code: package edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern;
  
  import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
  import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
  import edu.cmu.tetrad.algcomparison.utils.HasKnowledge;
  import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
  import edu.cmu.tetrad.annotation.AlgType;
  import edu.cmu.tetrad.data.DataModel;
  import edu.cmu.tetrad.data.DataSet;
  import edu.cmu.tetrad.data.DataType;
  import edu.cmu.tetrad.data.IKnowledge;
  import edu.cmu.tetrad.data.Knowledge2;
  import edu.cmu.tetrad.graph.EdgeListGraph;
  import edu.cmu.tetrad.graph.Graph;
  import edu.cmu.tetrad.graph.GraphUtils;
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.search.IndependenceTest;
  import edu.cmu.tetrad.util.Parameters;
  import edu.pitt.dbmi.algo.resampling.GeneralResamplingTest;
  import edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble;
  import java.util.List;
  
  /**
   * PC.
   *
   * @author jdramsey
   */
  @edu.cmu.tetrad.annotation.Algorithm(
          name = "MBFS",
          command = "mbfs",
          algoType = AlgType.search_for_Markov_blankets
  )
  public class MBFS implements Algorithm, HasKnowledge, TakesIndependenceWrapper {
  
      static final long serialVersionUID = 23L;
      private IndependenceWrapper test;
      private IKnowledge knowledge = new Knowledge2();
      private String targetName;
  
      public MBFS() {
      }
  
      public MBFS(IndependenceWrapper type) {
          this.test = type;
      }
  
      @Override
      public Graph search(DataModel dataSet, Parameters parameters) {
      	if (parameters.getInt("numberResampling") < 1) {
              IndependenceTest test = this.test.getTest(dataSet, parameters);
              edu.cmu.tetrad.search.Mbfs search = new edu.cmu.tetrad.search.Mbfs(test, parameters.getInt("depth"));
  
              search.setDepth(parameters.getInt("depth"));
              search.setKnowledge(knowledge);
  
              this.targetName = parameters.getString("targetName");
              if (targetName.isEmpty()) {
                  throw new IllegalArgumentException("Target variable name needs to be provided.");
              }
              
              if (test.getVariable(targetName) == null) {
                  throw new IllegalArgumentException("Target variable name '" + targetName + "' not found in dataset.");
              }
              
              Node target = test.getVariable(targetName);
              return search.search(target.getName());
          } else {
              MBFS algorithm = new MBFS(test);
  
              DataSet data = (DataSet) dataSet;
              GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt("numberResampling"));
              search.setKnowledge(knowledge);
  
              search.setPercentResampleSize(parameters.getDouble("percentResampleSize"));
              search.setResamplingWithReplacement(parameters.getBoolean("resamplingWithReplacement"));
              
              ResamplingEdgeEnsemble edgeEnsemble = ResamplingEdgeEnsemble.Highest;
              switch (parameters.getInt("resamplingEnsemble", 1)) {
                  case 0:
                      edgeEnsemble = ResamplingEdgeEnsemble.Preserved;
                      break;
                  case 1:
                      edgeEnsemble = ResamplingEdgeEnsemble.Highest;
                      break;
                  case 2:
                      edgeEnsemble = ResamplingEdgeEnsemble.Majority;
              }
              search.setEdgeEnsemble(edgeEnsemble);
              search.setAddOriginalDataset(parameters.getBoolean("addOriginalDataset"));
              
              search.setParameters(parameters);
              search.setVerbose(parameters.getBoolean("verbose"));
              return search.search();
          }
      }
  
      @Override
      public Graph getComparisonGraph(Graph graph) {
          Node target = graph.getNode(targetName);
          return GraphUtils.markovBlanketDag(target, new EdgeListGraph(graph));
      }
  
      @Override
      public String getDescription() {
          return "MBFS (Markov Blanket Fan Search) using " + test.getDescription();
      }
  
      @Override
      public DataType getDataType() {
          return test.getDataType();
      }
  
      @Override
      public List<String> getParameters() {
          List<String> parameters = test.getParameters();
          parameters.add("depth");
          parameters.add("targetName");
          // Resampling
          parameters.add("numberResampling");
          parameters.add("percentResampleSize");
          parameters.add("resamplingWithReplacement");
          parameters.add("resamplingEnsemble");
          parameters.add("addOriginalDataset");
          parameters.add("verbose");
          return parameters;
      }
  
      @Override
      public IKnowledge getKnowledge() {
          return knowledge;
      }
  
      @Override
      public void setKnowledge(IKnowledge knowledge) {
          this.knowledge = knowledge;
      }
  
      @Override
      public void setIndependenceWrapper(IndependenceWrapper test) {
          this.test = test;
      }
      
      @Override
      public IndependenceWrapper getIndependenceWrapper() {
          return test;
      }
  }
  