<commit_before>//  Experiment.java
//
//  Authors:
//       <NAME> <<EMAIL>>
//
//  Copyright (c) 2014 <NAME>
//
//  This program is free software: you can redistribute it and/or modify
//  it under the terms of the GNU Lesser General Public License as published by
//  the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
//
//  You should have received a copy of the GNU Lesser General Public License
//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
package jmetal.experiments;

import jmetal.experiments.util.*;
import jmetal.util.Configuration;
import jmetal.util.JMException;
import jmetal.util.parallel.MultithreadedAlgorithmRunner;

import java.io.*;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Properties;
import java.util.logging.Level;

/**
 * Created by <NAME> on 08/02/14.
 * Class for configuring and running experiments
 */
public class Experiment {
  protected String experimentName_;
  public String getExperimentName() {
    return experimentName_ ;
  }

  //List of the names of the algorithms to be executed
  protected String[] algorithmNameList_; 
  public String[] getAlgorithmNameList() {
    return algorithmNameList_ ;
  }

  //List of problems to be solved
  protected String[] problemList_; 
  public String[] getProblemList() {
    return problemList_ ;
  }

  //List of the files containing the pareto fronts corresponding 
  //to the problems in problemList_

  protected String[] paretoFrontFileList_; 
  public String[] getParetoFrontFileList() {
    return paretoFrontFileList_ ;
  }

  // List of the quality indicators to be applied
  protected String[] indicatorList_; 
  public String[] getIndicatorList() {
    return indicatorList_ ;
  }

  //Directory to store the results
  protected String experimentBaseDirectory_; 
  public String getExperimentBaseDirectory() {
    return experimentBaseDirectory_ ;
  }
  public void setExperimentBaseDirector(String directory) {
    experimentBaseDirectory_ = directory ;
  }

  //Directory to store the latex files
  protected String latexDirectory_; 
  public String getLatexDirectory() {
    return latexDirectory_ ;
  }
  public void setLatexDirectory(String directory) {
    latexDirectory_ = directory ;
  }

  //Directory containing the Pareto front files
  protected String paretoFrontDirectory_; 
  public String getParetoFrontDirectory() {
    return paretoFrontDirectory_ ; 
  }

  //Name of the file containing the output Pareto front
  protected String outputParetoFrontFile_;
  public String getOutputParetoFrontFile() {
    return outputParetoFrontFile_ ;
  }

  //Name of the file containing the output Pareto set
  protected String outputParetoSetFile_; 
  public String getOutputParetoSetFile() {
    return outputParetoSetFile_ ;
  }

  //Number of independent runs per algorithm
  protected int independentRuns_; 
  public int getIndependentRuns() {
    return independentRuns_ ;
  }

  //Parameter experiments.settings of each algorithm
  protected Settings[] algorithmSettings_; 
  public Settings[] getAlgorithmSettings() {
    return algorithmSettings_ ;
  }

  //Map used to send experiment parameters to threads
  HashMap<String, Object> map_; 

  //To indicate whether an indicator is to be minimized. Hard-coded
  // in the constructor
  protected HashMap<String, Boolean> indicatorMinimize_; 
  public HashMap<String, Boolean> indicatorMinimize() {
    return indicatorMinimize_ ;
  }

  protected boolean  runTheAlgorithms_ ;
  public boolean runTheAlgorithms() {
    return runTheAlgorithms_ ;
  }
  protected boolean  generateReferenceParetoFronts_ ;
  public boolean generateReferenceParetoFronts() {
    return generateReferenceParetoFronts_ ;
  }
  protected boolean  generateQualityIndicators_ ;
  public boolean generateQualityIndicators() {
    return generateQualityIndicators_ ;
  }
  protected boolean  generateLatexTables_ ;
  public boolean generateLatexTables() {
    return generateLatexTables_ ;
  }
  protected boolean  generateBoxplots_ ;
  public boolean generateBoxplots() {
    return generateBoxplots_ ;
  }
  protected boolean  generateWilcoxonTables_ ;
  public boolean generateWilcoxonTables() {
    return generateWilcoxonTables_ ;
  }
  protected boolean  generateFriedmanTables_ ;
  public boolean generateFriedmanTables() {
    return generateFriedmanTables_ ;
  }
  protected boolean  useConfigurationFilesForAlgorithms_ ;
  public boolean useConfigurationFilesForAlgorithms() {
    return useConfigurationFilesForAlgorithms_ ;
  }

  protected int boxplotRows_    ;
  public int getBoxplotRows() {
    return boxplotRows_ ;
  }

  protected int boxplotColumns_ ;
  public int getBoxplotColumns() {
    return boxplotColumns_ ;
  }
  protected boolean boxplotNotch_ ;
  public boolean getBoxplotNotch() {<commit_msg>Minor change in Experiment<commit_after>//  Experiment.java
//
//  Authors:
//       <NAME> <<EMAIL>>
//
//  Copyright (c) 2014 <NAME>
//
//  This program is free software: you can redistribute it and/or modify
//  it under the terms of the GNU Lesser General Public License as published by
//  the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
//
//  You should have received a copy of the GNU Lesser General Public License
//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
package jmetal.experiments;

import jmetal.experiments.util.*;
import jmetal.util.Configuration;
import jmetal.util.JMException;
import jmetal.util.parallel.MultithreadedAlgorithmRunner;

import java.io.*;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Properties;
import java.util.logging.Level;

/**
 * Created by <NAME> on 08/02/14.
 * Class for configuring and running experiments
 */
public class Experiment {
  protected String experimentName_;
  public String getExperimentName() {
    return experimentName_ ;
  }

  //List of the names of the algorithms to be executed
  protected String[] algorithmNameList_; 
  public String[] getAlgorithmNameList() {
    return algorithmNameList_ ;
  }

  //List of problems to be solved
  protected String[] problemList_; 
  public String[] getProblemList() {
    return problemList_ ;
  }

  //List of the files containing the pareto fronts corresponding 
  //to the problems in problemList_

  protected String[] paretoFrontFileList_; 
  public String[] getParetoFrontFileList() {
    return paretoFrontFileList_ ;
  }

  // List of the quality indicators to be applied
  protected String[] indicatorList_; 
  public String[] getIndicatorList() {
    return indicatorList_ ;
  }

  //Directory to store the results
  protected String experimentBaseDirectory_; 
  public String getExperimentBaseDirectory() {
    return experimentBaseDirectory_ ;
  }
  public void setExperimentBaseDirector(String directory) {
    experimentBaseDirectory_ = directory ;
  }

  //Directory to store the latex files
  protected String latexDirectory_; 
  public String getLatexDirectory() {
    return latexDirectory_ ;
  }
  public void setLatexDirectory(String directory) {
    latexDirectory_ = directory ;
  }

  //Directory containing the Pareto front files
  protected String paretoFrontDirectory_; 
  public String getParetoFrontDirectory() {
    return paretoFrontDirectory_ ; 
  }

  //Name of the file containing the output Pareto front
  protected String outputParetoFrontFile_;
  public String getOutputParetoFrontFile() {
    return outputParetoFrontFile_ ;
  }

  //Name of the file containing the output Pareto set
  protected String outputParetoSetFile_; 
  public String getOutputParetoSetFile() {
    return outputParetoSetFile_ ;
  }

  //Number of independent runs per algorithm
  protected int independentRuns_; 
  public int getIndependentRuns() {
    return independentRuns_ ;
  }

  //Parameter experiments.settings of each algorithm
  protected Settings[] algorithmSettings_; 
  public Settings[] getAlgorithmSettings() {
    return algorithmSettings_ ;
  }

  //Map used to send experiment parameters to threads
  HashMap<String, Object> map_; 

  //To indicate whether an indicator is to be minimized. Hard-coded
  // in the constructor
  protected HashMap<String, Boolean> indicatorMinimize_; 
  public HashMap<String, Boolean> indicatorMinimize() {
    return indicatorMinimize_ ;
  }

  protected boolean  runTheAlgorithms_ ;
  public boolean runTheAlgorithms() {
    return runTheAlgorithms_ ;
  }
  
  protected boolean  generateReferenceParetoFronts_ ;
  public boolean generateReferenceParetoFronts() {
    return generateReferenceParetoFronts_ ;
  }
  
  protected boolean  generateQualityIndicators_ ;
  public boolean generateQualityIndicators() {
    return generateQualityIndicators_ ;
  }
  
  protected boolean  generateLatexTables_ ;
  public boolean generateLatexTables() {
    return generateLatexTables_ ;
  }
  
  protected boolean  generateBoxplots_ ;
  public boolean generateBoxplots() {
    return generateBoxplots_ ;
  }
  
  protected boolean  generateWilcoxonTables_ ;
  public boolean generateWilcoxonTables() {
    return generateWilcoxonTables_ ;
  }
  
  protected boolean  generateFriedmanTables_ ;
  public boolean generateFriedmanTables() {
    return generateFriedmanTables_ ;
  }
  
  protected boolean  useConfigurationFilesForAlgorithms_ ;
  public boolean useConfigurationFilesForAlgorithms() {
    return useConfigurationFilesForAlgorithms_ ;
  }

  protected int boxplotRows_    ;
  public int getBoxplotRows() {
    return boxplotRows_ ;
  }

  protected int boxplotColumns_ ;
  public int getBoxplotColumns() {
    return boxplotColumns_ ;
  }
  protected boolean boxplotNotch_ ;
  public boolean getBoxplotNotch() {
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