Modifier and Type | Method and Description |
---|---|
OntologyHandle |
OntologyDatabase.getEmptyOntology(String name)
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet, it is created and the new ontology handle
is returned.
|
OntologyHandle |
OntologyDatabase.getOntology(String name)
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet, it is created and the new ontology handle
is returned.
|
OntologyHandle |
OntologyDatabase.getOntology(String name,
boolean create)
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet and the "create" flag is set to true, it
is created and the new ontology handle is returned.
|
Modifier and Type | Method and Description |
---|---|
Collection<OntologyHandle> |
OntologyDatabase.getOntologies()
Returns a list containing handles to all currently available ontologies.
|
Modifier and Type | Method and Description |
---|---|
void |
OntologyDatabase.deleteOntology(OntologyHandle ontology)
Deletes the ontology with the given handle.
|
Date |
OntologyDatabase.getOntologyModificationDate(OntologyHandle ontology)
Returns the modification date of the given ontology.
|
Collection<Node> |
OntologyDatabase.getRootNodes(OntologyHandle ontology)
Returns all the nodes that were marked as "root node" in the given
ontology.
|
void |
OntologyDatabase.updateOntologyModificationDate(OntologyHandle ontology)
Updates the modification date of the given ontology to now.
|
Constructor and Description |
---|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
Collection<NodeName> names)
Constructor of the Node class.
|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
Collection<NodeName> names,
boolean root)
Constructor of the Node class.
|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
NodeName name)
Constructor of the Node class.
|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
NodeName name,
boolean root)
Constructor of the Node class.
|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
String name)
Constructor of the Node class.
|
Node(OntologyDatabase db,
OntologyHandle handle,
int id,
String name,
boolean root)
Constructor of the Node class.
|
Modifier and Type | Method and Description |
---|---|
OntologyHandle |
OntologyDatabaseDriver.getEmptyOntology(String name)
Returns an empty instance of the ontology with the given name.
|
OntologyHandle |
NodeHandle.getOntology()
Returns the ontology handle.
|
OntologyHandle |
NodeDescriptor.getOntology()
Returns the ontology the described node belongs to.
|
OntologyHandle |
OntologyDatabaseDriver.getOntology(String name)
Returns the handle for the ontology with the given name or creates the
ontology if it does not exist.
|
abstract OntologyHandle |
OntologyDatabaseDriver.getOntology(String name,
boolean create)
Returns a the handle for the ontology with the given name or creates the
ontology if it does not exist.
|
Modifier and Type | Method and Description |
---|---|
abstract Collection<OntologyHandle> |
OntologyDatabaseDriver.getOntologies()
Returns a list containing all ontologies in the database and an empty
list if no ontologies are present.
|
Modifier and Type | Method and Description |
---|---|
abstract void |
OntologyDatabaseDriver.deleteOntology(OntologyHandle ontology)
Deletes the ontology with the given ontology handle.
|
abstract Date |
OntologyDatabaseDriver.getOntologyModificationDate(OntologyHandle ontology)
Returns the last update date for the given ontology handle.
|
abstract Collection<NodeDescriptor> |
OntologyDatabaseDriver.getRootNodes(OntologyHandle ontology)
Returns a list containing all root nodes in the given ontology.
|
abstract void |
OntologyDatabaseDriver.setOntologyModificationDate(OntologyHandle ontology,
Date date)
Returns the last update date for the given ontology handle.
|
Constructor and Description |
---|
Association(OntologyHandle ontology,
int sourceId,
int targetId)
Constructor of the Association class.
|
Association(OntologyHandle ontology,
int sourceId,
int targetId,
AssociationType type)
Constructor of the Association class.
|
NodeDescriptor(OntologyHandle handle,
int id,
Collection<NodeName> names)
Constructor of the NodeDescriptor class.
|
NodeDescriptor(OntologyHandle handle,
int id,
Collection<NodeName> names,
boolean root)
Constructor of the NodeDescriptor class.
|
NodeDescriptor(OntologyHandle handle,
int id,
NodeName name)
Constructor of the NodeDescriptor class.
|
NodeDescriptor(OntologyHandle handle,
int id,
NodeName name,
boolean root)
Constructor of the NodeDescriptor class.
|
NodeDescriptor(OntologyHandle handle,
int id,
String name)
Constructor of the NodeDescriptor class.
|
NodeDescriptor(OntologyHandle handle,
int id,
String name,
boolean root)
Constructor of the NodeDescriptor class.
|
NodeHandle(OntologyHandle ontology,
int id)
Constructor of the NodeHandle class.
|
Modifier and Type | Class and Description |
---|---|
protected class |
JDBCDatabaseDriver.JDBCOntologyHandle
The JDBCOntologyHandle class is the OntologyHandle type used by the JDBC
database.
|
protected class |
MemoryDatabaseDriver.MemoryDatabaseOntologyHandle
The JDBCOntologyHandle class is the OntologyHandle type used by the JDBC
database.
|
Modifier and Type | Method and Description |
---|---|
OntologyHandle |
JDBCDatabaseDriver.getOntology(String name,
boolean create) |
OntologyHandle |
MemoryDatabaseDriver.getOntology(String name,
boolean create) |
Modifier and Type | Method and Description |
---|---|
Collection<OntologyHandle> |
JDBCDatabaseDriver.getOntologies() |
Collection<OntologyHandle> |
MemoryDatabaseDriver.getOntologies() |
Modifier and Type | Method and Description |
---|---|
void |
JDBCDatabaseDriver.deleteOntology(OntologyHandle ontology) |
void |
MemoryDatabaseDriver.deleteOntology(OntologyHandle ontology) |
Date |
JDBCDatabaseDriver.getOntologyModificationDate(OntologyHandle ontology) |
Date |
MemoryDatabaseDriver.getOntologyModificationDate(OntologyHandle ontology) |
Collection<NodeDescriptor> |
JDBCDatabaseDriver.getRootNodes(OntologyHandle ontology) |
Collection<NodeDescriptor> |
MemoryDatabaseDriver.getRootNodes(OntologyHandle ontology) |
void |
JDBCDatabaseDriver.setOntologyModificationDate(OntologyHandle ontology,
Date date) |
void |
MemoryDatabaseDriver.setOntologyModificationDate(OntologyHandle ontology,
Date date) |
Modifier and Type | Method and Description |
---|---|
protected abstract void |
AbstractImporter.parseXML(OntologyHandle onto,
XMLStreamReader parser)
Flushes all data from xml into db.
|
Modifier and Type | Method and Description |
---|---|
protected void |
DrugBankImporter.parseXML(OntologyHandle onto,
XMLStreamReader parser)
Flushes all data from Drugbank xml into db.
|
Modifier and Type | Method and Description |
---|---|
protected void |
MeshImporter2.parseXML(OntologyHandle onto,
XMLStreamReader parser)
Flushes all data from desc xml(Mesh) into db.
|
protected void |
MeshImporter.parseXML(OntologyHandle onto,
XMLStreamReader parser)
Flushes all data from desc xml(Mesh) into db.
|
Modifier and Type | Method and Description |
---|---|
protected void |
NCBIImporter.parseXML(OntologyHandle onto,
XMLStreamReader parser) |
Modifier and Type | Method and Description |
---|---|
void |
AssociationList.flush(OntologyDatabase db,
OntologyHandle onto) |
protected void |
SmallImporter.parseXML(OntologyHandle onto,
XMLStreamReader parser) |
Copyright (C) 2013, 2014 Raphael Dickfelder, Jan Göpfert, Benjamin Paassen, Andreas Stöckel, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/scie