Uses of Interface
org.cytoscape.model.CyNetwork
Package
Description
This package provides Cytoscape version number, application-wide setting,
basic access to current network, selected networks, views and rendering engines.
This package provides application events/listeners, including
Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/
setSelectedNetwork.
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.
Tunable classes useful for command applications
This package provides an API for creating and managing
groups in Cytoscape.
This package contains the various events and listeners
related to group management, creation, and destruction.
Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
This package provides factory interfaces to be used by anyone wishing to provide
export or writing capabilities to the rest of Cytoscape.
This package provides a mechanism for executing remote jobs from within Cytoscape.
This package has the core interfaces of network and
table data structures that are foundational to Cytoscape.
This package contains the event interfaces necessary for communicating
with the classes in org.cytoscape.model.
This package contains rootnetwork and subnetwork extensions to the
CyNetwork interface that provide a more complex meta-network
data model.
This package contains the interfaces and classes necessary to capturing,
storing, and retrieving the state of a Cytoscape session.
This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
This package provides a variety of task factory interfaces for creating
new instances of network and other objects.
This package include a set of task factory interfaces that allow
the modification or editing of various objects within Cytoscape.
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.
This package contains a set of task factory interfaces used for
exporting or writing a variety of Cytoscape objects to files.
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.
Module for View Models and Visual Properties.
This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
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Uses of CyNetwork in org.cytoscape.application
Modifier and TypeMethodDescriptionCyApplicationManager.getCurrentNetwork()
Provides access to the current network.Modifier and TypeMethodDescriptionCyApplicationManager.getCurrentRenderingEngine()
Returns the rendering engine associated with the current network view.NetworkViewRenderer.getRenderingEngineFactory(String contextId)
CyApplicationManager.getSelectedNetworks()
Returns the list of selected networks.Modifier and TypeMethodDescriptionvoid
CyApplicationManager.setCurrentNetwork(CyNetwork net)
Sets the current network to the specified network.Modifier and TypeMethodDescriptionvoid
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
Modifier and TypeMethodDescriptionSetCurrentNetworkEvent.getNetwork()
Returns the network associated with this event.Modifier and TypeMethodDescriptionSetSelectedNetworksEvent.getNetworks()
Returns the list of networks selected.SetCurrentRenderingEngineEvent.getRenderingEngine()
Return the rendering engine (presentation) that has been set as current.ModifierConstructorDescriptionSetCurrentNetworkEvent(CyApplicationManager source, CyNetwork net)
Constructor.ModifierConstructorDescriptionSetCurrentRenderingEngineEvent(CyApplicationManager source, RenderingEngine<CyNetwork> engine)
Constructor.SetSelectedNetworksEvent(CyApplicationManager source, List<CyNetwork> networks)
Constructor. -
Uses of CyNetwork in org.cytoscape.command
Modifier and TypeMethodDescriptionStringToModel.getNetwork(String strNet)
Convert a string request for a network into aCyNetwork
.Modifier and TypeMethodDescriptionStringToModel.getEdgeList(CyNetwork net, String edgelist)
Convert a string request for a edgelist into a list ofCyEdge
s.StringToModel.getNodeList(CyNetwork net, String nodelist)
Convert a string request for a nodelist into a list ofCyNode
s. -
Uses of CyNetwork in org.cytoscape.command.util
Modifier and TypeMethodDescriptionEdgeList.getNetwork()
Return the network used by this EdgeListNodeList.getNetwork()
Get the network for this nodelistModifier and TypeMethodDescriptionvoid
EdgeList.setNetwork(CyNetwork network)
Set the network to be used by this EdgeListvoid
NodeList.setNetwork(CyNetwork network)
Set the network for this nodelist -
Uses of CyNetwork in org.cytoscape.group
Modifier and TypeMethodDescriptionCyGroup.getGroupNetwork()
Returns the network referenced by this group.Modifier and TypeMethodDescriptionCyGroup.getNetworkSet()
Return the list ofCyNetwork
s this group is in.Modifier and TypeMethodDescriptionvoid
CyGroup.addGroupToNetwork(CyNetwork network)
Add a group to an additional network.void
Collapse this group in the designated network.CyGroupFactory.createGroup(CyNetwork network, boolean register)
Creates a CyGroup object in the referenced network.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.CyGroupFactory.createGroup(CyNetwork network, CyNode node, boolean register)
Creates a CyGroup object in the referenced network from an existingCyNode
.CyGroupFactory.createGroup(CyNetwork network, CyNode node, List<CyNode> nodes, List<CyEdge> edges, boolean register)
Creates a CyGroup object in the referenced network from an existingCyNode
.void
Expand this group in the designated network.Return the group the corresponds to a particular node in aCyNetwork
.CyGroupManager.getGroupSet(CyNetwork network)
Provides the set of all the groups known to the groups manager in a particular network.CyGroupManager.getGroupsForNode(CyNode node, CyNetwork network)
Return the list ofCyGroup
s 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
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
ModifierConstructorDescriptionGroupAboutToBeRemovedEvent(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
Modifier and TypeFieldDescriptionprotected CyNetwork[]
AbstractCyNetworkReader.networks
Array of networks to be returned.Modifier and TypeMethodDescriptionAbstractCyNetworkReader.getNetworks()
CyNetworkReader.getNetworks()
Returns an array of networks read after executing the run() method ofTask
.Modifier and TypeMethodDescriptionCyNetworkReader.buildCyNetworkView(CyNetwork network)
A method to build aCyNetworkView
from one of the networks just read. -
Uses of CyNetwork in org.cytoscape.io.write
Modifier and TypeMethodDescriptionCyNetworkViewWriterFactory.createWriter(OutputStream os, CyNetwork network)
Creates a single Task that will write the specified network to the specified OutputStream.CyNetworkViewWriterManager.getWriter(CyNetwork network, CyFileFilter filter, File file)
Returns theCyWriter
Task that will attempt to write the specified network to the specified file of the specified file type.CyNetworkViewWriterManager.getWriter(CyNetwork network, CyFileFilter filter, OutputStream os)
Returns theCyWriter
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
Modifier and TypeMethodDescriptiondefault CyNetwork
CyJobDataService.getNetworkData(CyJobData data, String key)
Optional method to extract network data from aCyJobData
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.Modifier and TypeMethodDescriptiondefault 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 aCyJobData
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
Modifier and TypeMethodDescriptionCyNetworkFactory.createNetwork()
Returns a new, emptyCyNetwork
object.CyNetworkFactory.createNetwork(SavePolicy policy)
Returns a new, emptyCyNetwork
object.CyNetworkFactory.createNetworkWithPrivateTables()
Returns a new, emptyCyNetwork
object where the associated default tables are private.CyNetworkFactory.createNetworkWithPrivateTables(SavePolicy policy)
Returns a new, emptyCyNetwork
object where the associated default tables are private.CyNetworkManager.getNetwork(long id)
Returns the network corresponding to the provided IDCyTableMetadata.getNetwork()
Returns all the networks associated with this object's table.CyNetworkTableManager.getNetworkForTable(CyTable table)
Returns the network this table is registered with.CyNode.getNetworkPointer()
Returns the network referenced by this node.Modifier and TypeMethodDescriptionCyNetworkManager.getNetworkSet()
Provides the set of all the networks known to the network manager.CyNetworkTableManager.getNetworkSet()
Returns a read-only set of all networks managed by this instance.Modifier and TypeMethodDescriptionvoid
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.CyTableUtil.getEdgesInState(CyNetwork net, String columnName, boolean state)
A utility method that returns a list of edges that have a boolean attribute in theDEFAULT_ATTRS
namespace specified by columnName and are in the specified state.CyTableUtil.getNodesInState(CyNetwork net, String columnName, boolean state)
A utility method that returns a list of nodes that have a boolean attribute in theDEFAULT_ATTRS
namespace specified by columnName and are in the specified state.CyTableUtil.getSelectedEdges(CyNetwork network)
Equivalent toCyTableUtil.getSelectedNodes(CyNetwork network)
Equivalent toCyNetworkTableManager.getTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace)
Returns the table with the specified namespace and type from the network.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
Modifier and TypeMethodDescriptionSelectedNodesAndEdgesEvent.getNetwork()
Returns the CyNetwork event source.ModifierConstructorDescriptionAboutToRemoveEdgesEvent(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.SelectedNodesAndEdgesEvent(CyNetwork source, boolean isCurrentNetwork, boolean nodesChanged, boolean edgesChanged)
SetNetworkPointerEvent(CyNode node, CyNetwork network)
Constructs event.UnsetNetworkPointerEvent(CyNode node, CyNetwork network)
Constructs event. -
Uses of CyNetwork in org.cytoscape.model.subnetwork
Modifier and TypeInterfaceDescriptioninterface
CyRootNetwork is an interface for managing Cytoscape's meta-network implementation.interface
Modifier and TypeMethodDescriptionboolean
CyRootNetwork.containsNetwork(CyNetwork n)
Returns true if the network to be checked is a subnetwork of this root network and returns false otherwise.CyRootNetworkManager.getRootNetwork(CyNetwork n)
Converts a CyNetwork to a CyRootNetwork -
Uses of CyNetwork in org.cytoscape.session
Modifier and TypeMethodDescriptionCySession.getNetworks()
Returns a set of all CyNetwork objects contained in this Session.Modifier and TypeMethodDescriptionCyNetworkNaming.getSuggestedSubnetworkTitle(CyNetwork parentNetwork)
Generates a unique title for a subnetwork based on a parent network.Modifier and TypeMethodDescriptionReturns an instance of Builder that has at least been configured with the specified networks. -
Uses of CyNetwork in org.cytoscape.task
Modifier and TypeFieldDescriptionprotected CyNetwork
AbstractNetworkTask.network
The network that descendants of this class will operate on.Modifier and TypeFieldDescriptionprotected Collection<CyNetwork>
AbstractNetworkCollectionTask.networks
The collection of networks that descendants will operate on.Modifier and TypeMethodDescriptionNetworkTaskFactory.createTaskIterator(CyNetwork network)
Provisions this factory with theCyNetwork
that will be passed into any task created by it.default boolean
If this task factory implements theTogglable
interface then this method determines if the button or check box is on or off.boolean
Returns true if the supplied network is not null.boolean
Returns true if this task factory is ready to produce a TaskIterator.Modifier and TypeMethodDescriptionNetworkCollectionTaskFactory.createTaskIterator(Collection<CyNetwork> networks)
Provisions this factory with the collection of networks that will be passed into any task created by it.default boolean
NetworkCollectionTaskFactory.isOn(Collection<CyNetwork> networks)
If this task factory implements theTogglable
interface then this method determines if the button or check box is on or off.boolean
AbstractNetworkCollectionTaskFactory.isReady(Collection<CyNetwork> networks)
Returns true if the supplied collection is not null.boolean
NetworkCollectionTaskFactory.isReady(Collection<CyNetwork> networks)
Returns true if this task factory is ready to produce a task iterator.ModifierConstructorDescriptionAbstractNetworkTask(CyNetwork network)
Base class for tasks that need to operate on aCyNetwork
ModifierConstructorDescriptionAbstractNetworkCollectionTask(Collection<CyNetwork> networks)
Base Constructor for a task that will operate on a collection of networks -
Uses of CyNetwork in org.cytoscape.task.create
Modifier and TypeMethodDescriptionCloneNetworkTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that clones the given network.NewNetworkSelectedNodesAndEdgesTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.NewNetworkSelectedNodesOnlyTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that creates a new network from the selected nodes in the given network.Modifier and TypeMethodDescriptionCreateNetworkViewTaskFactory.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
Modifier and TypeMethodDescriptionEditNetworkTitleTaskFactory.createTaskIterator(CyNetwork network, String title)
Creates a task iterator for editing a network's title.Modifier and TypeMethodDescriptionImportDataTableTaskFactory.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.JoinTablesTaskTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
MapTableToNetworkTablesTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
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Uses of CyNetwork in org.cytoscape.task.select
Modifier and TypeMethodDescriptionSelectFromFileListTaskFactory.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
Modifier and TypeMethodDescriptionExportNetworkTaskFactory.createTaskIterator(CyNetwork network, File file)
Creates the task iterator for exporting networks. -
Uses of CyNetwork in org.cytoscape.util.json
Modifier and TypeMethodDescriptionReturns a JSON representation of a network and its relevant data.Returns a JSON representation of a single CyEdge and its relevant data.Returns a JSON representation of a single CyNode and its relevant data. -
Uses of CyNetwork in org.cytoscape.view.layout
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Uses of CyNetwork in org.cytoscape.view.model
Modifier and TypeMethodDescriptionCyNetworkViewFactory.createNetworkView(CyNetwork network)
Create aCyNetworkView
from aCyNetwork
object.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