Program: 58592
Project: 58592
Buggy source:
/** 
 * Load data from file using a token pattern.
 * @see org.caleydo.core.parser.ascii.microarray.MicroArrayLoader1Storage#loadData()
 * @see org.caleydo.core.command.ICommand#doCommand()
 */
public void doCommand(){
  LookupTableLoader loader=null;
  if (sFileName.contains("String_Node_Str")) {
    EOrganism eOrganism=((GeneticUseCase)GeneralManager.get().getUseCase(EDataDomain.GENETIC_DATA)).getOrganism();
    this.sFileName=sFileName.replace("String_Node_Str",eOrganism.toString());
  }
  IIDMappingManager genomeIdManager=generalManager.getIDMappingManager();
  EMappingType mappingType=EMappingType.valueOf(sLookupTableType);
  int iIndex=0;
  if (sFileName.equals("String_Node_Str")) {
    genomeIdManager.createMap(EMappingType.REFSEQ_MRNA_2_REFSEQ_MRNA_INT);
    Map hashTmp=genomeIdManager.getMap(EMappingType.REFSEQ_MRNA_2_REFSEQ_MRNA_INT);
    for (    Object sRefSeqID : genomeIdManager.getMap(EMappingType.DAVID_2_REFSEQ_MRNA).values()) {
      hashTmp.put(sRefSeqID,iIndex++);
    }
  }
 else   if (!sFileName.equals("String_Node_Str")) {
    loader=new LookupTableLoader(sFileName,mappingType);
    loader.setTokenSeperator(sLookupTableDelimiter);
    loader.setStartParsingStopParsingAtLine(iStartPareseFileAtLine,iStopParseFileAtLine);
    loader.loadData();
  }
  if (bResolveCodeMappingUsingCodeToId_LUT) {
    genomeIdManager.createCodeResolvedMap(mappingType,EMappingType.valueOf(sCodeResolvingLUTMappingType));
  }
  if (bCreateReverseMap) {
    if (sCodeResolvingLUTMappingType != null) {
      mappingType=EMappingType.valueOf(sCodeResolvingLUTMappingType);
    }
    EMappingType reverseMappingType=EMappingType.valueOf(mappingType.getTypeTarget().toString() + "String_Node_Str" + mappingType.getTypeOrigin().toString());
    genomeIdManager.createReverseMap(mappingType,reverseMappingType);
  }
  commandManager.runDoCommand(this);
}

Fixed version (ground truth):
/** 
 * Load data from file using a token pattern.
 * @see org.caleydo.core.command.ICommand#doCommand()
 */
public void doCommand(){
  LookupTableLoader loader=null;
  if (sFileName.contains("String_Node_Str")) {
    EOrganism eOrganism=((GeneticUseCase)GeneralManager.get().getUseCase(EDataDomain.GENETIC_DATA)).getOrganism();
    this.sFileName=sFileName.replace("String_Node_Str",eOrganism.toString());
  }
  IIDMappingManager genomeIdManager=generalManager.getIDMappingManager();
  EMappingType mappingType=EMappingType.valueOf(sLookupTableType);
  int iIndex=0;
  if (sFileName.equals("String_Node_Str")) {
    genomeIdManager.createMap(EMappingType.REFSEQ_MRNA_2_REFSEQ_MRNA_INT);
    Map hashTmp=genomeIdManager.getMap(EMappingType.REFSEQ_MRNA_2_REFSEQ_MRNA_INT);
    for (    Object sRefSeqID : genomeIdManager.getMap(EMappingType.DAVID_2_REFSEQ_MRNA).values()) {
      hashTmp.put(sRefSeqID,iIndex++);
    }
  }
 else   if (!sFileName.equals("String_Node_Str")) {
    loader=new LookupTableLoader(sFileName,mappingType);
    loader.setTokenSeperator(sLookupTableDelimiter);
    loader.setStartParsingStopParsingAtLine(iStartPareseFileAtLine,iStopParseFileAtLine);
    loader.loadData();
  }
  if (bResolveCodeMappingUsingCodeToId_LUT) {
    genomeIdManager.createCodeResolvedMap(mappingType,EMappingType.valueOf(sCodeResolvingLUTMappingType));
  }
  if (bCreateReverseMap) {
    if (sCodeResolvingLUTMappingType != null) {
      mappingType=EMappingType.valueOf(sCodeResolvingLUTMappingType);
    }
    EMappingType reverseMappingType=EMappingType.valueOf(mappingType.getTypeTarget().toString() + "String_Node_Str" + mappingType.getTypeOrigin().toString());
    genomeIdManager.createReverseMap(mappingType,reverseMappingType);
  }
  commandManager.runDoCommand(this);
}