Uses of Class
com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

Packages that use WritableDatabaseService

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.plugin	Provides the GeneiousPlugin interface and plugin related interfaces.

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

Subclasses of WritableDatabaseService in com.biomatters.geneious.publicapi.databaseservice

Modifier and Type	Class	Description
static class	WritableDatabaseService.DummyService	A dummy implementation of WritableDatabaseService that provides no functionality apart from a name and icons

Methods in com.biomatters.geneious.publicapi.databaseservice that return WritableDatabaseService

Modifier and Type	Method	Description
protected abstract WritableDatabaseService	WritableDatabaseService._getHiddenFolder(java.lang.String folderName, boolean isPerUserFolder)	The implementation method for getHiddenFolder(String, boolean)
protected WritableDatabaseService	WritableDatabaseService.DummyService._getHiddenFolder(java.lang.String folderName, boolean isPerUserFolder)
abstract WritableDatabaseService	WritableDatabaseService.createChildFolder(java.lang.String name)	Creates a child DatabaseService.
WritableDatabaseService	WritableDatabaseService.DummyService.createChildFolder(java.lang.String name)
WritableDatabaseService	WritableDatabaseService.createFolderViewFolder(java.lang.String folderName, AnnotatedPluginDocument folderViewDocument)	Creates a new child folder that contains a document that may be displayed for representing an entire view of the folder.
WritableDatabaseService	WritableDatabaseService.getChildService(java.lang.String name)	Gets a child service whose getFolderName() == name.
WritableDatabaseService	WritableDatabaseService.getDatabaseRoot()	Get the root folder of this database folder hierarchy.
WritableDatabaseService	WritableDatabaseService.DocumentToAdd.getDestination()
WritableDatabaseService	WritableDatabaseService.DummyService.getDocumentLocation(URN documentURN)
abstract WritableDatabaseService	WritableDatabaseService.getDocumentLocation(URN documentURN)	If this database contains this document in any user visible folder returns the WritableDatabaseService representing the folder that contains it.
WritableDatabaseService	WritableDatabaseService.getHiddenFolder(java.lang.String folderName, boolean isPerUserFolder)	Gets an existing or creates a new hidden folder as an immediate child of the root service of this database.
WritableDatabaseService	WritableDatabaseService.getPrimaryDatabaseRoot()	Returns the database root (see getDatabaseRoot()) for the primary database in this collection.

Methods in com.biomatters.geneious.publicapi.databaseservice that return types with arguments of type WritableDatabaseService

Modifier and Type	Method	Description
java.util.List<WritableDatabaseService>	WritableDatabaseService.createChildFolders(java.util.List<java.lang.String> folderNames, jebl.util.ProgressListener progressListener)	Creates one or more child folders.

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

Modifier and Type	Method	Description
abstract boolean	WritableDatabaseService.canMoveTo(WritableDatabaseService destination)	Checks whether the service can be moved to a new destination.
boolean	WritableDatabaseService.DummyService.canMoveTo(WritableDatabaseService destination)
protected java.lang.String	WritableDatabaseService.getReasonCantMoveTo(WritableDatabaseService destination)	Returns the reason why we can not move this folder to destination, or null if we can move.
boolean	WritableDatabaseService.isSameRootService(WritableDatabaseService anotherService)	Determines whether the root of this service (or this service itself if it is the root) is equal to the root of another service.
void	WritableDatabaseService.DummyService.moveTo(WritableDatabaseService destination)
abstract void	WritableDatabaseService.moveTo(WritableDatabaseService destination)	Move this entire database folder to a new location.

Method parameters in com.biomatters.geneious.publicapi.databaseservice with type arguments of type WritableDatabaseService

Modifier and Type	Method	Description
void	WritableDatabaseService.setFolderViewDocuments(java.util.Map<WritableDatabaseService,AnnotatedPluginDocument> folderViewDocuments, jebl.util.ProgressListener progressListener)	Sets folder view documents on multiple folders.

Constructors in com.biomatters.geneious.publicapi.databaseservice with parameters of type WritableDatabaseService

Constructor	Description
DocumentToAdd(WritableDatabaseService destination, AnnotatedPluginDocument document, java.lang.String overrideDocumentName)

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

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

Modifier and Type	Method	Description
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.addAndReturnGeneratedDocuments(java.util.List<AnnotatedPluginDocument> documents, boolean selectDocumentsImmediately, java.util.List<AnnotatedPluginDocument> additionalDocumentsToSelect, boolean giveResultsUniqueNames, WritableDatabaseService destination)	Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table, and returns the newly added documents
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.addAndReturnGeneratedDocuments(java.util.List<AnnotatedPluginDocument> documents, boolean selectDocumentsImmediately, java.util.List<AnnotatedPluginDocument> additionalDocumentsToSelect, WritableDatabaseService destination)	Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table, and returns the newly added documents
static void	DocumentUtilities.addGeneratedDocuments(java.util.List<AnnotatedPluginDocument> documents, boolean selectDocumentsImmediately, java.util.List<AnnotatedPluginDocument> additionalDocumentsToSelect, WritableDatabaseService destination)	Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table.
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.addGeneratedDocumentsWithLineage(java.util.List<AnnotatedPluginDocument> documents, boolean selectDocumentsImmediately, WritableDatabaseService destination, java.lang.String operationUniqueId, java.util.List<AnnotatedPluginDocument> parentDocuments, boolean giveResultsUniqueNames, jebl.util.ProgressListener progress)	Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table.
static java.util.List<AnnotatedPluginDocument>	DocumentUtilities.addGeneratedDocumentsWithLineage(java.util.List<AnnotatedPluginDocument> documents, boolean selectDocumentsImmediately, WritableDatabaseService destination, java.lang.String operationUniqueId, java.util.List<AnnotatedPluginDocument> parentDocuments, jebl.util.ProgressListener progress)	Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table.
static java.lang.String	DocumentUtilities.getUniqueNameForDocument(java.lang.String baseDocumentName, WritableDatabaseService mustBeUniqueIn)	Generate a document name that is unique to the given folder, based on the original name passed in.
static java.lang.String	DocumentUtilities.getUniqueNameForDocument(java.lang.String baseDocumentName, WritableDatabaseService mustBeUniqueIn, java.util.Collection<java.lang.String> mustNotBe)	Generate a document name that is unique to the given folder, based on the original name passed in.

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

Methods in com.biomatters.geneious.publicapi.plugin that return WritableDatabaseService

Modifier and Type	Method	Description
WritableDatabaseService	DocumentSelectionOption.FolderOrDocuments.getFolder()	Get the selected folder or null if a folder was not selected (documents are selected).
static WritableDatabaseService	ServiceUtilities.getResultsDestination()	Get the service to which results of the current operation will be saved.
WritableDatabaseService	DocumentOperationInput.getResultsLocation()
WritableDatabaseService	WritableDatabaseServiceTree.getSelectedService()	returns the currently selected service.
static WritableDatabaseService	ServiceUtilities.getUserSelectedFolder(java.awt.Component anyComponentInParentFrame)	Opens a dialog in which the user can choose one of their local database folders.
abstract WritableDatabaseService	DatabaseFolderImporter.importFolder(java.io.File folder, WritableDatabaseService destination, Options options, jebl.util.ProgressListener progress)	Import the external database to a Geneious WritableDatabaseService and report back the containing the added documents.

Methods in com.biomatters.geneious.publicapi.plugin that return types with arguments of type WritableDatabaseService

Modifier and Type	Method	Description
Options.Option<WritableDatabaseService,javax.swing.JComponent>	Options.addServiceOption(java.lang.String name, java.lang.String label, WritableDatabaseService defaultValue)	Add an option that allows the user to select a WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
Options.Option<WritableDatabaseService,javax.swing.JComponent>	Options.addServiceOption(java.lang.String name, java.lang.String label, WritableDatabaseService defaultValue, java.util.function.Predicate<GeneiousService> rootServiceValidator, boolean displayButton, boolean showNewFolderButton, boolean useStandardButtonLook, java.lang.String folderTreeDialogTitle, java.util.List<WritableDatabaseService> foldersToDisable)	Add an option that allows the user to select a WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
static java.util.List<WritableDatabaseService>	PluginUtilities.getWritableDatabaseServiceRoots()	Returns the root services of all installed WritableDatabaseServices.

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

Modifier and Type	Method	Description
Options.Option<WritableDatabaseService,javax.swing.JComponent>	Options.addServiceOption(java.lang.String name, java.lang.String label, WritableDatabaseService defaultValue)	Add an option that allows the user to select a WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
Options.Option<WritableDatabaseService,javax.swing.JComponent>	Options.addServiceOption(java.lang.String name, java.lang.String label, WritableDatabaseService defaultValue, java.util.function.Predicate<GeneiousService> rootServiceValidator, boolean displayButton, boolean showNewFolderButton, boolean useStandardButtonLook, java.lang.String folderTreeDialogTitle, java.util.List<WritableDatabaseService> foldersToDisable)	Add an option that allows the user to select a WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
abstract Options	DatabaseFolderImporter.getOptions(java.io.File folder, WritableDatabaseService destination, jebl.util.ProgressListener progress)	Provides some options applicable to this database importer to the user, or null if no user-specified options are required.
static java.util.List<AnnotatedPluginDocument>	PluginUtilities.importDocumentsToDatabase(java.io.File file, WritableDatabaseService destination, jebl.util.ProgressListener progress)	Imports documents from a file into a database.
abstract WritableDatabaseService	DatabaseFolderImporter.importFolder(java.io.File folder, WritableDatabaseService destination, Options options, jebl.util.ProgressListener progress)	Import the external database to a Geneious WritableDatabaseService and report back the containing the added documents.
void	PluginUtilities.WritableDatabaseServicesListener.serviceAdded(WritableDatabaseService service)	Called by Geneious when a new service has been added.
void	PluginUtilities.WritableDatabaseServicesListener.serviceRemoved(WritableDatabaseService service)	Called by Geneious when a service has been removed.
DocumentOperationInput	DocumentOperationInput.setResultsLocation(WritableDatabaseService resultsLocation)	Sets the results location to be used for this operation.
void	WritableDatabaseServiceTree.setSelectedService(WritableDatabaseService service)	Sets the currently selected service.

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

Modifier and Type	Method	Description
Options.Option<WritableDatabaseService,javax.swing.JComponent>	Options.addServiceOption(java.lang.String name, java.lang.String label, WritableDatabaseService defaultValue, java.util.function.Predicate<GeneiousService> rootServiceValidator, boolean displayButton, boolean showNewFolderButton, boolean useStandardButtonLook, java.lang.String folderTreeDialogTitle, java.util.List<WritableDatabaseService> foldersToDisable)	Add an option that allows the user to select a WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
void	WritableDatabaseServiceTree.updateModel(java.util.List<WritableDatabaseService> roots, java.util.Map<WritableDatabaseService,java.lang.Integer> documentCountsByService)	Update the tree in-place with a newly-generated model to reflect changes in the available services.
void	WritableDatabaseServiceTree.updateModel(java.util.List<WritableDatabaseService> roots, java.util.Map<WritableDatabaseService,java.lang.Integer> documentCountsByService)	Update the tree in-place with a newly-generated model to reflect changes in the available services.

Constructors in com.biomatters.geneious.publicapi.plugin with parameters of type WritableDatabaseService

Constructor	Description
FolderOrDocuments(WritableDatabaseService folder)	Create a FolderOrDocuments for a folder selection

Constructor parameters in com.biomatters.geneious.publicapi.plugin with type arguments of type WritableDatabaseService

Constructor	Description
WritableDatabaseServiceTree(java.util.List<WritableDatabaseService> roots, boolean showNumberOfDocumentsInFolder, java.util.Map<WritableDatabaseService,java.lang.Integer> documentCountsByService)	Create a new GUI component that lets the user choose a WritableDatabaseService from the root services supplied
WritableDatabaseServiceTree(java.util.List<WritableDatabaseService> roots, boolean showNumberOfDocumentsInFolder, java.util.Map<WritableDatabaseService,java.lang.Integer> documentCountsByService)	Create a new GUI component that lets the user choose a WritableDatabaseService from the root services supplied