@Override
public boolean isValidated(
String itemName,
FilterItemComparator filterItemComparator,
Object value,
String matchKey,
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
throws IOException, InterruptedException, ClassNotFoundException, SQLException,
MzMLUnmarshallerException, MathException {
PeptideFilterItem filterItem = PeptideFilterItem.getItem(itemName);
if (filterItem == null) {
throw new IllegalArgumentException(
"Filter item " + itemName + "not recognized as peptide filter item.");
}
String input = value.toString();
switch (filterItem) {
case proteinAccession:
PeptideMatch peptideMatch = identification.getPeptideMatch(matchKey);
return filterItemComparator.passes(
input,
peptideMatch
.getTheoreticPeptide()
.getParentProteins(identificationParameters.getSequenceMatchingPreferences()));
case proteinDescription:
peptideMatch = identification.getPeptideMatch(matchKey);
ArrayList<String> accessions =
peptideMatch
.getTheoreticPeptide()
.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
ArrayList<String> descriptions = new ArrayList<String>();
for (String accession : accessions) {
Header proteinHeader = SequenceFactory.getInstance().getHeader(accession);
descriptions.add(proteinHeader.getDescription());
}
return filterItemComparator.passes(input, descriptions);
case sequence:
return filterItemComparator.passes(input, Peptide.getSequence(matchKey));
case ptm:
peptideMatch = identification.getPeptideMatch(matchKey);
ArrayList<String> ptms;
PSPtmScores psPtmScores = new PSPtmScores();
psPtmScores = (PSPtmScores) peptideMatch.getUrParam(psPtmScores);
if (psPtmScores != null) {
ptms = psPtmScores.getScoredPTMs();
} else {
ptms = new ArrayList<String>(0);
}
return filterItemComparator.passes(input, ptms);
case nPSMs:
peptideMatch = identification.getPeptideMatch(matchKey);
Integer nPsms = peptideMatch.getSpectrumCount();
return filterItemComparator.passes(input, nPsms.toString());
case nValidatedPSMs:
nPsms = identificationFeaturesGenerator.getNValidatedSpectraForPeptide(matchKey);
return filterItemComparator.passes(input, nPsms.toString());
case nConfidentPSMs:
nPsms = identificationFeaturesGenerator.getNConfidentSpectraForPeptide(matchKey);
return filterItemComparator.passes(input, nPsms.toString());
case confidence:
PSParameter psParameter = new PSParameter();
psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
Double confidence = psParameter.getProteinConfidence();
return filterItemComparator.passes(input, confidence.toString());
case proteinInference:
psParameter = new PSParameter();
psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
Integer pi = psParameter.getProteinInferenceClass();
return filterItemComparator.passes(input, pi.toString());
case validationStatus:
psParameter = new PSParameter();
psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
Integer validation = psParameter.getMatchValidationLevel().getIndex();
return filterItemComparator.passes(input, validation.toString());
case stared:
psParameter = new PSParameter();
psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
String starred;
if (psParameter.isStarred()) {
starred = FilterItemComparator.trueFalse[0];
} else {
starred = FilterItemComparator.trueFalse[1];
}
return filterItemComparator.passes(input, starred);
default:
throw new IllegalArgumentException(
"Protein filter not implemented for item " + filterItem.name + ".");
}
}
/**
* Writes the desired section.
*
* @param identification the identification of the project
* @param identificationFeaturesGenerator the identification features generator of the project
* @param identificationParameters the identification parameters
* @param keys the keys of the protein matches to output
* @param nSurroundingAA the number of surrounding amino acids to export
* @param linePrefix the line prefix to use.
* @param validatedOnly whether only validated matches should be exported
* @param decoys whether decoy matches should be exported as well
* @param waitingHandler the waiting handler
* @throws IOException exception thrown whenever an error occurred while interacting with a file
* @throws SQLException thrown whenever an error occurred while interacting with the database
* @throws ClassNotFoundException thrown whenever an error occurred while deserializing a match
* from the database
* @throws InterruptedException thrown whenever a threading error occurred while interacting with
* the database
* @throws MzMLUnmarshallerException thrown whenever an error occurred while reading an mzML file
*/
public void writeSection(
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
ArrayList<String> keys,
int nSurroundingAA,
String linePrefix,
boolean validatedOnly,
boolean decoys,
WaitingHandler waitingHandler)
throws IOException, SQLException, ClassNotFoundException, InterruptedException,
MzMLUnmarshallerException {
if (waitingHandler != null) {
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}
if (header) {
writeHeader();
}
if (keys == null) {
keys = new ArrayList<String>(identification.getPeptideIdentification());
}
int line = 1;
if (waitingHandler != null) {
waitingHandler.setWaitingText("Exporting. Please Wait...");
waitingHandler.resetSecondaryProgressCounter();
waitingHandler.setMaxSecondaryProgressCounter(keys.size());
}
PSParameter psParameter = new PSParameter();
ArrayList<UrParameter> parameters = new ArrayList<UrParameter>(1);
parameters.add(psParameter);
PeptideMatchesIterator peptideMatchesIterator =
identification.getPeptideMatchesIterator(
keys, parameters, psmSection != null, parameters, waitingHandler);
while (peptideMatchesIterator.hasNext()) {
if (waitingHandler != null) {
if (waitingHandler.isRunCanceled()) {
return;
}
waitingHandler.increaseSecondaryProgressCounter();
}
PeptideMatch peptideMatch = peptideMatchesIterator.next();
String peptideKey = peptideMatch.getKey();
psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);
if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {
if (decoys
|| !peptideMatch
.getTheoreticPeptide()
.isDecoy(identificationParameters.getSequenceMatchingPreferences())) {
boolean first = true;
if (indexes) {
if (linePrefix != null) {
writer.write(linePrefix);
}
writer.write(line + "");
first = false;
}
for (ExportFeature exportFeature : peptideFeatures) {
if (!first) {
writer.addSeparator();
} else {
first = false;
}
PsPeptideFeature peptideFeature = (PsPeptideFeature) exportFeature;
writer.write(
getfeature(
identification,
identificationFeaturesGenerator,
identificationParameters,
keys,
nSurroundingAA,
linePrefix,
peptideMatch,
psParameter,
peptideFeature,
validatedOnly,
decoys,
waitingHandler));
}
writer.newLine();
if (psmSection != null) {
String psmSectionPrefix = "";
if (linePrefix != null) {
psmSectionPrefix += linePrefix;
}
psmSectionPrefix += line + ".";
writer.increaseDepth();
if (waitingHandler != null) {
waitingHandler.setDisplayProgress(false);
}
psmSection.writeSection(
identification,
identificationFeaturesGenerator,
identificationParameters,
peptideMatch.getSpectrumMatchesKeys(),
psmSectionPrefix,
nSurroundingAA,
validatedOnly,
decoys,
waitingHandler);
if (waitingHandler != null) {
waitingHandler.setDisplayProgress(true);
}
writer.decreseDepth();
}
line++;
}
}
}
}
/**
* Indicates whether the match designated by the match key validates the given item using the
* given comparator and value threshold.
*
* @param itemName the name of the item to filter on
* @param filterItemComparator the comparator to use
* @param value the value to use as a threshold
* @param spectrumKey the key of the match of interest
* @param peptideAssumption the assumption to validate
* @param identification the identification objects where to get identification matches from
* @param identificationFeaturesGenerator the identification feature generator where to get
* identification features
* @param identificationParameters the identification parameters used
* @param peptideSpectrumAnnotator the annotator to use to annotate spectra when filtering on PSM
* or assumptions
* @return a boolean indicating whether the match designated by the protein key validates the
* given item using the given comparator and value threshold.
* @throws java.io.IOException exception thrown whenever an exception occurred while reading or
* writing a file
* @throws java.lang.InterruptedException exception thrown whenever a threading issue occurred
* while validating that the match passes the filter
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* deserilalizing a match
* @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
* with a database
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
* @throws org.apache.commons.math.MathException exception thrown whenever an error occurred while
* doing statistics on a distribution
*/
public boolean isValidated(
String itemName,
FilterItemComparator filterItemComparator,
Object value,
String spectrumKey,
PeptideAssumption peptideAssumption,
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
throws IOException, InterruptedException, ClassNotFoundException, SQLException,
MzMLUnmarshallerException, MathException {
AssumptionFilterItem filterItem = AssumptionFilterItem.getItem(itemName);
if (filterItem == null) {
throw new IllegalArgumentException(
"Filter item " + itemName + "not recognized as spectrum assumption filter item.");
}
String input = value.toString();
switch (filterItem) {
case precrusorMz:
Precursor precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
Double mz = precursor.getMz();
return filterItemComparator.passes(input, mz.toString());
case precrusorRT:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
Double rt = precursor.getRt();
return filterItemComparator.passes(input, rt.toString());
case precrusorCharge:
Integer charge = peptideAssumption.getIdentificationCharge().value;
return filterItemComparator.passes(input, charge.toString());
case precrusorMzErrorDa:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
SearchParameters searchParameters = identificationParameters.getSearchParameters();
Double mzError =
Math.abs(
peptideAssumption.getDeltaMass(
precursor.getMz(),
false,
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection()));
return filterItemComparator.passes(input, mzError.toString());
case precrusorMzErrorPpm:
searchParameters = identificationParameters.getSearchParameters();
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
mzError =
Math.abs(
peptideAssumption.getDeltaMass(
precursor.getMz(),
true,
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection()));
return filterItemComparator.passes(input, mzError.toString());
case precrusorMzErrorStat:
searchParameters = identificationParameters.getSearchParameters();
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
mzError =
peptideAssumption.getDeltaMass(
precursor.getMz(),
identificationParameters.getSearchParameters().isPrecursorAccuracyTypePpm(),
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection());
NonSymmetricalNormalDistribution precDeviationDistribution =
identificationFeaturesGenerator.getMassErrorDistribution(
Spectrum.getSpectrumFile(spectrumKey));
Double p;
if (mzError > precDeviationDistribution.getMean()) {
p = precDeviationDistribution.getDescendingCumulativeProbabilityAt(mzError);
} else {
p = precDeviationDistribution.getCumulativeProbabilityAt(mzError);
}
return filterItemComparator.passes(input, p.toString());
case sequenceCoverage:
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
Peptide peptide = peptideAssumption.getPeptide();
AnnotationSettings annotationPreferences =
identificationParameters.getAnnotationPreferences();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> matches =
peptideSpectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
double nCovered = 0;
int nAA = peptide.getSequence().length();
for (int i = 0; i <= nAA; i++) {
ArrayList<IonMatch> matchesAtAa = matches.get(i);
if (matchesAtAa != null && !matchesAtAa.isEmpty()) {
nCovered++;
}
}
Double coverage = 100.0 * nCovered / nAA;
return filterItemComparator.passes(input, coverage.toString());
case algorithmScore:
Double score = peptideAssumption.getRawScore();
if (score == null) {
score = peptideAssumption.getScore();
}
return filterItemComparator.passes(input, score.toString());
case fileNames:
return filterItemComparator.passes(input, Spectrum.getSpectrumFile(spectrumKey));
case confidence:
PSParameter psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
Double confidence = psParameter.getProteinConfidence();
return filterItemComparator.passes(input, confidence.toString());
case validationStatus:
psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
Integer validation = psParameter.getMatchValidationLevel().getIndex();
return filterItemComparator.passes(input, validation.toString());
case stared:
psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
String starred;
if (psParameter.isStarred()) {
starred = FilterItemComparator.trueFalse[0];
} else {
starred = FilterItemComparator.trueFalse[1];
}
return filterItemComparator.passes(input, starred);
default:
throw new IllegalArgumentException(
"Protein filter not implemented for item " + filterItem.name + ".");
}
}
