/** Updates the mass shifts. */ protected void updateMassShifts() { if (theoreticalFragmentIons != null) { HashMap<Integer, ArrayList<Ion>> peptideFragmentIons = theoreticalFragmentIons.get(IonType.PEPTIDE_FRAGMENT_ION.index); ArrayList<Ion> ions = peptideFragmentIons.get(PeptideFragmentIon.A_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = peptideFragmentIons.get(PeptideFragmentIon.B_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = peptideFragmentIons.get(PeptideFragmentIon.C_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = peptideFragmentIons.get(PeptideFragmentIon.X_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } ions = peptideFragmentIons.get(PeptideFragmentIon.Y_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } ions = peptideFragmentIons.get(PeptideFragmentIon.Z_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } HashMap<Integer, ArrayList<Ion>> tagFragmentIons = theoreticalFragmentIons.get(IonType.TAG_FRAGMENT_ION.index); ions = tagFragmentIons.get(TagFragmentIon.A_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = tagFragmentIons.get(TagFragmentIon.B_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = tagFragmentIons.get(TagFragmentIon.C_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftNTerm); } } ions = tagFragmentIons.get(TagFragmentIon.X_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } ions = tagFragmentIons.get(TagFragmentIon.Y_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } ions = tagFragmentIons.get(TagFragmentIon.Z_ION); if (ions != null) { for (Ion ion : ions) { ion.setTheoreticMass(ion.getTheoreticMass() + massShift + massShiftCTerm); } } } }