Package com.biomatters.geneious.publicapi.implementations.sequence
Provides
SequenceDocument
implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.-
Interface Summary Interface Description SequenceTrack.Manager.Provider An interface implemented bySequenceDocuments
orSequenceAlignmentDocuments
to indicate they provide sequence tracks. -
Class Summary Class Description CombinedAlignmentAndAminoAcidSequenceDocument See documentation atCombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideGraphSequenceDocument See documentation atCombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideSequenceDocument See documentation atCombinedAlignmentAndSequenceDocument
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.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 bySequenceDocument.getSequenceAnnotations()
).SequenceTrack.Manager Manages all the tracks on a single sequence, including allowing tracks to added or removed. -
Enum Summary Enum Description OligoSequenceDocument.OligoType The possible types of oligos