/**
* Returns the possible neutral losses expected by default for a given peptide. /!\ this method
* will work only if the PTM found in the peptide are in the PTMFactory.
*
* @param spectrumIdentificationAssumption the spectrumIdentificationAssumption of interest
* @param sequenceMatchingPreferences the sequence matching settings for peptide to protein
* mapping
* @param ptmSequenceMatchingPreferences the sequence matching settings for PTM to peptide mapping
* @return the expected possible neutral losses
* @throws IOException exception thrown whenever an error occurred while interacting with a file
* while mapping potential modification sites
* @throws InterruptedException exception thrown whenever a threading issue occurred while mapping
* potential modification sites
* @throws ClassNotFoundException exception thrown whenever an error occurred while deserializing
* an object from the ProteinTree
* @throws SQLException exception thrown whenever an error occurred while interacting with the
* ProteinTree
*/
public static NeutralLossesMap getDefaultLosses(
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
throws IOException, InterruptedException, ClassNotFoundException, SQLException {
if (spectrumIdentificationAssumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) spectrumIdentificationAssumption;
return PeptideSpectrumAnnotator.getDefaultLosses(
peptideAssumption.getPeptide(),
sequenceMatchingPreferences,
ptmSequenceMatchingPreferences);
} else if (spectrumIdentificationAssumption instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) spectrumIdentificationAssumption;
return TagSpectrumAnnotator.getDefaultLosses(
tagAssumption.getTag(), ptmSequenceMatchingPreferences);
} else {
throw new IllegalArgumentException(
"Default neutral loss map not implemented for SpectrumIdentificationAssumption "
+ spectrumIdentificationAssumption.getClass()
+ ".");
}
}
/**
* Fills the PSM specific map.
*
* @param inputMap The input map
* @param waitingHandler the handler displaying feedback to the user
* @param shotgunProtocol information about the protocol
* @param identificationParameters the identification parameters
* @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
* with the back-end database
* @throws java.io.IOException exception thrown whenever an error occurred while reading an
* external file
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* deserializing an object
* @throws java.lang.InterruptedException exception thrown whenever a threading error occurred
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
*/
public void selectBestHitAndFillPsmMap(
InputMap inputMap,
WaitingHandler waitingHandler,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters)
throws SQLException, IOException, ClassNotFoundException, InterruptedException,
MzMLUnmarshallerException {
waitingHandler.setSecondaryProgressCounterIndeterminate(false);
waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());
PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
boolean multiSE = inputMap.isMultipleAlgorithms();
SequenceMatchingPreferences sequenceMatchingPreferences =
identificationParameters.getSequenceMatchingPreferences();
AnnotationSettings annotationPreferences = identificationParameters.getAnnotationPreferences();
PeptideAssumptionFilter idFilter = identificationParameters.getPeptideAssumptionFilter();
// Keep a map of the spectrum keys grouped by peptide
HashMap<String, ArrayList<String>> orderedPsmMap = null;
if (MemoryConsumptionStatus.memoryUsed() < 0.8) {
orderedPsmMap =
new HashMap<String, ArrayList<String>>(
identification.getSpectrumIdentificationMap().size());
}
PSParameter psParameter = new PSParameter();
for (String spectrumFileName : identification.getSpectrumFiles()) {
HashMap<String, ArrayList<String>> keysMap = null;
if (orderedPsmMap != null) {
keysMap = new HashMap<String, ArrayList<String>>();
}
PsmIterator psmIterator =
identification.getPsmIterator(spectrumFileName, null, true, waitingHandler);
while (psmIterator.hasNext()) {
SpectrumMatch advocateMatch = psmIterator.next();
String spectrumKey = advocateMatch.getKey();
// map of the peptide first hits for this spectrum: score -> max protein count -> max search
// engine votes -> amino acids annotated -> min mass deviation -> peptide sequence
HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>
peptideAssumptions =
new HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>();
// map of the tag first hits: score -> assumptions
HashMap<Double, ArrayList<TagAssumption>> tagAssumptions =
new HashMap<Double, ArrayList<TagAssumption>>();
ArrayList<String> identifications = new ArrayList<String>();
HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>> assumptions =
identification.getAssumptions(spectrumKey);
for (int searchEngine1 : assumptions.keySet()) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate1Map =
assumptions.get(searchEngine1);
double bestEvalue = Collections.min(advocate1Map.keySet());
for (SpectrumIdentificationAssumption assumption1 : advocate1Map.get(bestEvalue)) {
if (assumption1 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption1 = (PeptideAssumption) assumption1;
String id = peptideAssumption1.getPeptide().getKey();
if (!identifications.contains(id)) {
psParameter = (PSParameter) peptideAssumption1.getUrParam(psParameter);
double p;
if (multiSE && sequenceFactory.concatenatedTargetDecoy()) {
p = psParameter.getSearchEngineProbability();
} else {
p = peptideAssumption1.getScore();
}
int nSE = 1;
int proteinMax = 1;
for (String protein :
peptideAssumption1
.getPeptide()
.getParentProteins(sequenceMatchingPreferences)) {
Integer tempCount = proteinCount.get(protein);
if (tempCount != null && tempCount > proteinMax) {
proteinMax = tempCount;
}
}
for (int searchEngine2 : assumptions.keySet()) {
if (searchEngine1 != searchEngine2) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate2Map =
assumptions.get(searchEngine2);
boolean found = false;
ArrayList<Double> eValues2 = new ArrayList<Double>(advocate2Map.keySet());
Collections.sort(eValues2);
for (double eValue2 : eValues2) {
for (SpectrumIdentificationAssumption assumption2 :
advocate2Map.get(eValue2)) {
if (assumption2 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption2 = (PeptideAssumption) assumption2;
if (peptideAssumption1
.getPeptide()
.isSameSequenceAndModificationStatus(
peptideAssumption2.getPeptide(), sequenceMatchingPreferences)) {
PSParameter psParameter2 =
(PSParameter) peptideAssumption2.getUrParam(psParameter);
p = p * psParameter2.getSearchEngineProbability();
nSE++;
found = true;
break;
}
}
}
if (found) {
break;
}
}
}
}
identifications.add(id);
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
if (pMap == null) {
pMap =
new HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>(
advocate1Map.size());
peptideAssumptions.put(p, pMap);
}
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
if (proteinMaxMap == null) {
proteinMaxMap =
new HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>(1);
pMap.put(proteinMax, proteinMaxMap);
}
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
if (nSeMap == null) {
nSeMap =
new HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>(1);
proteinMaxMap.put(nSE, nSeMap);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
nSeMap.put(-1, coverageMap);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
coverageMap.put(-1.0, assumptionMap);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
} else {
MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap = nSeMap.get(-1);
if (coverageMap != null) {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
Peptide peptide = tempAssumption.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
tempAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
nSeMap.put(nIons, coverageMap);
}
nSeMap.remove(-1);
}
Peptide peptide = peptideAssumption1.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption1,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
coverageMap = nSeMap.get(nIons);
if (coverageMap == null) {
coverageMap = new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
coverageMap.put(-1.0, assumptionMap);
nSeMap.put(nIons, coverageMap);
} else {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
if (assumptionMap != null) {
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
double massError =
Math.abs(
tempAssumption.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
coverageMap.put(massError, assumptionMap);
}
coverageMap.remove(-1.0);
}
double massError =
Math.abs(
peptideAssumption1.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
assumptionMap = coverageMap.get(massError);
if (assumptionMap == null) {
assumptionMap = new HashMap<String, PeptideAssumption>(1);
coverageMap.put(massError, assumptionMap);
}
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
}
}
}
} else if (assumption1 instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) assumption1;
ArrayList<TagAssumption> assumptionList = tagAssumptions.get(bestEvalue);
if (assumptionList == null) {
assumptionList = new ArrayList<TagAssumption>();
tagAssumptions.put(bestEvalue, assumptionList);
}
assumptionList.add(tagAssumption);
}
}
}
SpectrumMatch spectrumMatch = new SpectrumMatch(spectrumKey);
if (!peptideAssumptions.isEmpty()) {
PeptideAssumption bestPeptideAssumption = null;
ArrayList<Double> ps = new ArrayList<Double>(peptideAssumptions.keySet());
Collections.sort(ps);
double retainedP = 0;
for (double p : ps) {
retainedP = p;
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
ArrayList<Integer> proteinMaxs = new ArrayList<Integer>(pMap.keySet());
Collections.sort(proteinMaxs, Collections.reverseOrder());
for (int proteinMax : proteinMaxs) {
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
ArrayList<Integer> nSEs = new ArrayList<Integer>(proteinMaxMap.keySet());
Collections.sort(nSEs, Collections.reverseOrder());
for (int nSE : nSEs) {
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
ArrayList<Integer> coverages = new ArrayList<Integer>(nSeMap.keySet());
Collections.sort(coverages, Collections.reverseOrder());
for (Integer coverage : coverages) {
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
nSeMap.get(coverage);
ArrayList<Double> minErrors = new ArrayList<Double>(coverageMap.keySet());
Collections.sort(minErrors);
for (double minError : minErrors) {
HashMap<String, PeptideAssumption> bestPeptideAssumptions =
coverageMap.get(minError);
ArrayList<String> sequences =
new ArrayList<String>(bestPeptideAssumptions.keySet());
Collections.sort(sequences);
for (String sequence : sequences) {
PeptideAssumption peptideAssumption = bestPeptideAssumptions.get(sequence);
if (idFilter.validateProteins(
peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
bestPeptideAssumption = peptideAssumption;
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
if (multiSE) {
// try to find the most likely modification localization based on the search engine
// results
HashMap<PeptideAssumption, ArrayList<Double>> assumptionPEPs =
new HashMap<PeptideAssumption, ArrayList<Double>>();
String bestAssumptionKey =
bestPeptideAssumption.getPeptide().getMatchingKey(sequenceMatchingPreferences);
for (int searchEngine : assumptions.keySet()) {
boolean found = false;
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocateMap =
assumptions.get(searchEngine);
ArrayList<Double> eValues = new ArrayList<Double>(advocateMap.keySet());
Collections.sort(eValues);
for (double eValue : eValues) {
for (SpectrumIdentificationAssumption assumption : advocateMap.get(eValue)) {
if (assumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
if (peptideAssumption
.getPeptide()
.getMatchingKey(sequenceMatchingPreferences)
.equals(bestAssumptionKey)) {
found = true;
boolean found2 = false;
for (PeptideAssumption assumption1 : assumptionPEPs.keySet()) {
if (assumption1
.getPeptide()
.sameModificationsAs(peptideAssumption.getPeptide())) {
found2 = true;
psParameter = (PSParameter) assumption.getUrParam(psParameter);
ArrayList<Double> peps = assumptionPEPs.get(assumption1);
peps.add(psParameter.getSearchEngineProbability());
break;
}
}
if (!found2) {
ArrayList<Double> peps = new ArrayList<Double>(1);
assumptionPEPs.put(peptideAssumption, peps);
psParameter = (PSParameter) assumption.getUrParam(psParameter);
peps.add(psParameter.getSearchEngineProbability());
}
}
}
}
if (found) {
break;
}
}
}
Double bestSeP = null;
int nSe = -1;
for (PeptideAssumption peptideAssumption : assumptionPEPs.keySet()) {
ArrayList<Double> peps = assumptionPEPs.get(peptideAssumption);
Double sep = Collections.min(peps);
if (bestSeP == null || bestSeP > sep) {
bestSeP = sep;
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
} else if (peps.size() > nSe) {
if (sep != null && (Math.abs(sep - bestSeP) <= 1e-10)) {
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
}
}
}
}
// create a PeptideShaker match based on the best search engine match
Peptide sePeptide = bestPeptideAssumption.getPeptide();
ArrayList<String> psProteins =
new ArrayList<String>(sePeptide.getParentProteins(sequenceMatchingPreferences));
ArrayList<ModificationMatch> psModificationMatches = null;
if (sePeptide.isModified()) {
psModificationMatches =
new ArrayList<ModificationMatch>(sePeptide.getNModifications());
for (ModificationMatch seModMatch : sePeptide.getModificationMatches()) {
psModificationMatches.add(
new ModificationMatch(
seModMatch.getTheoreticPtm(),
seModMatch.isVariable(),
seModMatch.getModificationSite()));
}
}
Peptide psPeptide = new Peptide(sePeptide.getSequence(), psModificationMatches);
psPeptide.setParentProteins(psProteins);
PeptideAssumption psAssumption =
new PeptideAssumption(
psPeptide,
1,
Advocate.peptideShaker.getIndex(),
bestPeptideAssumption.getIdentificationCharge(),
retainedP);
spectrumMatch.setBestPeptideAssumption(psAssumption);
if (orderedPsmMap != null) {
String peptideKey = psPeptide.getMatchingKey(sequenceMatchingPreferences);
ArrayList<String> spectrumKeys = keysMap.get(peptideKey);
if (spectrumKeys == null) {
spectrumKeys = new ArrayList<String>();
keysMap.put(peptideKey, spectrumKeys);
}
spectrumKeys.add(spectrumKey);
}
psParameter = new PSParameter();
psParameter.setSpectrumProbabilityScore(retainedP);
PSParameter matchParameter =
(PSParameter) bestPeptideAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
matchesValidator
.getPsmMap()
.addPoint(
psParameter.getPsmProbabilityScore(),
spectrumMatch,
sequenceMatchingPreferences);
psParameter.setSpecificMapKey(
spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
identification.updateSpectrumMatch(spectrumMatch);
}
}
if (!tagAssumptions.isEmpty()) {
ArrayList<Double> evalues = new ArrayList<Double>(tagAssumptions.keySet());
Double bestEvalue = Collections.min(evalues);
TagAssumption bestAssumption = tagAssumptions.get(bestEvalue).get(0);
spectrumMatch.setBestTagAssumption(bestAssumption);
identification.updateSpectrumMatch(spectrumMatch);
if (spectrumMatch.getBestPeptideAssumption() == null) {
psParameter = new PSParameter();
if (!multiSE) {
psParameter.setSpectrumProbabilityScore(bestEvalue);
}
PSParameter matchParameter = (PSParameter) bestAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
psParameter.setSpecificMapKey(
spectrumMatch.getBestTagAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
}
}
waitingHandler.increaseSecondaryProgressCounter();
if (waitingHandler.isRunCanceled()) {
return;
}
}
if (orderedPsmMap != null) {
ArrayList<String> orderedKeys =
new ArrayList<String>(
identification.getSpectrumIdentification(spectrumFileName).size());
for (ArrayList<String> keys : keysMap.values()) {
orderedKeys.addAll(keys);
}
orderedPsmMap.put(spectrumFileName, orderedKeys);
if (MemoryConsumptionStatus.memoryUsed() > 0.9) {
orderedPsmMap = null;
}
}
}
if (orderedPsmMap != null) {
metrics.setOrderedSpectrumKeys(orderedPsmMap);
}
// the protein count map is no longer needed
proteinCount.clear();
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}