Uses of Interface
org.cytoscape.model.CyNetwork

Packages that use CyNetwork

Package	Description
org.cytoscape.application	This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.application.events	This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
org.cytoscape.command	Interface to support execution of tasks as commands, including the ability to get a list of namespaces, commands, and arguments, and then execute those commands with a set of arguments.
org.cytoscape.command.util	Tunable classes useful for command applications
org.cytoscape.group	This package provides an API for creating and managing groups in Cytoscape.
org.cytoscape.group.events	This package contains the various events and listeners related to group management, creation, and destruction.
org.cytoscape.io.read	Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.write	This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
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.events	This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
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	This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.create	This package provides a variety of task factory interfaces for creating new instances of network and other objects.
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.task.select	This package includes a set of task factory interfaces for selecting, de-selecting and inverting selections of nodes, edges, or combinations of both based on specific criteria.
org.cytoscape.task.write	This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.view.layout	This package provides access to the available layout algorithms, as well as provides abstract layout classes and layout information containers for the convenience of implementing other layout algorithms.
org.cytoscape.view.model	Module for View Models and Visual Properties.
org.cytoscape.view.vizmap.gui	This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.

Uses of CyNetwork in org.cytoscape.application

Methods in org.cytoscape.application that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	CyApplicationManager.getCurrentNetwork() Provides access to the current network.

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

Modifier and Type	Method and Description
RenderingEngine<CyNetwork>	CyApplicationManager.getCurrentRenderingEngine() Returns the rendering engine associated with the current network view.
RenderingEngineFactory<CyNetwork>	NetworkViewRenderer.getRenderingEngineFactory(String contextId)
List<CyNetwork>	CyApplicationManager.getSelectedNetworks() Returns the list of selected networks.

Methods in org.cytoscape.application with parameters of type CyNetwork

Modifier and Type	Method and Description
void	CyApplicationManager.setCurrentNetwork(CyNetwork net) Sets the current network to the specified network.

Method parameters in org.cytoscape.application with type arguments of type CyNetwork

Modifier and Type	Method and Description
void	CyApplicationManager.setCurrentRenderingEngine(RenderingEngine<CyNetwork> engine) Sets the current rendering engine.
void	CyApplicationManager.setSelectedNetworks(List<CyNetwork> nets) Sets the networks specified as selected.

Uses of CyNetwork in org.cytoscape.application.events

Methods in org.cytoscape.application.events that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	SetCurrentNetworkEvent.getNetwork() Returns the network associated with this event.

Methods in org.cytoscape.application.events that return types with arguments of type CyNetwork

Modifier and Type	Method and Description
List<CyNetwork>	SetSelectedNetworksEvent.getNetworks() Returns the list of networks selected.
RenderingEngine<CyNetwork>	SetCurrentRenderingEngineEvent.getRenderingEngine() Return the rendering engine (presentation) that has been set as current.

Constructors in org.cytoscape.application.events with parameters of type CyNetwork

Constructor and Description
SetCurrentNetworkEvent(CyApplicationManager source, CyNetwork net) Constructor.

Constructor parameters in org.cytoscape.application.events with type arguments of type CyNetwork

Constructor and Description
SetCurrentRenderingEngineEvent(CyApplicationManager source, RenderingEngine<CyNetwork> engine) Constructor.
SetSelectedNetworksEvent(CyApplicationManager source, List<CyNetwork> networks) Constructor.

Uses of CyNetwork in org.cytoscape.command

Methods in org.cytoscape.command that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	StringToModel.getNetwork(String strNet) Convert a string request for a network into a CyNetwork.

Methods in org.cytoscape.command with parameters of type CyNetwork

Modifier and Type	Method and Description
List<CyEdge>	StringToModel.getEdgeList(CyNetwork net, String edgelist) Convert a string request for a edgelist into a list of CyEdges.
List<CyNode>	StringToModel.getNodeList(CyNetwork net, String nodelist) Convert a string request for a nodelist into a list of CyNodes.

Uses of CyNetwork in org.cytoscape.command.util

Methods in org.cytoscape.command.util that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	NodeList.getNetwork() Get the network for this nodelist
CyNetwork	EdgeList.getNetwork() Return the network used by this EdgeList

Methods in org.cytoscape.command.util with parameters of type CyNetwork

Modifier and Type	Method and Description
void	NodeList.setNetwork(CyNetwork network) Set the network for this nodelist
void	EdgeList.setNetwork(CyNetwork network) Set the network to be used by this EdgeList

Constructors in org.cytoscape.command.util with parameters of type CyNetwork

Constructor and Description
EdgeList(CyNetwork targetNetwork) Constructor for EdgeList when the network is known at time of creation.
NodeList(CyNetwork targetNetwork) Create a new NodeList object with an initial network

Uses of CyNetwork in org.cytoscape.group

Methods in org.cytoscape.group that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	CyGroup.getGroupNetwork() Returns the network referenced by this group.

Methods in org.cytoscape.group that return types with arguments of type CyNetwork

Modifier and Type	Method and Description
Set<CyNetwork>	CyGroup.getNetworkSet() Return the list of CyNetworks this group is in.

Methods in org.cytoscape.group with parameters of type CyNetwork

Modifier and Type	Method and Description
void	CyGroup.addGroupToNetwork(CyNetwork network) Add a group to an additional network.
void	CyGroup.collapse(CyNetwork network) Collapse this group in the designated network.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, boolean register) Creates a CyGroup object in the referenced network.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, CyNode node, boolean register) Creates a CyGroup object in the referenced network from an existing CyNode.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, CyNode node, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network from an existing CyNode.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network initially populated with the supplied nodes.
void	CyGroup.expand(CyNetwork network) Expand this group in the designated network.
CyGroup	CyGroupManager.getGroup(CyNode node, CyNetwork network) Return the group the corresponds to a particular node in a CyNetwork.
Set<CyGroup>	CyGroupManager.getGroupSet(CyNetwork network) Provides the set of all the groups known to the groups manager in a particular network.
List<CyGroup>	CyGroupManager.getGroupsForNode(CyNode node, CyNetwork network) Return the list of CyGroups this node is in for a particular network.
boolean	CyGroup.isCollapsed(CyNetwork network) Return whether this group is expanded or collapsed in the designated network.
boolean	CyGroupManager.isGroup(CyNode node, CyNetwork network) Test to see if this node represents a CyGroup in a particular CyNetwork.
boolean	CyGroup.isInNetwork(CyNetwork network) Check to see if this group is defined in a particular network.
void	CyGroup.removeGroupFromNetwork(CyNetwork network) Remove a group from a network.

Uses of CyNetwork in org.cytoscape.group.events

Constructors in org.cytoscape.group.events with parameters of type CyNetwork

Constructor and Description
GroupAboutToBeRemovedEvent(CyGroup source, CyNetwork network) Constructs event.
GroupAboutToCollapseEvent(CyGroup source, CyNetwork network, boolean collapsing) Constructs event.
GroupAddedToNetworkEvent(CyGroup source, CyNetwork network) Constructs event.
GroupCollapsedEvent(CyGroup source, CyNetwork network, boolean collapsed) Constructs event.

Uses of CyNetwork in org.cytoscape.io.read

Fields in org.cytoscape.io.read declared as CyNetwork

Modifier and Type	Field and Description
protected CyNetwork[]	AbstractCyNetworkReader.networks Array of networks to be returned.

Methods in org.cytoscape.io.read that return CyNetwork

Modifier and Type	Method and Description
CyNetwork[]	CyNetworkReader.getNetworks() Returns an array of networks read after executing the run() method of Task.
CyNetwork[]	AbstractCyNetworkReader.getNetworks()

Methods in org.cytoscape.io.read with parameters of type CyNetwork

Modifier and Type	Method and Description
CyNetworkView	CyNetworkReader.buildCyNetworkView(CyNetwork network) A method to build a CyNetworkView from one of the networks just read.

Uses of CyNetwork in org.cytoscape.io.write

Methods in org.cytoscape.io.write with parameters of type CyNetwork

Modifier and Type	Method and Description
CyWriter	CyNetworkViewWriterFactory.createWriter(OutputStream os, CyNetwork network) Creates a single Task that will write the specified network to the specified OutputStream.
CyWriter	CyNetworkViewWriterManager.getWriter(CyNetwork network, CyFileFilter filter, File file) Returns the CyWriter Task that will attempt to write the specified network to the specified file of the specified file type.
CyWriter	CyNetworkViewWriterManager.getWriter(CyNetwork network, CyFileFilter filter, OutputStream os) Returns the CyWriter Task that will attempt to write the specified network to the specified output steam of the specified file type.

Uses of CyNetwork in org.cytoscape.jobs

Methods in org.cytoscape.jobs that return CyNetwork

Modifier and Type	Method and Description
default CyNetwork	CyJobDataService.getNetworkData(CyJobData data, String key) Optional method to extract network data from a CyJobData object.
static CyNetwork	SUIDUtil.restoreNetwork(CyJob job, CyNetworkManager netManager, Long networkSUID, boolean clear) This method is used to restore a saved network based on the network SUID.

Methods in org.cytoscape.jobs with parameters of type CyNetwork

Modifier and Type	Method and 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.
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.
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 CyNetwork in org.cytoscape.model

Methods in org.cytoscape.model that return CyNetwork

Modifier and Type	Method and Description
CyNetwork	CyNetworkFactory.createNetwork() Returns a new, empty CyNetwork object.
CyNetwork	CyNetworkFactory.createNetwork(SavePolicy policy) Returns a new, empty CyNetwork object.
CyNetwork	CyNetworkFactory.createNetworkWithPrivateTables() Returns a new, empty CyNetwork object where the associated default tables are private.
CyNetwork	CyNetworkFactory.createNetworkWithPrivateTables(SavePolicy policy) Returns a new, empty CyNetwork object where the associated default tables are private.
CyNetwork	CyTableMetadata.getNetwork() Returns all the networks associated with this object's table.
CyNetwork	CyNetworkManager.getNetwork(long id) Returns the network corresponding to the provided ID
CyNetwork	CyNetworkTableManager.getNetworkForTable(CyTable table) Returns the network this table is registered with.
CyNetwork	CyNode.getNetworkPointer() Returns the network referenced by this node.

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

Modifier and Type	Method and Description
Set<CyNetwork>	CyNetworkTableManager.getNetworkSet() Returns a read-only set of all networks managed by this instance.
Set<CyNetwork>	CyNetworkManager.getNetworkSet() Provides the set of all the networks known to the network manager.

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

Modifier and Type	Method and Description
void	CyNetworkManager.addNetwork(CyNetwork network) Registers a network with the network manager and sets the network as current.
void	CyNetworkManager.addNetwork(CyNetwork network, boolean setCurrent) Registers a network with the network manager.
void	CyNetworkManager.destroyNetwork(CyNetwork network) Destroys a network.
static List<CyEdge>	CyTableUtil.getEdgesInState(CyNetwork net, String columnName, boolean state) A utility method that returns a list of edges that have a boolean attribute in the DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
static List<CyNode>	CyTableUtil.getNodesInState(CyNetwork net, String columnName, boolean state) A utility method that returns a list of nodes that have a boolean attribute in the DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
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.removeAllTables(CyNetwork network) Removes all tables associated with the given 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	CyNode.setNetworkPointer(CyNetwork network) Allows a network reference for this node to be set.
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 CyNetwork in org.cytoscape.model.events

Constructors in org.cytoscape.model.events with parameters of type CyNetwork

Constructor and Description
AboutToRemoveEdgesEvent(CyNetwork source, Collection<CyEdge> edges) Constructs event.
AboutToRemoveNodesEvent(CyNetwork source, Collection<CyNode> nodes) Constructs event.
AddedEdgesEvent(CyNetwork source, Collection<CyEdge> edges) Constructs event.
AddedNodesEvent(CyNetwork source, Collection<CyNode> nodes) Constructs event.
NetworkAboutToBeDestroyedEvent(CyNetworkManager source, CyNetwork net) Constructs event.
NetworkAddedEvent(CyNetworkManager source, CyNetwork net) Constructs event.
RemovedEdgesEvent(CyNetwork source) Constructs event.
RemovedNodesEvent(CyNetwork source) Constructs event.
SetNetworkPointerEvent(CyNode node, CyNetwork network) Constructs event.
UnsetNetworkPointerEvent(CyNode node, CyNetwork network) Constructs event.

Uses of CyNetwork in org.cytoscape.model.subnetwork

Subinterfaces of CyNetwork in org.cytoscape.model.subnetwork

Modifier and Type	Interface and 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.

Methods in org.cytoscape.model.subnetwork with parameters of type CyNetwork

Modifier and Type	Method and Description
boolean	CyRootNetwork.containsNetwork(CyNetwork n) Returns true if the network to be checked is a subnetwork of this root network and returns false otherwise.
CyRootNetwork	CyRootNetworkManager.getRootNetwork(CyNetwork n) Converts a CyNetwork to a CyRootNetwork

Uses of CyNetwork in org.cytoscape.session

Methods in org.cytoscape.session that return types with arguments of type CyNetwork

Modifier and Type	Method and Description
Set<CyNetwork>	CySession.getNetworks() Returns a set of all CyNetwork objects contained in this Session.

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

Modifier and Type	Method and Description
String	CyNetworkNaming.getSuggestedSubnetworkTitle(CyNetwork parentNetwork) Generates a unique title for a subnetwork based on a parent network.

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

Modifier and Type	Method and Description
CySession.Builder	CySession.Builder.networks(Set<CyNetwork> networks) Returns an instance of Builder that has at least been configured with the specified networks.

Uses of CyNetwork in org.cytoscape.task

Fields in org.cytoscape.task declared as CyNetwork

Modifier and Type	Field and Description
protected CyNetwork	AbstractNetworkTask.network The network that descendants of this class will operate on.

Fields in org.cytoscape.task with type parameters of type CyNetwork

Modifier and Type	Field and Description
protected Collection<CyNetwork>	AbstractNetworkCollectionTask.networks The collection of networks that descendants will operate on.

Methods in org.cytoscape.task with parameters of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	NetworkTaskFactory.createTaskIterator(CyNetwork network) Provisions this factory with the CyNetwork that will be passed into any task created by it.
boolean	NetworkTaskFactory.isReady(CyNetwork network) Returns true if this task factory is ready to produce a TaskIterator.
boolean	AbstractNetworkTaskFactory.isReady(CyNetwork network) Returns true if the supplied network is not null.

Method parameters in org.cytoscape.task with type arguments of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	NetworkCollectionTaskFactory.createTaskIterator(Collection<CyNetwork> networks) Provisions this factory with the collection of networks that will be passed into any task created by it.
boolean	NetworkCollectionTaskFactory.isReady(Collection<CyNetwork> networks) Returns true if this task factory is ready to produce a task iterator.
boolean	AbstractNetworkCollectionTaskFactory.isReady(Collection<CyNetwork> networks) Returns true if the supplied collection is not null.

Constructors in org.cytoscape.task with parameters of type CyNetwork

Constructor and Description
AbstractNetworkTask(CyNetwork network) Base class for tasks that need to operate on a CyNetwork

Constructor parameters in org.cytoscape.task with type arguments of type CyNetwork

Constructor and Description
AbstractNetworkCollectionTask(Collection<CyNetwork> networks) Base Constructor for a task that will operate on a collection of networks

Uses of CyNetwork in org.cytoscape.task.create

Methods in org.cytoscape.task.create with parameters of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	NewNetworkSelectedNodesOnlyTaskFactory.createTaskIterator(CyNetwork network) Returns a TaskIterator that creates a new network from the selected nodes in the given network.
TaskIterator	NewNetworkSelectedNodesAndEdgesTaskFactory.createTaskIterator(CyNetwork network) Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.
TaskIterator	CloneNetworkTaskFactory.createTaskIterator(CyNetwork network) Returns a TaskIterator that clones the given network.

Method parameters in org.cytoscape.task.create with type arguments of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	CreateNetworkViewTaskFactory.createTaskIterator(Collection<CyNetwork> networks, CyNetworkViewFactory factory) Use this method to create a network view for each of the passed networks.

Uses of CyNetwork in org.cytoscape.task.edit

Methods in org.cytoscape.task.edit with parameters of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	EditNetworkTitleTaskFactory.createTaskIterator(CyNetwork network, String title) Creates a task iterator for editing a network's title.

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

Modifier and Type	Method and 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	MapTableToNetworkTablesTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
TaskIterator	JoinTablesTaskTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, 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 CyNetwork in org.cytoscape.task.select

Methods in org.cytoscape.task.select with parameters of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	SelectFromFileListTaskFactory.createTaskIterator(CyNetwork network, File file) Creates a task iterator for selecting items of a network based on a file.

Uses of CyNetwork in org.cytoscape.task.write

Methods in org.cytoscape.task.write with parameters of type CyNetwork

Modifier and Type	Method and Description
TaskIterator	ExportNetworkTaskFactory.createTaskIterator(CyNetwork network, File file) Creates the task iterator for exporting networks.

Uses of CyNetwork in org.cytoscape.view.layout

Methods in org.cytoscape.view.layout with parameters of type CyNetwork

Modifier and Type	Method and Description
protected void	LayoutPartition.addNode(CyNetwork network, View<CyNode> nv, boolean locked) Add a node to this partition.

Uses of CyNetwork in org.cytoscape.view.model

Methods in org.cytoscape.view.model with parameters of type CyNetwork

Modifier and Type	Method and Description
CyNetworkView	CyNetworkViewFactory.createNetworkView(CyNetwork network) Create a CyNetworkView from a CyNetwork object.
Collection<CyNetworkView>	CyNetworkViewManager.getNetworkViews(CyNetwork network) Returns a collection of network views corresponding to the specified network, if found.
boolean	CyNetworkViewManager.viewExists(CyNetwork network) Determines whether a network view for the specified network is known to the network view manager.

Uses of CyNetwork in org.cytoscape.view.vizmap.gui

Methods in org.cytoscape.view.vizmap.gui that return types with arguments of type CyNetwork

Modifier and Type	Method and Description
RenderingEngine<CyNetwork>	DefaultViewPanel.getRenderingEngine() Deprecated.