Cytoscape (Cytoscape 2.2 API)

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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 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
`static int`	`FILE_GML`
`static int`	`FILE_SBML`
`static int`	`FILE_SIF`
`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 int`	`SELECT_EDGES_ONLY`
`static int`	`SELECT_NODES_AND_EDGES`
`static int`	`SELECT_NODES_ONLY`

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 title, boolean create_view)` 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`	`disableSquiggle()` Utility method to disable Squiggle function.
`static void`	`enableSquiggle()` Utility method to enable Squiggle function.
`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 between the two nodes (direction does not matter) 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 alias, 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 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 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 PropertyChangeSupport`	`getPropertyChangeSupport()`
`static cytoscape.giny.CytoscapeRootGraph`	`getRootGraph()` Return the CytoscapeRootGraph
`static int`	`getSelectionMode()` Gets the selection mode value.
`static SwingPropertyChangeSupport`	`getSwingPropertyChangeSupport()` Bound events are: NETWORK_CREATED NETWORK_DESTROYED ATTRIBUTES_ADDED CYTOSCAPE_EXIT
`static boolean`	`isSquiggleEnabled()` Returns the value of the global flag to indicate whether the Squiggle function is enabled.
`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)` 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`	`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

EXPRESSION_DATA_LOADED

public static String EXPRESSION_DATA_LOADED

NETWORK_DESTROYED

public static String NETWORK_DESTROYED

CYTOSCAPE_EXIT

public static String CYTOSCAPE_EXIT

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

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

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

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:

NETWORK_CREATED
NETWORK_DESTROYED
ATTRIBUTES_ADDED
CYTOSCAPE_EXIT

getPropertyChangeSupport

public static PropertyChangeSupport getPropertyChangeSupport()

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 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(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