/** Set the default preferences. */
private void setDefaultPreferences() {
searchParameters = new SearchParameters();
annotationPreferences.setAnnotationLevel(0.75);
annotationPreferences.useAutomaticAnnotation(true);
spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF);
spectrumCountingPreferences.setValidatedHits(true);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
processingPreferences = new ProcessingPreferences();
ptmScoringPreferences = new PTMScoringPreferences();
}
/**
* The spectrum annotator annotates peaks in a spectrum.
*
* @author Marc Vaudel
* @author Harald Barsnes
*/
public abstract class SpectrumAnnotator {
/** Enum of the possibilities for ties resolution when multiple peaks can be annotated. */
public enum TiesResolution {
/**
* The most intense peak is retained. If two peaks have the same intensity, the one with the
* most accurate m/z is retained.
*/
mostIntense,
/**
* The peak of most accurate m/z is retained. If two peaks have the same error the most intense
* is retained.
*/
mostAccurateMz;
}
/** The precursor charge as deduced by the search engine. */
protected int precursorCharge;
/** The theoretic fragment ions. */
protected HashMap<Integer, HashMap<Integer, ArrayList<Ion>>> theoreticalFragmentIons;
/** The Fragment factory which will generate the fragment ions. */
protected IonFactory fragmentFactory = IonFactory.getInstance();
/** The key of the currently loaded spectrum. */
private String spectrumKey = "";
/** The intensity limit to use. */
protected double intensityLimit = 0;
/** Index for the spectrum. */
private SpectrumIndex spectrumIndex;
/** The m/z tolerance for peak matching. */
protected double mzTolerance;
/** Boolean indicating whether the tolerance is in ppm (true) or in Dalton (false). */
protected boolean isPpm;
/** Minimal isotopic correction when matching an ion. */
protected static final boolean subtractIsotope = false;
/** The minimal isotope correction. By default only the monoisotopic peak is annotated (min=0). */
protected static final Integer minIsotopicCorrection = 0;
/** The maximal isotope correction. By default only the monoisotopic peak is annotated (max=0). */
protected static final Integer maxIsotopicCorrection = 0;
/** m/z shift applied to all theoretic peaks. */
protected double massShift = 0;
/** N-terminal m/z shift applied to all forward ions. */
protected double massShiftNTerm = 0;
/** C-terminal m/z shift applied to all reverse ions. */
protected double massShiftCTerm = 0;
/** The methods to use to select the best peak when multiple are possible. */
protected TiesResolution tiesResolution;
/**
* If provided, the annotator will only look for the ions included in the specific annotation
* settings.
*/
protected SpecificAnnotationSettings specificAnnotationSettings = null;
/** The cache to use for the ion match keys. */
protected IonMatchKeysCache ionMatchKeysCache = new IonMatchKeysCache();
/**
* Translates the list of ion matches into a vector of annotations which can be read by the
* SpectrumPanel.
*
* @param ionMatches list of ion matches
* @return vector of default spectrum annotations
*/
public static Vector<SpectrumAnnotation> getSpectrumAnnotation(ArrayList<IonMatch> ionMatches) {
Vector<SpectrumAnnotation> currentAnnotations = new Vector();
for (IonMatch ionMatch : ionMatches) {
currentAnnotations.add(
new DefaultSpectrumAnnotation(
ionMatch.peak.mz,
ionMatch.getAbsoluteError(minIsotopicCorrection, maxIsotopicCorrection),
SpectrumPanel.determineFragmentIonColor(ionMatch.ion, true),
ionMatch.getPeakAnnotation()));
}
return currentAnnotations;
}
/**
* 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;
}
/**
* Returns the peak to retain of the matched peaks according to the ties resolution setting.
*
* @param matchedPeaks the peaks matched
* @param ionMatch an ion match with the ion to be matched
* @return the peak to retain
*/
protected Peak getBestPeak(ArrayList<Peak> matchedPeaks, IonMatch ionMatch) {
Peak bestPeak = null;
switch (tiesResolution) {
case mostAccurateMz:
Double bestPeakError = null;
for (Peak peak : matchedPeaks) {
if (bestPeak == null) {
bestPeak = peak;
ionMatch.peak = peak;
bestPeakError = Math.abs(ionMatch.getError(isPpm));
} else {
ionMatch.peak = peak;
double peakError = Math.abs(ionMatch.getError(isPpm));
if (peakError < bestPeakError) {
bestPeak = peak;
bestPeakError = peakError;
} else if (peakError == bestPeakError && peak.intensity > bestPeak.intensity) {
bestPeak = peak;
}
}
}
return bestPeak;
case mostIntense:
for (Peak peak : matchedPeaks) {
if (bestPeak == null || peak.intensity > bestPeak.intensity) {
bestPeak = peak;
} else if (peak.intensity == bestPeak.intensity) {
ionMatch.peak = bestPeak;
bestPeakError = Math.abs(ionMatch.getError(isPpm));
ionMatch.peak = peak;
double peakError = Math.abs(ionMatch.getError(isPpm));
if (peakError < bestPeakError) {
bestPeak = peak;
}
}
}
return bestPeak;
default:
throw new UnsupportedOperationException(
"Ties resolution method " + tiesResolution + " not implemented.");
}
}
/**
* Sets a new spectrum to annotate.
*
* @param spectrum the spectrum to inspect
* @param intensityLimit the minimal intensity to account for
*/
protected void setSpectrum(MSnSpectrum spectrum, double intensityLimit) {
if (spectrumIndex == null
|| !spectrumKey.equals(spectrum.getSpectrumKey())
|| this.intensityLimit != intensityLimit) {
// Save spectrum number and intensity limit
spectrumKey = spectrum.getSpectrumKey();
this.intensityLimit = intensityLimit;
// See whether the index was previously stored
spectrumIndex = new SpectrumIndex();
spectrumIndex = (SpectrumIndex) spectrum.getUrParam(spectrumIndex);
// Create new index
spectrumIndex = new SpectrumIndex(spectrum.getPeakMap(), intensityLimit, mzTolerance, isPpm);
spectrum.addUrParam(spectrumIndex);
}
}
/**
* Sets a new m/z tolerance for peak matching.
*
* @param mzTolerance the new m/z tolerance (in m/z, Th)
* @param isPpm a boolean indicating whether the mass tolerance is in ppm or in Da
* @param tiesResolution the method used to resolve ties
*/
protected void setMassTolerance(
double mzTolerance, boolean isPpm, TiesResolution tiesResolution) {
if (mzTolerance != this.mzTolerance || tiesResolution != this.tiesResolution) {
// Clear previous index
spectrumIndex = null;
// Save new values
this.mzTolerance = mzTolerance;
this.isPpm = isPpm;
this.tiesResolution = tiesResolution;
}
}
/**
* 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 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 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 the currently matched ions with the given settings.
*
* @param spectrum the spectrum of interest
* @param annotationSettings the annotation settings
* @param specificAnnotationSettings the specific annotation settings
* @return the currently matched ions with the given settings
*/
public abstract ArrayList<IonMatch> getCurrentAnnotation(
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings);
/**
* Returns the spectrum currently inspected.
*
* @return the spectrum currently inspected
*/
public String getCurrentlyLoadedSpectrumKey() {
return spectrumKey;
}
/**
* Returns the m/z shift applied to the fragment ions.
*
* @return the m/z shift applied to the fragment ions
*/
public double getMassShift() {
return massShift;
}
/**
* Returns the N-terminal m/z shift applied to all forward ions.
*
* @return the N-terminal m/z shift applied to all forward ions
*/
public double getMassShiftNTerm() {
return massShiftNTerm;
}
/**
* Returns the C-terminal m/z shift applied to all reverse ions.
*
* @return the C-terminal m/z shift applied to all reverse ions
*/
public double getMassShiftCTerm() {
return massShiftNTerm;
}
/**
* Sets an m/z shift on all ions. The previous mass main shift will be removed.
*
* @param aMassShift the m/z shift to apply
*/
public void setMassShift(double aMassShift) {
this.massShift = aMassShift;
updateMassShifts();
}
/**
* Sets the m/z shifts. The previous mass shifts will be removed.
*
* @param aMassShift the m/z shift to apply
* @param aMassShiftNTerm the n-terminal mass shift to apply to all forward ions
* @param aMassShiftCTerm the c-terminal mass shift to apply to all reverse ions
*/
public void setMassShifts(double aMassShift, double aMassShiftNTerm, double aMassShiftCTerm) {
this.massShift = aMassShift;
this.massShiftNTerm = aMassShiftNTerm;
this.massShiftCTerm = aMassShiftCTerm;
updateMassShifts();
}
/**
* Sets the terminal m/z shifts.
*
* @param aMassShiftNTerm the n-terminal mass shift to apply to all forward ions
* @param aMassShiftCTerm the c-terminal mass shift to apply to all reverse ions
*/
public void setTerminalMassShifts(double aMassShiftNTerm, double aMassShiftCTerm) {
this.massShiftNTerm = aMassShiftNTerm;
this.massShiftCTerm = aMassShiftCTerm;
updateMassShifts();
}
/** 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);
}
}
}
}
/**
* 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()
+ ".");
}
}
/**
* This method matches the potential fragment ions of a given peptide with a given peak. Note:
* fragment ions need to be initiated by the SpectrumAnnotator extending class.
*
* @param specificAnnotationSettings the specific annotation settings
* @param peak The peak to match
* @return A list of potential ion matches
*/
protected ArrayList<IonMatch> matchPeak(
SpecificAnnotationSettings specificAnnotationSettings, Peak peak) {
ArrayList<IonMatch> result = new ArrayList<IonMatch>();
HashMap<Ion.IonType, HashSet<Integer>> ionTypes = specificAnnotationSettings.getIonTypes();
for (Ion.IonType ionType : ionTypes.keySet()) {
HashMap<Integer, ArrayList<Ion>> ionMap = theoreticalFragmentIons.get(ionType.index);
if (ionMap != null) {
HashSet<Integer> subtypes = ionTypes.get(ionType);
for (int subType : subtypes) {
ArrayList<Ion> ions = ionMap.get(subType);
if (ions != null) {
for (Ion ion : ions) {
for (int charge : specificAnnotationSettings.getSelectedCharges()) {
if (chargeValidated(ion, charge, specificAnnotationSettings.getPrecursorCharge())
&& lossesValidated(specificAnnotationSettings.getNeutralLossesMap(), ion)) {
IonMatch ionMatch = new IonMatch(peak, ion, charge);
if (Math.abs(
ionMatch.getError(
specificAnnotationSettings.isFragmentIonPpm(),
minIsotopicCorrection,
maxIsotopicCorrection))
<= specificAnnotationSettings.getFragmentIonAccuracy()) {
result.add(ionMatch);
}
}
}
}
}
}
}
}
return result;
}
/**
* Returns the expected ions in a map indexed by the possible charges.
*
* <p>Note that, except for +1 precursors, fragments ions will be expected to have a charge
* strictly smaller than the precursor ion charge.
*
* <p>Note: fragment ions need to be initiated by the SpectrumAnnotator extending class.
*
* @param specificAnnotationSettings the specific annotation settings
* @return an ArrayList of IonMatch containing the ion matches with the given settings
*/
protected HashMap<Integer, ArrayList<Ion>> getExpectedIons(
SpecificAnnotationSettings specificAnnotationSettings) {
HashMap<Integer, ArrayList<Ion>> result = new HashMap<Integer, ArrayList<Ion>>();
HashMap<Ion.IonType, HashSet<Integer>> ionTypes = specificAnnotationSettings.getIonTypes();
for (Ion.IonType ionType : ionTypes.keySet()) {
HashMap<Integer, ArrayList<Ion>> ionMap = theoreticalFragmentIons.get(ionType.index);
if (ionMap != null) {
HashSet<Integer> subtypes = ionTypes.get(ionType);
for (int subType : subtypes) {
ArrayList<Ion> ions = ionMap.get(subType);
if (ions != null) {
for (Ion ion : ions) {
if (lossesValidated(specificAnnotationSettings.getNeutralLossesMap(), ion)) {
for (int charge : specificAnnotationSettings.getSelectedCharges()) {
if (chargeValidated(ion, charge, precursorCharge)) {
ArrayList<Ion> resultsAtCharge = result.get(charge);
if (resultsAtCharge == null) {
resultsAtCharge = new ArrayList<Ion>();
result.put(charge, resultsAtCharge);
}
resultsAtCharge.add(ion);
}
}
}
}
}
}
}
}
return result;
}
/**
* 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;
}
}
public void importPeptideShakerFile(File aPsFile, final String resource) {
this.resource = resource;
this.currentPSFile = aPsFile;
loadGeneMapping();
loadEnzymes();
resetPtmFactory();
// setDefaultPreferences(); // @TODO: i tried re-adding this but then we get a null pointer, but
// the two below have to be added or the default neutral losses won't appear
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
// exceptionHandler = new ExceptionHandler(this);
new Thread("ProgressThread") {
@Override
public void run() {
jprog.setValue(10);
}
}.start();
Thread importThread =
new Thread("ImportThread") {
@Override
public void run() {
try {
// reset enzymes, ptms and preferences
loadEnzymes();
resetPtmFactory();
setDefaultPreferences();
try {
// close any open connection to an identification database
if (identification != null) {
identification.close();
}
} catch (Exception e) {
e.printStackTrace();
}
File experimentFile =
new File(
PeptideShaker.SERIALIZATION_DIRECTORY, PeptideShaker.experimentObjectName);
File matchFolder = new File(PeptideShaker.SERIALIZATION_DIRECTORY);
// empty the existing files in the matches folder
if (matchFolder.exists()) {
for (File file : matchFolder.listFiles()) {
if (file.isDirectory()) {
boolean deleted = Util.deleteDir(file);
if (!deleted) {
System.out.println("Failed to delete folder: " + file.getPath());
}
} else {
boolean deleted = file.delete();
if (!deleted) {
System.out.println("Failed to delete file: " + file.getPath());
}
}
}
}
final int BUFFER = 2048;
byte data[] = new byte[BUFFER];
FileInputStream fi = new FileInputStream(currentPSFile);
BufferedInputStream bis = new BufferedInputStream(fi, BUFFER);
try {
ArchiveInputStream tarInput =
new ArchiveStreamFactory().createArchiveInputStream(bis);
ArchiveEntry archiveEntry;
while ((archiveEntry = tarInput.getNextEntry()) != null) {
File destinationFile = new File(archiveEntry.getName());
File destinationFolder = destinationFile.getParentFile();
boolean destFolderExists = true;
if (!destinationFolder.exists()) {
destFolderExists = destinationFolder.mkdirs();
}
if (destFolderExists) {
FileOutputStream fos = new FileOutputStream(destinationFile);
BufferedOutputStream bos = new BufferedOutputStream(fos);
int count;
while ((count = tarInput.read(data, 0, BUFFER)) != -1
&& !progressDialog.isRunCanceled()) {
bos.write(data, 0, count);
}
bos.close();
fos.close();
// int progress = (int) (100 *
// tarInput.getBytesRead() / fileLength);
// progressDialog.setValue(progress);
} else {
System.out.println(
"Folder does not exist: \'"
+ destinationFolder.getAbsolutePath()
+ "\'. User preferences not saved.");
}
}
tarInput.close();
} catch (ArchiveException e) {
// Most likely an old project
experimentFile = currentPSFile;
e.printStackTrace();
}
fi.close();
bis.close();
fi.close();
MsExperiment tempExperiment = ExperimentIO.loadExperiment(experimentFile);
Sample tempSample = null;
PeptideShakerSettings experimentSettings = new PeptideShakerSettings();
if (tempExperiment.getUrParam(experimentSettings) instanceof PSSettings) {
// convert old settings files using utilities version 3.10.68 or older
// convert the old ProcessingPreferences object
PSSettings tempSettings =
(PSSettings) tempExperiment.getUrParam(experimentSettings);
ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
tempProcessingPreferences.setProteinFDR(
tempSettings.getProcessingPreferences().getProteinFDR());
tempProcessingPreferences.setPeptideFDR(
tempSettings.getProcessingPreferences().getPeptideFDR());
tempProcessingPreferences.setPsmFDR(
tempSettings.getProcessingPreferences().getPsmFDR());
// convert the old PTMScoringPreferences object
PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
tempPTMScoringPreferences.setaScoreCalculation(
tempSettings.getPTMScoringPreferences().aScoreCalculation());
tempPTMScoringPreferences.setaScoreNeutralLosses(
tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
tempPTMScoringPreferences.setFlrThreshold(
tempSettings.getPTMScoringPreferences().getFlrThreshold());
// missing gene refrences
GenePreferences genePreferences = getGenePreferences();
// String selectedSpecies = genePreferences.getCurrentSpecies();
// String speciesDatabase =
// genePreferences.getEnsemblDatabaseName(selectedSpecies);
experimentSettings =
new PeptideShakerSettings(
tempSettings.getSearchParameters(),
tempSettings.getAnnotationPreferences(),
tempSettings.getSpectrumCountingPreferences(),
tempSettings.getProjectDetails(),
tempSettings.getFilterPreferences(),
tempSettings.getDisplayPreferences(),
tempSettings.getMetrics(),
tempProcessingPreferences,
tempSettings.getIdentificationFeaturesCache(),
tempPTMScoringPreferences,
genePreferences,
new IdFilter());
;
} else {
experimentSettings =
(PeptideShakerSettings) tempExperiment.getUrParam(experimentSettings);
}
idFilter = experimentSettings.getIdFilter();
setAnnotationPreferences(experimentSettings.getAnnotationPreferences());
setSpectrumCountingPreferences(experimentSettings.getSpectrumCountingPreferences());
setPtmScoringPreferences(experimentSettings.getPTMScoringPreferences());
setProjectDetails(experimentSettings.getProjectDetails());
setSearchParameters(experimentSettings.getSearchParameters());
setProcessingPreferences(experimentSettings.getProcessingPreferences());
setMetrics(experimentSettings.getMetrics());
setDisplayPreferences(experimentSettings.getDisplayPreferences());
if (experimentSettings.getFilterPreferences() != null) {
setFilterPreferences(experimentSettings.getFilterPreferences());
} else {
setFilterPreferences(new FilterPreferences());
}
if (experimentSettings.getDisplayPreferences() != null) {
setDisplayPreferences(experimentSettings.getDisplayPreferences());
displayPreferences.compatibilityCheck(searchParameters.getModificationProfile());
} else {
setDisplayPreferences(new DisplayPreferences());
displayPreferences.setDefaultSelection(searchParameters.getModificationProfile());
}
ArrayList<Sample> samples = new ArrayList(tempExperiment.getSamples().values());
if (samples.size() == 1) {
tempSample = samples.get(0);
} else {
tempSample = samples.get(0);
String[] sampleNames = new String[samples.size()];
for (int cpt = 0; cpt < sampleNames.length; cpt++) {
sampleNames[cpt] = samples.get(cpt).getReference();
System.out.println(sampleNames[cpt]);
}
SampleSelection sampleSelection =
new SampleSelection(null, true, sampleNames, "sample");
sampleSelection.setVisible(false);
String choice = sampleSelection.getChoice();
for (Sample sampleTemp : samples) {
if (sampleTemp.getReference().equals(choice)) {
tempSample = sampleTemp;
break;
}
}
}
ArrayList<Integer> replicates =
new ArrayList(tempExperiment.getAnalysisSet(tempSample).getReplicateNumberList());
System.out.println(replicates);
int tempReplicate;
if (replicates.size() == 1) {
tempReplicate = replicates.get(0);
} else {
String[] replicateNames = new String[replicates.size()];
for (int cpt = 0; cpt < replicateNames.length; cpt++) {
replicateNames[cpt] = samples.get(cpt).getReference();
}
SampleSelection sampleSelection =
new SampleSelection(null, true, replicateNames, "replicate");
sampleSelection.setVisible(false);
Integer choice = new Integer(sampleSelection.getChoice());
tempReplicate = 0;
}
setProject(tempExperiment, tempSample, tempReplicate);
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification,
searchParameters,
idFilter,
metrics,
spectrumCountingPreferences);
if (experimentSettings.getIdentificationFeaturesCache() != null) {
identificationFeaturesGenerator.setIdentificationFeaturesCache(
experimentSettings.getIdentificationFeaturesCache());
}
// mainProgressDialog.setTitle("Loading FASTA File. Please
// Wait...");
try {
File providedFastaLocation =
experimentSettings.getSearchParameters().getFastaFile();
String fileName = providedFastaLocation.getName();
File projectFolder = currentPSFile.getParentFile();
File dataFolder = new File(projectFolder, "data");
// try to locate the FASTA file
if (providedFastaLocation.exists()) {
SequenceFactory.getInstance().loadFastaFile(providedFastaLocation);
} else if (new File(projectFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(projectFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(projectFolder, fileName));
} else if (new File(dataFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(dataFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(dataFolder, fileName));
} else {
// return error
System.out.println("fastafile is missing");
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("fastafile is missing");
}
// mainProgressDialog.setTitle("Locating Spectrum Files. Please
// Wait...");
for (String spectrumFileName : identification.getSpectrumFiles()) {
try {
File providedSpectrumLocation = projectDetails.getSpectrumFile(spectrumFileName);
// try to locate the spectrum file
if (providedSpectrumLocation == null || !providedSpectrumLocation.exists()) {
File projectFolder = currentPSFile.getParentFile();
File fileInProjectFolder = new File(projectFolder, spectrumFileName);
File dataFolder = new File(projectFolder, "data");
File fileInDataFolder = new File(dataFolder, spectrumFileName);
File fileInLastSelectedFolder =
new File(getLastSelectedFolder(), spectrumFileName);
if (fileInProjectFolder.exists()) {
projectDetails.addSpectrumFile(fileInProjectFolder);
} else if (fileInDataFolder.exists()) {
projectDetails.addSpectrumFile(fileInDataFolder);
} else if (fileInLastSelectedFolder.exists()) {
projectDetails.addSpectrumFile(fileInLastSelectedFolder);
} else {
System.out.println("error no file");
}
}
} catch (Exception e) {
clearData(true);
// clearPreferences();
e.printStackTrace();
System.out.println("error no file");
return;
}
}
objectsCache = new ObjectsCache();
objectsCache.setAutomatedMemoryManagement(true);
if (identification.isDB()) {
try {
String dbFolder =
new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY).getAbsolutePath();
identification.establishConnection(dbFolder, false, objectsCache);
} catch (Exception e) {
e.printStackTrace();
}
} else {
updateAnnotationPreferencesFromSearchSettings();
annotationPreferences.useAutomaticAnnotation(true);
}
int cpt = 1, nfiles = identification.getSpectrumFiles().size();
for (String fileName : identification.getSpectrumFiles()) {
// mainProgressDialog.setTitle("Importing Spectrum
// Files. Please Wait...");
try {
File mgfFile = projectDetails.getSpectrumFile(fileName);
spectrumFactory.addSpectra(mgfFile, progressDialog);
} catch (Exception e) {
clearData(true);
e.printStackTrace();
return;
}
}
boolean compatibilityIssue =
getSearchParameters().getIonSearched1() == null
|| getSearchParameters().getIonSearched2() == null;
if (compatibilityIssue) {
JOptionPane.showMessageDialog(
null,
"The annotation preferences for this project may have changed.\n\n"
+ "Note that PeptideShaker has substancially improved, we strongly\n"
+ "recommend reprocessing your identification files.",
"Annotation Preferences",
JOptionPane.INFORMATION_MESSAGE);
updateAnnotationPreferencesFromSearchSettings();
}
if (identification.getSpectrumIdentificationMap() == null) {
// 0.18 version, needs update of the spectrum mapping
identification.updateSpectrumMapping();
}
} catch (OutOfMemoryError error) {
System.out.println(
"Ran out of memory! (runtime.maxMemory(): "
+ Runtime.getRuntime().maxMemory()
+ ")");
Runtime.getRuntime().gc();
JOptionPane.showMessageDialog(
null,
"The task used up all the available memory and had to be stopped.\n"
+ "Memory boundaries are set in ../resources/conf/JavaOptions.txt.",
"Out Of Memory Error",
JOptionPane.ERROR_MESSAGE);
error.printStackTrace();
} catch (Exception exp) {
exp.printStackTrace();
}
}
};
importThread.setPriority(Thread.MAX_PRIORITY);
// importThread.start();
// while (importThread.isAlive()) {
// try {
// Thread.currentThread().sleep(100);
//
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
ExecutorService es = Executors.newCachedThreadPool();
es.execute(importThread);
es.shutdown();
try {
boolean finshed = es.awaitTermination(1, TimeUnit.DAYS);
System.gc();
return;
// t.start();
} catch (InterruptedException ex) {
System.err.println(ex.getMessage());
// Logger.getLogger(UpdatedOutputGenerator.class.getName()).log(Level.SEVERE, null, ex);
}
System.gc();
// return;
}
