java.lang.CharSequence)
  • com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph)
  • com.biomatters.geneious.publicapi.documents.sequence.ConstructorWrapper
  • com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph)
  • com.biomatters.geneious.publicapi.documents.sequence.ExternalSort<T>
  • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.ObjectInputStream (implements java.io.ObjectInput, java.io.ObjectStreamConstants)
      • com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.ObjectOutputStream (implements java.io.ObjectOutput, java.io.ObjectStreamConstants)
      • com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument (implements com.biomatters.geneious.publicapi.documents.sequence.PairedReads, com.biomatters.geneious.publicapi.documents.PluginDocument)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence (implements java.lang.CharSequence, java.lang.Comparable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
    • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence (implements com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Transformer
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder<T>
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
  • com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency

Interface Hierarchy

• com.biomatters.geneious.publicapi.documents.sequence.ExternalSort.Serializer<T>
• com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph
  • com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph.ImmutableGraphProvider
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
• com.biomatters.geneious.publicapi.documents.sequence.PairedReads
• com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument
  • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument
    • com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument
• com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider
• com.biomatters.geneious.publicapi.documents.XMLSerializable
  • com.biomatters.geneious.publicapi.documents.PluginDocument
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentListDocument
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
        • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph)
          • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
          • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations
        • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
          • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet