Graph

java.lang.Object
- prefuse.data.tuple.AbstractTupleSet
- - prefuse.data.tuple.CompositeTupleSet
  - - prefuse.data.Graph

All Implemented Interfaces:

TupleSet

Direct Known Subclasses:

Tree, VisualGraph
```
public class Graph
extends CompositeTupleSet
```
A Graph models a network of nodes connected by a collection of edges. Both nodes and edges can have any number of associated data fields. Additionally, edges are either directed or undirected, indicating a possible directionality of the connection. Each edge has both a source node and a target node, for a directed edge this indicates the directionality, for an undirected edge this is just an artifact of the order in which the nodes were specified when added to the graph.

Both nodes and edges are represented by backing data Table instances storing the data attributes. For edges, this table must also contain a source node field and a target node field. The default column name for these fields are DEFAULT_SOURCE_KEY and DEFAULT_TARGET_KEY, but these can be configured by the graph constructor. These columns should be integer valued, and contain either the row number for a corresponding node in the node table, or another unique identifier for a node. In this second case, the unique identifier must be included as a data field in the node table. This name of this column can be configured using the appropriate graph constructor. The default column name for this field is DEFAULT_NODE_KEY, which by default evaluates to null, indicating that no special node key should be used, just the direct node table row numbers. Though the source, target, and node key values completely specify the graph linkage structure, to make graph operations more efficient an additional table is maintained internally by the Graph class, storing node indegree and outdegree counts and adjacency lists for the inlinks and outlinks for all nodes.

Graph nodes and edges can be accessed by application code by either using the row numbers of the node and edge tables, which provide unique ids for each, or using the Node and Edge classes -- Tuple instances that provide object-oriented access to both node or edge data values and the backing graph structure. Node and Edge tuples are maintained by special TupleManager instances contained within this Graph. By default, they are not accessible from the backing node or edge tables directly. The reason for this is that these tables might be used in multiple graphs simultaneously. For example, a node data table could be used in a number of different graphs, exploring different possible linkages between those node. In short, use this Graph instance to request iterators over Node or Edge tuples, not the backing data tables.

All Graph instances also support an internally generated spanning tree, provided by the getSpanningTree() or getSpanningTree(Node) methods. This is particularly useful in visualization contexts that use an underlying tree structure to compute a graph layout.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`Graph.Listener` Listener class for tracking updates from node and edge tables, and their columns that determine the graph linkage structure.

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`DEFAULT_NODE_KEY` Default data field used to uniquely identify a node
`static java.lang.String`	`DEFAULT_SOURCE_KEY` Default data field used to denote the source node in an edge table
`static java.lang.String`	`DEFAULT_TARGET_KEY` Default data field used to denote the target node in an edge table
`static java.lang.String`	`EDGES` Data group name to identify the edges of this graph
`protected static java.lang.String`	`INDEGREE` In-degree data field for the links table
`static int`	`INEDGES` Indicates incoming edges (inlinks)
`protected static java.lang.String`	`INLINKS` In-links adjacency list data field for the links table
`protected static Schema`	`LINKS_SCHEMA` Schema used for the internal graph linkage table
`protected boolean`	`m_directed` Indicates if this graph is directed or undirected
`protected TupleManager`	`m_edgeTuples` TupleManager for managing Edge tuple instances
`protected Table`	`m_links` Table containing the adjacency lists for the graph
`protected boolean`	`m_longKey` Indicates if the key values are of type long
`protected Index`	`m_nidx` Reference to an index over the node key field
`protected java.lang.String`	`m_nkey` The node key field (for the Node table)
`protected TupleManager`	`m_nodeTuples` TupleManager for managing Node tuple instances
`protected java.lang.String`	`m_skey` The source node key field (for the Edge table)
`protected SpanningTree`	`m_spanning` The spanning tree over this graph
`protected java.lang.String`	`m_tkey` The target node key field (for the Edge table)
`static java.lang.String`	`NODES` Data group name to identify the nodes of this graph
`protected static java.lang.String`	`OUTDEGREE` Out-degree data field for the links table
`static int`	`OUTEDGES` Indicates outgoing edges (outlinks)
`protected static java.lang.String`	`OUTLINKS` Out-links adjacency list data field for the links table
`static int`	`UNDIRECTED` Indicates all edges, regardless of direction

Fields inherited from interface prefuse.data.tuple.TupleSet
EMPTY_ARRAY

Constructor Summary

Constructors
Constructor and Description
`Graph()` Creates a new, empty undirected Graph.
`Graph(boolean directed)` Creates a new, empty Graph.
`Graph(Table nodes, boolean directed)` Create a new Graph using the provided table of node data and an empty set of edges.
`Graph(Table nodes, boolean directed, java.lang.String nodeKey, java.lang.String sourceKey, java.lang.String targetKey)` Create a new Graph using the provided table of node data and an empty set of edges.
`Graph(Table nodes, Table edges, boolean directed)` Create a new Graph, using node table row numbers to uniquely identify nodes in the edge table's source and target fields.
`Graph(Table nodes, Table edges, boolean directed, java.lang.String sourceKey, java.lang.String targetKey)` Create a new Graph, using node table row numbers to uniquely identify nodes in the edge table's source and target fields.
`Graph(Table nodes, Table edges, boolean directed, java.lang.String nodeKey, java.lang.String sourceKey, java.lang.String targetKey)` Create a new Graph.

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`addEdge(int s, int t)` Add an edge to the graph.
`Edge`	`addEdge(Node s, Node t)` Add an edge to the graph.
`void`	`addGraphModelListener(GraphListener listnr)` Add a listener to be notified of changes to the graph.
`protected void`	`addLink(java.lang.String field, int len, int n, int e)` Internal method for adding a link to an adjacency list
`Node`	`addNode()` Add a new node to the graph.
`int`	`addNodeRow()` Add row to the node table, thereby adding a node to the graph.
`void`	`clear()` Clear this graph, removing all nodes and edges.
`protected void`	`clearEdges()` Internal method for clearing the edge table, removing all edges.
`void`	`clearSpanningTree()` Clear the internally stored spanning tree.
`protected Table`	`createLinkTable()` Instantiate and return the link table.
`void`	`dispose()` Dispose of this graph.
`protected boolean`	`edgeCheck(Edge e, boolean throwException)` Internal method for checking the validity of an edge.
`IntIterator`	`edgeRows()` Get an iterator over all edge ids (edge table row numbers).
`IntIterator`	`edgeRows(int node)` Get an iterator over all edge ids for edges incident on the given node.
`IntIterator`	`edgeRows(int node, int direction)` Get an iterator edge ids for edges incident on the given node.
`java.util.Iterator`	`edges()` Get an iterator over all edges in the graph.
`java.util.Iterator`	`edges(Node node)` Get an iterator over all Edges connected to the given Node in the graph.
`protected void`	`fireGraphEvent(Table t, int first, int last, int col, int type)` Fire a graph change event
`Node`	`getAdjacentNode(Edge e, Node n)` Given an Edge and an incident Node, return the other Node connected to the edge.
`int`	`getAdjacentNode(int edge, int node)` Given an edge id and an incident node id, return the node id for the other node connected to the edge.
`int`	`getDegree(int node)` Get the degree of a node, the number of edges for which a node is either the source or the target.
`int`	`getDegree(Node n)` Get the degree of a node, the number of edges for which a node is either the source or the target.
`Edge`	`getEdge(int e)` Get the Edge tuple instance corresponding to an edge id.
`int`	`getEdge(int source, int target)` Returns an edge from the source node to the target node.
`Edge`	`getEdge(Node source, Node target)` Get an Edge with given source and target Nodes.
`int`	`getEdgeCount()` Get the number of edges in this graph.
`TupleSet`	`getEdges()` Get the collection of edges as a TupleSet.
`java.lang.String`	`getEdgeSourceField()` Get the data field used to denote the source node in an edge table.
`Table`	`getEdgeTable()` Get the backing edge table.
`java.lang.String`	`getEdgeTargetField()` Get the data field used to denote the target node in an edge table.
`int`	`getInDegree(int node)` Get the in-degree of a node, the number of edges for which the node is the target.
`int`	`getInDegree(Node n)` Get the in-degree of a node, the number of edges for which the node is the target.
`long`	`getKey(int node)` Given a node id (a row number in the node table), get the value of the node key field.
`Node`	`getNode(int n)` Get the Node tuple instance corresponding to a node id.
`int`	`getNodeCount()` Get the number of nodes in this graph.
`Node`	`getNodeFromKey(long key)` Get the Node tuple corresponding to the input node key field value.
`int`	`getNodeIndex(long key)` Given a value of the node key field, get the node id (the row number in the node table).
`java.lang.String`	`getNodeKeyField()` Get the data field used to uniquely identify a node
`TupleSet`	`getNodes()` Get the collection of nodes as a TupleSet.
`Table`	`getNodeTable()` Get the backing node table.
`int`	`getOutDegree(int node)` Get the out-degree of a node, the number of edges for which the node is the source.
`int`	`getOutDegree(Node n)` Get the out-degree of a node, the number of edges for which the node is the source.
`Node`	`getSourceNode(Edge e)` Get the source Node for the given Edge instance.
`int`	`getSourceNode(int edge)` Get the source node id (node table row number) for the given edge id (edge table row number).
`Tree`	`getSpanningTree()` Return the current spanning tree over this graph.
`Tree`	`getSpanningTree(Node root)` Returns a spanning tree rooted at the specified node.
`Node`	`getTargetNode(Edge e)` Get the target Node for the given Edge instance.
`int`	`getTargetNode(int edge)` Get the target node id (node table row number) for the given edge id (edge table row number).
`IntIterator`	`inEdgeRows(int node)` Get an iterator over all edges that have the given node as a target.
`java.util.Iterator`	`inEdges(Node node)` Get an iterator over all in-linking edges to the given Node.
`protected void`	`init(Table nodes, Table edges, boolean directed, java.lang.String nodeKey, java.lang.String sourceKey, java.lang.String targetKey)` Initialize this Graph instance.
`protected void`	`initLinkTable()` Initialize the link table, which holds adjacency lists for this graph.
`java.util.Iterator`	`inNeighbors(Node n)` Get an iterator over all in-linking neighbor nodes for the given Node.
`boolean`	`isDirected()` Indicates if the edges of this graph are directed or undirected.
`java.util.Iterator`	`neighbors(Node n)` Get an iterator over all neighbor nodes for the given Node in the graph.
`protected boolean`	`nodeCheck(Node n, boolean throwException)` Internal method for checking the validity of a node.
`IntIterator`	`nodeRows()` Get an iterator over all node ids (node table row numbers).
`java.util.Iterator`	`nodes()` Get an iterator over all nodes in the graph.
`IntIterator`	`outEdgeRows(int node)` Get an iterator over all edges that have the given node as a source.
`java.util.Iterator`	`outEdges(Node node)` Get an iterator over all out-linking edges from the given Node.
`java.util.Iterator`	`outNeighbors(Node n)` Get an iterator over all out-linking neighbor nodes for the given Node.
`protected boolean`	`remLink(java.lang.String field, int len, int n, int e)` Internal method for removing a link from an adjacency list
`void`	`removeAllGraphModelListeners()` Removes all listeners on this graph
`boolean`	`removeEdge(Edge e)` Remove an edge from the graph.
`boolean`	`removeEdge(int edge)` Remove an edge from the graph.
`void`	`removeGraphModelListener(GraphListener listnr)` Remove a listener from this graph.
`boolean`	`removeNode(int node)` Remove a node from the graph, also removing all incident edges.
`boolean`	`removeNode(Node n)` Remove a node from the graph, also removing all incident edges.
`boolean`	`removeTuple(Tuple t)` If the given tuple is a Node or Edge in this graph, remove it.
`void`	`setEdgeTable(Table edges)` Updates this graph to use a different edge structure for the same nodes.
`void`	`setTupleManagers(TupleManager ntm, TupleManager etm)` Set the tuple managers used to manage the Node and Edge tuples of this Graph.
`java.util.Iterator`	`tuples()` Get an iterator over all the edges and nodes of this graph.
`java.util.Iterator`	`tuples(Predicate filter)` Get a filtered iterator over the edges and nodes of this graph.
`protected void`	`updateDegrees(int e, int incr)` Internal method for updating the linkage of this graph.
`protected void`	`updateDegrees(int e, int s, int t, int incr)` Internal method for updating the linkage of this graph.
`protected void`	`updateNodeData(int r, boolean added)` Update the link table to accomodate an inserted or deleted node

Methods inherited from class prefuse.data.tuple.CompositeTupleSet
addColumn, addColumn, addColumn, addColumn, addSet, addTuple, containsSet, containsTuple, getSet, getTupleCount, hasSet, isAddColumnSupported, removeAllSets, removeSet, setNames, sets, setTuple

Methods inherited from class prefuse.data.tuple.AbstractTupleSet
addColumns, addPropertyChangeListener, addPropertyChangeListener, addTupleSetListener, fireTupleEvent, fireTupleEvent, fireTupleEvent, getClientProperty, putClientProperty, removePropertyChangeListener, removePropertyChangeListener, removeTupleSetListener, tuples

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - INEDGES
```
public static final int INEDGES
```
    Indicates incoming edges (inlinks)
    
    See Also:
    Constant Field Values
  - OUTEDGES
```
public static final int OUTEDGES
```
    Indicates outgoing edges (outlinks)
    
    See Also:
    Constant Field Values
  - UNDIRECTED
```
public static final int UNDIRECTED
```
    Indicates all edges, regardless of direction
    
    See Also:
    Constant Field Values
  - DEFAULT_NODE_KEY
```
public static final java.lang.String DEFAULT_NODE_KEY
```
    Default data field used to uniquely identify a node
  - DEFAULT_SOURCE_KEY
```
public static final java.lang.String DEFAULT_SOURCE_KEY
```
    Default data field used to denote the source node in an edge table
  - DEFAULT_TARGET_KEY
```
public static final java.lang.String DEFAULT_TARGET_KEY
```
    Default data field used to denote the target node in an edge table
  - NODES
```
public static final java.lang.String NODES
```
    Data group name to identify the nodes of this graph
  - EDGES
```
public static final java.lang.String EDGES
```
    Data group name to identify the edges of this graph
  - m_links
```
protected Table m_links
```
    Table containing the adjacency lists for the graph
  - m_nodeTuples
```
protected TupleManager m_nodeTuples
```
    TupleManager for managing Node tuple instances
  - m_edgeTuples
```
protected TupleManager m_edgeTuples
```
    TupleManager for managing Edge tuple instances
  - m_directed
```
protected boolean m_directed
```
    Indicates if this graph is directed or undirected
  - m_spanning
```
protected SpanningTree m_spanning
```
    The spanning tree over this graph
  - m_nkey
```
protected java.lang.String m_nkey
```
    The node key field (for the Node table)
  - m_skey
```
protected java.lang.String m_skey
```
    The source node key field (for the Edge table)
  - m_tkey
```
protected java.lang.String m_tkey
```
    The target node key field (for the Edge table)
  - m_nidx
```
protected Index m_nidx
```
    Reference to an index over the node key field
  - m_longKey
```
protected boolean m_longKey
```
    Indicates if the key values are of type long
  - INDEGREE
```
protected static final java.lang.String INDEGREE
```
    In-degree data field for the links table
    
    See Also:
    Constant Field Values
  - OUTDEGREE
```
protected static final java.lang.String OUTDEGREE
```
    Out-degree data field for the links table
    
    See Also:
    Constant Field Values
  - INLINKS
```
protected static final java.lang.String INLINKS
```
    In-links adjacency list data field for the links table
    
    See Also:
    Constant Field Values
  - OUTLINKS
```
protected static final java.lang.String OUTLINKS
```
    Out-links adjacency list data field for the links table
    
    See Also:
    Constant Field Values
  - LINKS_SCHEMA
```
protected static final Schema LINKS_SCHEMA
```
    Schema used for the internal graph linkage table
- Constructor Detail
  - Graph
```
public Graph()
```
    Creates a new, empty undirected Graph.
  - Graph
```
public Graph(boolean directed)
```
    Creates a new, empty Graph.
    
    Parameters:
    directed - true for directed edges, false for undirected
  - Graph
```
public Graph(Table nodes,
     boolean directed)
```
    Create a new Graph using the provided table of node data and an empty set of edges.
    
    Parameters:
    nodes - the backing table to use for node data. Node instances of this graph will get their data from this table.
    directed - true for directed edges, false for undirected
  - Graph
```
public Graph(Table nodes,
     boolean directed,
     java.lang.String nodeKey,
     java.lang.String sourceKey,
     java.lang.String targetKey)
```
    Create a new Graph using the provided table of node data and an empty set of edges.
    
    Parameters:
    nodes - the backing table to use for node data. Node instances of this graph will get their data from this table.
    directed - true for directed edges, false for undirected
    nodeKey - data field used to uniquely identify a node. If this field is null, the node table row numbers will be used
    sourceKey - data field used to denote the source node in an edge table
    targetKey - data field used to denote the target node in an edge table
  - Graph
```
public Graph(Table nodes,
     Table edges,
     boolean directed)
```
    Create a new Graph, using node table row numbers to uniquely identify nodes in the edge table's source and target fields.
    
    Parameters:
    nodes - the backing table to use for node data. Node instances of this graph will get their data from this table.
    edges - the backing table to use for edge data. Edge instances of this graph will get their data from this table.
    directed - true for directed edges, false for undirected
  - Graph
```
public Graph(Table nodes,
     Table edges,
     boolean directed,
     java.lang.String sourceKey,
     java.lang.String targetKey)
```
    Create a new Graph, using node table row numbers to uniquely identify nodes in the edge table's source and target fields.
    
    Parameters:
    nodes - the backing table to use for node data. Node instances of this graph will get their data from this table.
    edges - the backing table to use for edge data. Edge instances of this graph will get their data from this table.
    directed - true for directed edges, false for undirected
    sourceKey - data field used to denote the source node in an edge table
    targetKey - data field used to denote the target node in an edge table
  - Graph
```
public Graph(Table nodes,
     Table edges,
     boolean directed,
     java.lang.String nodeKey,
     java.lang.String sourceKey,
     java.lang.String targetKey)
```
    Create a new Graph.
    
    Parameters:
    nodes - the backing table to use for node data. Node instances of this graph will get their data from this table.
    edges - the backing table to use for edge data. Edge instances of this graph will get their data from this table.
    directed - true for directed edges, false for undirected
    nodeKey - data field used to uniquely identify a node. If this field is null, the node table row numbers will be used
    sourceKey - data field used to denote the source node in an edge table
    targetKey - data field used to denote the target node in an edge table
- Method Detail
  - init
```
protected void init(Table nodes,
        Table edges,
        boolean directed,
        java.lang.String nodeKey,
        java.lang.String sourceKey,
        java.lang.String targetKey)
```
    Initialize this Graph instance.
    
    Parameters:
    nodes - the node table
    edges - the edge table
    directed - the edge directionality
    nodeKey - data field used to uniquely identify a node
    sourceKey - data field used to denote the source node in an edge table
    targetKey - data field used to denote the target node in an edge table
  - setTupleManagers
```
public void setTupleManagers(TupleManager ntm,
                    TupleManager etm)
```
    Set the tuple managers used to manage the Node and Edge tuples of this Graph.
    
    Parameters:
    ntm - the TupleManager to use for nodes
    etm - the TupleManager to use for edges
  - dispose
```
public void dispose()
```
    Dispose of this graph. Unregisters this graph as a listener to its included tables.
  - setEdgeTable
```
public void setEdgeTable(Table edges)
```
    Updates this graph to use a different edge structure for the same nodes. All other settings will remain the same (e.g., directionality, keys)
    
    Parameters:
    edges - the new edge table.
  - initLinkTable
```
protected void initLinkTable()
```
    Initialize the link table, which holds adjacency lists for this graph.
  - createLinkTable
```
protected Table createLinkTable()
```
    Instantiate and return the link table.
    
    Returns:
    the created link table
  - updateDegrees
```
protected void updateDegrees(int e,
                 int incr)
```
    Internal method for updating the linkage of this graph.
    
    Parameters:
    e - the edge id for the updated link
    incr - the increment value, 1 for an added link, -1 for a removed link
  - updateDegrees
```
protected void updateDegrees(int e,
                 int s,
                 int t,
                 int incr)
```
    Internal method for updating the linkage of this graph.
    
    Parameters:
    e - the edge id for the updated link
    s - the source node id for the updated link
    t - the target node id for the updated link
    incr - the increment value, 1 for an added link, -1 for a removed link
  - addLink
```
protected void addLink(java.lang.String field,
           int len,
           int n,
           int e)
```
    Internal method for adding a link to an adjacency list
    
    Parameters:
    field - which adjacency list (inlinks or outlinks) to use
    len - the length of the adjacency list
    n - the node id of the adjacency list to use
    e - the edge to add to the list
  - remLink
```
protected boolean remLink(java.lang.String field,
              int len,
              int n,
              int e)
```
    Internal method for removing a link from an adjacency list
    
    Parameters:
    field - which adjacency list (inlinks or outlinks) to use
    len - the length of the adjacency list
    n - the node id of the adjacency list to use
    e - the edge to remove from the list
    
    Returns:
    true if the link was removed successfully, false otherwise
  - updateNodeData
```
protected void updateNodeData(int r,
                  boolean added)
```
    Update the link table to accomodate an inserted or deleted node
    
    Parameters:
    r - the node id, also the row number into the link table
    added - indicates if a node was added or removed
  - getNodeKeyField
```
public java.lang.String getNodeKeyField()
```
    Get the data field used to uniquely identify a node
    
    Returns:
    the data field used to uniquely identify a node
  - getEdgeSourceField
```
public java.lang.String getEdgeSourceField()
```
    Get the data field used to denote the source node in an edge table.
    
    Returns:
    the data field used to denote the source node in an edge table.
  - getEdgeTargetField
```
public java.lang.String getEdgeTargetField()
```
    Get the data field used to denote the target node in an edge table.
    
    Returns:
    the data field used to denote the target node in an edge table.
  - getKey
```
public long getKey(int node)
```
    Given a node id (a row number in the node table), get the value of the node key field.
    
    Parameters:
    node - the node id
    
    Returns:
    the value of the node key field for the given node
  - getNodeIndex
```
public int getNodeIndex(long key)
```
    Given a value of the node key field, get the node id (the row number in the node table).
    
    Parameters:
    key - a node key field value
    
    Returns:
    the node id (the row number in the node table)
  - addNodeRow
```
public int addNodeRow()
```
    Add row to the node table, thereby adding a node to the graph.
    
    Returns:
    the node id (node table row number) of the added node
  - addNode
```
public Node addNode()
```
    Add a new node to the graph.
    
    Returns:
    the new Node instance
  - addEdge
```
public int addEdge(int s,
          int t)
```
    Add an edge to the graph. Both multiple edges between two nodes and edges from a node to itself are allowed.
    
    Parameters:
    s - the source node id
    t - the target node id
    
    Returns:
    the edge id (edge table row number) of the added edge
  - addEdge
```
public Edge addEdge(Node s,
           Node t)
```
    Add an edge to the graph.
    
    Parameters:
    s - the source Node
    t - the target Node
    
    Returns:
    the new Edge instance
  - removeNode
```
public boolean removeNode(int node)
```
    Remove a node from the graph, also removing all incident edges.
    
    Parameters:
    node - the node id (node table row number) of the node to remove
    
    Returns:
    true if the node was successfully removed, false if the node id was not found or was not valid
  - removeNode
```
public boolean removeNode(Node n)
```
    Remove a node from the graph, also removing all incident edges.
    
    Parameters:
    n - the Node to remove from the graph
    
    Returns:
    true if the node was successfully removed, false if the node was not found in this graph
  - removeEdge
```
public boolean removeEdge(int edge)
```
    Remove an edge from the graph.
    
    Parameters:
    edge - the edge id (edge table row number) of the edge to remove
    
    Returns:
    true if the edge was successfully removed, false if the edge was not found or was not valid
  - removeEdge
```
public boolean removeEdge(Edge e)
```
    Remove an edge from the graph.
    
    Parameters:
    e - the Edge to remove from the graph
    
    Returns:
    true if the edge was successfully removed, false if the edge was not found in this graph
  - clearEdges
```
protected void clearEdges()
```
    Internal method for clearing the edge table, removing all edges.
  - nodeCheck
```
protected boolean nodeCheck(Node n,
                boolean throwException)
```
    Internal method for checking the validity of a node.
    
    Parameters:
    n - the Node to check for validity
    throwException - true if this method should throw an Exception when an invalid node is encountered
    
    Returns:
    true is the node is valid, false if invalid
  - getNodes
```
public TupleSet getNodes()
```
    Get the collection of nodes as a TupleSet. Returns the same result as CompositeTupleSet.getSet(String) using NODES as the parameter.
    
    Returns:
    the nodes of this graph as a TupleSet instance
  - getNodeTable
```
public Table getNodeTable()
```
    Get the backing node table.
    
    Returns:
    the table of node values
  - getNodeCount
```
public int getNodeCount()
```
    Get the number of nodes in this graph.
    
    Returns:
    the number of nodes
  - getNode
```
public Node getNode(int n)
```
    Get the Node tuple instance corresponding to a node id.
    
    Parameters:
    n - a node id (node table row number)
    
    Returns:
    the Node instance corresponding to the node id
  - getNodeFromKey
```
public Node getNodeFromKey(long key)
```
    Get the Node tuple corresponding to the input node key field value. The node key field is used to find the node id (node table row number), which is then used to retrieve the Node tuple.
    
    Parameters:
    key - a node key field value
    
    Returns:
    the requested Node instance
  - getInDegree
```
public int getInDegree(int node)
```
    Get the in-degree of a node, the number of edges for which the node is the target.
    
    Parameters:
    node - the node id (node table row number)
    
    Returns:
    the in-degree of the node
  - getInDegree
```
public int getInDegree(Node n)
```
    Get the in-degree of a node, the number of edges for which the node is the target.
    
    Parameters:
    n - the Node instance
    
    Returns:
    the in-degree of the node
  - getOutDegree
```
public int getOutDegree(int node)
```
    Get the out-degree of a node, the number of edges for which the node is the source.
    
    Parameters:
    node - the node id (node table row number)
    
    Returns:
    the out-degree of the node
  - getOutDegree
```
public int getOutDegree(Node n)
```
    Get the out-degree of a node, the number of edges for which the node is the source.
    
    Parameters:
    n - the Node instance
    
    Returns:
    the out-degree of the node
  - getDegree
```
public int getDegree(int node)
```
    Get the degree of a node, the number of edges for which a node is either the source or the target.
    
    Parameters:
    node - the node id (node table row number)
    
    Returns:
    the total degree of the node
  - getDegree
```
public int getDegree(Node n)
```
    Get the degree of a node, the number of edges for which a node is either the source or the target.
    
    Parameters:
    n - the Node instance
    
    Returns:
    the total degree of the node
  - isDirected
```
public boolean isDirected()
```
    Indicates if the edges of this graph are directed or undirected.
    
    Returns:
    true if directed edges, false if undirected edges
  - edgeCheck
```
protected boolean edgeCheck(Edge e,
                boolean throwException)
```
    Internal method for checking the validity of an edge.
    
    Parameters:
    e - the Edge to check for validity
    throwException - true if this method should throw an Exception when an invalid node is encountered
    
    Returns:
    true is the edge is valid, false if invalid
  - getEdges
```
public TupleSet getEdges()
```
    Get the collection of edges as a TupleSet. Returns the same result as CompositeTupleSet.getSet(String) using EDGES as the parameter.
    
    Returns:
    the edges of this graph as a TupleSet instance
  - getEdgeTable
```
public Table getEdgeTable()
```
    Get the backing edge table.
    
    Returns:
    the table of edge values
  - getEdgeCount
```
public int getEdgeCount()
```
    Get the number of edges in this graph.
    
    Returns:
    the number of edges
  - getEdge
```
public Edge getEdge(int e)
```
    Get the Edge tuple instance corresponding to an edge id.
    
    Parameters:
    e - an edge id (edge table row number)
    
    Returns:
    the Node instance corresponding to the node id
  - getEdge
```
public int getEdge(int source,
          int target)
```
    Returns an edge from the source node to the target node. This method returns the first such edge found; in the case of multiple edges there may be more.
  - getEdge
```
public Edge getEdge(Node source,
           Node target)
```
    Get an Edge with given source and target Nodes. There may be times where there are multiple edges between two nodes; in those cases this method returns the first such edge found.
    
    Parameters:
    source - the source Node
    target - the target Node
    
    Returns:
    an Edge with given source and target nodes, or null if no such edge is found.
  - getSourceNode
```
public int getSourceNode(int edge)
```
    Get the source node id (node table row number) for the given edge id (edge table row number).
    
    Parameters:
    edge - an edge id (edge table row number)
    
    Returns:
    the source node id (node table row number)
  - getSourceNode
```
public Node getSourceNode(Edge e)
```
    Get the source Node for the given Edge instance.
    
    Parameters:
    e - an Edge instance
    
    Returns:
    the source Node of the edge
  - getTargetNode
```
public int getTargetNode(int edge)
```
    Get the target node id (node table row number) for the given edge id (edge table row number).
    
    Parameters:
    edge - an edge id (edge table row number)
    
    Returns:
    the target node id (node table row number)
  - getTargetNode
```
public Node getTargetNode(Edge e)
```
    Get the target Node for the given Edge instance.
    
    Parameters:
    e - an Edge instance
    
    Returns:
    the target Node of the edge
  - getAdjacentNode
```
public int getAdjacentNode(int edge,
                  int node)
```
    Given an edge id and an incident node id, return the node id for the other node connected to the edge.
    
    Parameters:
    edge - an edge id (edge table row number)
    node - a node id (node table row number). This node id must be connected to the edge
    
    Returns:
    the adjacent node id
  - getAdjacentNode
```
public Node getAdjacentNode(Edge e,
                   Node n)
```
    Given an Edge and an incident Node, return the other Node connected to the edge.
    
    Parameters:
    e - an Edge instance
    n - a Node instance. This node must be connected to the edge
    
    Returns:
    the adjacent Node
  - nodeRows
```
public IntIterator nodeRows()
```
    Get an iterator over all node ids (node table row numbers).
    
    Returns:
    an iterator over all node ids (node table row numbers)
  - edgeRows
```
public IntIterator edgeRows()
```
    Get an iterator over all edge ids (edge table row numbers).
    
    Returns:
    an iterator over all edge ids (edge table row numbers)
  - edgeRows
```
public IntIterator edgeRows(int node)
```
    Get an iterator over all edge ids for edges incident on the given node.
    
    Parameters:
    node - a node id (node table row number)
    
    Returns:
    an iterator over all edge ids for edges incident on the given node
  - edgeRows
```
public IntIterator edgeRows(int node,
                   int direction)
```
    Get an iterator edge ids for edges incident on the given node.
    
    Parameters:
    node - a node id (node table row number)
    direction - the directionality of the edges to include. One of INEDGES (for in-linking edges), OUTEDGES (for out-linking edges), or UNDIRECTED (for all edges).
    
    Returns:
    an iterator over all edge ids for edges incident on the given node
  - inEdgeRows
```
public IntIterator inEdgeRows(int node)
```
    Get an iterator over all edges that have the given node as a target. That is, edges that link into the given target node.
    
    Parameters:
    node - a node id (node table row number)
    
    Returns:
    an iterator over all edges that have the given node as a target
  - outEdgeRows
```
public IntIterator outEdgeRows(int node)
```
    Get an iterator over all edges that have the given node as a source. That is, edges that link out from the given source node.
    
    Parameters:
    node - a node id (node table row number)
    
    Returns:
    an iterator over all edges that have the given node as a source
  - nodes
```
public java.util.Iterator nodes()
```
    Get an iterator over all nodes in the graph.
    
    Returns:
    an iterator over Node instances
  - neighbors
```
public java.util.Iterator neighbors(Node n)
```
    Get an iterator over all neighbor nodes for the given Node in the graph.
    
    Parameters:
    n - a Node in the graph
    
    Returns:
    an iterator over all Nodes connected to the input node
  - inNeighbors
```
public java.util.Iterator inNeighbors(Node n)
```
    Get an iterator over all in-linking neighbor nodes for the given Node.
    
    Parameters:
    n - a Node in the graph
    
    Returns:
    an iterator over all Nodes that point to the input target node
  - outNeighbors
```
public java.util.Iterator outNeighbors(Node n)
```
    Get an iterator over all out-linking neighbor nodes for the given Node.
    
    Parameters:
    n - a Node in the graph
    
    Returns:
    an iterator over all Nodes pointed to by the input source node
  - edges
```
public java.util.Iterator edges()
```
    Get an iterator over all edges in the graph.
    
    Returns:
    an iterator over Edge instances
  - edges
```
public java.util.Iterator edges(Node node)
```
    Get an iterator over all Edges connected to the given Node in the graph.
    
    Parameters:
    node - a Node in the graph
    
    Returns:
    an iterator over all Edges connected to the input node
  - inEdges
```
public java.util.Iterator inEdges(Node node)
```
    Get an iterator over all in-linking edges to the given Node.
    
    Parameters:
    node - a Node in the graph
    
    Returns:
    an iterator over all in-linking edges to the input target node
  - outEdges
```
public java.util.Iterator outEdges(Node node)
```
    Get an iterator over all out-linking edges from the given Node.
    
    Parameters:
    node - a Node in the graph
    
    Returns:
    an iterator over all out-linking edges from the input source node
  - clear
```
public void clear()
```
    Clear this graph, removing all nodes and edges.
    
    Specified by:
    
    clear in interface TupleSet
    
    Overrides:
    
    clear in class CompositeTupleSet
    
    See Also:
    TupleSet.clear()
  - removeTuple
```
public boolean removeTuple(Tuple t)
```
    If the given tuple is a Node or Edge in this graph, remove it.
    
    Specified by:
    
    removeTuple in interface TupleSet
    
    Overrides:
    
    removeTuple in class CompositeTupleSet
    
    Parameters:
    t - the Tuple to remove
    
    Returns:
    true if the Tuple was found and removed, false otherwise
    See Also:
    TupleSet.removeTuple(prefuse.data.Tuple)
  - tuples
```
public java.util.Iterator tuples(Predicate filter)
```
    Get a filtered iterator over the edges and nodes of this graph.
    
    Specified by:
    
    tuples in interface TupleSet
    
    Overrides:
    
    tuples in class CompositeTupleSet
    
    Parameters:
    filter - predicate to apply to tuples in this set, only tuples for which the predicate evaluates to true are included in the iteration
    
    Returns:
    a filtered iterator over this set's tuples
    See Also:
    TupleSet.tuples(prefuse.data.expression.Predicate)
  - tuples
```
public java.util.Iterator tuples()
```
    Get an iterator over all the edges and nodes of this graph. The iterator will return all edges first, then all nodes.
    
    Specified by:
    
    tuples in interface TupleSet
    
    Overrides:
    
    tuples in class CompositeTupleSet
    
    Returns:
    an iterator over this set's tuples
    See Also:
    TupleSet.tuples()
  - getSpanningTree
```
public Tree getSpanningTree()
```
    Return the current spanning tree over this graph. If no spanning tree has been constructed, a SpanningTree rooted at the first valid node found in the node table will be generated. Spanning trees are generated using an unweighted breadth first search over the graph structure.
    
    Returns:
    a spanning tree over this graph
    See Also:
    getSpanningTree(Node), clearSpanningTree()
  - getSpanningTree
```
public Tree getSpanningTree(Node root)
```
    Returns a spanning tree rooted at the specified node. If the current spanning tree is already rooted at the given node, it is simply returned. Otherwise, the tree is reconstructed at the new root and made the current spanning tree for this Graph instance. Spanning trees are generated using an unweighted breadth first search over the graph structure.
    
    Parameters:
    root - the node at which to root the spanning tree.
    
    Returns:
    a spanning tree over this graph, rooted at the given root
    See Also:
    getSpanningTree(), clearSpanningTree()
  - clearSpanningTree
```
public void clearSpanningTree()
```
    Clear the internally stored spanning tree. Any new calls to a getSpanningTree() method will generate a new spanning tree instance as needed. This method is primarily useful for subclasses. For example, calling this method on a Tree instance will revert the state to the original rooted tree such that a sbusequent call to getSpanningTree() will return the backing Tree itself.
    
    See Also:
    getSpanningTree(), getSpanningTree(Node), Tree.getSpanningTree(Node)
  - addGraphModelListener
```
public void addGraphModelListener(GraphListener listnr)
```
    Add a listener to be notified of changes to the graph.
    
    Parameters:
    listnr - the listener to add
  - removeGraphModelListener
```
public void removeGraphModelListener(GraphListener listnr)
```
    Remove a listener from this graph.
    
    Parameters:
    listnr - the listener to remove
  - removeAllGraphModelListeners
```
public void removeAllGraphModelListeners()
```
    Removes all listeners on this graph
  - fireGraphEvent
```
protected void fireGraphEvent(Table t,
                  int first,
                  int last,
                  int col,
                  int type)
```
    Fire a graph change event
    
    Parameters:
    t - the backing table where the change occurred (either a node table or an edge table)
    first - the first modified table row
    last - the last (inclusive) modified table row
    col - the number of the column modified, or EventConstants.ALL_COLUMNS for operations affecting all columns
    type - the type of modification, one of EventConstants.INSERT, EventConstants.DELETE, or EventConstants.UPDATE.

Class Graph

Nested Class Summary

Field Summary

Fields inherited from interface prefuse.data.tuple.TupleSet

Constructor Summary

Method Summary

Methods inherited from class prefuse.data.tuple.CompositeTupleSet

Methods inherited from class prefuse.data.tuple.AbstractTupleSet

Methods inherited from class java.lang.Object

Field Detail

INEDGES

OUTEDGES

UNDIRECTED

DEFAULT_NODE_KEY

DEFAULT_SOURCE_KEY

DEFAULT_TARGET_KEY

NODES

EDGES

m_links

m_nodeTuples

m_edgeTuples

m_directed

m_spanning

m_nkey

m_skey

m_tkey

m_nidx

m_longKey

INDEGREE

OUTDEGREE

INLINKS

OUTLINKS

LINKS_SCHEMA

Constructor Detail

Graph

Graph

Graph

Graph

Graph

Graph

Graph

Method Detail

init

setTupleManagers

dispose

setEdgeTable

initLinkTable

createLinkTable

updateDegrees

updateDegrees

addLink

remLink

updateNodeData

getNodeKeyField

getEdgeSourceField

getEdgeTargetField

getKey

getNodeIndex

addNodeRow

addNode

addEdge

addEdge

removeNode

removeNode

removeEdge

removeEdge

clearEdges

nodeCheck

getNodes

getNodeTable

getNodeCount

getNode

getNodeFromKey

getInDegree

getInDegree

getOutDegree

getOutDegree

getDegree

getDegree

isDirected