Program: 36978
Project: 36978
Buggy source:
public static void main(String[] args){
  String propsFile="String_Node_Str";
  try {
    JWNL.initialize(new FileInputStream(propsFile));
  }
 catch (  Exception Ex) {
    Ex.printStackTrace();
  }
  concept=new ConceptizationStats();
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  String path=args[0];
  Inpath=path;
  String runas="String_Node_Str";
  if (args.length > 1)   runas=args[1];
  if (Arrays.asList(args).contains("String_Node_Str")) {
    int i=Arrays.asList(args).indexOf("String_Node_Str");
    outputDest=args[i + 1];
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    int i=Arrays.asList(args).indexOf("String_Node_Str");
    learnheaders=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    shouldTag=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    ExportLinkedData=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    Conceptization=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEFreqSQLTial=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doStats=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEinSQLTial=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEFine=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    TypeClassify=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doXMLInput=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    ComplexClassify=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doIE=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    printHelp();
    return;
  }
  classifiers.PragmaticClassifier pc=new classifiers.PragmaticClassifier("String_Node_Str");
  if (TypeClassify)   SimpleTableClassifier.init(TablInExMain.Inpath);
  if (ComplexClassify)   SimpleTableClassifier.initComplexity(Inpath);
  System.out.println("String_Node_Str" + path);
  File Dir=new File(path);
  File[] files=Dir.listFiles();
  Article article=new Article("String_Node_Str");
  boolean newrun=true;
  String LinkedDataFolder="String_Node_Str";
  if (ExportLinkedData) {
    boolean success=(new File(LinkedDataFolder)).mkdirs();
  }
  for (int a=0; a < files.length; a++) {
    if (ExportLinkedData) {
      linkedData=new DecompositionRDFWriter();
    }
    if (runas.toLowerCase().equals("String_Node_Str")) {
      article=runReadingloopOneFile(article,files[a],PMCXMLReader.class);
      for (int s=0; s < article.getTables().length; s++) {
        Cell[][] original_cells=new Cell[article.getTables()[s].cells.length][];
        for (int i=0; i < article.getTables()[s].cells.length; i++) {
          original_cells[i]=new Cell[article.getTables()[s].cells[i].length];
          for (int j=0; j < article.getTables()[s].cells[i].length; j++)           original_cells[i][j]=new Cell(article.getTables()[s].cells[i][j]);
        }
        article.getTables()[s].original_cells=original_cells;
      }
    }
    Decomposition ie=null;
    TrialIE2 tie=null;
    FreqIE tie2=null;
    IEArmBased21 tie3=null;
    if (doIE) {
      ie=new Decomposition(Inpath,newrun);
      newrun=false;
    }
    if (IEFreqSQLTial) {
      tie2=new FreqIE();
    }
    if (IEinSQLTial) {
      tie=new TrialIE2();
    }
    if (IEFine) {
      tie3=new IEArmBased21();
      informationClasses=ResourceReader.read("String_Node_Str");
    }
    if (Conceptization) {
      concept.ReadPatterns("String_Node_Str");
    }
    if (article != null && article.getTables() != null)     for (int j=0; j < article.getTables().length; j++) {
      Table t=article.getTables()[j];
      if (t.isHasHeader()) {
        t=TableSimplifier.MergeHeaders(t);
        t=TableSimplifier.MergeStubs(t);
      }
      t.PragmaticClass=pc.Classify(t);
    }
    if (doIE) {
      ie.ExtractData(article);
    }
    if (TablInExMain.ComplexClassify) {
      for (int i=0; i < article.getTables().length; i++) {
        SimpleTableClassifier.ClassifyTableByComplexity(article.getTables()[i]);
      }
    }
    if (IEinSQLTial) {
      tie.ExtractTrialData(article);
    }
    if (IEFreqSQLTial) {
      tie2.ExtractTrialData(article);
    }
    if (IEFine) {
      tie3.ExtractTrialData(article);
    }
    if (Conceptization) {
      concept.processArticle(article);
    }
    if (ExportLinkedData) {
      linkedData.printToFile(LinkedDataFolder + "String_Node_Str" + article.getPmc()+ "String_Node_Str");
    }
    for (int l=0; l < article.getTables().length; l++) {
      LinkedList<DataExtractionOutputObj> outputs=article.getTables()[l].output;
      for (      DataExtractionOutputObj out : outputs) {
        out.CreateOutput();
      }
    }
    Annotate annot=new Annotate();
    annot.AnnotateArticle(article);
  }
  int weight=0;
  int BMI=0;
  if (learnheaders) {
    LinkedHashMap lm=Utilities.sortHashMapByValuesD(headermap);
    Object[] ss=lm.keySet().toArray();
    String[] sa=new String[ss.length];
    int k=0;
    for (    Object o : ss) {
      sa[k]=(String)ss[k];
      k++;
    }
    PrintWriter writer;
    try {
      writer=new PrintWriter("String_Node_Str","String_Node_Str");
      for (      String name : sa) {
        String key=name.toString();
        String value=lm.get(name).toString();
        writer.println(key + "String_Node_Str" + value);
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str")|| key.toLowerCase().contains("String_Node_Str")) && (!key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str"))) {
          weight+=Integer.parseInt(lm.get(name).toString());
        }
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str"))) {
          BMI+=Integer.parseInt(lm.get(name).toString());
        }
      }
      writer.close();
    }
 catch (    FileNotFoundException e) {
      e.printStackTrace();
    }
catch (    UnsupportedEncodingException e) {
      e.printStackTrace();
    }
    lm=Utilities.sortHashMapByValuesD(stubmap);
    ss=lm.keySet().toArray();
    sa=new String[ss.length];
    k=0;
    for (    Object o : ss) {
      sa[k]=(String)ss[k];
      k++;
    }
    try {
      writer=new PrintWriter("String_Node_Str","String_Node_Str");
      for (      String name : sa) {
        String key=name.toString();
        String value=lm.get(name).toString();
        writer.println(key + "String_Node_Str" + value);
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str")|| key.toLowerCase().contains("String_Node_Str")) && (!key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str"))) {
          weight+=Integer.parseInt(lm.get(name).toString());
        }
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str"))) {
          BMI+=Integer.parseInt(lm.get(name).toString());
        }
      }
      writer.close();
    }
 catch (    FileNotFoundException e) {
      e.printStackTrace();
    }
catch (    UnsupportedEncodingException e) {
      e.printStackTrace();
    }
  }
  Statistics.CalculateStatistics();
  String stats=Statistics.makeOutputStatisticString();
  System.out.print(stats);
  concept.PrintConceptizationStats();
}

Fixed version (ground truth):
public static void main(String[] args){
  String propsFile="String_Node_Str";
  try {
    JWNL.initialize(new FileInputStream(propsFile));
  }
 catch (  Exception Ex) {
    Ex.printStackTrace();
  }
  concept=new ConceptizationStats();
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  System.out.println("String_Node_Str");
  String path=args[0];
  Inpath=path;
  String runas="String_Node_Str";
  if (args.length > 1)   runas=args[1];
  if (Arrays.asList(args).contains("String_Node_Str")) {
    int i=Arrays.asList(args).indexOf("String_Node_Str");
    outputDest=args[i + 1];
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    int i=Arrays.asList(args).indexOf("String_Node_Str");
    learnheaders=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    shouldTag=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    ExportLinkedData=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    Conceptization=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEFreqSQLTial=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doStats=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEinSQLTial=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    IEFine=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    TypeClassify=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doXMLInput=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    ComplexClassify=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    doIE=true;
  }
  if (Arrays.asList(args).contains("String_Node_Str")) {
    printHelp();
    return;
  }
  classifiers.PragmaticClassifier pc=new classifiers.PragmaticClassifier("String_Node_Str");
  if (TypeClassify)   SimpleTableClassifier.init(TablInExMain.Inpath);
  if (ComplexClassify)   SimpleTableClassifier.initComplexity(Inpath);
  System.out.println("String_Node_Str" + path);
  File Dir=new File(path);
  File[] files=Dir.listFiles();
  Article article=new Article("String_Node_Str");
  boolean newrun=true;
  String LinkedDataFolder="String_Node_Str";
  if (ExportLinkedData) {
    boolean success=(new File(LinkedDataFolder)).mkdirs();
  }
  for (int a=0; a < files.length; a++) {
    if (ExportLinkedData) {
      linkedData=new DecompositionRDFWriter();
    }
    if (runas.toLowerCase().equals("String_Node_Str")) {
      article=runReadingloopOneFile(article,files[a],PMCXMLReader.class);
      for (int s=0; s < article.getTables().length; s++) {
        if (article.getTables()[s].cells == null)         continue;
        Cell[][] original_cells=new Cell[article.getTables()[s].cells.length][];
        for (int i=0; i < article.getTables()[s].cells.length; i++) {
          original_cells[i]=new Cell[article.getTables()[s].cells[i].length];
          for (int j=0; j < article.getTables()[s].cells[i].length; j++)           original_cells[i][j]=new Cell(article.getTables()[s].cells[i][j]);
        }
        article.getTables()[s].original_cells=original_cells;
      }
    }
    Decomposition ie=null;
    TrialIE2 tie=null;
    FreqIE tie2=null;
    IEArmBased21 tie3=null;
    if (doIE) {
      ie=new Decomposition(Inpath,newrun);
      newrun=false;
    }
    if (IEFreqSQLTial) {
      tie2=new FreqIE();
    }
    if (IEinSQLTial) {
      tie=new TrialIE2();
    }
    if (IEFine) {
      tie3=new IEArmBased21();
      informationClasses=ResourceReader.read("String_Node_Str");
    }
    if (Conceptization) {
      concept.ReadPatterns("String_Node_Str");
    }
    if (article != null && article.getTables() != null)     for (int j=0; j < article.getTables().length; j++) {
      Table t=article.getTables()[j];
      if (t.isHasHeader()) {
        t=TableSimplifier.MergeHeaders(t);
        t=TableSimplifier.MergeStubs(t);
      }
      t.PragmaticClass=pc.Classify(t);
    }
    if (doIE) {
      ie.ExtractData(article);
    }
    if (TablInExMain.ComplexClassify) {
      for (int i=0; i < article.getTables().length; i++) {
        SimpleTableClassifier.ClassifyTableByComplexity(article.getTables()[i]);
      }
    }
    if (IEinSQLTial) {
      tie.ExtractTrialData(article);
    }
    if (IEFreqSQLTial) {
      tie2.ExtractTrialData(article);
    }
    if (IEFine) {
      tie3.ExtractTrialData(article);
    }
    if (Conceptization) {
      concept.processArticle(article);
    }
    if (ExportLinkedData) {
      linkedData.printToFile(LinkedDataFolder + "String_Node_Str" + article.getPmc()+ "String_Node_Str");
    }
    for (int l=0; l < article.getTables().length; l++) {
      LinkedList<DataExtractionOutputObj> outputs=article.getTables()[l].output;
      for (      DataExtractionOutputObj out : outputs) {
        out.CreateOutput();
      }
    }
    Annotate annot=new Annotate();
    annot.AnnotateArticle(article);
  }
  int weight=0;
  int BMI=0;
  if (learnheaders) {
    LinkedHashMap lm=Utilities.sortHashMapByValuesD(headermap);
    Object[] ss=lm.keySet().toArray();
    String[] sa=new String[ss.length];
    int k=0;
    for (    Object o : ss) {
      sa[k]=(String)ss[k];
      k++;
    }
    PrintWriter writer;
    try {
      writer=new PrintWriter("String_Node_Str","String_Node_Str");
      for (      String name : sa) {
        String key=name.toString();
        String value=lm.get(name).toString();
        writer.println(key + "String_Node_Str" + value);
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str")|| key.toLowerCase().contains("String_Node_Str")) && (!key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str"))) {
          weight+=Integer.parseInt(lm.get(name).toString());
        }
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str"))) {
          BMI+=Integer.parseInt(lm.get(name).toString());
        }
      }
      writer.close();
    }
 catch (    FileNotFoundException e) {
      e.printStackTrace();
    }
catch (    UnsupportedEncodingException e) {
      e.printStackTrace();
    }
    lm=Utilities.sortHashMapByValuesD(stubmap);
    ss=lm.keySet().toArray();
    sa=new String[ss.length];
    k=0;
    for (    Object o : ss) {
      sa[k]=(String)ss[k];
      k++;
    }
    try {
      writer=new PrintWriter("String_Node_Str","String_Node_Str");
      for (      String name : sa) {
        String key=name.toString();
        String value=lm.get(name).toString();
        writer.println(key + "String_Node_Str" + value);
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str")|| key.toLowerCase().contains("String_Node_Str")) && (!key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str") || !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str")|| !key.toLowerCase().contains("String_Node_Str"))) {
          weight+=Integer.parseInt(lm.get(name).toString());
        }
        if ((key.toLowerCase().contains("String_Node_Str") || key.toLowerCase().contains("String_Node_Str"))) {
          BMI+=Integer.parseInt(lm.get(name).toString());
        }
      }
      writer.close();
    }
 catch (    FileNotFoundException e) {
      e.printStackTrace();
    }
catch (    UnsupportedEncodingException e) {
      e.printStackTrace();
    }
  }
  Statistics.CalculateStatistics();
  String stats=Statistics.makeOutputStatisticString();
  System.out.print(stats);
  concept.PrintConceptizationStats();
}