Uses of Interface
cytoscape.CyNetwork

Packages that use CyNetwork

cytoscape	Core Cytoscape Classes.
cytoscape.actions	UI classes that are attached to menu items in the menu or tool bar of the window.
cytoscape.data	Basic data classes used by Cytoscape.
cytoscape.data.ontology
cytoscape.data.ontology.readers
cytoscape.data.readers	Reader classes for the basic data types in cytoscape.data.
cytoscape.data.writers
cytoscape.dialogs	UI classes for performing some action, generally more complicated than those contained in the cytoscape.actions package.
cytoscape.ding
cytoscape.giny
cytoscape.groups
cytoscape.layout	Classes providing some kind of graph layout functionality.
cytoscape.plugin	Classes related to Cytoscape plugins.
cytoscape.util	This package contains utility classes which are deemed generally useful, but which do not clearly belong to any other package.
cytoscape.util.swing
cytoscape.view	Classes that provide a window to display a graph and UI components connected to that window, such as the menus.
cytoscape.visual	Framework for generalized mappings from graph attributes to visual attributes.
cytoscape.visual.calculators	Objects that calculate from the data attributes the value for one visual attribute, such as color, shape, or size.
cytoscape.visual.mappings	The Mappings are used by Calculators to map graph attributes to visual attribute values.

Uses of CyNetwork in cytoscape

Fields in cytoscape declared as CyNetwork

protected static CyNetwork

Cytoscape.nullNetwork A null CyNetwork to give when there is no Current Network

Fields in cytoscape with type parameters of type CyNetwork

protected static Map<String,CyNetwork>	Cytoscape.networkMap
protected static LinkedList<CyNetwork>	Cytoscape.selectedNetworks The list analog to the currentNetworkID

Methods in cytoscape that return CyNetwork

static CyNetwork	Cytoscape.createNetwork(Collection nodes, Collection edges, String title) Creates a new Network.
static CyNetwork	Cytoscape.createNetwork(Collection nodes, Collection edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(Collection nodes, Collection edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(GraphReader reader, boolean create_view, CyNetwork parent) Creates a cytoscape.data.CyNetwork from a reader.
static CyNetwork	Cytoscape.createNetwork(int[] nodes, int[] edges, String title) Creates a new Network.
static CyNetwork	Cytoscape.createNetwork(int[] nodes, int[] edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(int[] nodes, int[] edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork
static CyNetwork	Cytoscape.createNetwork(String title) Creates a new, empty Network.
static CyNetwork	Cytoscape.createNetwork(String title, boolean create_view) Creates a new, empty Network.
static CyNetwork	Cytoscape.createNetwork(String title, CyNetwork parent, boolean create_view) Creates a new, empty Network.
static CyNetwork	Cytoscape.createNetworkFromFile(String location) Creates a CyNetwork from a file.
static CyNetwork	Cytoscape.createNetworkFromFile(String loc, boolean create_view) Creates a CyNetwork from a file.
static CyNetwork	Cytoscape.createNetworkFromURL(URL url, boolean create_view) Creates a CyNetwork from a URL.
static CyNetwork	Cytoscape.getCurrentNetwork() Return the Network that currently has the Focus.
CyNetwork	CyNetworkEvent.getNetwork() DOCUMENT ME!
static CyNetwork	Cytoscape.getNetwork(String id)
static CyNetwork	Cytoscape.getNullNetwork()

Methods in cytoscape that return types with arguments of type CyNetwork

protected static Map<String,CyNetwork>	Cytoscape.getNetworkMap() This Map has keys that are Strings ( network_ids ) and values that are networks.
static Set<CyNetwork>	Cytoscape.getNetworkSet() Return a List of all available CyNetworks
static List<CyNetwork>	Cytoscape.getSelectedNetworks() Returns the list of selected networks.

Methods in cytoscape with parameters of type CyNetwork

static void	Cytoscape.addNetwork(CyNetwork network, String title, CyNetwork parent, boolean create_view) Add a network to Cytoscape's internal list of networks.
void	CyNetwork.appendNetwork(CyNetwork network) Appends all of the nodes and edges in the given Network to this Network
static CyNetwork	Cytoscape.createNetwork(Collection nodes, Collection edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(Collection nodes, Collection edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(GraphReader reader, boolean create_view, CyNetwork parent) Creates a cytoscape.data.CyNetwork from a reader.
static CyNetwork	Cytoscape.createNetwork(int[] nodes, int[] edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	Cytoscape.createNetwork(int[] nodes, int[] edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork
static CyNetwork	Cytoscape.createNetwork(String title, CyNetwork parent, boolean create_view) Creates a new, empty Network.
static CyNetworkView	Cytoscape.createNetworkView(CyNetwork network) Creates a CyNetworkView, but doesn't do anything with it.
static CyNetworkView	Cytoscape.createNetworkView(CyNetwork network, String title) Creates a CyNetworkView, but doesn't do anything with it.
static CyNetworkView	Cytoscape.createNetworkView(CyNetwork network, String title, CyLayoutAlgorithm layout) Creates a CyNetworkView, but doesn't do anything with it.
static CyNetworkView	Cytoscape.createNetworkView(CyNetwork network, String title, CyLayoutAlgorithm layout, VisualStyle vs) Creates a CyNetworkView that is placed placed in a given visual style and rendered with a given layout algorithm.
static void	Cytoscape.destroyNetwork(CyNetwork network) destroys the given network
static void	Cytoscape.destroyNetwork(CyNetwork network, boolean destroy_unique) destroys the given network
static void	Cytoscape.destroyNetworkView(CyNetwork network) destroys the networkview, including any layout information
static boolean	CytoscapeModifiedNetworkManager.isModified(CyNetwork net)
static void	CytoscapeModifiedNetworkManager.setModified(CyNetwork net, String state) set the state of the network

Constructors in cytoscape with parameters of type CyNetwork

CyNetworkEvent(CyNetwork source, int type)
Creates a new CyNetworkEvent object.

Uses of CyNetwork in cytoscape.actions

Methods in cytoscape.actions with parameters of type CyNetwork

static void

CreateNetworkViewAction.createViewFromCurrentNetwork(CyNetwork cyNetwork) DOCUMENT ME!

Uses of CyNetwork in cytoscape.data

Methods in cytoscape.data with parameters of type CyNetwork

static void	Semantics.applyNamingServices(CyNetwork network) Deprecated.
static boolean	Semantics.areSynonyms(String firstName, String secondName, CyNetwork network) Deprecated.
static void	Semantics.assignCommonNames(CyNetwork network, BioDataServer bioDataServer) Deprecated.
static void	Semantics.assignSpecies(CyNetwork network) Deprecated.
static List	Semantics.getAllSynonyms(String name, CyNetwork network) Deprecated.
static String	Semantics.getInteractionType(CyNetwork network, Edge edge) Returns the interaction type of the given edge.
static String[]	Semantics.getInteractionTypes(CyNetwork network) Returns an array containing all of the unique interaction types present in the network.
static Set	Semantics.getSpeciesInNetwork(CyNetwork network) Deprecated.
static boolean	CyNetworkUtilities.saveSelectedNodeNames(CyNetworkView networkView, CyNetwork network, String filename) Saves all selected nodes in the current view to a file with the given name.
static boolean	CyNetworkUtilities.saveVisibleNodeNames(CyNetwork network, String filename) Saves all nodes in the given network to a file with the given name.
static boolean	CyNetworkUtilities.selectNodesStartingWith(CyNetwork network, String key, CyNetworkView networkView) Selects every node in the current view whose canonical name, label, or any known synonym starts with the string specified by the second argument.

Uses of CyNetwork in cytoscape.data.ontology

Constructors in cytoscape.data.ontology with parameters of type CyNetwork

GeneOntology(String name, String curator, String description, CyNetwork dag)

Ontology(String name, String curator, String description, CyNetwork dag)
Constructor.

Uses of CyNetwork in cytoscape.data.ontology.readers

Methods in cytoscape.data.ontology.readers that return CyNetwork

CyNetwork	OntologyReader.getDag() DOCUMENT ME!
CyNetwork	OBOFlatFileReader.getDag() DOCUMENT ME!

Uses of CyNetwork in cytoscape.data.readers

Methods in cytoscape.data.readers that return types with arguments of type CyNetwork

List<CyNetwork>	NestedNetworkReader.getNetworks() Returns all networks, whether nested or not.
List<CyNetwork>	NNFReader.getNetworks() Returns root network.
protected List<CyNetwork>	NNFParser.getNetworks()

Methods in cytoscape.data.readers with parameters of type CyNetwork

void	XGMMLReader.doPostProcessing(CyNetwork network) This method does all of our postprocessing after reading and parsing the file
void	InteractionsReader.doPostProcessing(CyNetwork net)
void	GraphReader.doPostProcessing(CyNetwork network) Execute whatever post-processing is required.
void	GMLReader.doPostProcessing(CyNetwork net) DOCUMENT ME!
void	AbstractGraphReader.doPostProcessing(CyNetwork network) Executes post-processing: no-op.
void	GMLWriter.writeGML(CyNetwork network, CyNetworkView view, List oldList) Given an object tree given in oldList, update it with the information provided in network and optional view (if view is not null).

Constructors in cytoscape.data.readers with parameters of type CyNetwork

MetadataParser(CyNetwork network)
Constructor.

MetadataParser(CyNetwork network, String metadataLabel)
Constructor.

Uses of CyNetwork in cytoscape.data.writers

Methods in cytoscape.data.writers with parameters of type CyNetwork

static String	InteractionWriter.getInteractionString(CyNetwork network) Returns a SIF formatted string of the specified network.
static String	InteractionWriter.getInteractionString(CyNetwork network, TaskMonitor taskMonitor) Returns a SIF formatted string of the specified network.
static void	InteractionWriter.writeInteractions(CyNetwork network, Writer writer) Writes a SIF formatted string of the specified network to the specified writer.
static void	InteractionWriter.writeInteractions(CyNetwork network, Writer writer, TaskMonitor taskMonitor) Writes a SIF formatted string of the specified network to the specified writer.

Constructors in cytoscape.data.writers with parameters of type CyNetwork

XGMMLWriter(CyNetwork network, CyNetworkView view)
Constructor.
Initialize data objects to be saved in XGMML file.

XGMMLWriter(CyNetwork network, CyNetworkView view, boolean noCytoscapeGraphics)
Constructor.
Initialize data objects to be saved in XGMML file.

Uses of CyNetwork in cytoscape.dialogs

Methods in cytoscape.dialogs that return CyNetwork

CyNetwork

SetNestedNetworkDialog.getSelectedNetwork()

Constructors in cytoscape.dialogs with parameters of type CyNetwork

NetworkMetaDataDialog(Frame parent, boolean modal, CyNetwork network)
Creates new form MetadataDialog

NetworkMetaDataTableModel(CyNetwork network)
Constructor for the network metadata table model.

Uses of CyNetwork in cytoscape.ding

Methods in cytoscape.ding that return CyNetwork

CyNetwork

DingNetworkView.getNetwork() DOCUMENT ME!

Constructors in cytoscape.ding with parameters of type CyNetwork

DingNetworkView(CyNetwork network, String title)
Creates a new DingNetworkView object.

Uses of CyNetwork in cytoscape.giny

Classes in cytoscape.giny that implement CyNetwork

class

FingCyNetwork FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the functionality formally provided by GraphObjAttributes.

Methods in cytoscape.giny that return CyNetwork

CyNetwork	CytoscapeRootGraph.createNetwork(Collection nodes, Collection edges) DOCUMENT ME!
CyNetwork	CytoscapeFingRootGraph.createNetwork(Collection nodes, Collection edges) DOCUMENT ME!
CyNetwork	CytoscapeRootGraph.createNetwork(int[] node_indices, int[] edge_indices) Uses Code copied from ColtRootGraph to create a new Network.
CyNetwork	CytoscapeFingRootGraph.createNetwork(int[] nodeInx, int[] edgeInx) Uses Code copied from ColtRootGraph to create a new Network.
CyNetwork	CytoscapeRootGraph.createNetwork(Node[] nodes, Edge[] edges) Uses Code copied from ColtRootGraph to create a new CyNetwork.
CyNetwork	CytoscapeFingRootGraph.createNetwork(Node[] nodes, Edge[] edges) Creates a new Network

Methods in cytoscape.giny with parameters of type CyNetwork

void	FingCyNetwork.appendNetwork(CyNetwork network) Appends all of the nodes and edges in teh given Network to this Network

Uses of CyNetwork in cytoscape.groups

Methods in cytoscape.groups that return CyNetwork

CyNetwork	CyGroupImpl.getGraphPerspective() Return a CyNetwork that represents the internal components of this group
CyNetwork	CyGroup.getGraphPerspective() Get the graph (network) that represents this network
CyNetwork	CyGroupImpl.getNetwork() Get the network this group is a member of
CyNetwork	CyGroup.getNetwork() Get the network for this group

Methods in cytoscape.groups with parameters of type CyNetwork

static CyGroup	CyGroupManager.copyGroup(CyGroup group, CyNetwork network) Create a copy of a group, potentially in a new network, and name the copy automatically.
static CyGroup	CyGroupManager.copyGroup(String newName, CyGroup group, CyNetwork network) Create a copy of a group, potentially in a new network, and name the copy with the provided new name.
static CyGroup	CyGroupManager.createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer, CyNetwork network) Create a new group with a list of nodes as initial members, and a precreated group node.
static CyGroup	CyGroupManager.createGroup(String groupName, List<CyNode> nodeList, List<CyEdge> innerEdgeList, List<CyEdge> outerEdgeList, String viewer, CyNetwork network) Create a new group by specifying all components.
static CyGroup	CyGroupManager.createGroup(String groupName, List<CyNode> nodeList, String viewer, CyNetwork network) Create a new group with a list of nodes as initial members.
static CyGroup	CyGroupManager.createGroup(String groupName, String viewer, CyNetwork network) Create a new, empty group.
static List<CyGroup>	CyGroupManager.getGroupList(CyNetwork network) Return the list of all groups for this network
void	CyGroupImpl.setNetwork(CyNetwork network, boolean notify) Set (or change) the network fro this group
void	CyGroup.setNetwork(CyNetwork network, boolean notify) Set the network for this group

Constructors in cytoscape.groups with parameters of type CyNetwork

CyGroupImpl(CyNode groupNode, List<CyNode> nodeList, List<CyEdge> internalEdges, List<CyEdge> externalEdges, CyNetwork network)
Constructor to create an empty group.

Uses of CyNetwork in cytoscape.layout

Fields in cytoscape.layout declared as CyNetwork

protected CyNetwork

AbstractLayout.network

Uses of CyNetwork in cytoscape.plugin

Methods in cytoscape.plugin that return CyNetwork

CyNetwork

CytoscapePlugin.interpretScript(String[] args, CyNetwork network) Take a CyNetwork as input along with some arguments, and return a CyNetwork, which can be the same, or different, it doesn't really matter, and is up to the individual plugin.

Methods in cytoscape.plugin with parameters of type CyNetwork

CyNetwork

CytoscapePlugin.interpretScript(String[] args, CyNetwork network) Take a CyNetwork as input along with some arguments, and return a CyNetwork, which can be the same, or different, it doesn't really matter, and is up to the individual plugin.

Uses of CyNetwork in cytoscape.util

Methods in cytoscape.util that return CyNetwork

static CyNetwork	GraphSetUtils.createDifferenceGraph(List networkList, boolean copyView, String title) Create a new graph which is the difference of multiple graphs.
static CyNetwork	GraphSetUtils.createDifferenceGraph2(List networkList, boolean copyView, String title) The way this works is that the 2nd and optional additional networks will be subtracted from the 1st network.
static CyNetwork	GraphSetUtils.createIntersectionGraph(List networkList, boolean copyView, String title) Create a new graph which is the intersection of multiple graphs.
static CyNetwork	GraphSetUtils.createUnionGraph(List networkList, boolean copyView, String title) Create a new graph which is the union of multiple graphs.
protected static CyNetwork	GraphSetUtils.performNetworkOperation(List networkList, int operation, boolean copyView, String title) Protected helper function that actually does the heavy lifting to perform the set operations.

Methods in cytoscape.util with parameters of type CyNetwork

static void	CyNetworkNaming.editNetworkTitle(CyNetwork network) This will prompt the user to edit the title of a given CyNetork, and after ensuring that the network title is not already in use, this will assign that title to the given CyNetwork
static String	CyNetworkNaming.getSuggestedSubnetworkTitle(CyNetwork parentNetwork) DOCUMENT ME!

Uses of CyNetwork in cytoscape.util.swing

Methods in cytoscape.util.swing that return CyNetwork

CyNetwork

NetworkSelectorPanel.getSelectedNetwork() If selected, return selected network.

Uses of CyNetwork in cytoscape.view

Methods in cytoscape.view that return CyNetwork

CyNetwork

CyNetworkView.getNetwork() Returns the network displayed by this object.

Methods in cytoscape.view with parameters of type CyNetwork

void	CytoscapeDesktop.setNewNetwork(CyNetwork newNetwork) DOCUMENT ME!
void	NetworkViewManager.updateNetworkTitle(CyNetwork network) DOCUMENT ME!
void	NetworkViewManager.updateNetworkTitle(CyNetwork network, String title) Method to update the network title on the JInternalFrame, but not in the network panel.
void	NetworkPanel.updateTitle(CyNetwork network) update a network title

Uses of CyNetwork in cytoscape.visual

Methods in cytoscape.visual that return CyNetwork

CyNetwork

VisualMappingManager.getNetwork() DOCUMENT ME!

Methods in cytoscape.visual with parameters of type CyNetwork

void	VisualMappingManager.applyEdgeAppearances(CyNetwork network, CyNetworkView network_view) Recalculates and reapplies all of the edge appearances.
void	VisualMappingManager.applyGlobalAppearances(CyNetwork network, CyNetworkView network_view) Recalculates and reapplies the global visual attributes.
void	VisualMappingManager.applyNodeAppearances(CyNetwork network, CyNetworkView network_view) Recalculates and reapplies all of the node appearances.
Color	GlobalAppearanceCalculator.calculateBackgroundColor(CyNetwork network) Currently no calculators are supported for global visual attributes, so this method simply returns the default background color.
void	EdgeAppearanceCalculator.calculateEdgeAppearance(EdgeAppearance appr, Edge edge, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
EdgeAppearance	EdgeAppearanceCalculator.calculateEdgeAppearance(Edge edge, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
Color	GlobalAppearanceCalculator.calculateEdgeReverseSelectionColor(CyNetwork network) DOCUMENT ME!
Color	GlobalAppearanceCalculator.calculateEdgeSelectionColor(CyNetwork network) DOCUMENT ME!
GlobalAppearance	GlobalAppearanceCalculator.calculateGlobalAppearance(CyNetwork network) Constructs a new GlobalAppearance object containing the values for the known global visual attributes.
void	GlobalAppearanceCalculator.calculateGlobalAppearance(GlobalAppearance appr, CyNetwork network) The supplied GlobalAppearance object will be changed to hold new values for the known global visual attributes.
void	NodeAppearanceCalculator.calculateNodeAppearance(NodeAppearance appr, Node node, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
NodeAppearance	NodeAppearanceCalculator.calculateNodeAppearance(Node node, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
Color	GlobalAppearanceCalculator.calculateNodeReverseSelectionColor(CyNetwork network) DOCUMENT ME!
Color	GlobalAppearanceCalculator.calculateNodeSelectionColor(CyNetwork network) DOCUMENT ME!

Uses of CyNetwork in cytoscape.visual.calculators

Methods in cytoscape.visual.calculators with parameters of type CyNetwork

void	Calculator.apply(Appearance appr, Edge e, CyNetwork net) DOCUMENT ME!
void	AbstractCalculator.apply(Appearance appr, Edge e, CyNetwork net) DOCUMENT ME!
void	Calculator.apply(Appearance appr, Node n, CyNetwork net) DOCUMENT ME!
void	AbstractCalculator.apply(Appearance appr, Node n, CyNetwork net) DOCUMENT ME!
protected JPanel	AbstractCalculator.getUI(CyAttributes attr, JDialog parent, CyNetwork network) Deprecated. will be removed in the next release (2.8 or 3.0)
JPanel	Calculator.getUI(JDialog parent, CyNetwork network) Deprecated. replaced by new VizMap GUI components. Will be removed in 2.8 or 3.0
JPanel	AbstractCalculator.getUI(JDialog parent, CyNetwork network) Deprecated. Will be removed next release (2.8 or 3.0)

Constructors in cytoscape.visual.calculators with parameters of type CyNetwork

AbstractCalculator.CalculatorUI.AttributeSelectorListener(JDialog parent, CyNetwork network, int mapIndex, int yPos, JPanel mapperUI)
Constructs an AttributeSelectorListener for the ObjectMapping at index mapIndex.

AbstractCalculator.CalculatorUI(CyAttributes attr, JDialog parent, CyNetwork network)
Deprecated.

Uses of CyNetwork in cytoscape.visual.mappings

Methods in cytoscape.visual.mappings with parameters of type CyNetwork

JPanel	ObjectMapping.getUI(JDialog parent, CyNetwork network) Deprecated.
JPanel	AbstractMapping.getUI(JDialog parent, CyNetwork network) Deprecated.
void	ObjectMapping.setControllingAttributeName(String attrName, CyNetwork network, boolean preserveMapping) Deprecated. Will be removed in 2.8. Use setControllingAttributeName(final String controllingAttrName) instead.
void	AbstractMapping.setControllingAttributeName(String attrName, CyNetwork network, boolean preserveMapping) Deprecated.