/**
* Returns the description of an item.
*
* @param key the key of the item
* @param itemType the type of the item
* @return the description of an item
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
private String getItemDescription(String key, Type itemType)
throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException,
InterruptedException {
Identification identification = peptideShakerGUI.getIdentification();
switch (itemType) {
case PROTEIN:
ProteinMatch proteinMatch = identification.getProteinMatch(key);
String mainMatch = proteinMatch.getMainMatch();
String description = sequenceFactory.getHeader(mainMatch).getSimpleProteinDescription();
String result = mainMatch;
for (String accession : ProteinMatch.getAccessions(key)) {
if (!accession.equals(mainMatch)) {
if (!result.equals(mainMatch)) {
result += ", ";
}
result += accession;
}
}
result += " - " + description;
return result;
case PEPTIDE:
PeptideMatch peptideMatch = identification.getPeptideMatch(key);
return peptideShakerGUI
.getDisplayFeaturesGenerator()
.getTaggedPeptideSequence(peptideMatch, true, true, true);
case SPECTRUM:
return Spectrum.getSpectrumTitle(key) + " (" + Spectrum.getSpectrumFile(key) + ")";
default:
return "Unknown";
}
}
/**
* Returns the desired spectrum.
*
* @param spectrumKey the key of the spectrum
* @return the desired spectrum
*/
public MSnSpectrum getSpectrum(String spectrumKey) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
try {
return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
} catch (Exception e) {
System.out.println(e.getMessage());
return null;
}
}
/**
* 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;
}
/**
* 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 + ".");
}
}