Uses of Interface
org.cytoscape.model.CyNetwork
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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 applicationsorg.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.util.json 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. -
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Uses of CyNetwork in org.cytoscape.application
Methods in org.cytoscape.application that return CyNetwork Modifier and Type Method 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 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 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 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 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 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 Description SetCurrentNetworkEvent(CyApplicationManager source, CyNetwork net)
Constructor.Constructor parameters in org.cytoscape.application.events with type arguments of type CyNetwork Constructor 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 Description CyNetwork
StringToModel. getNetwork(String strNet)
Convert a string request for a network into aCyNetwork
.Methods in org.cytoscape.command with parameters of type CyNetwork Modifier and Type Method Description List<CyEdge>
StringToModel. getEdgeList(CyNetwork net, String edgelist)
Convert a string request for a edgelist into a list ofCyEdge
s.List<CyNode>
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
Methods in org.cytoscape.command.util that return CyNetwork Modifier and Type Method Description CyNetwork
EdgeList. getNetwork()
Return the network used by this EdgeListCyNetwork
NodeList. getNetwork()
Get the network for this nodelistMethods in org.cytoscape.command.util with parameters of type CyNetwork Modifier and Type Method Description void
EdgeList. setNetwork(CyNetwork network)
Set the network to be used by this EdgeListvoid
NodeList. setNetwork(CyNetwork network)
Set the network for this nodelistConstructors in org.cytoscape.command.util with parameters of type CyNetwork Constructor 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 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 Description Set<CyNetwork>
CyGroup. getNetworkSet()
Return the list ofCyNetwork
s this group is in.Methods in org.cytoscape.group with parameters of type CyNetwork Modifier and Type Method 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, List<CyNode> nodes, List<CyEdge> edges, boolean register)
Creates a CyGroup object in the referenced network initially populated with the supplied nodes.CyGroup
CyGroupFactory. createGroup(CyNetwork network, CyNode node, boolean register)
Creates a CyGroup object in the referenced network from an existingCyNode
.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 existingCyNode
.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 aCyNetwork
.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 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
CyGroupManager. isGroup(CyNode node, CyNetwork network)
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 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 Description protected CyNetwork[]
AbstractCyNetworkReader. networks
Array of networks to be returned.Methods in org.cytoscape.io.read that return CyNetwork Modifier and Type Method Description CyNetwork[]
AbstractCyNetworkReader. getNetworks()
CyNetwork[]
CyNetworkReader. getNetworks()
Returns an array of networks read after executing the run() method ofTask
.Methods in org.cytoscape.io.read with parameters of type CyNetwork Modifier and Type Method Description CyNetworkView
CyNetworkReader. buildCyNetworkView(CyNetwork network)
A method to build aCyNetworkView
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 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 theCyWriter
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 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
Methods in org.cytoscape.jobs that return CyNetwork Modifier and Type Method Description default 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.Methods in org.cytoscape.jobs with parameters of type CyNetwork 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 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
Methods in org.cytoscape.model that return CyNetwork Modifier and Type Method Description CyNetwork
CyNetworkFactory. createNetwork()
Returns a new, emptyCyNetwork
object.CyNetwork
CyNetworkFactory. createNetwork(SavePolicy policy)
Returns a new, emptyCyNetwork
object.CyNetwork
CyNetworkFactory. createNetworkWithPrivateTables()
Returns a new, emptyCyNetwork
object where the associated default tables are private.CyNetwork
CyNetworkFactory. createNetworkWithPrivateTables(SavePolicy policy)
Returns a new, emptyCyNetwork
object where the associated default tables are private.CyNetwork
CyNetworkManager. getNetwork(long id)
Returns the network corresponding to the provided IDCyNetwork
CyTableMetadata. getNetwork()
Returns all the networks associated with this object's table.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 Description Set<CyNetwork>
CyNetworkManager. getNetworkSet()
Provides the set of all the networks known to the network manager.Set<CyNetwork>
CyNetworkTableManager. getNetworkSet()
Returns a read-only set of all networks managed by this instance.Methods in org.cytoscape.model with parameters of type CyNetwork Modifier and Type Method 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 theDEFAULT_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 theDEFAULT_ATTRS
namespace specified by columnName and are in the specified state.static List<CyEdge>
CyTableUtil. getSelectedEdges(CyNetwork network)
Equivalent tostatic List<CyNode>
CyTableUtil. getSelectedNodes(CyNetwork network)
Equivalent toCyTable
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
Methods in org.cytoscape.model.events that return CyNetwork Modifier and Type Method Description CyNetwork
SelectedNodesAndEdgesEvent. getNetwork()
Returns the CyNetwork event source.Constructors in org.cytoscape.model.events with parameters of type CyNetwork Constructor 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.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
Subinterfaces of CyNetwork 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
Methods in org.cytoscape.model.subnetwork with parameters of type CyNetwork Modifier and Type Method 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 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 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 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 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 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 Description TaskIterator
NetworkTaskFactory. createTaskIterator(CyNetwork network)
Provisions this factory with theCyNetwork
that will be passed into any task created by it.boolean
AbstractNetworkTaskFactory. isReady(CyNetwork network)
Returns true if the supplied network is not null.boolean
NetworkTaskFactory. isReady(CyNetwork network)
Returns true if this task factory is ready to produce a TaskIterator.Method parameters in org.cytoscape.task with type arguments of type CyNetwork Modifier and Type Method 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
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.Constructors in org.cytoscape.task with parameters of type CyNetwork Constructor Description AbstractNetworkTask(CyNetwork network)
Base class for tasks that need to operate on aCyNetwork
Constructor parameters in org.cytoscape.task with type arguments of type CyNetwork Constructor 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 Description TaskIterator
CloneNetworkTaskFactory. createTaskIterator(CyNetwork network)
Returns a TaskIterator that clones 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
NewNetworkSelectedNodesOnlyTaskFactory. createTaskIterator(CyNetwork network)
Returns a TaskIterator that creates a new network from the selected nodes in the given network.Method parameters in org.cytoscape.task.create with type arguments of type CyNetwork Modifier and Type Method 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 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 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)
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Uses of CyNetwork in org.cytoscape.task.select
Methods in org.cytoscape.task.select with parameters of type CyNetwork Modifier and Type Method 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 Description TaskIterator
ExportNetworkTaskFactory. createTaskIterator(CyNetwork network, File file)
Creates the task iterator for exporting networks. -
Uses of CyNetwork in org.cytoscape.util.json
Methods in org.cytoscape.util.json with parameters of type CyNetwork Modifier and Type Method Description String
CyJSONUtil. toJson(CyNetwork cyNetwork)
Returns a JSON representation of a network and its relevant data.String
CyJSONUtil. toJson(CyNetwork network, CyEdge cyEdge, CyColumn... columns)
Returns a JSON representation of a single CyEdge and its relevant data.String
CyJSONUtil. toJson(CyNetwork network, CyNode cyNode, CyColumn... columns)
Returns a JSON representation of a single CyNode and its relevant data. -
Uses of CyNetwork in org.cytoscape.view.layout
Methods in org.cytoscape.view.layout with parameters of type CyNetwork Modifier and Type Method 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 Description CyNetworkView
CyNetworkViewFactory. createNetworkView(CyNetwork network)
Create aCyNetworkView
from aCyNetwork
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 Description RenderingEngine<CyNetwork>
DefaultViewPanel. getRenderingEngine()
Deprecated.
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