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

Packages that use com.biomatters.geneious.publicapi.implementations.sequence

Package	Description
com.biomatters.geneious.publicapi.documents.types	Provides interfaces specifying the types of documents available in Geneious.
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.sequence	Provides SequenceDocument implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.
com.biomatters.geneious.publicapi.plugin	Provides the GeneiousPlugin interface and plugin related interfaces.
com.biomatters.geneious.publicapi.utilities	Provides various utility methods and classes, none of which are necessary for creating a plugin, but many plugins implentations will find these methods useful.

Classes in com.biomatters.geneious.publicapi.implementations.sequence used by com.biomatters.geneious.publicapi.documents.types

Class	Description
SequenceTrack.Manager.Provider	An interface implemented by SequenceDocuments or SequenceAlignmentDocuments to indicate they provide sequence tracks.

Classes in com.biomatters.geneious.publicapi.implementations.sequence used by com.biomatters.geneious.publicapi.implementations

Class	Description
DefaultNucleotideSequence	A plugin document holding one nucleotide sequence.
DefaultSequenceDocument	A default implementation of a sequence document.
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.

Classes in com.biomatters.geneious.publicapi.implementations.sequence used by com.biomatters.geneious.publicapi.implementations.sequence

Class	Description
CombinedAlignmentAndSequenceDocument	A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
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.
OligoSequenceDocument.OligoType	The possible types of oligos
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.

Classes in com.biomatters.geneious.publicapi.implementations.sequence used by com.biomatters.geneious.publicapi.plugin

Class	Description
CombinedAlignmentAndAminoAcidSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
DefaultSequenceDocument	A default implementation of a sequence document.
OligoSequenceDocument	A sequence document which represents an olgionucleotide such as a Primer or DNA probe.
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.

Classes in com.biomatters.geneious.publicapi.implementations.sequence used by com.biomatters.geneious.publicapi.utilities

Class	Description
DefaultSequenceDocument	A default implementation of a sequence document.