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 This signals when new attributes have been loaded and a few other large scale changes to attributes have been made.
protected static String	currentNetworkID
protected static String	currentNetworkViewID
static String	CYTOSCAPE_EXIT
static String	CYTOSCAPE_INITIALIZED
protected static CytoscapeRootGraph	cytoscapeRootGraph The shared RootGraph between all Networks
static String	DATASERVER_CHANGED
protected static CytoscapeDesktop	defaultDesktop
static String	EXPRESSION_DATA_LOADED
protected static ExpressionData	expressionData
static int	FILE_BIOPAX
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_PSI_MI
static int	FILE_SBML
static int	FILE_SIF
static int	FILE_XGMML
protected static CyLogger	logger
static String	NESTED_NETWORK_CREATED Fired every time a nested network is assigned to a node.
static String	NESTED_NETWORK_DESTROYED Fired every time a nested network is removed from a node.
static String	NETWORK_CREATED
static String	NETWORK_DESTROYED
static String	NETWORK_LOADED
static String	NETWORK_MODIFIED
static String	NETWORK_SAVED
static String	NETWORK_TITLE_MODIFIED
protected static Map<String,CyNetwork>	networkMap
protected static Map<String,CyNetworkView>	networkViewMap
static String	NEW_ATTRS_LOADED Fired every time new attributes are loaded and provides the CyAttributes that was modified as well as a set of the new attribute names..
protected static PropertyChangeSupport	newPcs
protected static CyNetwork	nullNetwork A null CyNetwork to give when there is no Current Network
protected static CyNetworkView	nullNetworkView A null CyNetworkView to give when there is no Current NetworkView
static String	ONTOLOGY_ROOT
protected static String	ontologyRootID
protected static SwingPropertyChangeSupport	pcs
protected static Object	pcs2
protected static Object	pcsO
static String	PREFERENCE_MODIFIED
static String	PREFERENCES_UPDATED
static String	PROXY_MODIFIED Specifies that the Proxy settings Cytoscape uses to connect to the internet have been changed.
static String	READER_CLIENT_KEY
static String	RESTORE_PLUGIN_STATE
static String	SAVE_PLUGIN_STATE
static String	SAVE_VIZMAP_PROPS
static int	SELECT_EDGES_ONLY
static int	SELECT_NODES_AND_EDGES
static int	SELECT_NODES_ONLY
protected static LinkedList<CyNetwork>	selectedNetworks The list analog to the currentNetworkID
protected static LinkedList<CyNetworkView>	selectedNetworkViews The list analog to the currentNetworkViewID
static Integer	SESSION_CHANGED
static int	SESSION_CLOSED
static String	SESSION_LOADED
static Integer	SESSION_NEW
static Integer	SESSION_OPENED
static String	SESSION_SAVED
static String	VIZMAP_LOADED
static String	VIZMAP_RESTORED
protected static VisualMappingManager	VMM

Constructor Summary

Cytoscape()

Method Summary

static void	addNetwork(CyNetwork network, String title, CyNetwork parent, boolean create_view) Add a network to Cytoscape's internal list of networks.
static OntologyServer	buildOntologyServer() This will replace the bioDataServer.
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(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 title, CyNetwork parent, boolean create_view) Creates a new, empty Network.
static CyNetwork	createNetworkFromFile(String location) Creates a CyNetwork from a file.
static CyNetwork	createNetworkFromFile(String loc, boolean create_view) Creates a CyNetwork from a file.
static CyNetwork	createNetworkFromURL(URL url, boolean create_view) Creates a CyNetwork from a URL.
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 CyNetworkView	createNetworkView(CyNetwork network, String title, CyLayoutAlgorithm layout) Creates a CyNetworkView, but doesn't do anything with it.
static CyNetworkView	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	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 network view.
static void	destroyNetworkView(String networkViewID) destroys the networkview, including any layout information
static void	ensureCapacity(int nodes, int edges) Ensure the capacity of Cytoscapce.
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) DOCUMENT ME!
static Bookmarks	getBookmarks() DOCUMENT ME!
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) Returns and edge if it exists, otherwise creates a directed edge.
static List	getCyEdgesList()
static CyNode	getCyNode(String alias)
static CyNode	getCyNode(String nodeID, boolean create)
static List	getCyNodesList()
static CytoscapeDesktop	getDesktop()
static CyAttributes	getEdgeAttributes() Gets Global Edge Attributes
static EqnAttrTracker	getEqnAttrTracker()
static ExpressionData	getExpressionData() DOCUMENT ME!
static ImportHandler	getImportHandler() DOCUMENT ME!
static CyNetwork	getNetwork(String id)
static CyAttributes	getNetworkAttributes() Gets Global Network Attributes.
protected static Map<String,CyNetwork>	getNetworkMap() This Map has keys that are Strings ( network_ids ) and values that are networks.
static Set<CyNetwork>	getNetworkSet() Return a List of all available CyNetworks
static CyNetworkView	getNetworkView(String network_id)
static Map<String,CyNetworkView>	getNetworkViewMap() This Map has keys that are Strings ( network_ids ) and values that are networkviews.
static CyAttributes	getNodeAttributes() Gets Global Node Attributes.
static CyNetwork	getNullNetwork()
static CyNetworkView	getNullNetworkView()
static CyAttributes	getOntologyAttributes() Gets Global Network Attributes.
static String	getOntologyRootID() DOCUMENT ME!
static OntologyServer	getOntologyServer() DOCUMENT ME!
static PropertyChangeSupport	getPropertyChangeSupport() DOCUMENT ME!
static RecentlyOpenedTracker	getRecentlyOpenedSessionTracker()
static CytoscapeRootGraph	getRootGraph() Return the CytoscapeRootGraph
static List<CyNetwork>	getSelectedNetworks() Returns the list of selected networks.
static List<CyNetworkView>	getSelectedNetworkViews() Returns the list of currently selected networks.
static int	getSelectionMode() Gets the selection mode value.
static int	getSessionstate() DOCUMENT ME!
static SwingPropertyChangeSupport	getSwingPropertyChangeSupport() Bound events are: NETWORK_CREATED NETWORK_DESTROYED CYTOSCAPE_EXIT
static VisualMappingManager	getVisualMappingManager() DOCUMENT ME!
static void	loadAttributes(String[] nodeAttrLocations, String[] edgeAttrLocations) Loads Node and Edge attribute data into Cytoscape from the given file locations.
static boolean	loadExpressionData(String filename, boolean copy_atts) Load Expression Data
static void	setBookmarks(Bookmarks pBookmarks) DOCUMENT ME!
static void	setCurrentNetwork(String id)
static boolean	setCurrentNetworkView(String id)
static void	setCurrentSessionFileName(String newName) Set the current session name.
static void	setExpressionData(ExpressionData expData) DOCUMENT ME!
static void	setOntologyRootID(String id) DOCUMENT ME!
static void	setSelectedNetworks(List<String> ids) Sets the list of selected networks.
static void	setSelectedNetworkViews(List<String> viewIDs) Sets the selected network views.
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) DOCUMENT ME!
static boolean	viewExists(String network_id)

Methods inherited from class java.lang.Object

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

Field Detail

ATTRIBUTES_CHANGED

public static String ATTRIBUTES_CHANGED

This signals when new attributes have been loaded and a few other large scale changes to attributes have been made. There is no equivalent in the CyAttributes events.

NETWORK_CREATED

public static String NETWORK_CREATED

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

SAVE_PLUGIN_STATE

public static final String SAVE_PLUGIN_STATE

See Also:

Constant Field Values

RESTORE_PLUGIN_STATE

public static final String RESTORE_PLUGIN_STATE

See Also:

Constant Field Values

NETWORK_MODIFIED

public static final String NETWORK_MODIFIED

See Also:

Constant Field Values

NETWORK_TITLE_MODIFIED

public static final String NETWORK_TITLE_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

ONTOLOGY_ROOT

public static final String ONTOLOGY_ROOT

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

PROXY_MODIFIED

public static final String PROXY_MODIFIED

Specifies that the Proxy settings Cytoscape uses to connect to the internet have been changed.

See Also:

Constant Field Values

NESTED_NETWORK_CREATED

public static final String NESTED_NETWORK_CREATED

Fired every time a nested network is assigned to a node. This event contains the following values:

• oldValue - CyNode whose nested network was set.
• newValue - The network assigned to the node above.

See Also:

Constant Field Values

NESTED_NETWORK_DESTROYED

public static final String NESTED_NETWORK_DESTROYED

Fired every time a nested network is removed from a node.

See Also:

Constant Field Values

NEW_ATTRS_LOADED

public static final String NEW_ATTRS_LOADED

Fired every time new attributes are loaded and provides the CyAttributes that was modified as well as a set of the new attribute names..

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

FILE_BIOPAX

public static int FILE_BIOPAX

FILE_PSI_MI

public static int FILE_PSI_MI

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 Integer SESSION_NEW

SESSION_OPENED

public static final Integer SESSION_OPENED

SESSION_CHANGED

public static final Integer SESSION_CHANGED

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

cytoscapeRootGraph

protected static CytoscapeRootGraph cytoscapeRootGraph

The shared RootGraph between all Networks

expressionData

protected static ExpressionData expressionData

pcsO

protected static Object pcsO

pcs

protected static SwingPropertyChangeSupport pcs

pcs2

protected static Object pcs2

newPcs

protected static PropertyChangeSupport newPcs

networkViewMap

protected static Map<String,CyNetworkView> networkViewMap

networkMap

protected static Map<String,CyNetwork> networkMap

defaultDesktop

protected static CytoscapeDesktop defaultDesktop

currentNetworkID

protected static String currentNetworkID

currentNetworkViewID

protected static String currentNetworkViewID

ontologyRootID

protected static String ontologyRootID

nullNetwork

protected static CyNetwork nullNetwork

A null CyNetwork to give when there is no Current Network

selectedNetworkViews

protected static LinkedList<CyNetworkView> selectedNetworkViews

The list analog to the currentNetworkViewID

selectedNetworks

protected static LinkedList<CyNetwork> selectedNetworks

The list analog to the currentNetworkID

nullNetworkView

protected static final CyNetworkView nullNetworkView

A null CyNetworkView to give when there is no Current NetworkView

VMM

protected static VisualMappingManager VMM

logger

protected static CyLogger logger

Constructor Detail

Cytoscape

public Cytoscape()

Method Detail

getImportHandler

public static ImportHandler getImportHandler()

DOCUMENT ME!

Returns:

DOCUMENT ME!

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.

getEqnAttrTracker

public static EqnAttrTracker getEqnAttrTracker()

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()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getVisualMappingManager

public static VisualMappingManager getVisualMappingManager()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getRootGraph

public static 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.

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

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. If the edge doesn't exist, then it creates an undirected edge. This method MIGHT be deprecated, or even removed, because Cytoscape shouldn't really be using undirected edges.

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)

Returns and edge if it exists, otherwise creates a directed edge.

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

getCurrentNetwork

public static CyNetwork getCurrentNetwork()

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

getNetworkSet

public static Set<CyNetwork> 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 NullNetworkView

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

getSelectedNetworkViews

public static List<CyNetworkView> getSelectedNetworkViews()

Returns the list of currently selected networks.

setSelectedNetworkViews

public static void setSelectedNetworkViews(List<String> viewIDs)

Sets the selected network views.

getSelectedNetworks

public static List<CyNetwork> getSelectedNetworks()

Returns the list of selected networks.

setSelectedNetworks

public static void setSelectedNetworks(List<String> ids)

Sets the list of selected networks.

getDesktop

public static CytoscapeDesktop getDesktop()

Returns:

the reference to the One CytoscapeDesktop

setCurrentNetwork

public static void setCurrentNetwork(String id)

setCurrentNetworkView

public static boolean setCurrentNetworkView(String id)

Returns:

true if there is network view, false if not

getNetworkMap

protected static Map<String,CyNetwork> getNetworkMap()

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

getNetworkViewMap

public static Map<String,CyNetworkView> 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 to be 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 network view.

destroyNetworkView

public static void destroyNetworkView(String networkViewID)

destroys the networkview, including any layout information

destroyNetworkView

public static void destroyNetworkView(CyNetwork network)

destroys the networkview, including any layout information

addNetwork

public static void addNetwork(CyNetwork network,
                              String title,
                              CyNetwork parent,
                              boolean create_view)

Add a network to Cytoscape's internal list of networks. This also fires the NETWORK_CREATED event and as a byproduct adds the network to the Network Panel.

Parameters:

network - the network to add

title - the title (name) of the network

parent - the parent of the network to be added

create_view - if true create the view for this network

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(String title,
                                      CyNetwork parent,
                                      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 loc,
                                              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:

loc - 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.

createNetworkFromURL

public static CyNetwork createNetworkFromURL(URL url,
                                             boolean create_view)

Creates a CyNetwork from a URL. The file type is determined by the suffix of the file or, if one does't exist, the contentType of the data. 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:

url - url 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(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

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.

getOntologyAttributes

public static CyAttributes getOntologyAttributes()

Gets Global Network Attributes.

Returns:

CyAttributes Object.

getExpressionData

public static ExpressionData getExpressionData()

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Returns:

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setExpressionData

public static void setExpressionData(ExpressionData expData)

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Parameters:

expData - DOCUMENT ME!

loadExpressionData

public static boolean loadExpressionData(String filename,
                                         boolean copy_atts)

Load Expression Data

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.

buildOntologyServer

public static OntologyServer buildOntologyServer()

This will replace the bioDataServer.

getOntologyServer

public static OntologyServer getOntologyServer()

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Returns:

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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

title - the title to use for the view

createNetworkView

public static CyNetworkView createNetworkView(CyNetwork network,
                                              String title,
                                              CyLayoutAlgorithm layout)

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

title - the title to use for the view

layout - the CyLayoutAlgorithm to use to lay this out by default

createNetworkView

public static CyNetworkView 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. The CyNetworkView will become the current view and have focus.

Parameters:

network - the network to create a view of

title - the title to use for the view

layout - the CyLayoutAlgorithm to use for layout. If null, will use the default layout (CyLayouts.getDefaultLayout()).

vs - the VisualStyle in which to render this new network. If null, the default visual style will be used.

firePropertyChange

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

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Parameters:

property_type - DOCUMENT ME!

old_value - DOCUMENT ME!

new_value - DOCUMENT ME!

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)

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Parameters:

state - DOCUMENT ME!

getSessionstate

public static int getSessionstate()

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Returns:

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createNewSession

public static void createNewSession()

Clear all networks and attributes and start a new session.

getOntologyRootID

public static String getOntologyRootID()

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Returns:

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setOntologyRootID

public static void setOntologyRootID(String id)

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Parameters:

id - DOCUMENT ME!

getBookmarks

public static Bookmarks getBookmarks()
                              throws JAXBException,
                                     IOException

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Returns:

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Throws:

JAXBException - DOCUMENT ME!

IOException - DOCUMENT ME!

setBookmarks

public static void setBookmarks(Bookmarks pBookmarks)

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Parameters:

pBookmarks - DOCUMENT ME!

getRecentlyOpenedSessionTracker

public static RecentlyOpenedTracker getRecentlyOpenedSessionTracker()