edu.cmu.tetrad.graph.Dag

All Implemented Interfaces:: Graph, TetradSerializable, Serializable

public final class Dag extends Object implements Graph

Represents a directed acyclic graph--that is, a graph containing only directed edges, with no cycles. Variables are permitted to be either measured or latent, with at most one edge per node pair, and no edges to self.

Version:

$Id: $Id

Author:

josephramsey

See Also:

Constructor Summary

Constructors

Constructor

Description

Dag()

Constructs a new directed acyclic graph (DAG).

Dag(Graph graph)

Constructs a new directed acyclic graph from the given graph object.

Dag(List<Node> nodes)

Constructor for Dag.
Method Summary

Modifier and Type

Method

Description

void

addAmbiguousTriple(Node x, Node y, Node z)

Adds an ambiguous triple to the list of ambiguous triples.

void

addAttribute(String key, Object value)

Adds an attribute to the graph.

boolean

addBidirectedEdge(Node node1, Node node2)

Adds a bidirectional edge between two nodes.

boolean

addDirectedEdge(Node node1, Node node2)

Adds a directed edge between two nodes.

void

addDottedUnderlineTriple(Node x, Node y, Node z)

Adds a dotted underline triple to the graph.

boolean

addEdge(Edge edge)

Adds a directed edge to the Directed Acyclic Graph (DAG).

boolean

addNode(Node node)

Adds a Node to the graph.

boolean

addNondirectedEdge(Node node1, Node node2)

Adds a nondirected edge between two nodes in the graph.

boolean

addPartiallyOrientedEdge(Node node1, Node node2)

Adds a partially oriented edge between two nodes.

void

addPropertyChangeListener(PropertyChangeListener e)

Adds a PropertyChangeListener to the underlying graph object.

void

addUnderlineTriple(Node x, Node y, Node z)

Adds an underline triple to the current object.

boolean

addUndirectedEdge(Node node1, Node node2)

Adds an undirected edge between two nodes.

void

clear()

clear.

boolean

containsEdge(Edge edge)

Checks if the given edge is present in the graph.

boolean

containsNode(Node node)

Checks if the given Node object is contained in the graph.

boolean

equals(Object o)

Compares this Graph object with the specified object for equality.

void

fullyConnect(Endpoint endpoint)

Fully connects the given endpoint.

List<Node>

getAdjacentNodes(Node node)

Retrieves the adjacent nodes of a given node in the graph.

Map<String,Object>

getAllAttributes()

getAllAttributes.

Set<Triple>

getAmbiguousTriples()

Returns a set of ambiguous triples.

Object

getAttribute(String key)

Retrieves the value associated with the given key in the attribute map.

List<Node>

getChildren(Node node)

Retrieves the children of a specified Node in the graph.

int

getDegree()

getDegree.

int

getDegree(Node node)

Returns the degree of a given node in the graph.

Edge

getDirectedEdge(Node node1, Node node2)

Returns the directed edge between the given nodes, if one exists in the graph.

Set<Triple>

getDottedUnderlines()

getDottedUnderlines.

Edge

getEdge(Node node1, Node node2)

Retrieves the edge between two nodes in the graph.

Set<Edge>

getEdges()

getEdges.

Set<Edge>

getEdges(Node node)

Returns a list of edges connected to the given node.

List<Edge>

getEdges(Node node1, Node node2)

Returns a list of edges between the specified nodes in the graph.

Endpoint

getEndpoint(Node node1, Node node2)

Returns the endpoint between two nodes in the graph.

int

getIndegree(Node node)

Returns the indegree of the specified node in the graph.

Node

getNode(String name)

Retrieves the node in the graph with the specified name.

List<String>

getNodeNames()

getNodeNames.

List<Node>

getNodes()

getNodes.

List<Node>

getNodesInTo(Node node, Endpoint n)

Retrieves a list of nodes in the given graph that have edges pointing into the specified node and endpoint.

List<Node>

getNodesOutTo(Node node, Endpoint n)

Retrieves a list of nodes that have outgoing edges to a specified node and endpoint.

int

getNumEdges()

getNumEdges.

int

getNumEdges(Node node)

Returns the number of edges connected to the specified node.

int

getNumNodes()

getNumNodes.

int

getOutdegree(Node node)

Returns the outdegree of the given node.

List<Node>

getParents(Node node)

Retrieves the list of parent nodes for a given node in the graph.

Set<Node>

getSepset(Node n1, Node n2, IndependenceTest test)

Returns the sepset between two given nodes in the graph.

TimeLagGraph

getTimeLagGraph()

getTimeLagGraph.

Set<Triple>

getUnderLines()

Retrieves the set of underlined triples.

boolean

isAdjacentTo(Node node1, Node node2)

Determines whether two nodes are adjacent in the graph.

boolean

isAmbiguousTriple(Node x, Node y, Node z)

Determines if a triple of nodes is ambiguous.

boolean

isChildOf(Node node1, Node node2)

Checks if the given node1 is a child of node2 in the graph.

boolean

isDefCollider(Node node1, Node node2, Node node3)

Checks if there is a definite collider between three nodes in the graph.

boolean

isDefNoncollider(Node node1, Node node2, Node node3)

Checks if three given nodes form a definite non-collider in a graph.

boolean

isExogenous(Node node)

Checks whether a given node is exogenous.

boolean

isParameterizable(Node node)

Checks if the given node is parameterizable.

boolean

isParentOf(Node node1, Node node2)

Determines if a given node is a parent of another node in the graph.

boolean

isTimeLagModel()

isTimeLagModel.

boolean

isUnderlineTriple(Node x, Node y, Node z)

Determines if a triple of nodes is underlined.

Paths

paths()

paths.

void

removeAmbiguousTriple(Node x, Node y, Node z)

Removes an ambiguous triple from the list of ambiguous triples.

void

removeAttribute(String key)

Removes an attribute from the graph.

void

removeDottedUnderlineTriple(Node x, Node y, Node z)

Removes a dotted underline triple from the set of triples.

boolean

removeEdge(Edge edge)

Removes a given edge from the graph.

boolean

removeEdge(Node node1, Node node2)

Removes the edge between two nodes in the graph.

boolean

removeEdges(Node node1, Node node2)

Removes an edge between two nodes.

boolean

removeEdges(Collection<Edge> edges)

Removes the given edges from the graph.

boolean

removeNode(Node node)

Removes the specified node from the graph.

boolean

removeNodes(List<Node> nodes)

Removes the specified nodes from the graph.

void

removeTriplesNotInGraph()

Removes triples from the graph that contain nodes not present in the graph or are not adjacent to each other.

void

removeUnderlineTriple(Node x, Node y, Node z)

Removes an underline triple from the list of underline triples.

void

reorientAllWith(Endpoint endpoint)

Reorients all edges in a Directed Acyclic Graph (DAG) with a single endpoint type.

static Dag

serializableInstance()

Generates a simple exemplar of this class to test serialization.

void

setAmbiguousTriples(Set<Triple> triples)

Sets the ambiguous triples for the object.

void

setDottedUnderLineTriples(Set<Triple> triples)

Sets the dotted underline triples for the given set of Triples.

boolean

setEndpoint(Node from, Node to, Endpoint endPoint)

Sets the endpoint of a directed edge between two nodes in a graph.

void

setNodes(List<Node> nodes)

Set the nodes of the graph.

void

setUnderLineTriples(Set<Triple> triples)

Sets the underlined triples.

Graph

subgraph(List<Node> nodes)

Returns a subgraph of the current graph consisting only of the specified nodes.

String

toString()

toString.

void

transferAttributes(Graph graph)

Transfers attributes from the given graph to the current graph.

void

transferNodesAndEdges(Graph graph)

Transfers nodes and edges from the given graph to the current graph.

Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.graph.Graph
existsSemidirectedPath, isAncestorOf

Constructor Details
- Dag
  
  public Dag()
  
  Constructs a new directed acyclic graph (DAG).
- Dag
  
  public Dag(List<Node> nodes)
  
  Constructor for Dag.
  
  Parameters:
  
  nodes - a List object
- Dag
  
  public Dag(Graph graph) throws IllegalArgumentException
  
  Constructs a new directed acyclic graph from the given graph object.
  
  Parameters:
  
  graph - the graph to base the new DAG on.
  
  Throws:
  
  IllegalArgumentException - if the given graph cannot for some reason be converted into a DAG.
Method Details
- serializableInstance
  
  public static Dag serializableInstance()
  
  Generates a simple exemplar of this class to test serialization.
  
  Returns:
  
  a Dag object
- addBidirectedEdge
  
  public boolean addBidirectedEdge(Node node1, Node node2)
  
  Adds a bidirectional edge between two nodes.
  
  Specified by:
  
  addBidirectedEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to connect (a Node object)
  
  node2 - the second node to connect (a Node object)
  
  Returns:
  
  true if the bidirectional edge was successfully added, false otherwise
- addDirectedEdge
  
  public boolean addDirectedEdge(Node node1, Node node2)
  
  Adds a directed edge between two nodes.
  
  Specified by:
  
  addDirectedEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to connect (source node)
  
  node2 - the second node to connect (target node)
  
  Returns:
  
  true if the directed edge is successfully added, false otherwise
- addUndirectedEdge
  
  public boolean addUndirectedEdge(Node node1, Node node2)
  
  Adds an undirected edge between two nodes.
  
  Specified by:
  
  addUndirectedEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to connect (a Node object)
  
  node2 - the second node to connect (a Node object)
  
  Returns:
  
  true if the undirected edge is successfully added, false otherwise
- addNondirectedEdge
  
  public boolean addNondirectedEdge(Node node1, Node node2)
  
  Adds a nondirected edge between two nodes in the graph.
  
  Specified by:
  
  addNondirectedEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to connect (a Node object)
  
  node2 - the second node to connect (a Node object)
  
  Returns:
  
  true if the edge was successfully added, false otherwise
- addPartiallyOrientedEdge
  
  public boolean addPartiallyOrientedEdge(Node node1, Node node2)
  
  Adds a partially oriented edge between two nodes.
  
  Specified by:
  
  addPartiallyOrientedEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to be connected
  
  node2 - the second node to be connected
  
  Returns:
  
  true if the partially oriented edge is added successfully, false otherwise
  
  Throws:
  
  UnsupportedOperationException - if the graph is a directed acyclic graph (DAG)
- addEdge
  
  public boolean addEdge(Edge edge)
  
  Adds a directed edge to the Directed Acyclic Graph (DAG).
  
  Specified by:
  
  addEdge in interface Graph
  
  Parameters:
  
  edge - the directed Edge object to be added
  
  Returns:
  
  true if the edge is successfully added, false otherwise
  
  Throws:
  
  IllegalArgumentException - if the provided edge is not a directed edge or adding the edge would result in a cycle
- addNode
  
  public boolean addNode(Node node)
  
  Adds a Node to the graph.
  
  Specified by:
  
  addNode in interface Graph
  
  Parameters:
  
  node - the Node object to be added
  
  Returns:
  
  true if the Node is successfully added, false otherwise
- addPropertyChangeListener
  
  public void addPropertyChangeListener(PropertyChangeListener e)
  
  Adds a PropertyChangeListener to the underlying graph object.
  
  Specified by:
  
  addPropertyChangeListener in interface Graph
  
  Parameters:
  
  e - the PropertyChangeListener to be added
- clear
  
  public void clear()
  
  clear.
  
  Specified by:
  
  clear in interface Graph
- containsEdge
  
  public boolean containsEdge(Edge edge)
  
  Checks if the given edge is present in the graph.
  
  Specified by:
  
  containsEdge in interface Graph
  
  Parameters:
  
  edge - the edge to check if present in the graph
  
  Returns:
  
  true if the edge is present in the graph, false otherwise
- containsNode
  
  public boolean containsNode(Node node)
  
  Checks if the given Node object is contained in the graph.
  
  Specified by:
  
  containsNode in interface Graph
  
  Parameters:
  
  node - The Node object to check for containment. Must not be null.
  
  Returns:
  
  true if the Node object is contained in the graph, false otherwise.
- equals
  
  public boolean equals(Object o)
  
  Compares this Graph object with the specified object for equality.
  
  Specified by:
  
  equals in interface Graph
  
  Overrides:
  
  equals in class Object
  
  Parameters:
  
  o - the object to compare this graph with
  
  Returns:
  
  true if the specified object is equal to this graph, false otherwise
- fullyConnect
  
  public void fullyConnect(Endpoint endpoint)
  
  Fully connects the given endpoint.
  
  Specified by:
  
  fullyConnect in interface Graph
  
  Parameters:
  
  endpoint - The endpoint to fully connect.
  
  Throws:
  
  UnsupportedOperationException - If the endpoint is a single endpoint type and cannot be fully connected.
- reorientAllWith
  
  public void reorientAllWith(Endpoint endpoint)
  
  Reorients all edges in a Directed Acyclic Graph (DAG) with a single endpoint type.
  
  Specified by:
  
  reorientAllWith in interface Graph
  
  Parameters:
  
  endpoint - The type of endpoint to reorient all edges with. Must be an instance of `edu.cmu.tetrad.graph.Endpoint`.
  
  Throws:
  
  UnsupportedOperationException - if attempting to reorient all edges in a DAG with a single endpoint type.
- getAdjacentNodes
  
  public List<Node> getAdjacentNodes(Node node)
  
  Retrieves the adjacent nodes of a given node in the graph.
  
  Specified by:
  
  getAdjacentNodes in interface Graph
  
  Parameters:
  
  node - the node for which to retrieve adjacent nodes
  
  Returns:
  
  a List of nodes that are adjacent to the given node
- getChildren
  
  public List<Node> getChildren(Node node)
  
  Retrieves the children of a specified Node in the graph.
  
  Specified by:
  
  getChildren in interface Graph
  
  Parameters:
  
  node - The Node object whose children are to be retrieved.
  
  Returns:
  
  A List of Node objects representing the children of the specified node.
- getDegree
  
  public int getDegree()
  
  getDegree.
  
  Specified by:
  
  getDegree in interface Graph
  
  Returns:
  
  a int
- getEdge
  
  public Edge getEdge(Node node1, Node node2)
  
  Retrieves the edge between two nodes in the graph.
  
  Specified by:
  
  getEdge in interface Graph
  
  Parameters:
  
  node1 - a Node object representing the first node
  
  node2 - a Node object representing the second node
  
  Returns:
  
  the edge between node1 and node2, or null if no such edge exists
- getDirectedEdge
  
  public Edge getDirectedEdge(Node node1, Node node2)
  
  Returns the directed edge between the given nodes, if one exists in the graph.
  
  Specified by:
  
  getDirectedEdge in interface Graph
  
  Parameters:
  
  node1 - the first Node object
  
  node2 - the second Node object
  
  Returns:
  
  the directed edge between the given nodes, or null if no edge exists
- getEdges
  
  public Set<Edge> getEdges(Node node)
  
  Returns a list of edges connected to the given node.
  
  Specified by:
  
  getEdges in interface Graph
  
  Parameters:
  
  node - a Node object representing the node
  
  Returns:
  
  a list of Edge objects connected to the node
- getEdges
  
  public List<Edge> getEdges(Node node1, Node node2)
  
  Returns a list of edges between the specified nodes in the graph.
  
  Specified by:
  
  getEdges in interface Graph
  
  Parameters:
  
  node1 - the first node in the edge pair. Must not be null.
  
  node2 - the second node in the edge pair. Must not be null.
  
  Returns:
  
  a list of edges between the specified nodes. Returns an empty list if no edges are found.
- getEdges
  
  public Set<Edge> getEdges()
  
  getEdges.
  
  Specified by:
  
  getEdges in interface Graph
  
  Returns:
  
  a Set object
- getEndpoint
  
  public Endpoint getEndpoint(Node node1, Node node2)
  
  Returns the endpoint between two nodes in the graph.
  
  Specified by:
  
  getEndpoint in interface Graph
  
  Parameters:
  
  node1 - a Node object representing the first node
  
  node2 - a Node object representing the second node
  
  Returns:
  
  the Endpoint object representing the endpoint between the two nodes
- getIndegree
  
  public int getIndegree(Node node)
  
  Returns the indegree of the specified node in the graph.
  
  Specified by:
  
  getIndegree in interface Graph
  
  Parameters:
  
  node - the node for which to find the indegree
  
  Returns:
  
  the indegree of the specified node
- getDegree
  
  public int getDegree(Node node)
  
  Returns the degree of a given node in the graph.
  
  Specified by:
  
  getDegree in interface Graph
  
  Parameters:
  
  node - the node whose degree needs to be calculated
  
  Returns:
  
  the degree of the node
- getNode
  
  public Node getNode(String name)
  
  Retrieves the node in the graph with the specified name.
  
  Specified by:
  
  getNode in interface Graph
  
  Parameters:
  
  name - a String object representing the name of the node
  
  Returns:
  
  the Node object found in the graph with the specified name
- getNodes
  
  public List<Node> getNodes()
  
  getNodes.
  
  Specified by:
  
  getNodes in interface Graph
  
  Returns:
  
  a List object
- setNodes
  
  public void setNodes(List<Node> nodes)
  
  Set the nodes of the graph.
  
  Specified by:
  
  setNodes in interface Graph
  
  Parameters:
  
  nodes - A list of Node objects representing the nodes to be set.
- getNodeNames
  
  public List<String> getNodeNames()
  
  getNodeNames.
  
  Specified by:
  
  getNodeNames in interface Graph
  
  Returns:
  
  a List object
- getNumEdges
  
  public int getNumEdges()
  
  getNumEdges.
  
  Specified by:
  
  getNumEdges in interface Graph
  
  Returns:
  
  a int
- getNumEdges
  
  public int getNumEdges(Node node)
  
  Returns the number of edges connected to the specified node.
  
  Specified by:
  
  getNumEdges in interface Graph
  
  Parameters:
  
  node - the node for which to retrieve the number of edges
  
  Returns:
  
  the number of edges connected to the specified node
- getNumNodes
  
  public int getNumNodes()
  
  getNumNodes.
  
  Specified by:
  
  getNumNodes in interface Graph
  
  Returns:
  
  a int
- getOutdegree
  
  public int getOutdegree(Node node)
  
  Returns the outdegree of the given node.
  
  Specified by:
  
  getOutdegree in interface Graph
  
  Parameters:
  
  node - a Node object
  
  Returns:
  
  the outdegree of the node
- getParents
  
  public List<Node> getParents(Node node)
  
  Retrieves the list of parent nodes for a given node in the graph.
  
  Specified by:
  
  getParents in interface Graph
  
  Parameters:
  
  node - the node for which to retrieve the parent nodes
  
  Returns:
  
  the list of parent nodes for the given node
- isAdjacentTo
  
  public boolean isAdjacentTo(Node node1, Node node2)
  
  Determines whether two nodes are adjacent in the graph.
  
  Specified by:
  
  isAdjacentTo in interface Graph
  
  Parameters:
  
  node1 - The first node to check adjacency.
  
  node2 - The second node to check adjacency.
  
  Returns:
  
  true if the nodes are adjacent, false otherwise.
- isChildOf
  
  public boolean isChildOf(Node node1, Node node2)
  
  Checks if the given node1 is a child of node2 in the graph.
  
  Specified by:
  
  isChildOf in interface Graph
  
  Parameters:
  
  node1 - the first Node object to be checked
  
  node2 - the second Node object to be checked against
  
  Returns:
  
  true if node1 is a child of node2, false otherwise
- isParentOf
  
  public boolean isParentOf(Node node1, Node node2)
  
  Determines if a given node is a parent of another node in the graph.
  
  Specified by:
  
  isParentOf in interface Graph
  
  Parameters:
  
  node1 - the first node to be compared.
  
  node2 - the second node to be compared.
  
  Returns:
  
  true if node1 is a parent of node2, false otherwise.
- isDefNoncollider
  
  public boolean isDefNoncollider(Node node1, Node node2, Node node3)
  
  Checks if three given nodes form a definite non-collider in a graph.
  
  Specified by:
  
  isDefNoncollider in interface Graph
  
  Parameters:
  
  node1 - the first node
  
  node2 - the second node
  
  node3 - the third node
  
  Returns:
  
  true if the three nodes form a definite non-collider, false otherwise
- isDefCollider
  
  public boolean isDefCollider(Node node1, Node node2, Node node3)
  
  Checks if there is a definite collider between three nodes in the graph.
  
  Specified by:
  
  isDefCollider in interface Graph
  
  Parameters:
  
  node1 - the first node to check
  
  node2 - the second node to check
  
  node3 - the third node to check
  
  Returns:
  
  true if there is a definite collider, false otherwise
- isExogenous
  
  public boolean isExogenous(Node node)
  
  Checks whether a given node is exogenous.
  
  Specified by:
  
  isExogenous in interface Graph
  
  Parameters:
  
  node - A Node object representing the node to be checked.
  
  Returns:
  
  True if the given node is exogenous, false otherwise.
- getNodesInTo
  
  public List<Node> getNodesInTo(Node node, Endpoint n)
  
  Retrieves a list of nodes in the given graph that have edges pointing into the specified node and endpoint.
  
  Specified by:
  
  getNodesInTo in interface Graph
  
  Parameters:
  
  node - the node to check for incoming edges
  
  n - the endpoint to check for incoming edges
  
  Returns:
  
  a list of nodes with edges pointing into the specified node and endpoint
- getNodesOutTo
  
  public List<Node> getNodesOutTo(Node node, Endpoint n)
  
  Retrieves a list of nodes that have outgoing edges to a specified node and endpoint.
  
  Specified by:
  
  getNodesOutTo in interface Graph
  
  Parameters:
  
  node - The node to which the outgoing edges lead.
  
  n - The endpoint to which the outgoing edges connect to the specified node.
  
  Returns:
  
  A list of nodes that have outgoing edges to the specified node and endpoint.
- removeEdge
  
  public boolean removeEdge(Edge edge)
  
  Removes a given edge from the graph.
  
  Specified by:
  
  removeEdge in interface Graph
  
  Parameters:
  
  edge - the edge to be removed
  
  Returns:
  
  true if the edge was successfully removed, false otherwise
- removeEdge
  
  public boolean removeEdge(Node node1, Node node2)
  
  Removes the edge between two nodes in the graph.
  
  Specified by:
  
  removeEdge in interface Graph
  
  Parameters:
  
  node1 - the first node to remove the edge from
  
  node2 - the second node to remove the edge to
  
  Returns:
  
  true if the edge was successfully removed, false otherwise
- removeEdges
  
  public boolean removeEdges(Node node1, Node node2)
  
  Removes an edge between two nodes.
  
  Specified by:
  
  removeEdges in interface Graph
  
  Parameters:
  
  node1 - the first node
  
  node2 - the second node
  
  Returns:
  
  true if the edge was successfully removed, false otherwise
- removeEdges
  
  public boolean removeEdges(Collection<Edge> edges)
  
  Removes the given edges from the graph.
  
  Specified by:
  
  removeEdges in interface Graph
  
  Parameters:
  
  edges - a collection of edges to be removed from the graph
  
  Returns:
  
  true if all the edges were successfully removed, false otherwise
- removeNode
  
  public boolean removeNode(Node node)
  
  Removes the specified node from the graph.
  
  Specified by:
  
  removeNode in interface Graph
  
  Parameters:
  
  node - the node to be removed from the graph
  
  Returns:
  
  true if the node was successfully removed, false otherwise
- removeNodes
  
  public boolean removeNodes(List<Node> nodes)
  
  Removes the specified nodes from the graph.
  
  Specified by:
  
  removeNodes in interface Graph
  
  Parameters:
  
  nodes - a List of nodes to remove
  
  Returns:
  
  true if the nodes were successfully removed, false otherwise
- setEndpoint
  
  public boolean setEndpoint(Node from, Node to, Endpoint endPoint)
  
  Sets the endpoint of a directed edge between two nodes in a graph.
  
  Specified by:
  
  setEndpoint in interface Graph
  
  Parameters:
  
  from - the starting node of the edge
  
  to - the ending node of the edge
  
  endPoint - the endpoint of the directed edge
  
  Returns:
  
  true if the endpoint was successfully set, false otherwise
- subgraph
  
  public Graph subgraph(List<Node> nodes)
  
  Returns a subgraph of the current graph consisting only of the specified nodes.
  
  Specified by:
  
  subgraph in interface Graph
  
  Parameters:
  
  nodes - a list of nodes to include in the subgraph
  
  Returns:
  
  a new Graph object representing the subgraph
- toString
  
  public String toString()
  
  toString.
  
  Specified by:
  
  toString in interface Graph
  
  Overrides:
  
  toString in class Object
  
  Returns:
  
  a String object
- transferNodesAndEdges
  
  public void transferNodesAndEdges(Graph graph) throws IllegalArgumentException
  
  Transfers nodes and edges from the given graph to the current graph.
  
  Specified by:
  
  transferNodesAndEdges in interface Graph
  
  Parameters:
  
  graph - the graph from which nodes and edges are to be pilfered
  
  Throws:
  
  IllegalArgumentException - if the graph is null, or if adding a node/edge fails
  
  NullPointerException - if no graph is provided
- transferAttributes
  
  public void transferAttributes(Graph graph) throws IllegalArgumentException
  
  Transfers attributes from the given graph to the current graph.
  
  Specified by:
  
  transferAttributes in interface Graph
  
  Parameters:
  
  graph - a Graph object representing the graph from which attributes will be transferred
  
  Throws:
  
  IllegalArgumentException - if the graph is null
- paths
  
  public Paths paths()
  
  paths.
  
  Specified by:
  
  paths in interface Graph
  
  Returns:
  
  a Paths object
- isParameterizable
  
  public boolean isParameterizable(Node node)
  
  Checks if the given node is parameterizable.
  
  Specified by:
  
  isParameterizable in interface Graph
  
  Parameters:
  
  node - the node to be checked for parameterizability
  
  Returns:
  
  true if the node is parameterizable, false otherwise
- isTimeLagModel
  
  public boolean isTimeLagModel()
  
  isTimeLagModel.
  
  Specified by:
  
  isTimeLagModel in interface Graph
  
  Returns:
  
  a boolean
- getTimeLagGraph
  
  public TimeLagGraph getTimeLagGraph()
  
  getTimeLagGraph.
  
  Specified by:
  
  getTimeLagGraph in interface Graph
  
  Returns:
  
  a TimeLagGraph object
- getSepset
  
  public Set<Node> getSepset(Node n1, Node n2, IndependenceTest test)
  
  Returns the sepset between two given nodes in the graph.
  
  Specified by:
  
  getSepset in interface Graph
  
  Parameters:
  
  n1 - the first node
  
  n2 - the second node
  
  test - the independence test to be used
  
  Returns:
  
  a set of nodes representing the sepset between n1 and n2
- getAllAttributes
  
  public Map<String,Object> getAllAttributes()
  
  getAllAttributes.
  
  Specified by:
  
  getAllAttributes in interface Graph
  
  Returns:
  
  a Map object
- getAttribute
  
  public Object getAttribute(String key)
  
  Retrieves the value associated with the given key in the attribute map.
  
  Specified by:
  
  getAttribute in interface Graph
  
  Parameters:
  
  key - the key of the attribute to be retrieved
  
  Returns:
  
  the value associated with the given key
- removeAttribute
  
  public void removeAttribute(String key)
  
  Removes an attribute from the graph.
  
  Specified by:
  
  removeAttribute in interface Graph
  
  Parameters:
  
  key - the key of the attribute to remove
- addAttribute
  
  public void addAttribute(String key, Object value)
  
  Adds an attribute to the graph.
  
  Specified by:
  
  addAttribute in interface Graph
  
  Parameters:
  
  key - the key of the attribute
  
  value - the value of the attribute
- getAmbiguousTriples
  
  public Set<Triple> getAmbiguousTriples()
  
  Returns a set of ambiguous triples.
  
  Specified by:
  
  getAmbiguousTriples in interface Graph
  
  Returns:
  
  a set of ambiguous triples
- setAmbiguousTriples
  
  public void setAmbiguousTriples(Set<Triple> triples)
  
  Sets the ambiguous triples for the object.
  
  Specified by:
  
  setAmbiguousTriples in interface Graph
  
  Parameters:
  
  triples - a set of Triple objects representing ambiguous triples
- getUnderLines
  
  public Set<Triple> getUnderLines()
  
  Retrieves the set of underlined triples.
  
  Specified by:
  
  getUnderLines in interface Graph
  
  Returns:
  
  The set of underlined triples as a Set of Triple objects.
- 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)
  
  Determines if a triple of nodes is ambiguous.
  
  Specified by:
  
  isAmbiguousTriple in interface Graph
  
  Parameters:
  
  x - the first node in the triple.
  
  y - the second node in the triple.
  
  z - the third node in the triple.
  
  Returns:
  
  true if the triple is ambiguous, false otherwise.
- isUnderlineTriple
  
  public boolean isUnderlineTriple(Node x, Node y, Node z)
  
  Determines if a triple of nodes is underlined.
  
  Specified by:
  
  isUnderlineTriple in interface Graph
  
  Parameters:
  
  x - the first Node in the triple
  
  y - the second Node in the triple
  
  z - the third Node in the triple
  
  Returns:
  
  true if the triple is underlined, false otherwise
- addAmbiguousTriple
  
  public void addAmbiguousTriple(Node x, Node y, Node z)
  
  Adds an ambiguous triple to the list of ambiguous triples. An ambiguous triple consists of three nodes: x, y, and z.
  
  Specified by:
  
  addAmbiguousTriple in interface Graph
  
  Parameters:
  
  x - the first node in the ambiguous triple
  
  y - the second node in the ambiguous triple
  
  z - the third node in the ambiguous triple
- addUnderlineTriple
  
  public void addUnderlineTriple(Node x, Node y, Node z)
  
  Adds an underline triple to the current object.
  
  Specified by:
  
  addUnderlineTriple in interface Graph
  
  Parameters:
  
  x - The first Node object in the triple.
  
  y - The second Node object in the triple.
  
  z - The third Node object in the triple.
- addDottedUnderlineTriple
  
  public void addDottedUnderlineTriple(Node x, Node y, Node z)
  
  Adds a dotted underline triple to the graph.
  
  Specified by:
  
  addDottedUnderlineTriple in interface Graph
  
  Parameters:
  
  x - The first node of the triple.
  
  y - The second node of the triple.
  
  z - The third node of the triple.
- removeAmbiguousTriple
  
  public void removeAmbiguousTriple(Node x, Node y, Node z)
  
  Removes an ambiguous triple from the list of ambiguous triples.
  
  Specified by:
  
  removeAmbiguousTriple in interface Graph
  
  Parameters:
  
  x - The first node of the triple.
  
  y - The second node of the triple.
  
  z - The third node of the triple.
- removeUnderlineTriple
  
  public void removeUnderlineTriple(Node x, Node y, Node z)
  
  Removes an underline triple from the list of underline triples.
  
  Specified by:
  
  removeUnderlineTriple in interface Graph
  
  Parameters:
  
  x - The first Node object in the underline triple.
  
  y - The second Node object in the underline triple.
  
  z - The third Node object in the underline triple.
- removeDottedUnderlineTriple
  
  public void removeDottedUnderlineTriple(Node x, Node y, Node z)
  
  Removes a dotted underline triple from the set of triples.
  
  Specified by:
  
  removeDottedUnderlineTriple in interface Graph
  
  Parameters:
  
  x - the first node of the triple to be removed
  
  y - the second node of the triple to be removed
  
  z - the third node of the triple to be removed
- setUnderLineTriples
  
  public void setUnderLineTriples(Set<Triple> triples)
  
  Sets the underlined triples.
  
  Specified by:
  
  setUnderLineTriples in interface Graph
  
  Parameters:
  
  triples - a set of triples to be set as underlined
- setDottedUnderLineTriples
  
  public void setDottedUnderLineTriples(Set<Triple> triples)
  
  Sets the dotted underline triples for the given set of Triples. Clears the existing dotted underline triples and adds the new ones from the set.
  
  Specified by:
  
  setDottedUnderLineTriples in interface Graph
  
  Parameters:
  
  triples - a Set of Triples to set as dotted underline triples
- removeTriplesNotInGraph
  
  public void removeTriplesNotInGraph()
  
  Removes triples from the graph that contain nodes not present in the graph or are not adjacent to each other.
  
  Specified by:
  
  removeTriplesNotInGraph in interface Graph

Class Dag

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface edu.cmu.tetrad.graph.Graph

Constructor Details

Dag

Dag

Dag

Method Details

serializableInstance

addBidirectedEdge

addDirectedEdge

addUndirectedEdge

addNondirectedEdge

addPartiallyOrientedEdge

addEdge

addNode

addPropertyChangeListener

clear

containsEdge

containsNode

equals

fullyConnect

reorientAllWith

getAdjacentNodes

getChildren

getDegree

getEdge

getDirectedEdge

getEdges

getEdges

getEdges

getEndpoint

getIndegree

getDegree

getNode

getNodes

setNodes

getNodeNames

getNumEdges

getNumEdges

getNumNodes

getOutdegree

getParents

isAdjacentTo

isChildOf

isParentOf

isDefNoncollider

isDefCollider

isExogenous

getNodesInTo

getNodesOutTo

removeEdge

removeEdge

removeEdges

removeEdges

removeNode

removeNodes

setEndpoint

subgraph

toString

transferNodesAndEdges

transferAttributes

paths

isParameterizable

isTimeLagModel

getTimeLagGraph

getSepset

getAllAttributes

getAttribute

removeAttribute

addAttribute

getAmbiguousTriples

setAmbiguousTriples

getUnderLines

getDottedUnderlines

isAmbiguousTriple

isUnderlineTriple

addAmbiguousTriple