Package edu.cmu.tetrad.graph

Class EdgeListGraph

java.lang.Object

edu.cmu.tetrad.graph.EdgeListGraph

All Implemented Interfaces:

Graph, TripleClassifier, TetradSerializable, Serializable

public class EdgeListGraph
extends Object
implements Graph, TripleClassifier

Stores a graph a list of lists of edges adjacent to each node in the graph, with an additional list storing all of the edges in the graph. The edges are of the form N1 *-# N2. Multiple edges may be added per node pair to this graph, with the caveat that all edges of the form N1 *-# N2 will be considered equal. For example, if the edge X --> Y is added to the graph, another edge X --> Y may not be added, although an edge Y --> X may be added. Edges from nodes to themselves may also be added.> 0

Version:

$Id: $Id

Author:

josephramsey, Erin Korber additions summer 2004

See Also:

• Endpoint
• Serialized Form

Constructor Summary

Constructors

Constructor	Description
EdgeListGraph()	Constructs a new (empty) EdgeListGraph.
EdgeListGraph(EdgeListGraph graph)	Constructor for EdgeListGraph.
EdgeListGraph(Graph graph)	Constructs a EdgeListGraph using the nodes and edges of the given graph.
EdgeListGraph(List<Node> nodes)	Constructs a new graph, with no edges, using the given variable names.

Method Summary

Modifier and Type	Method	Description
void	addAmbiguousTriple(Node x, Node y, Node z)	addAmbiguousTriple.
void	addAttribute(String key, Object value)	addAttribute.
boolean	addBidirectedEdge(Node node1, Node node2)	Adds a bidirected edges <-> to the graph.
boolean	addDirectedEdge(Node node1, Node node2)	Adds a directed edge --> to the graph.
void	addDottedUnderlineTriple(Node x, Node y, Node z)	addDottedUnderlineTriple.
boolean	addEdge(Edge edge)	Adds the specified edge to the graph, provided it is not already in the graph.
boolean	addNode(Node node)	Adds a node to the graph.
boolean	addNondirectedEdge(Node node1, Node node2)	Adds a nondirected edges o-o to the graph.
boolean	addPartiallyOrientedEdge(Node node1, Node node2)	Adds a partially oriented edge o-> to the graph.
void	addPropertyChangeListener(PropertyChangeListener l)	Adds a PropertyChangeListener to the graph.
void	addUnderlineTriple(Node x, Node y, Node z)	addUnderlineTriple.
boolean	addUndirectedEdge(Node node1, Node node2)	Adds an undirected edge --- to the graph.
void	changeName(String name, String newName)	changeName.
void	clear()	Removes all nodes (and therefore all edges) from the graph.
boolean	containsEdge(Edge edge)	Determines whether this graph contains the given edge.
boolean	containsNode(Node node)	Determines whether this graph contains the given node.
boolean	equals(Object o)	Determines whether this graph is equal to some other graph, in the sense that they contain the same nodes and the sets of edges defined over these nodes in the two graphs are isomorphic typewise.
boolean	existsSemidirectedPath(Node node1, Node node2)	Determines whether one node is an ancestor of another.
void	fullyConnect(Endpoint endpoint)	Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.
List<Node>	getAdjacentNodes(Node node)	getAdjacentNodes.
Map<String,Object>	getAllAttributes()	getAllAttributes.
Set<Triple>	getAmbiguousTriples()	Getter for the field ambiguousTriples.
Object	getAttribute(String key)	getAttribute.
List<Node>	getChildren(Node node)	getChildren.
int	getDegree()	getDegree.
int	getDegree(Node node)	getDegree.
Edge	getDirectedEdge(Node node1, Node node2)	getDirectedEdge.
Set<Triple>	getDottedUnderlines()	getDottedUnderlines.
Edge	getEdge(Node node1, Node node2)	getEdge.
Set<Edge>	getEdges()	getEdges.
Set<Edge>	getEdges(Node node)	getEdges.
List<Edge>	getEdges(Node node1, Node node2)	getEdges.
Endpoint	getEndpoint(Node node1, Node node2)	getEndpoint.
int	getIndegree(Node node)	getIndegree.
Node	getNode(String name)	getNode.
List<String>	getNodeNames()	getNodeNames.
List<Node>	getNodes()	getNodes.
List<Node>	getNodesInTo(Node node, Endpoint endpoint)	Nodes adjacent to the given node with the given proximal endpoint.
List<Node>	getNodesOutTo(Node node, Endpoint endpoint)	Nodes adjacent to the given node with the given distal endpoint.
int	getNumEdges()	getNumEdges.
int	getNumEdges(Node node)	getNumEdges.
int	getNumNodes()	getNumNodes.
int	getOutdegree(Node node)	getOutdegree.
List<Node>	getParents(Node node)	getParents.
Set<Node>	getSepset(Node x, Node y, int maxLength)	Retrieves the set of nodes that form the sepset between two given nodes.
Set<Node>	getSepset(Node x, Node y, IndependenceTest test)	Returns the set of nodes that form the separating set between two given nodes.
Set<Node>	getSepsetContaining(Node x, Node y, Set<Node> containing, int maxLength)	Retrieves the set of nodes that form the sepset between two given nodes.
TimeLagGraph	getTimeLagGraph()	getTimeLagGraph.
List<String>	getTriplesClassificationTypes()	getTriplesClassificationTypes.
List<List<Triple>>	getTriplesLists(Node node)	getTriplesLists.
Set<Triple>	getUnderLines()	getUnderLines.
int	hashCode()
boolean	isAdjacentTo(Node node1, Node node2)	isAdjacentTo.
boolean	isAmbiguousTriple(Node x, Node y, Node z)	States whether r-s-r is an underline triple or not.
boolean	isAncestorOf(Node node1, Node node2)	Determines whether one node is an ancestor of another.
boolean	isChildOf(Node node1, Node node2)	isChildOf.
boolean	isDefCollider(Node node1, Node node2, Node node3)	Added by ekorber, 2004/6/9.
boolean	isDefNoncollider(Node node1, Node node2, Node node3)	Added by ekorber, 2004/6/9.
boolean	isExogenous(Node node)	isExogenous.
boolean	isMSeparatedFrom(Node x, Node y, Set<Node> z)	Determines whether x and y are d-separated given z.
boolean	isParameterizable(Node node)	isParameterizable.
boolean	isParentOf(Node node1, Node node2)	Determines whether node1 is a parent of node2.
boolean	isTimeLagModel()	isTimeLagModel.
boolean	isUnderlineTriple(Node x, Node y, Node z)	States whether r-s-r is an underline triple or not.
Paths	paths()	paths.
void	removeAmbiguousTriple(Node x, Node y, Node z)	removeAmbiguousTriple.
void	removeAttribute(String key)	removeAttribute.
void	removeDottedUnderlineTriple(Node x, Node y, Node z)	removeDottedUnderlineTriple.
boolean	removeEdge(Edge edge)	Removes the given edge from the graph.
boolean	removeEdge(Node node1, Node node2)	Removes an edge between two given nodes.
boolean	removeEdges(Node node1, Node node2)	Removes all edges connecting node A to node B.
boolean	removeEdges(Collection<Edge> edges)	Iterates through the list and removes any permissible edges found.
boolean	removeNode(Node node)	Removes a node from the graph.
boolean	removeNodes(List<Node> newNodes)	Iterates through the list and removes any permissible nodes found.
void	removeTriplesNotInGraph()	removeTriplesNotInGraph.
void	removeUnderlineTriple(Node x, Node y, Node z)	removeUnderlineTriple.
void	reorientAllWith(Endpoint endpoint)	Reorients all edges in the graph with the given endpoint.
static EdgeListGraph	serializableInstance()	Generates a simple exemplar of this class to test serialization.
void	setAmbiguousTriples(Set<Triple> triples)	setAmbiguousTriples.
void	setDottedUnderLineTriples(Set<Triple> triples)	setDottedUnderLineTriples.
boolean	setEndpoint(Node from, Node to, Endpoint endPoint)	Sets the endpoint type at the 'to' end of the edge from 'from' to 'to' to the given endpoint.
void	setNodes(List<Node> nodes)	setNodes.
void	setUnderLineTriples(Set<Triple> triples)	setUnderLineTriples.
Graph	subgraph(List<Node> nodes)	Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.
String	toString()	toString.
void	transferAttributes(Graph graph)	transferAttributes.
void	transferNodesAndEdges(Graph graph)	Transfers nodes and edges from one graph to another.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Details

EdgeListGraph

public EdgeListGraph()

Constructs a new (empty) EdgeListGraph.

EdgeListGraph

public EdgeListGraph(Graph graph)
              throws IllegalArgumentException

Constructs a EdgeListGraph using the nodes and edges of the given graph. If this cannot be accomplished successfully, an exception is thrown. Note that any graph constraints from the given graph are forgotten in the new graph.

Parameters:

graph - the graph from which nodes and edges are is to be extracted.

Throws:

IllegalArgumentException - if a duplicate edge is added.

EdgeListGraph

public EdgeListGraph(EdgeListGraph graph)
              throws IllegalArgumentException

Constructor for EdgeListGraph.

Parameters:

graph - a EdgeListGraph object

Throws:

IllegalArgumentException - if any.

EdgeListGraph

public EdgeListGraph(List<Node> nodes)

Constructs a new graph, with no edges, using the given variable names.

Parameters:

nodes - a List object

Method Details

serializableInstance

public static EdgeListGraph serializableInstance()

Generates a simple exemplar of this class to test serialization.

Returns:

a EdgeListGraph object

addDirectedEdge

public boolean addDirectedEdge(Node node1,
 Node node2)

Adds a directed edge --> to the graph.

Adds a directed edge to the graph from node A to node B.

Specified by:

addDirectedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

addUndirectedEdge

public boolean addUndirectedEdge(Node node1,
 Node node2)

Adds an undirected edge --- to the graph.

Adds an undirected edge to the graph from node A to node B.

Specified by:

addUndirectedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

addNondirectedEdge

public boolean addNondirectedEdge(Node node1,
 Node node2)

Adds a nondirected edges o-o to the graph.

Adds a nondirected edge to the graph from node A to node B.

Specified by:

addNondirectedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

addPartiallyOrientedEdge

public boolean addPartiallyOrientedEdge(Node node1,
 Node node2)

Adds a partially oriented edge o-> to the graph.

Adds a partially oriented edge to the graph from node A to node B.

Specified by:

addPartiallyOrientedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

addBidirectedEdge

public boolean addBidirectedEdge(Node node1,
 Node node2)

Adds a bidirected edges <-> to the graph.

Adds a bidirected edge to the graph from node A to node B.

Specified by:

addBidirectedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

isDefNoncollider

public boolean isDefNoncollider(Node node1,
 Node node2,
 Node node3)

Added by ekorber, 2004/6/9.

IllegalArgument exception raised (by isDirectedFromTo(getEndpoint) or by getEdge) if there are multiple edges between any of the node pairs.

Specified by:

isDefNoncollider in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

node3 - a Node object

Returns:

true if node 2 is a definite noncollider between 1 and 3

isDefCollider

public boolean isDefCollider(Node node1,
 Node node2,
 Node node3)

Added by ekorber, 2004/6/9.

Specified by:

isDefCollider in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

node3 - a Node object

Returns:

true if node 2 is a definite collider between 1 and 3

getChildren

public List<Node> getChildren(Node node)

getChildren.

Specified by:

getChildren in interface Graph

Parameters:

node - a Node object

Returns:

a mutable list of children for a node.

getDegree

public int getDegree()

getDegree.

Specified by:

getDegree in interface Graph

Returns:

the connectivity of the graph.

getEdge

public Edge getEdge(Node node1,
 Node node2)

getEdge.

Specified by:

getEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

the edge connecting node1 and node2, provided a unique such edge exists.

getDirectedEdge

public Edge getDirectedEdge(Node node1,
 Node node2)

getDirectedEdge.

Specified by:

getDirectedEdge in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

the directed edge from node1 to node2, if there is one.

getParents

public List<Node> getParents(Node node)

getParents.

Specified by:

getParents in interface Graph

Parameters:

node - a Node object

Returns:

the list of parents for a node.

isAncestorOf

public boolean isAncestorOf(Node node1,
 Node node2)

Determines whether one node is an ancestor of another. Including this here for caching purposes.

Specified by:

isAncestorOf in interface Graph

Parameters:

node1 - The first node.

node2 - The second node.

Returns:

True if the first node is an ancestor of the second, false if not.

existsSemidirectedPath

public boolean existsSemidirectedPath(Node node1,
 Node node2)

Determines whether one node is an ancestor of another. Including this here for caching purposes.

Specified by:

existsSemidirectedPath in interface Graph

Parameters:

node1 - The first node.

node2 - The second node.

Returns:

True if the first node is an ancestor of the second, false if not.

getIndegree

public int getIndegree(Node node)

getIndegree.

Specified by:

getIndegree in interface Graph

Parameters:

node - a Node object

Returns:

the number of arrow endpoints adjacent to a node.

getDegree

public int getDegree(Node node)

getDegree.

Specified by:

getDegree in interface Graph

Parameters:

node - a Node object

Returns:

the number of arrow endpoints adjacent to a node.

getOutdegree

public int getOutdegree(Node node)

getOutdegree.

Specified by:

getOutdegree in interface Graph

Parameters:

node - a Node object

Returns:

the number of null endpoints adjacent to an edge.

isAdjacentTo

public boolean isAdjacentTo(Node node1,
 Node node2)

isAdjacentTo.

Determines whether some edge or other exists between two nodes.

Specified by:

isAdjacentTo in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

true iff node1 is adjacent to node2 in the graph.

isChildOf

public boolean isChildOf(Node node1,
 Node node2)

isChildOf.

Determines whether one node is a child of another.

Specified by:

isChildOf in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

true iff node1 is a child of node2 in the graph.

getSepset

public Set<Node> getSepset(Node x,
 Node y,
 IndependenceTest test)

Returns the set of nodes that form the separating set between two given nodes. A separating set is a set of nodes that, when conditioned on, renders the given nodes d-separated.

Specified by:

getSepset in interface Graph

Parameters:

x - the first node

y - the second node

test - the independence test to use

Returns:

the set of nodes that form the separating set between the two given nodes

getSepset

public Set<Node> getSepset(Node x,
 Node y,
 int maxLength)

Retrieves the set of nodes that form the sepset between two given nodes. This method needs specifically to be called on the EdgeListGraph class, as it is not implemented in the Graph interface.

Parameters:

x - The first node.

y - The second node.

maxLength - The maximum length of the paths to consider.

Returns:

The set of nodes that form the sepset between the two given nodes.

getSepsetContaining

public Set<Node> getSepsetContaining(Node x,
 Node y,
 Set<Node> containing,
 int maxLength)

Retrieves the set of nodes that form the sepset between two given nodes. This method needs specifically

Parameters:

x - The first node.

y - The second node.

containing - The set of nodes that must be contained in the sepset.

maxLength - The maximum length of the paths to consider.

Returns:

The set of nodes that form the sepset between the two given nodes.

isMSeparatedFrom

public boolean isMSeparatedFrom(Node x,
 Node y,
 Set<Node> z)

Determines whether x and y are d-separated given z.

Parameters:

x - a Node object

y - a Node object

z - a Set object

Returns:

True if the nodes in x are all d-separated from nodes in y given nodes in z, false if not.

isParentOf

public boolean isParentOf(Node node1,
 Node node2)

Determines whether node1 is a parent of node2.

Determines whether one node is a parent of another.

Specified by:

isParentOf in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

a boolean

See Also:

• isChildOf(edu.cmu.tetrad.graph.Node, edu.cmu.tetrad.graph.Node)
• getParents(edu.cmu.tetrad.graph.Node)
• getChildren(edu.cmu.tetrad.graph.Node)

transferNodesAndEdges

public void transferNodesAndEdges(Graph graph)
                           throws IllegalArgumentException

Transfers nodes and edges from one graph to another. One way this is used is to change graph types. One constructs a new graph based on the old graph, and this method is called to transfer the nodes and edges of the old graph to the new graph.

Transfers nodes and edges from one graph to another. One way this is used is to change graph types. One constructs a new graph based on the old graph, and this method is called to transfer the nodes and edges of the old graph to the new graph.

Specified by:

transferNodesAndEdges in interface Graph

Parameters:

graph - the graph from which nodes and edges are to be pilfered.

Throws:

IllegalArgumentException - This exception is thrown if adding some node.

transferAttributes

public void transferAttributes(Graph graph)
                        throws IllegalArgumentException

transferAttributes.

Specified by:

transferAttributes in interface Graph

Parameters:

graph - a Graph object

Throws:

IllegalArgumentException - if any.

paths

public Paths paths()

paths.

Specified by:

paths in interface Graph

Returns:

a Paths object

isExogenous

public boolean isExogenous(Node node)

isExogenous.

Determines whether a node in a graph is exogenous.

Specified by:

isExogenous in interface Graph

Parameters:

node - a Node object

Returns:

true iff the given node is exogenous in the graph.

getAdjacentNodes

public List<Node> getAdjacentNodes(Node node)

getAdjacentNodes.

Specified by:

getAdjacentNodes in interface Graph

Parameters:

node - a Node object

Returns:

a mutable list of nodes adjacent to the given node.

removeEdge

public boolean removeEdge(Node node1,
 Node node2)

Removes an edge between two given nodes.

Removes the edge connecting the two given nodes.

Specified by:

removeEdge in interface Graph

Parameters:

node1 - The first node.

node2 - The second node.

Returns:

true if the edge between node1 and node2 was successfully removed, false otherwise.

getEndpoint

public Endpoint getEndpoint(Node node1,
 Node node2)

getEndpoint.

Specified by:

getEndpoint in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

the endpoint along the edge from node to node2 at the node2 end.

setEndpoint

public boolean setEndpoint(Node from,
 Node to,
 Endpoint endPoint)
                    throws IllegalArgumentException

Sets the endpoint type at the 'to' end of the edge from 'from' to 'to' to the given endpoint. Note: NOT CONSTRAINT SAFE

If there is currently an edge from node1 to node2, sets the endpoint at node2 to the given endpoint; if there is no such edge, adds an edge --# where # is the given endpoint. Setting an endpoint to null, provided there is exactly one edge connecting the given nodes, removes the edge. (If there is more than one edge, an exception is thrown.)

Specified by:

setEndpoint in interface Graph

Parameters:

from - a Node object

to - a Node object

endPoint - a Endpoint object

Returns:

a boolean

Throws:

IllegalArgumentException

getNodesInTo

public List<Node> getNodesInTo(Node node,
 Endpoint endpoint)

Nodes adjacent to the given node with the given proximal endpoint.

Nodes adjacent to the given node with the given proximal endpoint.

Specified by:

getNodesInTo in interface Graph

Parameters:

node - a Node object

endpoint - a Endpoint object

Returns:

a List object

getNodesOutTo

public List<Node> getNodesOutTo(Node node,
 Endpoint endpoint)

Nodes adjacent to the given node with the given distal endpoint.

( Nodes adjacent to the given node with the given distal endpoint.

Specified by:

getNodesOutTo in interface Graph

Parameters:

node - a Node object

endpoint - a Endpoint object

Returns:

a List object

addEdge

public boolean addEdge(Edge edge)

Adds the specified edge to the graph, provided it is not already in the graph.

Adds an edge to the graph.

Specified by:

addEdge in interface Graph

Parameters:

edge - a Edge object

Returns:

true if the edge was added, false if not.

addNode

public boolean addNode(Node node)

Adds a node to the graph. Precondition: The proposed name of the node cannot already be used by any other node in the same graph.

Adds a node to the graph. Precondition: The proposed name of the node cannot already be used by any other node in the same graph.

Specified by:

addNode in interface Graph

Parameters:

node - a Node object

Returns:

true if nodes were added, false if not.

getEdges

public Set<Edge> getEdges()

getEdges.

Specified by:

getEdges in interface Graph

Returns:

the set of edges in the graph. No particular ordering of the edges in the list is guaranteed.

containsEdge

public boolean containsEdge(Edge edge)

Determines whether this graph contains the given edge.

Determines if the graph contains a particular edge.

Specified by:

containsEdge in interface Graph

Parameters:

edge - a Edge object

Returns:

true iff the graph contain 'edge'.

containsNode

public boolean containsNode(Node node)

Determines whether this graph contains the given node.

Determines whether the graph contains a particular node.

Specified by:

containsNode in interface Graph

Parameters:

node - a Node object

Returns:

true iff the graph contains 'node'.

getEdges

public Set<Edge> getEdges(Node node)

getEdges.

Specified by:

getEdges in interface Graph

Parameters:

node - a Node object

Returns:

the set of edges connected to a particular node. No particular ordering of the edges in the list is guaranteed.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Determines whether this graph is equal to some other graph, in the sense that they contain the same nodes and the sets of edges defined over these nodes in the two graphs are isomorphic typewise. That is, if node A and B exist in both graphs, and if there are, e.g., three edges between A and B in the first graph, two of which are directed edges and one of which is an undirected edge, then in the second graph there must also be two directed edges and one undirected edge between nodes A and B.

Specified by:

equals in interface Graph

Overrides:

equals in class Object

Parameters:

o - a Object object

Returns:

a boolean

fullyConnect

public void fullyConnect(Endpoint endpoint)

Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.

Resets the graph so that it is fully connects it using #-# edges, where # is the given endpoint.

Specified by:

fullyConnect in interface Graph

Parameters:

endpoint - a Endpoint object

reorientAllWith

public void reorientAllWith(Endpoint endpoint)

Reorients all edges in the graph with the given endpoint.

Specified by:

reorientAllWith in interface Graph

Parameters:

endpoint - a Endpoint object

getNode

public Node getNode(String name)

getNode.

Specified by:

getNode in interface Graph

Parameters:

name - a String object

Returns:

the node with the given string name. In case of accidental duplicates, the first node encountered with the given name is returned. In case no node exists with the given name, null is returned.

getNumNodes

public int getNumNodes()

getNumNodes.

Specified by:

getNumNodes in interface Graph

Returns:

the number of nodes in the graph.

getNumEdges

public int getNumEdges()

getNumEdges.

Specified by:

getNumEdges in interface Graph

Returns:

the number of edges in the (entire) graph.

getNumEdges

public int getNumEdges(Node node)

getNumEdges.

Specified by:

getNumEdges in interface Graph

Parameters:

node - a Node object

Returns:

the number of edges in the graph which are connected to a particular node.

getNodes

public List<Node> getNodes()

getNodes.

Specified by:

getNodes in interface Graph

Returns:

the list of nodes for the graph.

setNodes

public void setNodes(List<Node> nodes)

setNodes.

Specified by:

setNodes in interface Graph

Parameters:

nodes - a List object

clear

public void clear()

Removes all nodes (and therefore all edges) from the graph.

Removes all nodes (and therefore all edges) from the graph.

Specified by:

clear in interface Graph

removeEdge

public boolean removeEdge(Edge edge)

Removes the given edge from the graph.

Removes an edge from the graph. (Note: It is dangerous to make a recursive call to this method (as it stands) from a method containing certain types of iterators. The problem is that if one uses an iterator that iterates over the edges of node A or node B, and tries in the process to remove those edges using this method, a concurrent modification exception will be thrown.)

Specified by:

removeEdge in interface Graph

Parameters:

edge - a Edge object

Returns:

true if the edge was removed, false if not.

removeEdges

public boolean removeEdges(Collection<Edge> edges)

Iterates through the list and removes any permissible edges found. The order in which edges are added is the order in which they are presented in the iterator.

Removes any relevant edge objects found in this collection. G

Specified by:

removeEdges in interface Graph

Parameters:

edges - a Collection object

Returns:

true if edges were added, false if not.

removeEdges

public boolean removeEdges(Node node1,
 Node node2)

Removes all edges connecting node A to node B. In most cases, this will remove at most one edge, but since multiple edges are permitted in some graph implementations, the number will in some cases be greater than one.

Removes all edges connecting node A to node B.

Specified by:

removeEdges in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

true if edges were removed, false if not.

removeNode

public boolean removeNode(Node node)

Removes a node from the graph.

Removes a node from the graph.

Specified by:

removeNode in interface Graph

Parameters:

node - a Node object

Returns:

true if the node was removed, false if not.

removeNodes

public boolean removeNodes(List<Node> newNodes)

Iterates through the list and removes any permissible nodes found. The order in which nodes are removed is the order in which they are presented in the iterator.

Removes any relevant node objects found in this collection.

Specified by:

removeNodes in interface Graph

Parameters:

newNodes - a List object

Returns:

true if nodes were added, false if not.

toString

public String toString()

toString.

Specified by:

toString in interface Graph

Overrides:

toString in class Object

Returns:

a string representation of the graph.

subgraph

public Graph subgraph(List<Node> nodes)

Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.

Specified by:

subgraph in interface Graph

Parameters:

nodes - a List object

Returns:

a Graph object

getEdges

public List<Edge> getEdges(Node node1,
 Node node2)

getEdges.

Specified by:

getEdges in interface Graph

Parameters:

node1 - a Node object

node2 - a Node object

Returns:

the edges connecting node1 and node2.

getNodeNames

public List<String> getNodeNames()

getNodeNames.

Specified by:

getNodeNames in interface Graph

Returns:

the names of the nodes, in the order of getNodes.

isParameterizable

public boolean isParameterizable(Node node)

isParameterizable.

Specified by:

isParameterizable in interface Graph

Parameters:

node - a Node object

Returns:

true if the given node is parameterizable.

isTimeLagModel

public boolean isTimeLagModel()

isTimeLagModel.

Specified by:

isTimeLagModel in interface Graph

Returns:

true if this is a time lag model, in which case getTimeLagGraph() returns the graph.

getTimeLagGraph

public TimeLagGraph getTimeLagGraph()

getTimeLagGraph.

Specified by:

getTimeLagGraph in interface Graph

Returns:

the underlying time lag model, if there is one; otherwise, returns null.

changeName

public void changeName(String name,
 String newName)

changeName.

Parameters:

name - a String object

newName - a String object

getAllAttributes

public Map<String,Object> getAllAttributes()

getAllAttributes.

Specified by:

getAllAttributes in interface Graph

Returns:

a Map object

getAttribute

public Object getAttribute(String key)

getAttribute.

Specified by:

getAttribute in interface Graph

Parameters:

key - a String object

Returns:

a Object object

removeAttribute

public void removeAttribute(String key)

removeAttribute.

Specified by:

removeAttribute in interface Graph

Parameters:

key - a String object

addAttribute

public void addAttribute(String key,
 Object value)

addAttribute.

Specified by:

addAttribute in interface Graph

Parameters:

key - a String object

value - a Object object

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Adds a PropertyChangeListener to the graph.

Specified by:

addPropertyChangeListener in interface Graph

Parameters:

l - a PropertyChangeListener object

getAmbiguousTriples

public Set<Triple> getAmbiguousTriples()

Getter for the field ambiguousTriples.

Specified by:

getAmbiguousTriples in interface Graph

Returns:

a Set object

setAmbiguousTriples

public void setAmbiguousTriples(Set<Triple> triples)

setAmbiguousTriples.

Specified by:

setAmbiguousTriples in interface Graph

Parameters:

triples - a Set object

getUnderLines

public Set<Triple> getUnderLines()

getUnderLines.

Specified by:

getUnderLines in interface Graph

Returns:

a Set object

getDottedUnderlines

public Set<Triple> getDottedUnderlines()

getDottedUnderlines.

Specified by:

getDottedUnderlines in interface Graph

Returns:

a Set object

isAmbiguousTriple

public boolean isAmbiguousTriple(Node x,
 Node y,
 Node z)

States whether r-s-r is an underline triple or not.

States whether r-s-r is an underline triple or not.

Specified by:

isAmbiguousTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

Returns:

a boolean

isUnderlineTriple

public boolean isUnderlineTriple(Node x,
 Node y,
 Node z)

States whether r-s-r is an underline triple or not.

States whether r-s-r is an underline triple or not.

Specified by:

isUnderlineTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

Returns:

a boolean

addAmbiguousTriple

public void addAmbiguousTriple(Node x,
 Node y,
 Node z)

addAmbiguousTriple.

Specified by:

addAmbiguousTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

addUnderlineTriple

public void addUnderlineTriple(Node x,
 Node y,
 Node z)

addUnderlineTriple.

Specified by:

addUnderlineTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

addDottedUnderlineTriple

public void addDottedUnderlineTriple(Node x,
 Node y,
 Node z)

addDottedUnderlineTriple.

Specified by:

addDottedUnderlineTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

removeAmbiguousTriple

public void removeAmbiguousTriple(Node x,
 Node y,
 Node z)

removeAmbiguousTriple.

Specified by:

removeAmbiguousTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

removeUnderlineTriple

public void removeUnderlineTriple(Node x,
 Node y,
 Node z)

removeUnderlineTriple.

Specified by:

removeUnderlineTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

removeDottedUnderlineTriple

public void removeDottedUnderlineTriple(Node x,
 Node y,
 Node z)

removeDottedUnderlineTriple.

Specified by:

removeDottedUnderlineTriple in interface Graph

Parameters:

x - a Node object

y - a Node object

z - a Node object

setUnderLineTriples

public void setUnderLineTriples(Set<Triple> triples)

setUnderLineTriples.

Specified by:

setUnderLineTriples in interface Graph

Parameters:

triples - a Set object

setDottedUnderLineTriples

public void setDottedUnderLineTriples(Set<Triple> triples)

setDottedUnderLineTriples.

Specified by:

setDottedUnderLineTriples in interface Graph

Parameters:

triples - a Set object

removeTriplesNotInGraph

public void removeTriplesNotInGraph()

removeTriplesNotInGraph.

Specified by:

removeTriplesNotInGraph in interface Graph

getTriplesClassificationTypes

public List<String> getTriplesClassificationTypes()

getTriplesClassificationTypes.

Specified by:

getTriplesClassificationTypes in interface TripleClassifier

Returns:

the names of the triple classifications. Coordinates with getTriplesList

getTriplesLists

public List<List<Triple>> getTriplesLists(Node node)

getTriplesLists.

Specified by:

getTriplesLists in interface TripleClassifier

Parameters:

node - a Node object

Returns:

a List object