Uses of Interface
org.cytoscape.model.CyNode
Package
Description
This package provides application events/listeners, including
Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/
setSelectedNetwork.
This package defines the various interfaces, abstract classes, and enums
that represent the Cytoscape Swing Application API.
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 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 provides base classes for common task factory types as well as their associated task types found in Cytoscape.
This package includes a set of task factory interfaces showing and hiding
nodes and edges within network views.
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.
Definitions for View-Model related events and their listeners.
This package provides support for graphical annotations associated with a Cytoscape
CyNetworkView
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Uses of CyNode in org.cytoscape.application.events
Modifier and TypeMethodDescriptionSetCurrentNetworkEvent.getSelectedNodes()
SetCurrentNetworkEvent.getUnselectedNodes()
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Uses of CyNode in org.cytoscape.application.swing
Modifier and TypeMethodDescriptionCyNodeViewContextMenuFactory.createMenuItem
(CyNetworkView netView, View<CyNode> nodeView) This method should return a CyMenuItem to be added to the context menu of the specified node view. -
Uses of CyNode in org.cytoscape.command
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Uses of CyNode in org.cytoscape.command.util
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Uses of CyNode in org.cytoscape.group
Modifier and TypeMethodDescriptionCyGroup.getGroupNode()
Return theCyNode
that represents this group in the network.Modifier and TypeMethodDescriptionCyGroup.getNodeList()
Returns the list of nodes contained within this group.Modifier and TypeMethodDescriptionCyGroupFactory.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
.Return the group the corresponds to a particular node in aCyNetwork
.CyGroupManager.getGroupsForNode
(CyNode node) Return the list ofCyGroup
s this node is in.CyGroupManager.getGroupsForNode
(CyNode node, CyNetwork network) Return the list ofCyGroup
s this node is in for a particular network.boolean
Modifier and TypeMethodDescriptionvoid
Add a list of nodes and their edgesCyGroupFactory.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, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network from an existingCyNode
.void
CyGroup.removeNodes
(List<CyNode> nodes) Remove a set of nodes and their edges from a group -
Uses of CyNode in org.cytoscape.group.events
ModifierConstructorDescriptionGroupNodesAddedEvent
(CyGroup source, CyNode node) Constructs event.GroupNodesRemovedEvent
(CyGroup source, CyNode node) Constructs event.ModifierConstructorDescriptionGroupNodesAddedEvent
(CyGroup source, List<CyNode> nodes) Constructs event.GroupNodesRemovedEvent
(CyGroup source, List<CyNode> nodes) Constructs event. -
Uses of CyNode in org.cytoscape.io.read
Modifier and TypeMethodDescriptionAbstractCyNetworkReader.getNodeMap()
Returns map from key value to existing CyNode. -
Uses of CyNode in org.cytoscape.model
Modifier and TypeMethodDescriptionCyNetwork.addNode()
This method is used to create and add a node to this network.CyNetwork.getNode
(long suid) Return the CyNode that has the SUID.CyEdge.getSource()
Returns the source node determining this edge.CyEdge.getTarget()
Returns the target node determining this edge.Modifier and TypeMethodDescriptionCyNetwork.getNeighborList
(CyNode node, CyEdge.Type edgeType) Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.CyNetwork.getNodeList()
Return a list of the nodes in this network.CyTableUtil.getNodesInState
(CyNetwork net, String columnName, boolean state) A utility method that returns a list of nodes that have a boolean attribute in theCyNetwork.DEFAULT_ATTRS
namespace specified by columnName and are in the specified state.CyTableUtil.getSelectedNodes
(CyNetwork network) Equivalent toModifier and TypeMethodDescriptionThis method is used to create and add an edge to this network.boolean
CyNetwork.containsEdge
(CyNode from, CyNode to) Determine if this CyNetwork contains an edge between two nodes.boolean
CyNetwork.containsNode
(CyNode node) Determine if this CyNetwork contains a particular node.CyNetwork.getAdjacentEdgeIterable
(CyNode node, CyEdge.Type edgeType) Gets an Iteable of edges that connect to this node.CyNetwork.getAdjacentEdgeList
(CyNode node, CyEdge.Type edgeType) Get the list of edges that connect to this node.CyNetwork.getConnectingEdgeList
(CyNode source, CyNode target, CyEdge.Type edgeType) Get the list of edges that connect two nodes.CyNetwork.getNeighborList
(CyNode node, CyEdge.Type edgeType) Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.Modifier and TypeMethodDescriptionboolean
CyNetwork.removeNodes
(Collection<CyNode> node) Remove a node from the network and delete the node (if it only exists in this network). -
Uses of CyNode in org.cytoscape.model.events
Modifier and TypeMethodDescriptionAboutToRemoveNodesEvent.getNodes()
Returns the collection of nodes about to be removed.SelectedNodesAndEdgesEvent.getSelectedNodes()
Returns all the nodes in the network that are currently selected.SelectedNodesAndEdgesEvent.getUnselectedNodes()
Returns all the nodes in the network that are currently unselected.ModifierConstructorDescriptionSetNetworkPointerEvent
(CyNode node, CyNetwork network) Constructs event.UnsetNetworkPointerEvent
(CyNode node, CyNetwork network) Constructs event.ModifierConstructorDescriptionAboutToRemoveNodesEvent
(CyNetwork source, Collection<CyNode> nodes) Constructs event.AddedNodesEvent
(CyNetwork source, Collection<CyNode> nodes) Constructs event. -
Uses of CyNode in org.cytoscape.model.subnetwork
Modifier and TypeMethodDescriptionCySubNetwork.addNode()
A shortcut method that Creates a newCyNode
in both this subnetwork AND in theCyRootNetwork
.Modifier and TypeMethodDescriptionA shortcut method that Creates a newCyEdge
in both this subnetwork AND in theCyRootNetwork
.boolean
Adds a node to thisCySubNetwork
.void
CyRootNetwork.restoreNode
(CyNode node) Causes the given node to (temporarily) remain in the root network even if it has already been removed from all subnetworks.Modifier and TypeMethodDescriptionCyRootNetwork.addSubNetwork
(Iterable<CyNode> nodes, Iterable<CyEdge> edges) CyRootNetwork.addSubNetwork
(Iterable<CyNode> nodes, Iterable<CyEdge> edges, SavePolicy policy) boolean
CySubNetwork.removeNodes
(Collection<CyNode> node) Removes a node from thisCySubNetwork
but not from theCyRootNetwork
. -
Uses of CyNode in org.cytoscape.task
Modifier and TypeFieldDescriptionAbstractNodeViewTask.nodeView
The node view that descendants of this class will operate on.Modifier and TypeMethodDescriptionNodeViewTaskFactory.createTaskIterator
(View<CyNode> nodeView, CyNetworkView networkView) Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.default boolean
NodeViewTaskFactory.isOn
(View<CyNode> nodeView, CyNetworkView networkView) If this task factory implements theTogglable
interface then this method determines if the button or check box is on or off.boolean
AbstractNodeViewTaskFactory.isReady
(View<CyNode> nodeView, CyNetworkView networkView) Returns true of the supplied network and node views are not null.boolean
NodeViewTaskFactory.isReady
(View<CyNode> nodeView, CyNetworkView networkView) Returns true if the node view and network view are in a state that is ready to be processed by the generated tasks and false otherwise.ModifierConstructorDescriptionAbstractNodeViewTask
(View<CyNode> nodeView, CyNetworkView netView) Base class constructor for all tasks that need to operate on a node view and possibly its associated network view. -
Uses of CyNode in org.cytoscape.task.hide
Modifier and TypeMethodDescriptionHideTaskFactory.createTaskIterator
(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges) Creates a task iterator that will hide the given nodes and edges.UnHideTaskFactory.createTaskIterator
(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges) Creates a task iterator that will show the given nodes and edges. -
Uses of CyNode in org.cytoscape.util.json
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Uses of CyNode in org.cytoscape.view.layout
Modifier and TypeFieldDescriptionCyLayoutAlgorithm.ALL_NODE_VIEWS
A convenience declaration for an empty set signifying that all node views should be laid out when creating the task iterator.AbstractLayoutTask.nodesToLayOut
The node views that will be laid out by the algorithm.Modifier and TypeMethodDescriptionLayoutNode.getNode()
Accessor function to return the Node associated with this LayoutNode.Modifier and TypeMethodDescriptionLayoutNode.getNodeView()
Accessor function to return the Viewassociated with this LayoutNode. Modifier and TypeMethodDescriptionprotected void
Add a node to this partition.CyLayoutAlgorithm.createTaskIterator
(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute) Creates a task iterator containing the layout tasks.boolean
AbstractLayoutAlgorithm.isReady
(CyNetworkView view, Object tunableContext, Set<View<CyNode>> nodesToLayout, String attributeName) boolean
CyLayoutAlgorithm.isReady
(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute) Returns true if the task factory is ready to produce a task iterator.static List<LayoutPartition>
PartitionUtil.partition
(CyNetworkView networkView, Collection<CyNode> nodeSet, EdgeWeighter edgeWeighter) Partition the graph -- this builds the LayoutEdge and LayoutNode arrays as a byproduct.ModifierConstructorDescriptionAbstractLayoutTask
(String displayName, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo) Constructor.AbstractParallelPartitionLayoutTask
(String displayName, boolean singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo) Creates a new AbstractPartitionLayoutTask object.AbstractPartitionLayoutTask
(String displayName, boolean singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo) Creates a new AbstractPartitionLayoutTask object.LayoutNode
(View<CyNode> nodeView, int index, CyRow row) The main constructor for a LayoutNode.LayoutPartition
(CyNetworkView networkView, Collection<View<CyNode>> nodeSet, EdgeWeighter edgeWeighter) LayoutPartition: use this constructor to create a LayoutPartition that includes the entire network. -
Uses of CyNode in org.cytoscape.view.model
Modifier and TypeMethodDescriptionCyNetworkViewSnapshot.getMutableNodeView
(long suid) Returns the mutable node View for the given view SUID, or null if the node view no longer exists in the mutable network view.CyNetworkView.getNodeView
(CyNode node) Returns a View for a specified Node.CyNetworkViewSnapshot.getNodeView
(long suid) Returns the immutable node View for the given view SUID.CyNetworkView.getNodeViews()
Returns a list of Views for all CyNodes in the network.CyNetworkView.getNodeViewsIterable()
Returns an Iterable for all node views in the network.SnapshotEdgeInfo.getSourceNodeView()
Returns the source node view;SnapshotEdgeInfo.getTargetNodeView()
Returns the target node view;CyNetworkViewSnapshot.getTrackedNodes
(Object key) Returns nodes that were configured to have their VisualProperties tracked usingCyNetworkViewFactoryConfig.addTrackedVisualProperty(Object, VisualProperty, java.util.function.Predicate)
and pass the predicate.Modifier and TypeMethodDescriptionCyNetworkView.getNodeView
(CyNode node) Returns a View for a specified Node.Modifier and TypeMethodDescriptionCyNetworkViewSnapshot.getAdjacentEdgeIterable
(View<CyNode> node) Returns an Iterable that contains the edges that are adjacent (connected) to the given node.CyNetworkViewSnapshot.getNodeInfo
(View<CyNode> node) Returns an object that provides more information about the given node. -
Uses of CyNode in org.cytoscape.view.model.events
Modifier and TypeMethodDescriptionAddedNodeViewsEvent.getNodeViews()
Returns new node view object.ModifierConstructorDescriptionAboutToRemoveNodeViewsEvent
(CyNetworkView source, Collection<View<CyNode>> payload) Creates the event for about to be removed node views.AddedNodeViewsEvent
(CyNetworkView source, Collection<View<CyNode>> nodeViews) Creates the event for a new node view. -
Uses of CyNode in org.cytoscape.view.model.spacial
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Uses of CyNode in org.cytoscape.view.presentation.annotations
ArrowAnnotation.setTarget(View)
instead.