SequenceDocumentWithEditableAnnotations (Geneious Public API)

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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`setAnnotations(java.util.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 Detail
  - setAnnotations
```
void setAnnotations(java.util.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()