Uses of Interface
org.cytoscape.model.CyIdentifiable

Packages that use CyIdentifiable

Package	Description
org.cytoscape.application.swing	This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
org.cytoscape.jobs	This package provides a mechanism for executing remote jobs from within Cytoscape.
org.cytoscape.model	This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
org.cytoscape.model.subnetwork	This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.session	This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
org.cytoscape.task.edit	This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
org.cytoscape.util.json
org.cytoscape.view.model	Module for View Models and Visual Properties.
org.cytoscape.view.model.table
org.cytoscape.view.presentation.annotations	This package provides support for graphical annotations associated with a Cytoscape CyNetworkView.
org.cytoscape.view.presentation.customgraphics	This package provides an API for augmenting a RenderingEngines node rendering with custom graphics.
org.cytoscape.view.presentation.property	Implementations of basic VisualProperty objects and VisualLexicons.
org.cytoscape.view.presentation.property.table
org.cytoscape.view.vizmap	Visual Mapping basic API module.
org.cytoscape.view.vizmap.gui.editor	Provides editors for Visual Properties and editor managers for VizMap GUI.
org.cytoscape.view.vizmap.mappings	APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.

Uses of CyIdentifiable in org.cytoscape.application.swing

Methods in org.cytoscape.application.swing that return types with arguments of type CyIdentifiable

Modifier and Type	Method	Description
Class<? extends CyIdentifiable>	TableToolBarComponent.getTableType()

Uses of CyIdentifiable in org.cytoscape.jobs

Methods in org.cytoscape.jobs that return types with arguments of type CyIdentifiable

Modifier and Type	Method	Description
static Map<Long,CyIdentifiable>	SUIDUtil.restoreSUIDs(CyJob job, CyNetwork network, List<Long> oldIds, boolean clear)	Method to restore Cytoscape objects based on a list of SUIDs that were sent to the remote service as saved in the hidden table.

Method parameters in org.cytoscape.jobs with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
default CyJobData	CyJobDataService.addData(CyJobData data, String key, CyNetwork network, List<? extends CyIdentifiable> nodesAndEdges, List<String> nodeColumns, List<String> edgeColumns)	An optional method to add network data to a CyJobData item.
default CyJobData	CyJobDataService.addData(CyJobData data, String key, CyNetworkView networkView, List<? extends CyIdentifiable> nodesAndEdges, List<VisualProperty<?>> properties)	An optional method to add network view data to a CyJobData item.
static void	SUIDUtil.saveSUIDs(CyJob job, CyNetwork network, List<? extends CyIdentifiable> objs)	This method may be used to save a list of SUIDs that have been sent to a remote service so that they may be restored later

Uses of CyIdentifiable in org.cytoscape.model

Subinterfaces of CyIdentifiable in org.cytoscape.model

Modifier and Type	Interface	Description
interface	CyColumn	This class describes a column in a CyTable.
interface	CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
interface	CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
interface	CyNode	An object that represents a node (vertex) within a network of nodes and edges.
interface	CyRow	This interface represents one row in a CyTable.
interface	CyTable	A simple representation of a table object consisting of rows and columns.

Methods in org.cytoscape.model that return types with arguments of type CyIdentifiable

Modifier and Type	Method	Description
Class<? extends CyIdentifiable>	CyNetworkTableManager.getTableType(CyTable table)	Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.

Methods in org.cytoscape.model with parameters of type CyIdentifiable

Modifier and Type	Method	Description
CyRow	CyNetwork.getRow(CyIdentifiable entry)	A convenience method that returns the row in the default table for this object.
CyRow	CyNetwork.getRow(CyIdentifiable entry, String namespace)	Returns the row for the specified table name for this object.

Method parameters in org.cytoscape.model with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
Set<CyTable>	CyTableManager.getLocalTables(Class<? extends CyIdentifiable> type)	Returns set of all local tables for the given data type.
CyTable	CyNetwork.getTable(Class<? extends CyIdentifiable> type, String namespace)	Returns the table with the specified namespace and type from this network.
CyTable	CyNetworkTableManager.getTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace)	Returns the table with the specified namespace and type from the network.
Map<String,CyTable>	CyNetworkTableManager.getTables(CyNetwork network, Class<? extends CyIdentifiable> type)	Returns a read-only map of all of the tables for the specified type from the network.
void	CyNetworkTableManager.removeTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace)	Removes the table with the specified namespace and type from the network.
void	CyNetworkTableManager.setTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace, CyTable table)	Associates the given table to the network using the specified namespace and type.

Uses of CyIdentifiable in org.cytoscape.model.subnetwork

Subinterfaces of CyIdentifiable in org.cytoscape.model.subnetwork

Modifier and Type	Interface	Description
interface	CyRootNetwork	CyRootNetwork is an interface for managing Cytoscape's meta-network implementation.
interface	CySubNetwork	A CySubNetwork is a CyNetwork that is contained within a parent CyNetwork.

Uses of CyIdentifiable in org.cytoscape.session

Methods in org.cytoscape.session with type parameters of type CyIdentifiable

Modifier and Type	Method	Description
<T extends CyIdentifiable> T	CySession.getObject(Long oldSUID, Class<T> type)	When a session is restored, Cytoscape automatically generates new SUIDs.
<T extends CyIdentifiable> T	CySession.getObject(String oldId, Class<T> type)	When a session is restored, Cytoscape automatically generates new SUIDs.

Method parameters in org.cytoscape.session with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
CySession.Builder	CySession.Builder.objectMap(Map<Class<? extends CyIdentifiable>,Map<Object,? extends CyIdentifiable>> map)	Returns an instance of Builder that has at least been configured with the specified old ID maps.
CySession.Builder	CySession.Builder.objectMap(Map<Class<? extends CyIdentifiable>,Map<Object,? extends CyIdentifiable>> map)	Returns an instance of Builder that has at least been configured with the specified old ID maps.

Uses of CyIdentifiable in org.cytoscape.task.edit

Method parameters in org.cytoscape.task.edit with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
TaskIterator	ImportDataTableTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, boolean loadToUnassignedTable, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)	Creates a task iterator for importing a table data in a network data table.
TaskIterator	JoinTablesTaskTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
TaskIterator	MapTableToNetworkTablesTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
TaskIterator	MergeTablesTaskFactory.createTaskIterator(CyTable sourceTable, CyTable targetTable, List<String> sourceColumnsList, String sourceKeyColumn, boolean mergeColumnVirtual, boolean mapToNetworks, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)	Creates a task iterator for merging two data tables.

Uses of CyIdentifiable in org.cytoscape.util.json

Methods in org.cytoscape.util.json with parameters of type CyIdentifiable

Modifier and Type	Method	Description
String	CyJSONUtil.toJson(CyIdentifiable cyIdentifiable)	Returns a reference (via SUID) for a CyIdentifiable.

Method parameters in org.cytoscape.util.json with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
String	CyJSONUtil.cyIdentifiablesToJson(Collection<? extends CyIdentifiable> collection)	Returns a list of references (via SUID) for a collection of CyIdentifiable.

Uses of CyIdentifiable in org.cytoscape.view.model

Subinterfaces of CyIdentifiable in org.cytoscape.view.model

Modifier and Type	Interface	Description
interface	CyNetworkView	Additional methods for CyNetworkView.
interface	CyNetworkViewSnapshot	An immutable snapshot of a CyNetworkView created using the CyNetworkView.createSnapshot() method.
interface	NullCyNetworkView	A CyNetwork with no corresponding view.
interface	View<S>	The base interface that defines methods used to set visual properties for nodes, edges, and networks.

Methods in org.cytoscape.view.model that return types with arguments of type CyIdentifiable

Modifier and Type	Method	Description
Collection<View<? extends CyIdentifiable>>	CyNetworkView.getAllViews()	Returns a list of all View including those for Nodes, Edges, and Network.
Class<? extends CyIdentifiable>	AbstractVisualProperty.getTargetDataType()
Class<? extends CyIdentifiable>	VisualProperty.getTargetDataType()	VisualProperty is always associated with a data type.

Constructor parameters in org.cytoscape.view.model with type arguments of type CyIdentifiable

Modifier	Constructor	Description
	AbstractVisualProperty(T defaultValue, Range<T> range, String id, String displayName, Class<? extends CyIdentifiable> targetObjectDataType)	Constructor to set all immutable fields.

Uses of CyIdentifiable in org.cytoscape.view.model.table

Subinterfaces of CyIdentifiable in org.cytoscape.view.model.table

Modifier and Type	Interface	Description
interface	CyColumnView	This interface is meant for internal use, it should not be used by Apps.
interface	CyTableView	Additional methods for table views.

Uses of CyIdentifiable in org.cytoscape.view.presentation.annotations

Method parameters in org.cytoscape.view.presentation.annotations with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
void	ArrowAnnotation.setTarget(View<? extends CyIdentifiable> target)	Set the target for this arrow assuming the target is a View object.

Uses of CyIdentifiable in org.cytoscape.view.presentation.customgraphics

Methods in org.cytoscape.view.presentation.customgraphics that return types with arguments of type CyIdentifiable

Modifier and Type	Method	Description
default Set<Class<? extends CyIdentifiable>>	CyCustomGraphics2Factory.getSupportedTargetTypes()	Returns all the target types supported by this factory, usually CyNode and CyColumn.
default Set<Class<? extends CyIdentifiable>>	CyCustomGraphicsFactory.getSupportedTargetTypes()	Returns all the target types supported by this factory, usually CyNode and CyColumn.

Method parameters in org.cytoscape.view.presentation.customgraphics with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
void	Cy2DGraphicLayer.draw(Graphics2D g, Shape shape, CyNetworkView networkView, View<? extends CyIdentifiable> view)	This method is called by Cytoscape when a CyNetworkView is being updated in order to let the custom graphics draw onto its Graphics2D object.
List<T>	CyCustomGraphics.getLayers(CyNetworkView networkView, View<? extends CyIdentifiable> grView)	Get layers that belong to this object.

Uses of CyIdentifiable in org.cytoscape.view.presentation.property

Constructor parameters in org.cytoscape.view.presentation.property with type arguments of type CyIdentifiable

Modifier	Constructor	Description
	ArrowShapeVisualProperty(ArrowShape defaultValue, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	BooleanVisualProperty(Boolean def, String id, String displayName, Boolean ignoreDefault, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	BooleanVisualProperty(Boolean def, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	DefaultVisualizableVisualProperty(String id, String displayName, Class<? extends CyIdentifiable> modelDataType)
	DoubleVisualProperty(Double def, Range<Double> range, String id, String displayName, boolean ignoreDefault, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	DoubleVisualProperty(Double def, Range<Double> range, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	EdgeStackingVisualProperty(EdgeStacking defaultValue, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)
	FontVisualProperty(Font def, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	IntegerVisualProperty(Integer def, Range<Integer> range, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	LineTypeVisualProperty(LineType defaultValue, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	NodeShapeVisualProperty(NodeShape defaultValue, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	ObjectPositionVisualProperty(ObjectPosition defaultValue, String id, String displayName, Class<? extends CyIdentifiable> targetObjectDataType)
	PaintVisualProperty(Paint def, Range<Paint> range, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	StringVisualProperty(String def, Range<String> range, String id, String displayName, boolean ignoreDefault, Class<? extends CyIdentifiable> modelDataType)	Constructor.
	StringVisualProperty(String def, Range<String> range, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)	Constructor.

Uses of CyIdentifiable in org.cytoscape.view.presentation.property.table

Constructor parameters in org.cytoscape.view.presentation.property.table with type arguments of type CyIdentifiable

Modifier	Constructor	Description
	CellFormatVisualProperty(CellFormat def, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)
	TableModeVisualProperty(TableMode defaultValue, String id, String displayName, Class<? extends CyIdentifiable> modelDataType)

Uses of CyIdentifiable in org.cytoscape.view.vizmap

Method parameters in org.cytoscape.view.vizmap with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
void	VisualMappingFunction.apply(CyRow row, View<? extends CyIdentifiable> view)	Apply mapping to the view model.
void	VisualStyle.apply(CyRow row, View<? extends CyIdentifiable> view)	Apply Visual Property values only to the given View Object (node or edge).

Uses of CyIdentifiable in org.cytoscape.view.vizmap.gui.editor

Method parameters in org.cytoscape.view.vizmap.gui.editor with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
PropertyEditor	EditorManager.getDataTableComboBoxEditor(Class<? extends CyIdentifiable> targetObjectType)	Attribute selector for the given table entry type.

Uses of CyIdentifiable in org.cytoscape.view.vizmap.mappings

Method parameters in org.cytoscape.view.vizmap.mappings with type arguments of type CyIdentifiable

Modifier and Type	Method	Description
void	AbstractVisualMappingFunction.apply(CyRow row, View<? extends CyIdentifiable> view)