/**
* 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.");
}
}
/**
* Returns a boolean indicating whether the neutral losses of the given fragment ion fit the
* requirement of the given neutral losses map.
*
* @param neutralLosses map of expected neutral losses: neutral loss
* @param theoreticIon the ion of interest
* @return a boolean indicating whether the neutral losses of the given fragment ion are fit the
* requirement of the given neutral losses map
*/
public boolean lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon) {
if (theoreticIon.hasNeutralLosses()) {
for (NeutralLoss neutralLoss : theoreticIon.getNeutralLosses()) {
if (!isAccounted(neutralLosses, neutralLoss, theoreticIon)) {
return false;
}
}
}
return true;
}
/**
* 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;
}
/**
* Convenience method to match a reporter ion in a spectrum. The charge is assumed to be 1.
*
* @param theoreticIon the theoretic ion to look for
* @param charge the charge of the ion
* @param spectrum the spectrum
* @param massTolerance the mass tolerance to use
* @return a list of all the ion matches
* @throws java.lang.InterruptedException exception thrown if the thread is interrupted
*/
public static ArrayList<IonMatch> matchReporterIon(
Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)
throws InterruptedException {
ArrayList<IonMatch> result = new ArrayList<IonMatch>(1);
double targetMass = theoreticIon.getTheoreticMz(charge);
for (double mz : spectrum.getOrderedMzValues()) {
if (Math.abs(mz - targetMass) <= massTolerance) {
result.add(new IonMatch(spectrum.getPeakMap().get(mz), theoreticIon, charge));
}
if (mz > targetMass + massTolerance) {
break;
}
}
return result;
}
/**
* Matches a theoretic ion in the spectrum. Returns an IonMatch containing the ion and the peak.
* Null if not found.
*
* @param theoreticIon the theoretic ion
* @param inspectedCharge the expected charge
* @return the IonMatch between the ion and the peak
*/
protected IonMatch matchInSpectrum(Ion theoreticIon, Integer inspectedCharge) {
Double fragmentMz = theoreticIon.getTheoreticMz(inspectedCharge);
// Get the peaks matching the desired m/z
ArrayList<Peak> matchedPeaks = spectrumIndex.getMatchingPeaks(fragmentMz);
if (matchedPeaks.isEmpty()) {
return null;
}
// Select the most accurate or most intense according to the annotation settings
IonMatch ionMatch = new IonMatch(null, theoreticIon, inspectedCharge);
ionMatch.peak =
(matchedPeaks.size() == 1) ? matchedPeaks.get(0) : getBestPeak(matchedPeaks, ionMatch);
return ionMatch;
}
/** 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);
}
}
}
}