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

Interface SequenceDocumentWithEditableAnnotations

All Superinterfaces:

PluginDocument, SequenceDocument, XMLSerializable

All Known Subinterfaces:

EditableNucleotideGraphSequenceDocument, EditableSequenceDocument

All Known Implementing Classes:

CombinedAlignmentAndAminoAcidSequenceDocument, CombinedAlignmentAndNucleotideGraphSequenceDocument, CombinedAlignmentAndNucleotideSequenceDocument, CombinedAlignmentAndSequenceDocument, DefaultAminoAcidSequence, DefaultNucleotideGraphSequence, DefaultNucleotideSequence, DefaultSequenceDocument, OligoSequenceDocument

public interface SequenceDocumentWithEditableAnnotations
extends SequenceDocument

An extension of a SequenceDocument that allows its annotations to be changed. Also see EditableSequenceDocument which allows even more properties of the sequence to be edited.

NoteSequenceListDocument implementations may not notice changes to their sequences that are edited alone using this API. The SequenceListDocument must also be informed about the change using the ExtendedEditableSequenceListDocument API.

Since:

API 4.14 (Geneious 5.1)

Nested Class Summary

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.sequence.SequenceDocument

SequenceDocument.Alphabet, SequenceDocument.Transformer

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

XMLSerializable.OldVersionCompatible, XMLSerializable.VersionSupportType

Field Summary

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.sequence.SequenceDocument

GENOME_SEQUENCE_THRESHOLD

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

ROOT_ELEMENT_NAME

Method Summary

Modifier and Type	Method	Description
void	setAnnotations(List<SequenceAnnotation> annotations)	Sets new annotations on this document, replacing the existing ones.

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.sequence.SequenceDocument

getCharSequence, getSequenceAnnotations, getSequenceLength, getSequenceString, isCircular

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

fromXML, toXML

Method Details

setAnnotations

void setAnnotations(List<SequenceAnnotation> annotations)

Sets new annotations on this document, replacing the existing ones. This does not replace annotations on SequenceTracks

Parameters:

annotations - New annotations to set on this document.

Since:

API 4.14 (Geneious 5.1)

See Also:

• SequenceDocument.getSequenceAnnotations()