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///////////////////////////////////////////////////////////////////////////////
// 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.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import java.io.Serial;
import java.util.SortedSet;
import java.util.TreeSet;
import static edu.cmu.tetrad.graph.GraphUtils.removeNonSkeletonEdges;
/**
* RemoveNonSkeletonEdgesModel class.
*
* @author kaalpurush
* @version $Id: $Id
*/
public class RemoveNonSkeletonEdgesModel extends KnowledgeBoxModel {
@Serial
private static final long serialVersionUID = 23L;
/**
* The graph with non-skeleton edges removed.
*/
private Graph resultGraph = new EdgeListGraph();
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BayesPmWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(BayesPmWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(GraphWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.StandardizedSemImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(StandardizedSemImWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(SemImWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemPmWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(SemPmWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(DataWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.TimeLagGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(TimeLagGraphWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(GeneralizedSemImWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BayesImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(BayesImWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(SemGraphWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(GeneralizedSemPmWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(DagWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.DirichletBayesImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(DirichletBayesImWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BuildPureClustersRunner} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(BuildPureClustersRunner wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.PurifyRunner} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(PurifyRunner wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.MeasurementModelWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(MeasurementModelWrapper wrapper, Parameters params) {
this((KnowledgeBoxInput) wrapper, params);
}
/**
* Constructor for RemoveNonSkeletonEdgesModel.
*
* @param input a {@link KnowledgeBoxInput} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public RemoveNonSkeletonEdgesModel(KnowledgeBoxInput input, Parameters params) {
this(params, input);
}
/**
* Constructor from dataWrapper edge
*
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param input a {@link KnowledgeBoxInput} object
*/
public RemoveNonSkeletonEdgesModel(Parameters params, KnowledgeBoxInput input) {
super(new KnowledgeBoxInput[]{input}, params);
if (input == null) {
throw new NullPointerException();
}
SortedSet variableNodes = new TreeSet<>(input.getVariables());
SortedSet variableNames = new TreeSet<>(input.getVariableNames());
this.resultGraph = input.getResultGraph();
/*
* @serial @deprecated
*/
Knowledge knowledge = new Knowledge();
for (Node v : input.getVariables()) {
knowledge.addVariable(v.getName());
}
createKnowledge(params);
TetradLogger.getInstance().log("Knowledge");
// This is a conundrum. At this point I dont know whether I am in a
// simulation or not. If in a simulation, I should print the knowledge.
// If not, I should wait for resetParams to be called. For now I'm
// printing the knowledge if it's not empty.
if (!((Knowledge) params.get("knowledge", new Knowledge())).isEmpty()) {
String message = params.get("knowledge", new Knowledge()).toString();
TetradLogger.getInstance().log(message);
}
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.RemoveNonSkeletonEdgesModel} object
* @see TetradSerializableUtils
*/
public static RemoveNonSkeletonEdgesModel serializableInstance() {
return new RemoveNonSkeletonEdgesModel(new Parameters(), GraphWrapper.serializableInstance());
}
private void createKnowledge(Parameters params) {
Knowledge knowledge = getKnowledge();
if (knowledge == null) {
return;
}
knowledge.clear();
if (this.resultGraph == null) {
throw new NullPointerException("I couldn't find a parent graph.");
}
removeNonSkeletonEdges(resultGraph, knowledge);
}
/**
* Getter for the field resultGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getResultGraph() {
return this.resultGraph;
}
}
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