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 Deprecated. this event should not be used, it is not fired
static String	CYTOSCAPE_EXIT
static String	CYTOSCAPE_INITIALIZED
static String	DATASERVER_CHANGED
static String	EXPRESSION_DATA_LOADED
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 xgmml -- XGMML
static int	FILE_GML
static int	FILE_SBML
static int	FILE_SIF
static int	FILE_XGMML
static String	NETWORK_CREATED
static String	NETWORK_DESTROYED
static String	NETWORK_LOADED
static String	NETWORK_MODIFIED
static String	NETWORK_SAVED
static String	PREFERENCE_MODIFIED
static String	PREFERENCES_UPDATED
static String	READER_CLIENT_KEY
static String	SAVE_VIZMAP_PROPS
static int	SELECT_EDGES_ONLY
static int	SELECT_NODES_AND_EDGES
static int	SELECT_NODES_ONLY
static int	SESSION_CHANGED
static int	SESSION_CLOSED
static String	SESSION_LOADED
static int	SESSION_NEW
static int	SESSION_OPENED
static String	SESSION_SAVED
static String	VIZMAP_LOADED
static String	VIZMAP_RESTORED

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(Collection nodes, Collection edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork.
static CyNetwork	createNetwork(cytoscape.data.readers.GraphReader reader, boolean create_view, CyNetwork parent) Creates a cytoscape.data.CyNetwork from a reader.
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(int[] nodes, int[] edges, String child_title, CyNetwork parent, boolean create_view) Creates a new Network, that inherits from the given ParentNetwork
static CyNetwork	createNetwork(String title) Creates a new, empty Network.
static CyNetwork	createNetwork(String title, boolean create_view) Creates a new, empty Network.
static CyNetwork	createNetwork(String location, int file_type, boolean canonicalize, BioDataServer biodataserver, String species) Deprecated. It will be removed in April 2007 Use CyNetwork createNetworkFromFile(String location, boolean create_view) instead. File type is no longer needed as ImportHandler now manages all file types.
static CyNetwork	createNetworkFromFile(String location) Creates a CyNetwork from a file.
static CyNetwork	createNetworkFromFile(String location, boolean create_view) Creates a CyNetwork from a file.
static CyNetwork	createNetworkFromProject(CyProject project, BioDataServer bioDataServer) Deprecated. Will be removed Oct 2006. This is not apparently used, so don't start. This functionality has been subsumed by Cytoscape Sessions.
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	createNewSession() Clear all networks and attributes and start a new session.
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	disableSquiggle() Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
static void	enableSquiggle() Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
static void	ensureCapacity(int nodes, int edges) Ensure the capacity of Cytoscapce.
static void	exit() Deprecated. Use exit(returnVal) instead. This will be removed in Sept 2006.
static void	exit(int returnVal) 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 String	getCurrentSessionFileName() Get name of the current session file.
static CyEdge	getCyEdge(Node node_1, Node node_2, String attribute, Object attribute_value, boolean create) Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.
static CyEdge	getCyEdge(Node source, Node target, String attribute, Object attribute_value, boolean create, boolean directed) Gets the first CyEdge found between the two nodes that has the given value for the given attribute.
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 nodeID, boolean create)
static List	getCyNodesList()
static CytoscapeObj	getCytoscapeObj() Deprecated.
static CytoscapeDesktop	getDesktop()
static CyAttributes	getEdgeAttributes() Gets Global Edge Attributes
static String[]	getEdgeAttributesList() Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static Object	getEdgeAttributeValue(Edge edge, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static cytoscape.data.GraphObjAttributes	getEdgeNetworkData() Deprecated. Use getEdgeAttributes() instead. This method will be removed in September, 2006.
static ExpressionData	getExpressionData()
static cytoscape.data.ImportHandler	getImportHandler()
static CyNetwork	getNetwork(String id)
static CyAttributes	getNetworkAttributes() Gets Global Network Attributes.
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 CyAttributes	getNodeAttributes() Gets Global Node Attributes.
static String[]	getNodeAttributesList() Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static String[]	getNodeAttributesList(Edge[] edges) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static String[]	getNodeAttributesList(Node[] nodes) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static Object	getNodeAttributeValue(Node node, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static cytoscape.data.GraphObjAttributes	getNodeNetworkData() Deprecated. Use getNodeAttributes() instead. This method will be removed in September, 2006.
static CyNetwork	getNullNetwork()
static CyNetworkView	getNullNetworkView()
static PropertyChangeSupport	getPropertyChangeSupport()
static cytoscape.giny.CytoscapeRootGraph	getRootGraph() Return the CytoscapeRootGraph
static int	getSelectionMode() Gets the selection mode value.
static int	getSessionstate()
static SwingPropertyChangeSupport	getSwingPropertyChangeSupport() Bound events are: NETWORK_CREATED NETWORK_DESTROYED CYTOSCAPE_EXIT
static VisualMappingManager	getVisualMappingManager()
static boolean	isSquiggleEnabled() Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
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 void	setCurrentSessionFileName(String newName) Set the current session name.
static boolean	setEdgeAttributeValue(Edge edge, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static void	setExpressionData(ExpressionData expData)
static boolean	setNodeAttributeValue(Node node, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
static void	setSelectionMode(int selectionMode) Sets the specified selection mode on all views.
static void	setSelectionMode(int selectionMode, GraphView view) Utility method to set the selection mode on the specified GraphView.
static void	setSessionState(int state)
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

Deprecated. this event should not be used, it is not fired

Please consult CyAttributes documentation for event listening

See Also:

CyAttributes

DATASERVER_CHANGED

public static String DATASERVER_CHANGED

EXPRESSION_DATA_LOADED

public static String EXPRESSION_DATA_LOADED

NETWORK_DESTROYED

public static String NETWORK_DESTROYED

CYTOSCAPE_INITIALIZED

public static String CYTOSCAPE_INITIALIZED

CYTOSCAPE_EXIT

public static String CYTOSCAPE_EXIT

SESSION_SAVED

public static String SESSION_SAVED

SESSION_LOADED

public static String SESSION_LOADED

VIZMAP_RESTORED

public static String VIZMAP_RESTORED

SAVE_VIZMAP_PROPS

public static String SAVE_VIZMAP_PROPS

VIZMAP_LOADED

public static String VIZMAP_LOADED

NETWORK_MODIFIED

public static final String NETWORK_MODIFIED

See Also:

Constant Field Values

NETWORK_SAVED

public static final String NETWORK_SAVED

See Also:

Constant Field Values

NETWORK_LOADED

public static final String NETWORK_LOADED

See Also:

Constant Field Values

PREFERENCE_MODIFIED

public static final String PREFERENCE_MODIFIED

See Also:

Constant Field Values

PREFERENCES_UPDATED

public static final String PREFERENCES_UPDATED

See Also:

Constant Field Values

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
• xgmml -- XGMML

FILE_GML

public static int FILE_GML

FILE_SIF

public static int FILE_SIF

FILE_SBML

public static int FILE_SBML

FILE_XGMML

public static int FILE_XGMML

SELECT_NODES_ONLY

public static final int SELECT_NODES_ONLY

See Also:

Constant Field Values

SELECT_EDGES_ONLY

public static final int SELECT_EDGES_ONLY

See Also:

Constant Field Values

SELECT_NODES_AND_EDGES

public static final int SELECT_NODES_AND_EDGES

See Also:

Constant Field Values

SESSION_NEW

public static final int SESSION_NEW

See Also:

Constant Field Values

SESSION_OPENED

public static final int SESSION_OPENED

See Also:

Constant Field Values

SESSION_CHANGED

public static final int SESSION_CHANGED

See Also:

Constant Field Values

SESSION_CLOSED

public static final int SESSION_CLOSED

See Also:

Constant Field Values

READER_CLIENT_KEY

public static final String READER_CLIENT_KEY

See Also:

Constant Field Values

Constructor Detail

Cytoscape

public Cytoscape()

Method Detail

getImportHandler

public static cytoscape.data.ImportHandler getImportHandler()

getNullNetworkView

public static CyNetworkView getNullNetworkView()

Returns:

a nullNetworkView object. This is NOT simply a null object.

getNullNetwork

public static CyNetwork getNullNetwork()

Returns:

the nullNetwork CyNetwork. This is NOT simply a null object.

exit

public static void exit()

Deprecated. Use exit(returnVal) instead. This will be removed in Sept 2006.

Shuts down Cytoscape, after giving plugins time to react.

exit

public static void exit(int returnVal)

Shuts down Cytoscape, after giving plugins time to react.

Parameters:

returnVal - The return value. Zero indicates success, non-zero otherwise.

getSwingPropertyChangeSupport

public static SwingPropertyChangeSupport getSwingPropertyChangeSupport()

Bound events are:

1. NETWORK_CREATED
2. NETWORK_DESTROYED
3. CYTOSCAPE_EXIT

getPropertyChangeSupport

public static PropertyChangeSupport getPropertyChangeSupport()

getVisualMappingManager

public static VisualMappingManager getVisualMappingManager()

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 nodeID,
                               boolean create)

Parameters:

nodeID - 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 KONO: 5/4/2006 Since we removed the canonicalName, no "canonicalization" is necessary. This method uses given nodeID as the identifier.

getCyEdge

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

Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.

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 and if attribute is Semantics.INTERACTION

Returns:

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

getCyEdge

public static CyEdge getCyEdge(Node source,
                               Node target,
                               String attribute,
                               Object attribute_value,
                               boolean create,
                               boolean directed)

Gets the first CyEdge found between the two nodes that has the given value for the given attribute. If direction flag is set, then direction is taken into account, A->B is NOT equivalent to B->A

Parameters:

source - one end of the edge

target - 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 and if attribute is Semantics.INTERACTION

directed - take direction into account, source->target is NOT target->source

Returns:

returns an existing CyEdge if present, or creates one if create is true and attribute is Semantics.INTERACTION, 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)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Returns 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)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Returns the requested Attribute for the given Edge

getNodeAttributesList

public static String[] getNodeAttributesList()

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all availble Attributes for the Nodes in this CyNetwork.

getNodeAttributesList

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all available Attributes for the given Nodes.

getEdgeAttributesList

public static String[] getEdgeAttributesList()

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all availble Attributes for the Edges in this CyNetwork.

getNodeAttributesList

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all available Attributes for the given Edges

setNodeAttributeValue

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

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)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

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 the nullNetwork (see getNullNetwork()) 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(String title,
                                      boolean create_view)

Creates a new, empty Network.

Parameters:

title - the title of the new network.

create_view - if the size of the network is under the node limit, create a view

createNetwork

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

Creates a new Network. A view will be created automatically.

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. A view will be created automatically.

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. A view will be created automatically.

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

child_title - the title of the new network.

parent - the parent of the this Network

createNetwork

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

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.

parent - the parent of the this Network

create_view - whether or not a view will be created

createNetwork

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

Creates a new Network, that inherits from the given ParentNetwork. A view will be created automatically.

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

parent - the parent of the this Network

createNetwork

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

Creates a new Network, that inherits from the given ParentNetwork.

Parameters:

nodes - the indeces of nodes

edges - the indeces of edges

parent - the parent of the this Network

create_view - whether or not a view will be created

createNetworkFromFile

public static CyNetwork createNetworkFromFile(String location)

Creates a CyNetwork from a file. The file type is determined by the suffix of the file.* Uses the new ImportHandler and thus the passed in location should be a file of a recognized "Graph Nature". The "Nature" of a file is a new way to tell what a file is beyond it's filetype e.g. galFiltered.sif is, in addition to being a .sif file, the file is also of Graph "Nature". Other files of Graph Nature include GML and XGMML. Beyond Graph Nature there are Node, Edge, and Properties Nature. A view will be created automatically.

Parameters:

location - the location of the file

createNetworkFromFile

public static CyNetwork createNetworkFromFile(String location,
                                              boolean create_view)

Creates a CyNetwork from a file. The file type is determined by the suffix of the file.* Uses the new ImportHandler and thus the passed in location should be a file of a recognized "Graph Nature". The "Nature" of a file is a new way to tell what a file is beyond it's filetype e.g. galFiltered.sif is, in addition to being a .sif file, the file is also of Graph "Nature". Other files of Graph Nature include GML and XGMML. Beyond Graph Nature there are Node, Edge, and Properties Nature.

Parameters:

location - location of importable file

create_view - whether or not a view will be created

Returns:

a network based on the specified file or null if the file type is supported but the file is not of Graph Nature.

createNetwork

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

Deprecated. It will be removed in April 2007 Use CyNetwork createNetworkFromFile(String location, boolean create_view) instead. File type is no longer needed as ImportHandler now manages all file types.

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. A view will be created automatically.

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

createNetwork

public static CyNetwork createNetwork(cytoscape.data.readers.GraphReader reader,
                                      boolean create_view,
                                      CyNetwork parent)

Creates a cytoscape.data.CyNetwork from a reader. Neccesary with cesssions.

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. This operation assumes the reader is of type .xgmml since this should only be called by the cessions reader which opens .xgmml files from the zipped cytoscape session.

Parameters:

reader - the graphreader that will read in the network

create_view - whether or not a view will be created

getCytoscapeObj

public static CytoscapeObj getCytoscapeObj()

Deprecated.

getNodeNetworkData

public static cytoscape.data.GraphObjAttributes getNodeNetworkData()

Deprecated. Use getNodeAttributes() instead. This method will be removed in September, 2006.

Gets Node Network Data: GraphObjAttributes.

Returns:

GraphObjAttributes Object.

getEdgeNetworkData

public static cytoscape.data.GraphObjAttributes getEdgeNetworkData()

Deprecated. Use getEdgeAttributes() instead. This method will be removed in September, 2006.

Gets Edge Network Data: GraphObjAttributes.

Returns:

GraphObjAttributes Object.

getNodeAttributes

public static CyAttributes getNodeAttributes()

Gets Global Node Attributes.

Returns:

CyAttributes Object.

getEdgeAttributes

public static CyAttributes getEdgeAttributes()

Gets Global Edge Attributes

Returns:

CyAttributes Object.

getNetworkAttributes

public static CyAttributes getNetworkAttributes()

Gets Global Network Attributes.

Returns:

CyAttributes Object.

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)

Deprecated. Will be removed Oct 2006. This is not apparently used, so don't start. This functionality has been subsumed by Cytoscape Sessions.

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

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

Parameters:

network - the network to create a view of

firePropertyChange

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

enableSquiggle

public static void enableSquiggle()

Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

Utility method to enable Squiggle function.

disableSquiggle

public static void disableSquiggle()

Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

Utility method to disable Squiggle function.

isSquiggleEnabled

public static boolean isSquiggleEnabled()

Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

Returns the value of the global flag to indicate whether the Squiggle function is enabled.

getSelectionMode

public static int getSelectionMode()

Gets the selection mode value.

setSelectionMode

public static void setSelectionMode(int selectionMode)

Sets the specified selection mode on all views.

Parameters:

selectionMode - SELECT_NODES_ONLY, SELECT_EDGES_ONLY, or SELECT_NODES_AND_EDGES.

setSelectionMode

public static void setSelectionMode(int selectionMode,
                                    GraphView view)

Utility method to set the selection mode on the specified GraphView.

Parameters:

selectionMode - SELECT_NODES_ONLY, SELECT_EDGES_ONLY, or SELECT_NODES_AND_EDGES.

view - the GraphView to set the selection mode on.

getCurrentSessionFileName

public static String getCurrentSessionFileName()

Get name of the current session file.

Returns:

current session file name

setCurrentSessionFileName

public static void setCurrentSessionFileName(String newName)

Set the current session name.

Parameters:

newName -

setSessionState

public static void setSessionState(int state)

getSessionstate

public static int getSessionstate()

createNewSession

public static void createNewSession()

Clear all networks and attributes and start a new session.