Package com.biomatters.geneious.publicapi.implementations.sequence

package com.biomatters.geneious.publicapi.implementations.sequence

Provides SequenceDocument implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.

Related Packages

Package	Description
com.biomatters.geneious.publicapi.implementations	Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.
com.biomatters.geneious.publicapi.implementations.structure	Provides MolecularStructureDocument implementations for many commonly used 3D structure documents.

Class	Description
CombinedAlignmentAndAminoAcidSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideGraphSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndSequenceDocument	A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
DefaultAminoAcidSequence	A plugin document holding one amino acid sequence.
DefaultNucleotideGraphSequence	An implementation of an editable chromatogram.
DefaultNucleotideSequence	A plugin document holding one nucleotide sequence.
DefaultSequenceDocument	A default implementation of a sequence document.
DefaultSequenceDocument.Cache	Used for controlling caching of the char sequence and annotations controlled from this class.
NucleotideCounter	Counts the frequency of AT and GC nucleotides, including counting S as GC and W as AT.
OligoSequenceDocument	A sequence document which represents an olgionucleotide such as a Primer or DNA probe.
OligoSequenceDocument.OligoType	The possible types of oligos
SequencePropertiesStorage	Provides supporting functionality for sequence classes that need to store various sequence properties and serialise those to XML.
SequenceTrack	A Sequence Track is a list of annotations that is associated with a sequence (in addition to those supplied by SequenceDocument.getSequenceAnnotations()).
SequenceTrack.Manager	Manages all the tracks on a single sequence, including allowing tracks to added or removed.
SequenceTrack.Manager.Provider	An interface implemented by SequenceDocuments or SequenceAlignmentDocuments to indicate they provide sequence tracks.