Program: 57629
Project: 57629
Buggy source:
public void loadPathwaysByType(PathwayDatabase pathwayDatabase){
  GeneralManager generalManager=GeneralManager.get();
  Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + pathwayDatabase.getName() + "String_Node_Str"));
  BufferedReader file=null;
  String line=null;
  String fileName="String_Node_Str";
  String pathwayPath=pathwayDatabase.getXMLPath();
  IPathwayResourceLoader pathwayResourceLoader=null;
  Organism organism=GeneralManager.get().getBasicInfo().getOrganism();
  if (pathwayDatabase.getType() == PathwayDatabaseType.KEGG) {
    if (organism == Organism.HOMO_SAPIENS) {
      fileName="String_Node_Str";
    }
 else     if (organism == Organism.MUS_MUSCULUS) {
      fileName="String_Node_Str";
    }
 else {
      throw new IllegalStateException("String_Node_Str" + organism);
    }
    generalManager.getSWTGUIManager().setProgressBarTextFromExternalThread("String_Node_Str");
  }
 else   if (pathwayDatabase.getType() == PathwayDatabaseType.BIOCARTA) {
    if (organism == Organism.HOMO_SAPIENS) {
      fileName="String_Node_Str";
    }
 else     if (organism == Organism.MUS_MUSCULUS) {
      fileName="String_Node_Str";
    }
 else {
      throw new IllegalStateException("String_Node_Str" + organism);
    }
    generalManager.getSWTGUIManager().setProgressBarTextFromExternalThread("String_Node_Str");
  }
  PathwayManager.get().createPathwayResourceLoader(pathwayDatabase.getType());
  pathwayResourceLoader=PathwayManager.get().getPathwayResourceLoader(pathwayDatabase.getType());
  try {
    if (pathwayDatabase.getType() == PathwayDatabaseType.KEGG || pathwayDatabase.getType() == PathwayDatabaseType.BIOCARTA)     file=pathwayResourceLoader.getResource(fileName);
 else     file=GeneralManager.get().getResourceLoader().getResource(fileName);
    StringTokenizer tokenizer;
    String pathwayName;
    while ((line=file.readLine()) != null) {
      tokenizer=new StringTokenizer(line,"String_Node_Str");
      pathwayName=tokenizer.nextToken();
      if (!pathwayName.endsWith("String_Node_Str") && !line.contains("String_Node_Str") && !line.contains("String_Node_Str")) {
        continue;
      }
      PathwayManager.get().getXmlParserManager().parseXmlFileByName(pathwayPath + pathwayName);
      currentPathwayGraph.setWidth(Integer.valueOf(tokenizer.nextToken()).intValue());
      currentPathwayGraph.setHeight(Integer.valueOf(tokenizer.nextToken()).intValue());
      int iImageWidth=currentPathwayGraph.getWidth();
      int iImageHeight=currentPathwayGraph.getHeight();
      if (iImageWidth == -1 || iImageHeight == -1) {
        Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + iImageWidth + "String_Node_Str"+ iImageHeight));
      }
    }
  }
 catch (  FileNotFoundException e) {
    throw new IllegalStateException("String_Node_Str" + fileName + "String_Node_Str");
  }
catch (  IOException e) {
    throw new IllegalStateException("String_Node_Str" + fileName);
  }
  Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + pathwayDatabase.getName() + "String_Node_Str"));
}

Fixed version (ground truth):
public void loadPathwaysByType(PathwayDatabase pathwayDatabase){
  GeneralManager generalManager=GeneralManager.get();
  Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + pathwayDatabase.getName() + "String_Node_Str"));
  BufferedReader file=null;
  String line=null;
  String fileName="String_Node_Str";
  String pathwayPath=pathwayDatabase.getXMLPath();
  IPathwayResourceLoader pathwayResourceLoader=null;
  Organism organism=GeneralManager.get().getBasicInfo().getOrganism();
  if (pathwayDatabase.getType() == PathwayDatabaseType.KEGG) {
    if (organism == Organism.HOMO_SAPIENS) {
      fileName="String_Node_Str";
    }
 else     if (organism == Organism.MUS_MUSCULUS) {
      fileName="String_Node_Str";
    }
 else {
      throw new IllegalStateException("String_Node_Str" + organism);
    }
    generalManager.getSWTGUIManager().setProgressBarTextFromExternalThread("String_Node_Str");
  }
 else   if (pathwayDatabase.getType() == PathwayDatabaseType.BIOCARTA) {
    if (organism == Organism.HOMO_SAPIENS) {
      fileName="String_Node_Str";
    }
 else     if (organism == Organism.MUS_MUSCULUS) {
      fileName="String_Node_Str";
    }
 else {
      throw new IllegalStateException("String_Node_Str" + organism);
    }
    generalManager.getSWTGUIManager().setProgressBarTextFromExternalThread("String_Node_Str");
  }
  PathwayManager.get().createPathwayResourceLoader(pathwayDatabase.getType());
  pathwayResourceLoader=PathwayManager.get().getPathwayResourceLoader(pathwayDatabase.getType());
  if (pathwayResourceLoader == null)   return;
  try {
    if (pathwayDatabase.getType() == PathwayDatabaseType.KEGG || pathwayDatabase.getType() == PathwayDatabaseType.BIOCARTA)     file=pathwayResourceLoader.getResource(fileName);
 else     file=GeneralManager.get().getResourceLoader().getResource(fileName);
    StringTokenizer tokenizer;
    String pathwayName;
    while ((line=file.readLine()) != null) {
      tokenizer=new StringTokenizer(line,"String_Node_Str");
      pathwayName=tokenizer.nextToken();
      if (!pathwayName.endsWith("String_Node_Str") && !line.contains("String_Node_Str") && !line.contains("String_Node_Str")) {
        continue;
      }
      PathwayManager.get().getXmlParserManager().parseXmlFileByName(pathwayPath + pathwayName);
      currentPathwayGraph.setWidth(Integer.valueOf(tokenizer.nextToken()).intValue());
      currentPathwayGraph.setHeight(Integer.valueOf(tokenizer.nextToken()).intValue());
      int iImageWidth=currentPathwayGraph.getWidth();
      int iImageHeight=currentPathwayGraph.getHeight();
      if (iImageWidth == -1 || iImageHeight == -1) {
        Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + iImageWidth + "String_Node_Str"+ iImageHeight));
      }
    }
  }
 catch (  FileNotFoundException e) {
    throw new IllegalStateException("String_Node_Str" + fileName + "String_Node_Str");
  }
catch (  IOException e) {
    throw new IllegalStateException("String_Node_Str" + fileName);
  }
  Logger.log(new Status(IStatus.INFO,"String_Node_Str","String_Node_Str" + pathwayDatabase.getName() + "String_Node_Str"));
}