/**
* Returns a boolean indicating whether the neutral loss should be accounted for.
*
* @param neutralLosses map of expected neutral losses
* @param neutralLoss the neutral loss of interest
* @param ion the fragment ion of interest
* @return boolean indicating whether the neutral loss should be considered
*/
public boolean isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion) {
if (neutralLosses == null || neutralLosses.isEmpty()) {
return false;
}
for (String neutralLossName : neutralLosses.getAccountedNeutralLosses()) {
NeutralLoss neutralLossRef = NeutralLoss.getNeutralLoss(neutralLossName);
if (neutralLoss.isSameAs(neutralLossRef)) {
switch (ion.getType()) {
case PEPTIDE_FRAGMENT_ION:
PeptideFragmentIon peptideFragmentIon = ((PeptideFragmentIon) ion);
switch (ion.getSubType()) {
case PeptideFragmentIon.A_ION:
case PeptideFragmentIon.B_ION:
case PeptideFragmentIon.C_ION:
return neutralLosses.getForwardStart(neutralLossName)
<= peptideFragmentIon.getNumber();
case PeptideFragmentIon.X_ION:
case PeptideFragmentIon.Y_ION:
case PeptideFragmentIon.Z_ION:
return neutralLosses.getRewindStart(neutralLossName)
<= peptideFragmentIon.getNumber();
default:
throw new UnsupportedOperationException(
"Fragment ion type "
+ ion.getSubTypeAsString()
+ " not implemented in the spectrum annotator.");
}
case TAG_FRAGMENT_ION:
TagFragmentIon tagFragmentIon = ((TagFragmentIon) ion);
switch (ion.getSubType()) {
case TagFragmentIon.A_ION:
case TagFragmentIon.B_ION:
case TagFragmentIon.C_ION:
return neutralLosses.getForwardStart(neutralLossName) <= tagFragmentIon.getNumber();
case TagFragmentIon.X_ION:
case TagFragmentIon.Y_ION:
case TagFragmentIon.Z_ION:
return neutralLosses.getRewindStart(neutralLossName) <= tagFragmentIon.getNumber();
default:
throw new UnsupportedOperationException(
"Fragment ion type "
+ ion.getSubTypeAsString()
+ " not implemented in the spectrum annotator.");
}
default:
return true;
}
}
}
return false;
}
/**
* Returns a boolean indicating whether the given charge can be found on the given fragment ion.
*
* @param theoreticIon the ion of interest
* @param charge the candidate charge
* @param precursorCharge the precursor charge
* @return a boolean indicating whether the given charge can be found on the given fragment ion
*/
public boolean chargeValidated(Ion theoreticIon, int charge, int precursorCharge) {
if (charge == 1) {
return true;
}
switch (theoreticIon.getType()) {
case IMMONIUM_ION:
case RELATED_ION: // note: it is possible to implement higher charges but then modify
// IonMatch.getPeakAnnotation(boolean html) as well to see the charge
// displayed on the spectrum
return false;
case REPORTER_ION: // note: it is possible to implement higher charges but then modify
// IonMatch.getPeakAnnotation(boolean html) as well to see the charge
// displayed on the spectrum
return false;
case PEPTIDE_FRAGMENT_ION:
PeptideFragmentIon peptideFragmentIon = ((PeptideFragmentIon) theoreticIon);
return charge <= peptideFragmentIon.getNumber() && charge < precursorCharge;
case TAG_FRAGMENT_ION:
TagFragmentIon tagFragmentIon = ((TagFragmentIon) theoreticIon);
return charge <= tagFragmentIon.getNumber() && charge < precursorCharge;
case PRECURSOR_ION:
return charge >= precursorCharge;
default:
throw new UnsupportedOperationException(
"Ion type "
+ theoreticIon.getTypeAsString()
+ " not implemented in the spectrum annotator.");
}
}