com.biomatters.geneious.publicapi.documents.sequence

Interface NucleotideGraphSequenceDocument

All Superinterfaces:

NucleotideGraph, NucleotideSequenceDocument, PluginDocument, SequenceDocument, XMLSerializable

All Known Subinterfaces:

ChromatogramDocument, EditableNucleotideGraphSequenceDocument

All Known Implementing Classes:

CombinedAlignmentAndNucleotideGraphSequenceDocument, DefaultNucleotideGraphSequence

public interface NucleotideGraphSequenceDocument
extends NucleotideSequenceDocument, NucleotideGraph

A nucleotide sequence with an underlying "graph".

Nested Class Summary

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

SequenceDocument.Alphabet, SequenceDocument.Transformer

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

PluginDocument.ReferencedDocumentsAlwaysLoaded, PluginDocument.ReferencedDocumentsNotLoaded, PluginDocument.SizeRequiredToLoadIntoMemoryProvider

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

XMLSerializable.OldVersionCompatible, XMLSerializable.VersionSupportType

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

NucleotideGraph.ImmutableGraphProvider

Field Summary

Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument

NICE_NAME

Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

GENOME_SEQUENCE_THRESHOLD

Fields inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

FILE_DATA_ATTRIBUTE_NAME, MAXIMUM_HTML_LENGTH, MODIFIED_DATE_FIELD

Fields inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

ROOT_ELEMENT_NAME

Method Summary

Methods inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

getCharSequence, getSequenceAnnotations, getSequenceLength, getSequenceString, isCircular

Methods inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

getCreationDate, getDescription, getDisplayableFields, getFieldValue, getName, getURN, toHTML

Methods inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

fromXML, toXML

Methods inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

getChromatogramLength, getChromatogramPositionForResidue, getChromatogramValue, getSequenceLength, getSequenceQuality, hasChromatogramPositionsForResidues, hasChromatogramValues, hasSequenceQualities