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.algcomparison.utils.TakesInitialGraph;
  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.search.SearchGraphUtils;
  import edu.cmu.tetrad.util.Parameters;
  import edu.pitt.dbmi.algo.resampling.GeneralResamplingTest;
  import edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble;
  import java.util.List;
  
  /**
   * CPC.
   *
   * @author jdramsey
   */
  @edu.cmu.tetrad.annotation.Algorithm(
          name = "Variants of PC",
          command = "pc-all",
          algoType = AlgType.forbid_latent_common_causes
  )
  public class PcAll implements Algorithm, TakesInitialGraph, HasKnowledge, TakesIndependenceWrapper {
  
      static final long serialVersionUID = 23L;
      private IndependenceWrapper test;
      private Algorithm algorithm = null;
      private Graph initialGraph = null;
      private IKnowledge knowledge = new Knowledge2();
  
      public PcAll() {
      }
  
      public PcAll(IndependenceWrapper test) {
          this.test = test;
      }
  
      public PcAll(IndependenceWrapper test, Algorithm algorithm) {
          this.test = test;
          this.algorithm = algorithm;
      }
  
      @Override
      public Graph search(DataModel dataSet, Parameters parameters) {
          if (parameters.getInt("numberResampling") < 1) {
              edu.cmu.tetrad.search.PcAll.ColliderDiscovery colliderDiscovery;
  
              switch (parameters.getInt("colliderDiscoveryRule")) {
                  case 1:
                      colliderDiscovery = edu.cmu.tetrad.search.PcAll.ColliderDiscovery.FAS_SEPSETS;
                      break;
                  case 2:
                      colliderDiscovery = edu.cmu.tetrad.search.PcAll.ColliderDiscovery.CONSERVATIVE;
                      break;
                  case 3:
                      colliderDiscovery = edu.cmu.tetrad.search.PcAll.ColliderDiscovery.MAX_P;
                      break;
                  default:
                      throw new IllegalArgumentException("Not a choice.");
              }
  
              edu.cmu.tetrad.search.PcAll.ConflictRule conflictRule;
  
              switch (parameters.getInt("conflictRule")) {
                  case 1:
                      conflictRule = edu.cmu.tetrad.search.PcAll.ConflictRule.OVERWRITE;
                      break;
                  case 2:
                      conflictRule = edu.cmu.tetrad.search.PcAll.ConflictRule.BIDIRECTED;
                      break;
                  case 3:
                      conflictRule = edu.cmu.tetrad.search.PcAll.ConflictRule.PRIORITY;
                      break;
                  default:
                      throw new IllegalArgumentException("Not a choice.");
              }
  
              edu.cmu.tetrad.search.PcAll search = new edu.cmu.tetrad.search.PcAll(test.getTest(dataSet, parameters), initialGraph);
              search.setDepth(parameters.getInt("depth"));
              search.setKnowledge(knowledge);
  
              if (parameters.getBoolean("stableFAS")) {
                  search.setFasType(edu.cmu.tetrad.search.PcAll.FasType.STABLE);
              } else {
                  search.setFasType(edu.cmu.tetrad.search.PcAll.FasType.REGULAR);
              }
  
              if (parameters.getBoolean("concurrentFAS")) {
                  search.setConcurrent(edu.cmu.tetrad.search.PcAll.Concurrent.YES);
              } else {
                  search.setConcurrent(edu.cmu.tetrad.search.PcAll.Concurrent.NO);
              }
  
              search.setColliderDiscovery(colliderDiscovery);
              search.setConflictRule(conflictRule);
              search.setUseHeuristic(parameters.getBoolean("useMaxPOrientationHeuristic"));
              search.setMaxPathLength(parameters.getInt("maxPOrientationMaxPathLength"));
              search.setVerbose(parameters.getBoolean("verbose"));
  
              return search.search();
          } else {
              PcAll pcAll = new PcAll(test, algorithm);
  
              if (initialGraph != null) {
                  pcAll.setInitialGraph(initialGraph);
              }
  
              DataSet data = (DataSet) dataSet;
              GeneralResamplingTest search = new GeneralResamplingTest(data, pcAll, 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) {
          return SearchGraphUtils.patternForDag(new EdgeListGraph(graph));
      }
  
      @Override
      public String getDescription() {
          return "PC using " + test.getDescription() + (algorithm != null ? " with initial graph from "
                  + algorithm.getDescription() : "");
      }
  
      @Override
      public DataType getDataType() {
          return test.getDataType();
      }
  
      @Override
      public List<String> getParameters() {
          List<String> parameters = test.getParameters();
          parameters.add("stableFAS");
          parameters.add("concurrentFAS");
          parameters.add("colliderDiscoveryRule");
          parameters.add("conflictRule");
          parameters.add("depth");
          parameters.add("useMaxPOrientationHeuristic");
          parameters.add("maxPOrientationMaxPathLength");
          // 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 Graph getInitialGraph() {
          return initialGraph;
      }
  
      @Override
      public void setInitialGraph(Graph initialGraph) {
          this.initialGraph = initialGraph;
      }
  
      @Override
      public void setInitialGraph(Algorithm algorithm) {
          this.algorithm = algorithm;
      }
  
      @Override
      public void setIndependenceWrapper(IndependenceWrapper test) {
          this.test = test;
      }
      
      @Override
      public IndependenceWrapper getIndependenceWrapper() {
          return test;
      }
  
  }