Program: 59072
Project: 59072
Buggy source:
public final ArrayList<Vec3f> getMappingColorArrayByVertexRep(final PathwayVertexGraphItemRep pathwayVertexRep){
  if (pathwayVertexRep == null) {
    return new ArrayList<Vec3f>();
  }
  if (pathwayVertexRep.getPathwayVertexGraphItem().getType().equals(EPathwayVertexType.gene)) {
    ArrayList<Vec3f> arMappingColor=new ArrayList<Vec3f>();
    if (pathwayVertexRep.getAllItemsByProp(EGraphItemProperty.ALIAS_PARENT).size() > 1) {
      arMappingColor.add(new Vec3f(0,1,1));
    }
 else {
      int iDavidId=generalManager.getPathwayItemManager().getDavidIdByPathwayVertexGraphItemId(pathwayVertexRep.getPathwayVertexGraphItem().getId());
      int iExpressionStorageIndex=genomeIdManager.getIdIntFromIntByMapping(iDavidId,EMappingType.DAVID_2_EXPRESSION_STORAGE_ID);
      if (iExpressionStorageIndex == -1) {
        arMappingColor.add(new Vec3f(-1,-1,-1));
        return arMappingColor;
      }
      Iterator<IStorage> iterMappingStorage=alMappingStorage.iterator();
      IStorage expressionStorage=null;
      while (iterMappingStorage.hasNext()) {
        expressionStorage=iterMappingStorage.next();
        float fExpressionValue=expressionStorage.getFloat(EDataRepresentation.NORMALIZED,iExpressionStorageIndex);
        arMappingColor.add(expressionColorMapper.colorMappingLookup(fExpressionValue));
      }
    }
    return arMappingColor;
  }
 else   if (pathwayVertexRep.getPathwayVertexGraphItem().getType().equals(EPathwayVertexType.enzyme)) {
    ArrayList<Vec3f> arMappingColor=new ArrayList<Vec3f>();
    arMappingColor.add(new Vec3f(-1,-1,-1));
    return arMappingColor;
  }
  return new ArrayList<Vec3f>();
}

Fixed version (ground truth):
public final ArrayList<Vec3f> getMappingColorArrayByVertexRep(final PathwayVertexGraphItemRep pathwayVertexRep){
  if (pathwayVertexRep == null) {
    return new ArrayList<Vec3f>();
  }
  if (pathwayVertexRep.getType().equals(EPathwayVertexType.gene)) {
    ArrayList<Vec3f> arMappingColor=new ArrayList<Vec3f>();
    if (pathwayVertexRep.getAllItemsByProp(EGraphItemProperty.ALIAS_PARENT).size() > 1) {
      arMappingColor.add(new Vec3f(0,1,1));
    }
 else {
      int iDavidId=generalManager.getPathwayItemManager().getDavidIdByPathwayVertexGraphItemId(pathwayVertexRep.getAllItemsByProp(EGraphItemProperty.ALIAS_PARENT).get(0).getId());
      int iExpressionStorageIndex=genomeIdManager.getIdIntFromIntByMapping(iDavidId,EMappingType.DAVID_2_EXPRESSION_STORAGE_ID);
      if (iExpressionStorageIndex == -1) {
        arMappingColor.add(new Vec3f(-1,-1,-1));
        return arMappingColor;
      }
      Iterator<IStorage> iterMappingStorage=alMappingStorage.iterator();
      IStorage expressionStorage=null;
      while (iterMappingStorage.hasNext()) {
        expressionStorage=iterMappingStorage.next();
        float fExpressionValue=expressionStorage.getFloat(EDataRepresentation.NORMALIZED,iExpressionStorageIndex);
        arMappingColor.add(expressionColorMapper.colorMappingLookup(fExpressionValue));
      }
    }
    return arMappingColor;
  }
 else   if (pathwayVertexRep.getType().equals(EPathwayVertexType.enzyme)) {
    ArrayList<Vec3f> arMappingColor=new ArrayList<Vec3f>();
    arMappingColor.add(new Vec3f(-1,-1,-1));
    return arMappingColor;
  }
  return new ArrayList<Vec3f>();
}