code: ///////////////////////////////////////////////////////////////////////////////
  // 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 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.tetrad.gene.tetrad.gene.simexp;
  
  import edu.cmu.tetrad.gene.tetrad.gene.history.*;
  import edu.cmu.tetrad.gene.tetrad.gene.simulation.MeasurementSimulator;
  import edu.cmu.tetrad.util.NumberFormatUtil;
  import edu.cmu.tetrad.util.Parameters;
  
  import java.io.FileNotFoundException;
  import java.io.FileOutputStream;
  import java.io.PrintStream;
  import java.text.NumberFormat;
  
  /**
   * Implements a particular simulation for experimental purposes.
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class LinearSimExp1 {
  
      /**
       * The measurement simulator.
       */
      private MeasurementSimulator simulator;
  
      public LinearSimExp1(String stub) {
          this.simulator = new MeasurementSimulator(new Parameters());
          UpdateFunction function = createFunction();
          GeneHistory history = createHistory(function);
          this.simulator.setRawDataSaved(true);
          this.simulator.setNumDishes(8);
          this.simulator.simulate(history);
  
          try {
              PrintStream out =
                      new PrintStream(new FileOutputStream(stub + "meas.dat"));
              printMeasuredData(out);
              out.close();
  
              PrintStream out2 =
                      new PrintStream(new FileOutputStream(stub + "raw.dat"));
              printRawData(out2);
              out2.close();
          }
          catch (FileNotFoundException e) {
              e.printStackTrace();
          }
      }
  
      public static void main(String[] args) {
          new LinearSimExp1(args[0]);
      }
  
      private UpdateFunction createFunction() {
          String[] factors = new String[]{"G1", "G2", "G3"};
  
          LagGraph lagGraph = new BasicLagGraph();
          lagGraph.addFactor(factors[0]);
          lagGraph.addFactor(factors[1]);
          lagGraph.addFactor(factors[2]);
  
          lagGraph.addEdge(factors[0], new LaggedFactor(factors[0], 1));
          lagGraph.addEdge(factors[1], new LaggedFactor(factors[0], 1));
          lagGraph.addEdge(factors[1], new LaggedFactor(factors[1], 1));
          lagGraph.addEdge(factors[1], new LaggedFactor(factors[2], 1));
          lagGraph.addEdge(factors[2], new LaggedFactor(factors[2], 1));
  
          LinearFunction function = new LinearFunction(lagGraph);
  
          function.setIntercept("G1", 0.05);
          function.setCoefficient("G1", new LaggedFactor("G1", 1), 0.5);
          function.setIntercept("G2", 0.1);
          function.setCoefficient("G2", new LaggedFactor("G1", 1), 0.6);
          function.setIntercept("G3", 0.2);
          function.setCoefficient("G2", new LaggedFactor("G2", 1), 0.7);
          function.setIntercept("G3", 0.3);
          function.setCoefficient("G2", new LaggedFactor("G3", 1), 0.8);
          function.setIntercept("G3", 0.4);
          function.setCoefficient("G3", new LaggedFactor("G3", 1), 0.9);
  
          /*
          function.setIntercept(0, 0.0);
          function.setCoefficient(0, 0, 0.5);
          function.setIntercept(1, 0.1);
          function.setCoefficient(1, 0, 1.5);
          function.setCoefficient(1, 1, -1.5);
          function.setCoefficient(1, 2, +1.3);
          function.setIntercept(2, -1.8);
          function.setCoefficient(2, 0, 1.1);
          */
  
          System.out.println(function);
  
          return function;
      }
  
      private GeneHistory createHistory(UpdateFunction function) {
          BasalInitializer initializer = new BasalInitializer(function, 0.0, 1.0);
          return new GeneHistory(initializer, function);
      }
  
      private void printRawData(PrintStream out) {
          double[][][] data = this.simulator.getRawData();
          GeneHistory history = this.simulator.getHistory();
          UpdateFunction updateFunction = history.getUpdateFunction();
          int[] timeSteps = this.simulator.getTimeSteps();
  
          out.print("Dish\tInd\t");
          for (int i = 0; i < timeSteps.length; i++) {
              for (int j = 0; j < updateFunction.getNumFactors(); j++) {
                  out.print("G" + j + ":t" + timeSteps[i] + "\t");
              }
          }
          out.println();
  
          NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
  
          int cellsPerDish = simulator.getNumCellsPerDish();
  
          for (int i = 0; i < data[0][0].length; i++) {
              out.print((i / cellsPerDish + 1) + "\t");
              out.print((i + 1) + "\t");
              for (int j = 0; j < data[0].length; j++) {
                  for (int k = 0; k < data.length; k++) {
                      out.print(nf.format(data[k][j][i]) + "\t");
                  }
              }
              out.println();
          }
      }
  
      private void printMeasuredData(PrintStream out) {
          double[][][] data = this.simulator.getMeasuredData();
          GeneHistory history = this.simulator.getHistory();
          UpdateFunction updateFunction = history.getUpdateFunction();
          int[] timeSteps = this.simulator.getTimeSteps();
  
          out.print("Dish\tChip\t");
  
          for (int i = 0; i < timeSteps.length; i++) {
              for (int j = 0; j < updateFunction.getNumFactors(); j++) {
                  out.print("G" + j + ":t" + timeSteps[i] + "\t");
              }
          }
          out.println();
  
          NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
          int samplesPerDish = simulator.getNumSamplesPerDish();
  
          for (int i = 0; i < data[0][0].length; i++) {
              out.print((i / samplesPerDish + 1) + "\t");
              out.print((i + 1) + "\t");
              for (int j = 0; j < data[0].length; j++) {
                  for (int k = 0; k < data.length; k++) {
                      out.print(nf.format(data[k][j][i]) + "\t");
                  }
              }
              out.println();
          }
      }
  }
  
  
  
  
  
  