Program: 58775
Project: 58775
Buggy source:
@Override public void doCommand(){
  generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sFileName + "String_Node_Str"+ sTokenPattern+ "String_Node_Str"+ iAlStorageIDs.toString()));
  TabularAsciiDataReader loader=new TabularAsciiDataReader(sFileName);
  loader.setTokenPattern(sTokenPattern);
  loader.setTargetStorages(iAlStorageIDs);
  loader.setStartParsingStopParsingAtLine(iStartParseFileAtLine,iStopParseFileAtLine);
  if (!sTokenSeparator.isEmpty()) {
    loader.setTokenSeperator(sTokenSeparator);
  }
  loader.loadData();
  generalManager.getGUIBridge().setFileNameCurrentDataSet(sFileName);
  if (sGenesTreeFileName != null) {
    if (sGenesTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sGenesTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree=treePorter.importTree(sGenesTreeFileName);
      ISet set=generalManager.getUseCase().getSet();
      set.setClusteredTreeGenes(tree);
    }
  }
  if (sExperimentsTreeFileName != null) {
    if (sExperimentsTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sExperimentsTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree=treePorter.importTree(sExperimentsTreeFileName);
      ISet set=generalManager.getUseCase().getSet();
      set.setClusteredTreeExps(tree);
    }
  }
  commandManager.runDoCommand(this);
}

Fixed version (ground truth):
@Override public void doCommand(){
  generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sFileName + "String_Node_Str"+ sTokenPattern+ "String_Node_Str"+ iAlStorageIDs.toString()));
  TabularAsciiDataReader loader=new TabularAsciiDataReader(sFileName);
  loader.setTokenPattern(sTokenPattern);
  loader.setTargetStorages(iAlStorageIDs);
  loader.setStartParsingStopParsingAtLine(iStartParseFileAtLine,iStopParseFileAtLine);
  if (!sTokenSeparator.isEmpty()) {
    loader.setTokenSeperator(sTokenSeparator);
  }
  bParsingOK=loader.loadData();
  generalManager.getGUIBridge().setFileNameCurrentDataSet(sFileName);
  if (sGenesTreeFileName != null) {
    if (sGenesTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sGenesTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree=treePorter.importTree(sGenesTreeFileName);
      ISet set=generalManager.getUseCase().getSet();
      set.setClusteredTreeGenes(tree);
    }
  }
  if (sExperimentsTreeFileName != null) {
    if (sExperimentsTreeFileName.equals("String_Node_Str") == false) {
      generalManager.getLogger().log(new Status(Status.INFO,GeneralManager.PLUGIN_ID,"String_Node_Str" + sExperimentsTreeFileName));
      TreePorter treePorter=new TreePorter();
      Tree<ClusterNode> tree=treePorter.importTree(sExperimentsTreeFileName);
      ISet set=generalManager.getUseCase().getSet();
      set.setClusteredTreeExps(tree);
    }
  }
  commandManager.runDoCommand(this);
}