cytoscape
Class Cytoscape

java.lang.Object
  cytoscape.Cytoscape

public abstract class Cytoscape

extends Object

This class, Cytoscape is the primary class in the API. All Nodes and Edges must be created using the methods getCyNode and getCyEdge, available only in this class. Once A node or edge is created using these methods it can then be added to a CyNetwork, where it can be used algorithmically.

The methods get/setNode/EdgeAttributeValue allow you to assocate data with nodes or edges. That data is then carried into all CyNetworks where that Node/Edge is present.

Field Summary

static String	ATTRIBUTES_CHANGED
static String	CYTOSCAPE_EXIT
static int	FILE_BY_SUFFIX When creating a network, use one of the standard suffixes to have it parsed correctly sif -- Simple Interaction File gml -- Graph Markup Languange sbml -- SBML
static int	FILE_GML
static int	FILE_SBML
static int	FILE_SIF
static String	NETWORK_CREATED
static String	NETWORK_DESTROYED

Constructor Summary

Cytoscape()

Method Summary

static void	clearCytoscape() Deprecated. WARNING: this should only be used under special circumstances.
static CyNetwork	createNetwork(Collection nodes, Collection edges, String title) Creates a new Network
static CyNetwork	createNetwork(Collection nodes, Collection edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork
static CyNetwork	createNetwork(int[] nodes, int[] edges, String title) Creates a new Network
static CyNetwork	createNetwork(int[] nodes, int[] edges, String child_title, CyNetwork parent) Creates a new Network, that inherits from the given ParentNetwork
static CyNetwork	createNetwork(String title) Creates a new, empty Network.
static CyNetwork	createNetwork(String location, int file_type, boolean canonicalize, BioDataServer biodataserver, String species) Creates a cytoscape.data.CyNetwork from a file.
static CyNetwork	createNetworkFromFile(String location) Creates a cytoscape.data.CyNetwork from a file.
static CyNetwork	createNetworkFromProject(CyProject project, BioDataServer bioDataServer) Constructs a network using information from a CyProject argument that contains information on the location of the graph file, any node/edge attribute files, and a possible expression data file.
static CyNetworkView	createNetworkView(CyNetwork network) Creates a CyNetworkView, but doesn't do anything with it.
static CyNetworkView	createNetworkView(CyNetwork network, String title) Creates a CyNetworkView, but doesn't do anything with it.
static void	destroyNetwork(CyNetwork network) destroys the given network
static void	destroyNetwork(CyNetwork network, boolean destroy_unique) destroys the given network
static void	destroyNetwork(String network_id) destroys the given network
static void	destroyNetworkView(CyNetwork network) destroys the networkview, including any layout information
static void	destroyNetworkView(CyNetworkView view) destroys the networkview, including any layout information
static void	destroyNetworkView(String network_view_id) destroys the networkview, including any layout information
static void	ensureCapacity(int nodes, int edges) Ensure the capacity of Cytoscapce.
static void	exit() Shuts down Cytoscape, after giving plugins time to react.
static void	firePropertyChange(String property_type, Object old_value, Object new_value)
static BioDataServer	getBioDataServer()
static CyNetwork	getCurrentNetwork() Return the Network that currently has the Focus.
static CyNetworkView	getCurrentNetworkView() Return the CyNetworkView that currently has the focus.
static CyEdge	getCyEdge(Node node_1, Node node_2, String attribute, Object attribute_value, boolean create) Gets the first CyEdge found.
static CyEdge	getCyEdge(String source_alias, String edge_name, String target_alias, String interaction_type)
static List	getCyEdgesList()
static CyNode	getCyNode(String alias)
static CyNode	getCyNode(String alias, boolean create)
static List	getCyNodesList()
static CytoscapeObj	getCytoscapeObj() Deprecated.
static CytoscapeDesktop	getDesktop()
static String[]	getEdgeAttributesList() Return all availble Attributes for the Edges in this CyNetwork
static Object	getEdgeAttributeValue(Edge edge, String attribute) Return the requested Attribute for the given Edge
static cytoscape.data.GraphObjAttributes	getEdgeNetworkData() Deprecated. This should not be used by any user-code
static ExpressionData	getExpressionData()
static CyNetwork	getNetwork(String id)
static Set	getNetworkSet() Return a List of all available CyNetworks
static CyNetworkView	getNetworkView(String network_id)
static Map	getNetworkViewMap() This Map has keys that are Strings ( network_ids ) and values that are networkviews.
static String[]	getNodeAttributesList() Return all availble Attributes for the Nodes in this CyNetwork
static String[]	getNodeAttributesList(Edge[] edges) Return all available Attributes for the given Edges
static String[]	getNodeAttributesList(Node[] nodes) Return all available Attributes for the given Nodes
static Object	getNodeAttributeValue(Node node, String attribute) Return the requested Attribute for the given Node
static cytoscape.data.GraphObjAttributes	getNodeNetworkData() Deprecated. This should not be used by any user-code
static cytoscape.giny.CytoscapeRootGraph	getRootGraph() Return the CytoscapeRootGraph
static SwingPropertyChangeSupport	getSwingPropertyChangeSupport() Bound events are: NETWORK_CREATED NETWORK_DESTROYED ATTRIBUTES_ADDED CYTOSCAPE_EXIT
static void	loadAttributes(String[] nodeAttrLocations, String[] edgeAttrLocations) Loads Node and Edge attribute data into Cytoscape from the given file locations.
static void	loadAttributes(String[] nodeAttrLocations, String[] edgeAttrLocations, boolean canonicalize, BioDataServer bioDataServer, String species) Loads Node and Edge attribute data into Cytoscape from the given file locations.
static BioDataServer	loadBioDataServer(String location) A BioDataServer should be loadable from a file systems file or from a URL.
static boolean	loadExpressionData(String filename, boolean copy_atts) Load Expression Data
static void	setCurrentNetwork(String id) Deprecated.
static boolean	setCurrentNetworkView(String id) Deprecated.
static boolean	setEdgeAttributeValue(Edge edge, String attribute, Object value) Return the requested Attribute for the given Edge
static void	setExpressionData(ExpressionData expData)
static boolean	setNodeAttributeValue(Node node, String attribute, Object value) Return the requested Attribute for the given Node
static void	setSpecies() Deprecated. argh!...
static boolean	viewExists(String network_id)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NETWORK_CREATED

public static String NETWORK_CREATED

ATTRIBUTES_CHANGED

public static String ATTRIBUTES_CHANGED

NETWORK_DESTROYED

public static String NETWORK_DESTROYED

CYTOSCAPE_EXIT

public static String CYTOSCAPE_EXIT

FILE_BY_SUFFIX

public static int FILE_BY_SUFFIX

When creating a network, use one of the standard suffixes to have it parsed correctly

• sif -- Simple Interaction File
• gml -- Graph Markup Languange
• sbml -- SBML

FILE_GML

public static int FILE_GML

FILE_SIF

public static int FILE_SIF

FILE_SBML

public static int FILE_SBML

Constructor Detail

Cytoscape

public Cytoscape()

Method Detail

exit

public static void exit()

Shuts down Cytoscape, after giving plugins time to react.

getSwingPropertyChangeSupport

public static SwingPropertyChangeSupport getSwingPropertyChangeSupport()

Bound events are:

1. NETWORK_CREATED
2. NETWORK_DESTROYED
3. ATTRIBUTES_ADDED
4. CYTOSCAPE_EXIT

getRootGraph

public static cytoscape.giny.CytoscapeRootGraph getRootGraph()

Return the CytoscapeRootGraph

ensureCapacity

public static void ensureCapacity(int nodes,
                                  int edges)

Ensure the capacity of Cytoscapce. This is to prevent the inefficiency of adding nodes one at a time.

clearCytoscape

public static void clearCytoscape()

Deprecated. WARNING: this should only be used under special circumstances.

getCyNodesList

public static List getCyNodesList()

Returns:

all CyNodes that are present in Cytoscape

getCyEdgesList

public static List getCyEdgesList()

Returns:

all CyEdges that are present in Cytoscape

getCyNode

public static CyNode getCyNode(String alias)

Parameters:

alias - an alias of a node

Returns:

will return a node, if one exists for the given alias

getCyNode

public static CyNode getCyNode(String alias,
                               boolean create)

Parameters:

alias - an alias of a node

create - will create a node if one does not exist

Returns:

will always return a node, if create is true

getCyEdge

public static CyEdge getCyEdge(Node node_1,
                               Node node_2,
                               String attribute,
                               Object attribute_value,
                               boolean create)

Gets the first CyEdge found.

Parameters:

node_1 - one end of the edge

node_2 - the other end of the edge

attribute - the attribute of the edge to be searched, a common one is Semantics.INTERACTION

attribute_value - a value for the attribute, like "pp"

create - will create an edge if one does not exist

Returns:

returns an existing CyEdge if present, or creates one if create is true, otherwise returns null.

getCyEdge

public static CyEdge getCyEdge(String source_alias,
                               String edge_name,
                               String target_alias,
                               String interaction_type)

Parameters:

source_alias - an alias of a node

edge_name - the name of the node

target_alias - an alias of a node

Returns:

will always return an edge

getNodeAttributeValue

public static Object getNodeAttributeValue(Node node,
                                           String attribute)

Return the requested Attribute for the given Node

Parameters:

node - the given CyNode

attribute - the name of the requested attribute

Returns:

the value for the give node, for the given attribute

getEdgeAttributeValue

public static Object getEdgeAttributeValue(Edge edge,
                                           String attribute)

Return the requested Attribute for the given Edge

getNodeAttributesList

public static String[] getNodeAttributesList()

Return all availble Attributes for the Nodes in this CyNetwork

getNodeAttributesList

public static String[] getNodeAttributesList(Node[] nodes)

Return all available Attributes for the given Nodes

getEdgeAttributesList

public static String[] getEdgeAttributesList()

Return all availble Attributes for the Edges in this CyNetwork

getNodeAttributesList

public static String[] getNodeAttributesList(Edge[] edges)

Return all available Attributes for the given Edges

setNodeAttributeValue

public static boolean setNodeAttributeValue(Node node,
                                            String attribute,
                                            Object value)

Return the requested Attribute for the given Node

Parameters:

node - the given CyNode

attribute - the name of the requested attribute

value - the value to be set

Returns:

if it overwrites a previous value

setEdgeAttributeValue

public static boolean setEdgeAttributeValue(Edge edge,
                                            String attribute,
                                            Object value)

Return the requested Attribute for the given Edge

setSpecies

public static void setSpecies()

Deprecated. argh!...

getCurrentNetwork

public static CyNetwork getCurrentNetwork()

Return the Network that currently has the Focus. Can be different from getCurrentNetworkView

getNetworkSet

public static Set getNetworkSet()

Return a List of all available CyNetworks

getNetwork

public static CyNetwork getNetwork(String id)

Returns:

the CyNetwork that has the given identifier or null if there is no such network

getNetworkView

public static CyNetworkView getNetworkView(String network_id)

Returns:

a CyNetworkView for the given ID, if one exists, otherwise returns null

viewExists

public static boolean viewExists(String network_id)

Returns:

if a view exists for a given network id

getCurrentNetworkView

public static CyNetworkView getCurrentNetworkView()

Return the CyNetworkView that currently has the focus. Can be different from getCurrentNetwork

getDesktop

public static CytoscapeDesktop getDesktop()

Returns:

the reference to the One CytoscapeDesktop

setCurrentNetwork

public static void setCurrentNetwork(String id)

Deprecated.

setCurrentNetworkView

public static boolean setCurrentNetworkView(String id)

Deprecated.

Returns:

true if there is network view, false if not

getNetworkViewMap

public static Map getNetworkViewMap()

This Map has keys that are Strings ( network_ids ) and values that are networkviews.

destroyNetwork

public static void destroyNetwork(String network_id)

destroys the given network

destroyNetwork

public static void destroyNetwork(CyNetwork network)

destroys the given network

destroyNetwork

public static void destroyNetwork(CyNetwork network,
                                  boolean destroy_unique)

destroys the given network

Parameters:

network - the network tobe destroyed

destroy_unique - if this is true, then all Nodes and Edges that are in this network, but no other are also destroyed.

destroyNetworkView

public static void destroyNetworkView(CyNetworkView view)

destroys the networkview, including any layout information

destroyNetworkView

public static void destroyNetworkView(String network_view_id)

destroys the networkview, including any layout information

destroyNetworkView

public static void destroyNetworkView(CyNetwork network)

destroys the networkview, including any layout information

createNetwork

public static CyNetwork createNetwork(String title)

Creates a new, empty Network.

Parameters:

title - the title of the new network.

createNetwork

public static CyNetwork createNetwork(int[] nodes,
                                      int[] edges,
                                      String title)

Creates a new Network

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

title - the title of the new network.

createNetwork

public static CyNetwork createNetwork(Collection nodes,
                                      Collection edges,
                                      String title)

Creates a new Network

Parameters:

nodes - a collection of nodes

edges - a collection of edges

title - the title of the new network.

createNetwork

public static CyNetwork createNetwork(int[] nodes,
                                      int[] edges,
                                      String child_title,
                                      CyNetwork parent)

Creates a new Network, that inherits from the given ParentNetwork

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

child_title - the title of the new network.

createNetwork

public static CyNetwork createNetwork(Collection nodes,
                                      Collection edges,
                                      String child_title,
                                      CyNetwork parent)

Creates a new Network, that inherits from the given ParentNetwork

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

createNetworkFromFile

public static CyNetwork createNetworkFromFile(String location)

Creates a cytoscape.data.CyNetwork from a file. The file type is determined by the suffice of the file

• sif -- Simple Interaction File
• gml -- Graph Markup Languange
• sbml -- SBML

Parameters:

location - the location of the file

createNetwork

public static CyNetwork createNetwork(String location,
                                      int file_type,
                                      boolean canonicalize,
                                      BioDataServer biodataserver,
                                      String species)

Creates a cytoscape.data.CyNetwork from a file. The passed variable determines the type of file, i.e. GML, SIF, SBML, etc.

This operation may take a long time to complete. It is a good idea NOT to call this method from the AWT event handling thread.

Parameters:

location - the location of the file

file_type - the type of file GML, SIF, SBML, etc.

canonicalize - this will set the preferred display name to what is on the server.

biodataserver - provides the name conversion service

species - the species used by the BioDataServer

getCytoscapeObj

public static CytoscapeObj getCytoscapeObj()

Deprecated.

getNodeNetworkData

public static cytoscape.data.GraphObjAttributes getNodeNetworkData()

Deprecated. This should not be used by any user-code

getEdgeNetworkData

public static cytoscape.data.GraphObjAttributes getEdgeNetworkData()

Deprecated. This should not be used by any user-code

getExpressionData

public static ExpressionData getExpressionData()

setExpressionData

public static void setExpressionData(ExpressionData expData)

loadExpressionData

public static boolean loadExpressionData(String filename,
                                         boolean copy_atts)

Load Expression Data

loadAttributes

public static void loadAttributes(String[] nodeAttrLocations,
                                  String[] edgeAttrLocations,
                                  boolean canonicalize,
                                  BioDataServer bioDataServer,
                                  String species)

Loads Node and Edge attribute data into Cytoscape from the given file locations. Currently, the only supported attribute types are of the type "name = value".

Parameters:

nodeAttrLocations - an array of node attribute file locations. May be null.

edgeAttrLocations - an array of edge attribute file locations. May be null.

canonicalize - convert to the preffered name on the biodataserver

bioDataServer - provides the name conversion service

species - the species to use with the bioDataServer's

loadAttributes

public static void loadAttributes(String[] nodeAttrLocations,
                                  String[] edgeAttrLocations)

Loads Node and Edge attribute data into Cytoscape from the given file locations. Currently, the only supported attribute types are of the type "name = value".

Parameters:

nodeAttrLocations - an array of node attribute file locations. May be null.

edgeAttrLocations - an array of edge attribute file locations. May be null.

createNetworkFromProject

public static CyNetwork createNetworkFromProject(CyProject project,
                                                 BioDataServer bioDataServer)

Constructs a network using information from a CyProject argument that contains information on the location of the graph file, any node/edge attribute files, and a possible expression data file. If the data server argument is non-null and the project requests canonicalization, the data server will be used for name resolution given the names in the graph/attributes files.

See Also:

CyProject

loadBioDataServer

public static BioDataServer loadBioDataServer(String location)

A BioDataServer should be loadable from a file systems file or from a URL.

getBioDataServer

public static BioDataServer getBioDataServer()

Returns:

the BioDataServer that was loaded, should not be null, but not contain any data.

createNetworkView

public static CyNetworkView createNetworkView(CyNetwork network)

Creates a CyNetworkView, but doesn't do anything with it. Ifnn's you want to use it @link {CytoscapeDesktop}

Parameters:

network - the network to create a view of

createNetworkView

public static CyNetworkView createNetworkView(CyNetwork network,
                                              String title)

Creates a CyNetworkView, but doesn't do anything with it. Ifnn's you want to use it @link {CytoscapeDesktop}

Parameters:

network - the network to create a view of

firePropertyChange

public static void firePropertyChange(String property_type,
                                      Object old_value,
                                      Object new_value)