Program: 58708
Project: 58708
Buggy source:
@Override public void doCommand(){
  generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + loadDataParameters.getFileName() + "String_Node_Str"+ loadDataParameters.getInputPattern()+ "String_Node_Str"+ iAlStorageIDs.toString()));
  TabularAsciiDataReader loader=new TabularAsciiDataReader(loadDataParameters.getFileName());
  loader.setTokenPattern(loadDataParameters.getInputPattern());
  loader.setTargetStorages(iAlStorageIDs);
  if (loadDataParameters.isUseExperimentClusterInfo())   loader.enableExperimentClusterInfo();
  loader.setStartParsingStopParsingAtLine(loadDataParameters.getStartParseFileAtLine(),loadDataParameters.getStopParseFileAtLine());
  if (loadDataParameters.getDelimiter() != null && loadDataParameters.getDelimiter().isEmpty()) {
    loader.setTokenSeperator(loadDataParameters.getDelimiter());
  }
  bParsingOK=loader.loadData();
  generalManager.getGUIBridge().setFileNameCurrentDataSet(loadDataParameters.getFileName());
  String geneTreeFileName=loadDataParameters.getGeneTreeFileName();
  if (geneTreeFileName != null) {
    if (geneTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + geneTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree;
      try {
        tree=treePorter.importTree(geneTreeFileName);
        ISet set=generalManager.getUseCase().getSet();
        set.setClusteredTreeGenes(tree);
      }
 catch (      FileNotFoundException e) {
        e.printStackTrace();
      }
catch (      JAXBException e) {
        e.printStackTrace();
      }
    }
  }
  String experimentsTreeFileName=loadDataParameters.getExperimentsFileName();
  if (experimentsTreeFileName != null) {
    if (experimentsTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + experimentsTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree;
      try {
        tree=treePorter.importTree(experimentsTreeFileName);
        ISet set=generalManager.getUseCase().getSet();
        set.setClusteredTreeExps(tree);
      }
 catch (      FileNotFoundException e) {
        e.printStackTrace();
      }
catch (      JAXBException e) {
        e.printStackTrace();
      }
    }
  }
  commandManager.runDoCommand(this);
}

Fixed version (ground truth):
@Override public void doCommand(){
  generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + loadDataParameters.getFileName() + "String_Node_Str"+ loadDataParameters.getInputPattern()+ "String_Node_Str"+ iAlStorageIDs.toString()));
  TabularAsciiDataReader loader=new TabularAsciiDataReader(loadDataParameters.getFileName());
  loader.setTokenPattern(loadDataParameters.getInputPattern());
  loader.setTargetStorages(iAlStorageIDs);
  if (loadDataParameters.isUseExperimentClusterInfo())   loader.enableExperimentClusterInfo();
  loader.setStartParsingStopParsingAtLine(loadDataParameters.getStartParseFileAtLine(),loadDataParameters.getStopParseFileAtLine());
  if (loadDataParameters.getDelimiter() != null && !loadDataParameters.getDelimiter().isEmpty()) {
    loader.setTokenSeperator(loadDataParameters.getDelimiter());
  }
  bParsingOK=loader.loadData();
  generalManager.getGUIBridge().setFileNameCurrentDataSet(loadDataParameters.getFileName());
  String geneTreeFileName=loadDataParameters.getGeneTreeFileName();
  if (geneTreeFileName != null) {
    if (geneTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + geneTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree;
      try {
        tree=treePorter.importTree(geneTreeFileName);
        ISet set=generalManager.getUseCase().getSet();
        set.setClusteredTreeGenes(tree);
      }
 catch (      FileNotFoundException e) {
        e.printStackTrace();
      }
catch (      JAXBException e) {
        e.printStackTrace();
      }
    }
  }
  String experimentsTreeFileName=loadDataParameters.getExperimentsFileName();
  if (experimentsTreeFileName != null) {
    if (experimentsTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + experimentsTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree;
      try {
        tree=treePorter.importTree(experimentsTreeFileName);
        ISet set=generalManager.getUseCase().getSet();
        set.setClusteredTreeExps(tree);
      }
 catch (      FileNotFoundException e) {
        e.printStackTrace();
      }
catch (      JAXBException e) {
        e.printStackTrace();
      }
    }
  }
  GeneralManager.get().getUseCase().setLoadDataParameters(loadDataParameters);
  commandManager.runDoCommand(this);
}