Uses of Interface
com.biomatters.geneious.publicapi.documents.PluginDocument

Packages that use PluginDocument

Package	Description
com.biomatters.geneious.publicapi.databaseservice	Provides the interface and associated classes for defining a database service which is a service that appears on the left-hand side of the main Geneious window and provides the user with access to a database, for example NCBI or the local database for storing the user's documents.
com.biomatters.geneious.publicapi.documents	Provides interfaces and classes for defining documents in Geneious and related interfaces and classes for dealing with XMLSerialization.
com.biomatters.geneious.publicapi.documents.sequence	Provides interfaces specifying the types of sequence and alignment documents in Geneious, together with concrete classes used by sequence documents such as SequenceAnnotation and SequenceCharSequence.
com.biomatters.geneious.publicapi.documents.types	Provides interfaces specifying the types of documents available in Geneious.
com.biomatters.geneious.publicapi.implementations	Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.
com.biomatters.geneious.publicapi.implementations.sequence	Provides SequenceDocument implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.
com.biomatters.geneious.publicapi.implementations.structure	Provides MolecularStructureDocument implementations for many commonly used 3D structure documents.
com.biomatters.geneious.publicapi.plugin	Provides the GeneiousPlugin interface and plugin related interfaces.

Uses of PluginDocument in com.biomatters.geneious.publicapi.databaseservice

Subinterfaces of PluginDocument in com.biomatters.geneious.publicapi.databaseservice

Modifier and Type	Interface	Description
interface	FolderViewDocument	A PluginDocument may implement this interface to indicate that it provides information about the results of a search.

Methods in com.biomatters.geneious.publicapi.databaseservice with parameters of type PluginDocument

Modifier and Type	Method	Description
protected void	CompositeRetrieveCallback._add(PluginDocument document, java.util.Map<java.lang.String,java.lang.Object> searchResultProperties)	Report back one retrieved document.
protected abstract void	RetrieveCallback._add(PluginDocument document, java.util.Map<java.lang.String,java.lang.Object> searchResultProperties)	Report back one retrieved document.
boolean	RetrieveCallback.add(PluginDocument document, java.util.Map<java.lang.String,java.lang.Object> searchResultProperties)	A wrapper method that forwards its arguments to RetrieveCallback._add(com.biomatters.geneious.publicapi.documents.PluginDocument, java.util.Map) only if this retrieval hasn't been canceled.

Uses of PluginDocument in com.biomatters.geneious.publicapi.documents

Classes in com.biomatters.geneious.publicapi.documents with type parameters of type PluginDocument

Modifier and Type	Class	Description
class	DocumentSearchCache<T extends PluginDocument>	Class which caches the results of a search for a particular type of document and automatically updates to include newly added documents of the particular type when they are added to the user's database.

Subinterfaces of PluginDocument in com.biomatters.geneious.publicapi.documents

Modifier and Type	Interface	Description
interface	SummaryDocument	Any summary document should "implement" this empty interface to enable special handling of summary documents inside Geneious.

Classes in com.biomatters.geneious.publicapi.documents that implement PluginDocument

Modifier and Type	Class	Description
class	AbstractPluginDocument	This class provides a "Field based" implementation of a Plugin documents.
class	AliasDocument	An alias document created using 'Edit->Paste Alias' or programmatically using AliasDocument.createAlias(AnnotatedPluginDocument).
class	DocumentCollection	This class provides a field based document that stores a collection of other documents.
class	OperationRecordDocument	Stores references to the input and output documents a from single DocumentOperation.

Methods in com.biomatters.geneious.publicapi.documents with type parameters of type PluginDocument

Modifier and Type	Method	Description
static <T extends PluginDocument> DocumentSearchCache<T>	DocumentSearchCache.getDocumentSearchCacheFor(DocumentType<T> documentType)	Gets a cache for the given document type, creating the cache if necessary and caching the cache so that future calls to this method return the same cache.

Methods in com.biomatters.geneious.publicapi.documents that return PluginDocument

Modifier and Type	Method	Description
abstract PluginDocument	AnnotatedPluginDocument.getDocument()	Returns the underlying document which is wrapped inside this AnnotatedPluginDocument.
abstract PluginDocument	AnnotatedPluginDocument.getDocumentOrCrash()	A convenience method that calls getDocumentOrThrow(RuntimeException.class).
abstract PluginDocument	AnnotatedPluginDocument.getDocumentOrNull()	A convenience method that calls getDocumentOrThrow(true,ProgressListener.EMPTY,...) but instead of throwing an exception if the document cannot be loaded, returns null.
abstract <T extends java.lang.Exception> PluginDocument	AnnotatedPluginDocument.getDocumentOrThrow(boolean warnIfCantLoad, jebl.util.ProgressListener progressListener, java.lang.Class<T> exceptionClass)	Returns the underlying document.
abstract <T extends java.lang.Exception> PluginDocument	AnnotatedPluginDocument.getDocumentOrThrow(java.lang.Class<T> exceptionClass)	Equivalent to calling getDocumentOrThrow(true,ProgressListener.EMPTY,exceptionClass)

Methods in com.biomatters.geneious.publicapi.documents that return types with arguments of type PluginDocument

Modifier and Type	Method	Description
abstract java.lang.Class<? extends PluginDocument>	AnnotatedPluginDocument.getDocumentClass()	Get the class of the underlying document without loading it.

Methods in com.biomatters.geneious.publicapi.documents with parameters of type PluginDocument

Modifier and Type	Method	Description
static void	DocumentUtilities.addGeneratedPluginDocument(PluginDocument document, boolean selectDocumentImmediately)	Adds a newly generated document that will appear in the user's local database.
static AnnotatedPluginDocument	DocumentUtilities.createAnnotatedPluginDocument(PluginDocument document)	Equivalent to createAnnotatedPluginDocument(document,ProgressListener.EMPTY)
static AnnotatedPluginDocument	DocumentUtilities.createAnnotatedPluginDocument(PluginDocument document, URN urn, jebl.util.ProgressListener progressListener)	Creates an AnnotatedPluginDocument from a PluginDocument with a specific URN.
static AnnotatedPluginDocument	DocumentUtilities.createAnnotatedPluginDocument(PluginDocument document, jebl.util.ProgressListener progressListener)	Creates an AnnotatedPluginDocument from a PluginDocument.
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.createAnnotatedPluginDocuments(PluginDocument document)	creates a list of AnnotatedPluginDocuments from a single of PluginDocument.
static AnnotatedPluginDocument	DocumentUtilities.getAnnotatedPluginDocumentThatContains(PluginDocument pluginDocument)	Gets the AnnotatedPluginDocument that contains the given PluginDocument.
static org.jdom.Element	XMLSerializer.pluginDocumentToXml(PluginDocument pluginDocument, jebl.util.ProgressListener progressListener)	Converts a PluginDocument to XML, handling the case where the PluginDocument may or may not implement XMLSerializableWithProgress.
static org.jdom.Element	XMLSerializer.pluginDocumentToXml(Geneious.MajorVersion version, PluginDocument pluginDocument, jebl.util.ProgressListener progressListener)	Converts a PluginDocument to XML, handling the case where the PluginDocument may or may not implement XMLSerializableWithProgress.

Method parameters in com.biomatters.geneious.publicapi.documents with type arguments of type PluginDocument

Modifier and Type	Method	Description
static void	DocumentUtilities.addGeneratedPluginDocuments(java.util.List<PluginDocument> documents, boolean selectDocumentsImmediately)	Adds newly generated documents that will appear in the user's local database.
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.createAnnotatedPluginDocuments(java.util.List<? extends PluginDocument> documents)	Creates a list of AnnotatedPluginDocuments from a list of PluginDocuments.
boolean	AnnotatedPluginDocument.isPluginDocumentInstanceOf(java.lang.Class<? extends PluginDocument> cl)

Uses of PluginDocument in com.biomatters.geneious.publicapi.documents.sequence

Subinterfaces of PluginDocument in com.biomatters.geneious.publicapi.documents.sequence

Modifier and Type	Interface	Description
interface	AminoAcidSequenceDocument	An interface for an Amino Acid sequence.
interface	ChromatogramDocument	Deprecated. Check for instanceof NucleotideGraphSequenceDocument instead.
interface	EditableNucleotideGraphSequenceDocument	A mutable nucleotide sequence with residue graph.
interface	EditableSequenceDocument	An extensions of a SequenceDocument that can be edited.
interface	NucleotideGraphSequenceDocument	A nucleotide sequence with an underlying "graph".
interface	NucleotideSequenceDocument	An interface for a nucleotide sequence.
interface	SequenceAlignmentListDocument	A document representing a list of alignments.
interface	SequenceDocument	Interface representing one sequence.
interface	SequenceDocumentWithEditableAnnotations	An extension of a SequenceDocument that allows its annotations to be changed.

Classes in com.biomatters.geneious.publicapi.documents.sequence that implement PluginDocument

Modifier and Type	Class	Description
class	DefaultSequenceListDocument	A default implementation of a SequenceListDocument.
class	ImmutableSequence	An implementation of a SequenceDocument that is immutable and has very low memory usage.
class	ImmutableSequenceImplementation	Despite this class being public, it is only public for implementation reasons.
class	SequenceAlignmentDocument	An alignment or contig of sequences.

Uses of PluginDocument in com.biomatters.geneious.publicapi.documents.types

Subinterfaces of PluginDocument in com.biomatters.geneious.publicapi.documents.types

Modifier and Type	Interface	Description
interface	EditableSameTaxaTreesDocument	A mutable tree set.
interface	JournalArticleDocument	Interface for plugin documents containing a Journal Article.
interface	MolecularStructureDocument	Interface representing 3D model data of a molecular structure.
interface	PublicationDocument	Interface for plugin documents containing a publication.
interface	RootedTreeDocument	A document containing one (rooted) tree.
interface	SameTaxaTreesDocument	A document containing a list of trees.
interface	TaxonomyDocument	A plugin document containing one TaxonomyDocument.Taxon, which holds information (rank, scientific name and alternative names) about one taxon in a taxonomy, and a reference to its parent taxon (if any).
interface	TreeDocument	The common base for all documents that hold one or several trees.

Classes in com.biomatters.geneious.publicapi.documents.types that implement PluginDocument

Modifier and Type	Class	Description
class	PhylogenyDocument	A document containing an alignment and one or more trees whose tips are the sequences (i.e.

Uses of PluginDocument in com.biomatters.geneious.publicapi.implementations

Classes in com.biomatters.geneious.publicapi.implementations that implement PluginDocument

Modifier and Type	Class	Description
class	CodonUsageTableDocument	A document storing a table of codon usage frequencies.
class	DefaultAlignmentDocument	An implementation of a SequenceAlignmentDocument.
class	DefaultPhylogenyDocument	An implementation of a Phylogeny document.
class	DefaultSameTaxaTreesDocument	A default implementation of a plugin document holding a list of trees.
class	DefaultTreeDocument	A default implementation of a plugin document holding a tree.
class	TextDocument	A document containing text that can be marked up in various formats such as html.

Methods in com.biomatters.geneious.publicapi.implementations with parameters of type PluginDocument

Modifier and Type	Method	Description
static void	SequenceExtractionUtilities.copyDocumentFields(PluginDocument source, AbstractPluginDocument target, boolean isTranslation)	Copy important document fields (such as organism, taxonomy and common name) from any PluginDocument to any AbstractPluginDocument

Uses of PluginDocument in com.biomatters.geneious.publicapi.implementations.sequence

Classes in com.biomatters.geneious.publicapi.implementations.sequence that implement PluginDocument

Modifier and Type	Class	Description
class	CombinedAlignmentAndAminoAcidSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
class	CombinedAlignmentAndNucleotideGraphSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
class	CombinedAlignmentAndNucleotideSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
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 with parameters of type PluginDocument

Modifier and Type	Method	Description
SequenceTrack.Manager	SequenceTrack.Manager.createGapInsertingManager(PluginDocument associatedPluginDocument, SequenceGapInformation sequenceGapInformation, boolean reverseToo, org.virion.jam.util.SimpleListener listenerToNotifyAboutDirectChangesToGappedManager)	Creates a new manager that inserts gaps into annotations relative to this manager.
SequenceTrack.Manager	SequenceTrack.Manager.createGapRemovingManager(PluginDocument associatedPluginDocument, SequenceGapInformation sequenceGapInformation, boolean reverseToo, org.virion.jam.util.SimpleListener listenerToNotifyAboutDirectChangesToGappedManager)	Creates a new manager that removes gaps from annotations relative to this manager.
static SequenceTrack.Manager	SequenceTrack.Manager.readObject(PluginDocument associatedPluginDocument, java.io.DataInput in)	Reads this object from a DataInput.

Constructors in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type PluginDocument

Constructor	Description
Manager(PluginDocument associatedPluginDocument)	Constructs a new empty manager with no tracks.
Manager(PluginDocument associatedPluginDocument, org.jdom.Element element)	Recreates a manager from XML.

Uses of PluginDocument in com.biomatters.geneious.publicapi.implementations.structure

Classes in com.biomatters.geneious.publicapi.implementations.structure that implement PluginDocument

Modifier and Type	Class	Description
class	CmlDocument	A Cml molecular structure document.
class	DefaultMolecularStructureDocument	An implementation of a MolecularStructureDocument.
class	GprDocument	A Gpr molecular structure document.
class	HinDocument	A Hin molecular structure document.
class	MolDocument	A Mol molecular structure document.
class	NwoDocument	A Nwo molecular structure document.
class	PdbDocument	A PDB molecular structure document.
class	XyzDocument	An XYZ molecular structure document.

Uses of PluginDocument in com.biomatters.geneious.publicapi.plugin

Subinterfaces of PluginDocument in com.biomatters.geneious.publicapi.plugin

Modifier and Type	Interface	Description
static interface	DocumentSelectionOption.DoNotRememberInPreferences	An interface that documents used in a DocumentSelectionOption may implement so that the option doesn't cache their instance and reuse it on future instances of these options.

Methods in com.biomatters.geneious.publicapi.plugin with parameters of type PluginDocument

Modifier and Type	Method	Description
abstract AnnotatedPluginDocument	DocumentFileImporter.ImportCallback.addDocument(PluginDocument document)	Report back one imported PluginDocument.
AnnotatedPluginDocument	DocumentOperation.OperationCallback.addDocument(PluginDocument doc, boolean dontSelectDocumentWhenComplete, jebl.util.ProgressListener progress)	returns a document from the operaiton while the operation is still in progress.
void	DocumentFileExporter.export(java.io.File file, PluginDocument[] documents, jebl.util.ProgressListener progressListener, Options options)	Do the actual exporting from PluginDocuments.
abstract SequenceAnnotationGenerator.AnnotationGeneratorResult	SequenceAnnotationGenerator.SingleSequenceResultGenerator.generate(PluginDocument document, SequenceAnnotationGenerator.SelectionRange selectionRange, jebl.util.ProgressListener progressListener)	Generate annotations for a single sequence.
static boolean	DocumentType.isAlignment(PluginDocument document)
static boolean	DocumentType.isAlignmentAndNotSequence(PluginDocument document)
static boolean	DocumentType.isAminoAcidSequence(PluginDocument document)
static boolean	DocumentType.isNucleotideSequence(PluginDocument document)
static boolean	DocumentType.isSequence(PluginDocument document)
static boolean	DocumentType.isSequenceList(PluginDocument document)

Method parameters in com.biomatters.geneious.publicapi.plugin with type arguments of type PluginDocument

Modifier and Type	Method	Description
SequenceDocument	SequenceSelection.SequenceIndex.getSequenceFromPluginDocuments(java.util.List<PluginDocument> selectedDocuments)	Gets the selected sequence corresponding to this sequence index for these documents