org.cytoscape.model
Interface CyNetwork

All Superinterfaces:

CyDisposable, CyIdentifiable

All Known Subinterfaces:

CyRootNetwork, CySubNetwork

public interface CyNetwork
extends CyIdentifiable, CyDisposable

CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape. Specifically, CyNetwork represents a multi-graph as multiple edges may exist between nodes. Edges may be directed, undirected, or both.

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

Field Summary

static String	DEFAULT_ATTRS The name of the default public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
static String	HIDDEN_ATTRS The name of the default hidden CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
static String	LOCAL_ATTRS The name of the local public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
static String	NAME A String column created by default for every CyNetwork that holds the name of the entry.
static String	SELECTED A boolean column created by default for every CyNode or CyEdge that holds the selection state of the entry.

Fields inherited from interface org.cytoscape.model.CyIdentifiable

SUID

Method Summary

CyEdge	addEdge(CyNode source, CyNode target, boolean isDirected) This method is used to create and add an edge to this network.
CyNode	addNode() This method is used to create and add a node to this network.
boolean	containsEdge(CyEdge edge) Determine if this CyNetwork contains a particular edge.
boolean	containsEdge(CyNode from, CyNode to) Determine if this CyNetwork contains an edge between two nodes.
boolean	containsNode(CyNode node) Determine if this CyNetwork contains a particular node.
Iterable<CyEdge>	getAdjacentEdgeIterable(CyNode node, CyEdge.Type edgeType) Gets an Iteable of edges that connect to this node.
List<CyEdge>	getAdjacentEdgeList(CyNode node, CyEdge.Type edgeType) Get the list of edges that connect to this node.
List<CyEdge>	getConnectingEdgeList(CyNode source, CyNode target, CyEdge.Type edgeType) Get the list of edges that connect two nodes.
CyTable	getDefaultEdgeTable() A convenience method returns the default attribute table for the edges of this network.
CyTable	getDefaultNetworkTable() A convenience method returns the default attribute table for this network.
CyTable	getDefaultNodeTable() A convenience method returns the default attribute table for the nodes of this network.
CyEdge	getEdge(long suid) Return the CyEdge that has the SUID.
int	getEdgeCount() Return the number of edges in this network.
List<CyEdge>	getEdgeList() Return a list of the edges in this network.
List<CyNode>	getNeighborList(CyNode node, CyEdge.Type edgeType) Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.
CyNode	getNode(long suid) Return the CyNode that has the SUID.
int	getNodeCount() Return the number of nodes in this network.
List<CyNode>	getNodeList() Return a list of the nodes in this network.
CyRow	getRow(CyIdentifiable entry) A convenience method that returns the row in the default table for this object.
CyRow	getRow(CyIdentifiable entry, String namespace) Returns the row for the specified table name for this object.
SavePolicy	getSavePolicy() Returns how (or if) this CyNetwork should be saved.
CyTable	getTable(Class<? extends CyIdentifiable> type, String namespace) Returns the table with the specified namespace and type from this network.
boolean	removeEdges(Collection<CyEdge> edges) Remove an edge from the network and delete the edge (if it only exists in this network).
boolean	removeNodes(Collection<CyNode> node) Remove a node from the network and delete the node (if it only exists in this network).

Methods inherited from interface org.cytoscape.model.CyIdentifiable

getSUID

Methods inherited from interface org.cytoscape.model.CyDisposable

dispose

Field Detail

SELECTED

static final String SELECTED

A boolean column created by default for every CyNode or CyEdge that holds the selection state of the entry.

See Also:

Constant Field Values

DEFAULT_ATTRS

static final String DEFAULT_ATTRS

The name of the default public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges. Other CyTables may also be associated with networks -- see CyTableManager for more information. The table should be referenced using this constant: CyNetwork.DEFAULT_ATTRS.

See Also:

Constant Field Values

LOCAL_ATTRS

static final String LOCAL_ATTRS

The name of the local public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges. This table contains attributes which are specific to only this network. -- see CyTableManager for more information. The table should be referenced using this constant: CyNetwork.DEFAULT_ATTRS.

See Also:

Constant Field Values

HIDDEN_ATTRS

static final String HIDDEN_ATTRS

The name of the default hidden CyTable that is created by default for CyNetworks, CyNodes, and CyEdges. Other CyTables may also be associated with networks -- see CyTableManager for more information.

See Also:

Constant Field Values

NAME

static final String NAME

A String column created by default for every CyNetwork that holds the name of the entry.

See Also:

Constant Field Values

Method Detail

addNode

CyNode addNode()

This method is used to create and add a node to this network.

Returns:

the created node

removeNodes

boolean removeNodes(Collection<CyNode> node)

Remove a node from the network and delete the node (if it only exists in this network). See CyRootNetwork for information about having the same node in two networks.
To delete a single node it is convenient to do it this way: network.removeNodes(Collections.singletonList(node));

Parameters:

node - the node to be deleted

Returns:

true if the node was successfully deleted

addEdge

CyEdge addEdge(CyNode source,
               CyNode target,
               boolean isDirected)

This method is used to create and add an edge to this network.

Parameters:

source - the source (or start) of the edge

target - the target (or end) of the edge

isDirected - if 'true' this is a directed edge

Returns:

the created edge

removeEdges

boolean removeEdges(Collection<CyEdge> edges)

Remove an edge from the network and delete the edge (if it only exists in this network). See CyRootNetwork for information about having the same edge in two networks.
To delete a single edge it is convenient to do it this way: network.removeEdges(Collections.singletonList(edge));

Parameters:

edges - the edges to be deleted

Returns:

true if the edge was successfully deleted

getNodeCount

int getNodeCount()

Return the number of nodes in this network.

Returns:

the number of nodes

getEdgeCount

int getEdgeCount()

Return the number of edges in this network.

Returns:

the number of edges

getNodeList

List<CyNode> getNodeList()

Return a list of the nodes in this network. The list will be empty if there are no nodes in the network. This method should never return null. Modifying this list (if allowed by the implementation) has no effect on the network.

Returns:

the node list

getEdgeList

List<CyEdge> getEdgeList()

Return a list of the edges in this network. The list will be empty if there are no edges in the network. This method should never return null. Modifying this list (if allowed by the implementation) has no effect on the network.

Returns:

the edge list

containsNode

boolean containsNode(CyNode node)

Determine if this CyNetwork contains a particular node.

Parameters:

node - the node to check

Returns:

true if this network contains the node

containsEdge

boolean containsEdge(CyEdge edge)

Determine if this CyNetwork contains a particular edge.

Parameters:

edge - the edge to check

Returns:

true if this network contains the edge

containsEdge

boolean containsEdge(CyNode from,
                     CyNode to)

Determine if this CyNetwork contains an edge between two nodes. Note that if the edge is directed, the source and targets must match.

Parameters:

from - the source of the edge

to - the target of the edge

Returns:

true if this network contains the edge

getNode

CyNode getNode(long suid)

Return the CyNode that has the SUID. To iterate over all nodes, iterate over getNodeList(). We make no guarantees on what represent valid values for the index. The only valid indices are those accessed from existing nodes.

Parameters:

suid - the SUID of the CyNode to get

Returns:

the associated CyNode or null if there is no node with that index in this network.

getEdge

CyEdge getEdge(long suid)

Return the CyEdge that has the SUID. To iterate over all edges, iterate over getEdgeList(). We make no guarantees on what represent valid values for the index. The only valid indices are those accessed from existing edges.

Parameters:

suid - the SUID of the CyEdge to get

Returns:

the associated CyEdge or null if there is no edge with that index in this network.

getNeighborList

List<CyNode> getNeighborList(CyNode node,
                             CyEdge.Type edgeType)

Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType. The CyEdge.Type enum is used to determine whether the list includes undirected, directed, incoming, or outgoing edges. The list will be empty if there are no neighbor nodes found. This method should never return null. Modifying this list (if allowed by the implementation) has no effect on the network. This method only returns immediate neighbors.

Parameters:

node - the node whose neighbors we're looking for

edgeType - the directionality of the edges we're interested in

Returns:

the list of nodes that neighbor this node

getAdjacentEdgeList

List<CyEdge> getAdjacentEdgeList(CyNode node,
                                 CyEdge.Type edgeType)

Get the list of edges that connect to this node. The CyEdge.Type enum is used to determine whether the list includes undirected, directed, incoming, or outgoing edges. The list will be empty if there are no adjacent edges found. This method should never return null. Modifying this list (if allowed by the implementation) has no effect on the network.

Parameters:

node - the node whose edges we're looking for

edgeType - the directionality of the edges we're interested in

Returns:

the list of edges that are adjacent to this one

getAdjacentEdgeIterable

Iterable<CyEdge> getAdjacentEdgeIterable(CyNode node,
                                         CyEdge.Type edgeType)

Gets an Iteable of edges that connect to this node. The CyEdge.Type enum is used to determine whether the list includes undirected, directed, incoming, or outgoing edges. The iterable will be empty if there are no adjacent edges found. This method should never return null. Modifying this list (if allowed by the implementation) has no effect on the network. The Iterable implementation may be more efficient because it doesn't necessarily need to create a list first. However, that depends on implementation details, so you should evaluate the method performance yourself.

Parameters:

node - the node whose edges we're looking for

edgeType - the directionality of the edges we're interested in

Returns:

the Iterable of edges that are adjacent to this one

getConnectingEdgeList

List<CyEdge> getConnectingEdgeList(CyNode source,
                                   CyNode target,
                                   CyEdge.Type edgeType)

Get the list of edges that connect two nodes. The CyEdge.Type enum is used to determine whether the list includes undirected, directed, incoming, or outgoing edges. The list will be empty if no connecting edges are found. This method should never return null. This method will NOT find the shortest path between two nodes that are not already immediate neighbors. Modifying this list (if allowed by the implementation) has no effect on the network.

Parameters:

source - the source node

target - the target node

edgeType - the directionality of the edges we're interested in

Returns:

the list of edges that include source and target and directed edges.

getDefaultNetworkTable

CyTable getDefaultNetworkTable()

A convenience method returns the default attribute table for this network. This is equivalent to CyNetworkTableManager.getTableMap(this,CyNetwork.class,CyNetwork.DEFAULT_ATTRS);

Returns:

The default attribute table for this network.

getDefaultNodeTable

CyTable getDefaultNodeTable()

A convenience method returns the default attribute table for the nodes of this network. This is equivalent to CyNetworkTableManager.getTable(this,CyNode.class,CyNetwork.DEFAULT_ATTRS);

Returns:

The default attribute table for the nodes of this network.

getDefaultEdgeTable

CyTable getDefaultEdgeTable()

A convenience method returns the default attribute table for the edges of this network. This is equivalent to CyNetworkTableManager.getTableMap(this,CyEdge.class,CyNetwork.DEFAULT_ATTRS);

Returns:

The default attribute table for the edges of this network.

getTable

CyTable getTable(Class<? extends CyIdentifiable> type,
                 String namespace)

Returns the table with the specified namespace and type from this network.

Parameters:

type - Type of CyIdentifiable associated with the table.

namespace - the namespace the table should belong to.

Returns:

the table with the specified namespace and type from the network.

getRow

CyRow getRow(CyIdentifiable entry,
             String namespace)

Returns the row for the specified table name for this object. A null entry or a an entry not found in this network will return null, but otherwise every node or edge in the network is guaranteed to have a row.

Parameters:

entry - The entry (node, edge, network) whose row we're looking for.

namespace - the namespace of the table from which to extract the row.

Returns:

the row in the table of the specified name for this object.

getRow

CyRow getRow(CyIdentifiable entry)

A convenience method that returns the row in the default table for this object. This method is equivalent to calling getCyRow(entry,DEFAULT_ATTRS). A null entry or a an entry not found in this network will return null.

Parameters:

entry - The entry (node, edge, network) whose row we're looking for.

Returns:

the row in the default table for this object.

getSavePolicy

SavePolicy getSavePolicy()

Returns how (or if) this CyNetwork should be saved.

Returns:

how (or if) this CyNetwork should be saved.