Usage notes

mzIdentML files (.mzid)

When dealing with mzIdentML files (.mzid) you will encounter AbstractParamType. In the definition of mzIdentML both cvParam and userParam inherit from it and both cvParam and userParam can be stored in the same list. Thus, when you get such a list, you'll need to cast manually to the concrete type like so:

List<AbstractParamType> paramGroup = blabla.getParamGroup();
for (AbstractParamType param : paramGroup) {

	if (param instanceof CVParamType) {
		CVParamType p = (CVParamType)param;
		// do something with cvParam

	} else if (param instanceof UserParamType) {
		UserParamType p = (UserParamType)param;
		// do something with userParam

	}
}