Protein Fragmentation

JPLPeptideFragmenter is making the fragmentation of a given JPLPeptide precursor, and a set of given JPLFragmentationType(s).

	JPLPeptide precursorSeq = 
	    new JPLPeptideBuilder("DELHIVEAEAMNYEGSPIK").build();
	
	JPLPeptideFragmenter fragmenter =
	    new JPLPeptideFragmenter.Builder(EnumSet.of(
	        JPLFragmentationType.BY, JPLFragmentationType.PRECURSOR,
	        JPLFragmentationType.IMMONIUM)).build();
	
	fragmenter.setFragmentablePrecursor(precursorSeq, 1);
	fragmenter.generateFragments();
	
	JPLTheoMSnPeakList bypiPl = fragmenter.getPeakList();