edu.cmu.tetradapp.model.TimeLagGraphWrapper Maven / Gradle / Ivy
///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// This program is free software; you can redistribute it and/or modify //
// it under the terms of the GNU General Public License as published by //
// the Free Software Foundation; either version 2 of the License, or //
// (at your option) any later version. //
// //
// This program is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
// along with this program; if not, write to the Free Software //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.data.KnowledgeBoxInput;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Holds a tetrad dag with all of the constructors necessary for it to serve as a model for the tetrad application.
*
* @author josephramsey
*/
public class TimeLagGraphWrapper implements GraphSource, KnowledgeBoxInput {
private static final long serialVersionUID = 23L;
/**
* @serial Can be null.
*/
private String name;
/**
* @serial Cannot be null.
*/
private TimeLagGraph graph;
private Parameters parameters;
//=============================CONSTRUCTORS==========================//
public TimeLagGraphWrapper(Parameters parameters) {
this.graph = new TimeLagGraph();
this.parameters = parameters;
log();
}
public TimeLagGraphWrapper(TimeLagGraph graph, Parameters parameters) {
if (graph == null) {
throw new NullPointerException("Tetrad dag must not be null.");
}
this.graph = graph;
this.parameters = parameters;
log();
}
public TimeLagGraphWrapper(GraphWrapper graphWrapper) {
if (graphWrapper == null) {
throw new NullPointerException("No graph wrapper.");
}
this.parameters = graphWrapper.getParameters();
TimeLagGraph graph = new TimeLagGraph();
Graph _graph = graphWrapper.getGraph();
for (Node node : _graph.getNodes()) {
Node _node = node.like(node.getName() + ":0");
_node.setNodeType(node.getNodeType());
graph.addNode(_node);
}
for (Edge edge : _graph.getEdges()) {
if (!Edges.isDirectedEdge(edge)) {
throw new IllegalArgumentException();
}
Node from = edge.getNode1();
Node to = edge.getNode2();
Node _from = graph.getNode(from.getName(), 1);
Node _to = graph.getNode(to.getName(), 0);
graph.addDirectedEdge(_from, _to);
}
this.graph = graph;
int numLags = 1; // need to fix this!
List variables = graph.getNodes();
List laglist = new ArrayList<>();
Knowledge knowledge1 = new Knowledge();
int lag;
for (Node node : variables) {
String varName = node.getName();
String tmp;
if (varName.indexOf(':') == -1) {
lag = 0;
} else {
tmp = varName.substring(varName.indexOf(':') + 1);
lag = Integer.parseInt(tmp);
}
laglist.add(lag);
}
numLags = Collections.max(laglist);
for (Node node : variables) {
String varName = node.getName();
String tmp;
if (varName.indexOf(':') == -1) {
lag = 0;
} else {
tmp = varName.substring(varName.indexOf(':') + 1);
lag = Integer.parseInt(tmp);
}
laglist.add(lag);
knowledge1.addToTier(numLags - lag, node.getName());
}
System.out.println("Knowledge in graph = " + knowledge1);
}
public TimeLagGraphWrapper() {
this.graph = new TimeLagGraph();
log();
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @see TetradSerializableUtils
*/
public static TimeLagGraphWrapper serializableInstance() {
return new TimeLagGraphWrapper(new TimeLagGraph(),
new Parameters());
}
//============================PRIVATE METHODS========================//
private void log() {
TetradLogger.getInstance().log("info", "Directed Acyclic Graph (DAG)");
TetradLogger.getInstance().log("graph", this.graph + "");
}
/**
* Adds semantic checks to the default deserialization method. This method must have the standard signature for a
* readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any
* semantic checks can be specified and do not need to stay the same from version to version. A readObject method of
* this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the
* class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for
* help.
*/
private void readObject(ObjectInputStream s)
throws IOException, ClassNotFoundException {
s.defaultReadObject();
if (this.graph == null) {
throw new NullPointerException();
}
}
public Graph getGraph() {
return this.graph;
}
public void setGraph(TimeLagGraph graph) {
this.graph = graph;
}
public String getName() {
return this.name;
}
public void setName(String name) {
this.name = name;
}
public Graph getSourceGraph() {
return getGraph();
}
public Graph getResultGraph() {
return getGraph();
}
public List getVariableNames() {
return getGraph().getNodeNames();
}
public List getVariables() {
return getGraph().getNodes();
}
public Knowledge getKnowledge() {
int numLags = 1; // need to fix this!
List variables = this.graph.getNodes();
List laglist = new ArrayList<>();
Knowledge knowledge1 = new Knowledge();
int lag;
for (Node node : variables) {
String varName = node.getName();
String tmp;
if (varName.indexOf(':') == -1) {
lag = 0;
} else {
tmp = varName.substring(varName.indexOf(':') + 1);
lag = Integer.parseInt(tmp);
}
laglist.add(lag);
}
numLags = Collections.max(laglist);
for (Node node : variables) {
String varName = node.getName();
String tmp;
if (varName.indexOf(':') == -1) {
lag = 0;
} else {
tmp = varName.substring(varName.indexOf(':') + 1);
lag = Integer.parseInt(tmp);
}
laglist.add(lag);
knowledge1.addToTier(numLags - lag, node.getName());
}
System.out.println("Knowledge in graph = " + knowledge1);
return knowledge1;
}
public Parameters getParameters() {
return this.parameters;
}
}
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