/** 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);
}
}
}
}
