Uses of Interface
com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
-
Packages that use EditableSequenceDocument Package Description com.biomatters.geneious.publicapi.documents.sequence Provides interfaces specifying the types ofsequence
andalignment
documents in Geneious, together with concrete classes used by sequence documents such asSequenceAnnotation
andSequenceCharSequence
.com.biomatters.geneious.publicapi.implementations.sequence ProvidesSequenceDocument
implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.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. -
-
Uses of EditableSequenceDocument in com.biomatters.geneious.publicapi.documents.sequence
Subinterfaces of EditableSequenceDocument in com.biomatters.geneious.publicapi.documents.sequence Modifier and Type Interface Description interface
EditableNucleotideGraphSequenceDocument
A mutable nucleotide sequence with residue graph. -
Uses of EditableSequenceDocument in com.biomatters.geneious.publicapi.implementations.sequence
Classes in com.biomatters.geneious.publicapi.implementations.sequence that implement EditableSequenceDocument Modifier and Type Class Description class
CombinedAlignmentAndAminoAcidSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndNucleotideGraphSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndNucleotideSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndSequenceDocument
A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.class
DefaultAminoAcidSequence
A plugin document holding one amino acid sequence.class
DefaultNucleotideGraphSequence
An implementation of an editable chromatogram.class
DefaultNucleotideSequence
A plugin document holding one nucleotide sequence.class
DefaultSequenceDocument
A default implementation of a sequence document.class
OligoSequenceDocument
A sequence document which represents an olgionucleotide such as a Primer or DNA probe.Methods in com.biomatters.geneious.publicapi.implementations.sequence that return EditableSequenceDocument Modifier and Type Method Description EditableSequenceDocument
CombinedAlignmentAndSequenceDocument. getSequenceDocument()
Get the sequence document contained within this documentConstructors in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type EditableSequenceDocument Constructor Description CombinedAlignmentAndSequenceDocument(EditableSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView)
Construct a new CombinedAlignmentAndSequenceDocument. -
Uses of EditableSequenceDocument in com.biomatters.geneious.publicapi.utilities
Methods in com.biomatters.geneious.publicapi.utilities with parameters of type EditableSequenceDocument Modifier and Type Method Description static void
SequenceUtilities. setOriginalResidueNumbering(EditableSequenceDocument document, int startIndex, boolean isReverse)
set the original residue numbering of a document the residue index of a document will appear shifted if the user has "show original residue numbers" selected in the sequence view
-