Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator

Package eu.isas.peptideshaker.recalibration

Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator

eu.isas.peptideshaker.recalibration.SpectrumRecalibrator
This class recalibrates spectra. @author Marc Vaudel

     */
    public static void exportPepnovoTrainingFiles(File destinationFolder, Identification identification, AnnotationPreferences annotationPreferences, Double fdr, Double fnr,
            boolean recalibrate, WaitingHandler waitingHandler) throws IOException, MzMLUnmarshallerException, SQLException, ClassNotFoundException, InterruptedException {


        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
        SpectrumRecalibrator spectrumRecalibrator = new SpectrumRecalibrator();


        PSMaps psMaps = new PSMaps();
        psMaps = (PSMaps) identification.getUrParam(psMaps);
        PsmSpecificMap psmTargetDecoyMap = psMaps.getPsmSpecificMap();


        int progress = 1;


        for (String fileName : spectrumFactory.getMgfFileNames()) {


            if (recalibrate) {
                if (waitingHandler != null) {
                    if (waitingHandler.isRunCanceled()) {
                        break;
                    }


                    waitingHandler.setWaitingText("Recalibrating Spectra. Please Wait... (" + progress + "/" + spectrumFactory.getMgfFileNames().size() + ")");
                    waitingHandler.setSecondaryProgressCounter(0);
                    waitingHandler.setSecondaryProgressCounterIndeterminate(false);
                    waitingHandler.setMaxSecondaryProgressCounter(2 * spectrumFactory.getNSpectra(fileName));
                }


                spectrumRecalibrator.estimateErrors(fileName, identification, annotationPreferences, waitingHandler);
            }


            PSParameter psParameter = new PSParameter();
            identification.loadSpectrumMatchParameters(fileName, psParameter, waitingHandler);


            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.setWaitingText("Selecting Good PSMs. Please Wait... (" + progress + "/" + spectrumFactory.getMgfFileNames().size() + ")");
                // reset the progress bar
                waitingHandler.resetSecondaryProgressCounter();
                waitingHandler.setMaxSecondaryProgressCounter(spectrumFactory.getSpectrumTitles(fileName).size());
            }


            ArrayList<String> keys = new ArrayList<String>();
            for (String spectrumTitle : spectrumFactory.getSpectrumTitles(fileName)) {


                String spectrumKey = Spectrum.getSpectrumKey(fileName, spectrumTitle);
                if (identification.matchExists(spectrumKey)) {
                    psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                    Integer charge = new Integer(psParameter.getSpecificMapKey());
                    String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
                    Double fdrThreshold = getFdrThreshold(psmTargetDecoyMap, charge, spectrumTitle, fdr);
                    double confidenceLevel = getHighConfidenceThreshold(psmTargetDecoyMap, charge, spectrumFile, fdrThreshold);
                    if (psParameter.getPsmConfidence() >= confidenceLevel) {
                        keys.add(spectrumKey);
                    }
                }
                if (waitingHandler != null) {
                    if (waitingHandler.isRunCanceled()) {
                        return;
                    }
                    waitingHandler.increaseSecondaryProgressCounter();
                }
            }
            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.setWaitingText("Loading PSMs. Please Wait... (" + progress + "/"
                        + spectrumFactory.getMgfFileNames().size() + ")");
            }
            identification.loadSpectrumMatches(keys, waitingHandler);


            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.setWaitingText("Exporting PepNovo Training Files. Please Wait... (" + progress + "/" + spectrumFactory.getMgfFileNames().size() + ").");
                // reset the progress bar
                waitingHandler.resetSecondaryProgressCounter();
                waitingHandler.setMaxSecondaryProgressCounter(spectrumFactory.getSpectrumTitles(fileName).size());
            }


            File file = new File(destinationFolder, getGoodSetFileName(fileName));
            BufferedWriter writerGood = new BufferedWriter(new FileWriter(file));
            file = new File(destinationFolder, getBadSetFileName(fileName));
            BufferedWriter writerBad = new BufferedWriter(new FileWriter(file));
            BufferedWriter writerRecalibration = null;
            if (recalibrate) {
                file = new File(destinationFolder, getRecalibratedFileName(fileName));
                writerRecalibration = new BufferedWriter(new FileWriter(file));
            }


            try {
                for (String spectrumTitle : spectrumFactory.getSpectrumTitles(fileName)) {


                    String spectrumKey = Spectrum.getSpectrumKey(fileName, spectrumTitle);


                    MSnSpectrum spectrum = null;
                    if (recalibrate) {
                        spectrum = spectrumRecalibrator.recalibrateSpectrum(fileName, spectrumTitle, true, true);
                        spectrum.writeMgf(writerRecalibration);
                    }
                    if (identification.matchExists(spectrumKey)) {
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                        Integer charge = new Integer(psParameter.getSpecificMapKey());
                        String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
                        Double fdrThreshold = getFdrThreshold(psmTargetDecoyMap, charge, spectrumTitle, fdr);
                        double confidenceLevel = getHighConfidenceThreshold(psmTargetDecoyMap, charge, spectrumFile, fdrThreshold);
                        if (psParameter.getPsmConfidence() >= confidenceLevel) {
                            if (spectrum == null) {
                                spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                            }
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                String sequence = spectrumMatch.getBestPeptideAssumption().getPeptide().getSequence();
                                HashMap<String, String> tags = new HashMap<String, String>();
                                tags.put("SEQ", sequence);
                                spectrum.writeMgf(writerGood, tags);
                            }
                        }
                        confidenceLevel = getLowConfidenceThreshold(psmTargetDecoyMap, charge, spectrumFile, fnr, fdrThreshold);
                        if (psParameter.getPsmConfidence() <= confidenceLevel) {
                            if (spectrum == null) {
                                spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                            }
                            spectrum.writeMgf(writerBad);
                        }
                    }


                    if (waitingHandler != null) {
                        if (waitingHandler.isRunCanceled()) {
                            return;
                        }
                        waitingHandler.increaseSecondaryProgressCounter();
                    }
                }
            } finally {
                writerBad.close();
                writerGood.close();
                if (writerRecalibration != null) {
                    writerRecalibration.close();
                }
            }


            spectrumRecalibrator.clearErrors(fileName);
            progress++;
        }
    }

View Full Code Here

    public static void writeRecalibratedSpectra(boolean recalibratePrecursors, boolean recalibrateFragmentIons, File folder,
            Identification identification, AnnotationPreferences annotationPreferences, WaitingHandler waitingHandler)
            throws IOException, MzMLUnmarshallerException, SQLException, ClassNotFoundException, InterruptedException {


        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
        SpectrumRecalibrator spectrumRecalibrator = new SpectrumRecalibrator();


        int progress = 1;


        for (String fileName : spectrumFactory.getMgfFileNames()) {


            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    break;
                }


                waitingHandler.setWaitingText("Recalibrating Spectra. Inspecting Mass Deviations. Please Wait... (" + progress + "/" + spectrumFactory.getMgfFileNames().size() + ")");
                waitingHandler.resetSecondaryProgressCounter();
                waitingHandler.setSecondaryProgressCounterIndeterminate(false);
                waitingHandler.setMaxSecondaryProgressCounter(2 * spectrumFactory.getNSpectra(fileName));
            }


            spectrumRecalibrator.estimateErrors(fileName, identification, annotationPreferences, waitingHandler);


            // Debug part
            if (debug) {


                RunMzDeviation runMzDeviation = spectrumRecalibrator.getRunMzDeviations(fileName);


                File debugFile = new File(folder, "debug" + getRecalibratedFileName(fileName) + "_precursors.txt");
                BufferedWriter debugWriter = new BufferedWriter(new FileWriter(debugFile));
                debugWriter.write("rt\tgrade\toffset");
                debugWriter.newLine();


                for (double key : runMzDeviation.getPrecursorRTList()) {


                    if (waitingHandler != null && waitingHandler.isRunCanceled()) {
                        break;
                    }


                    debugWriter.write(key + "\t");
                    debugWriter.write(runMzDeviation.getSlope(key) + "\t");
                    debugWriter.write(runMzDeviation.getOffset(key) + "\t");
                    debugWriter.newLine();
                }


                debugWriter.flush();
                debugWriter.close();


                debugFile = new File(folder, getRecalibratedFileName(fileName) + "_fragments.txt");
                debugWriter = new BufferedWriter(new FileWriter(debugFile));


                for (double rtKey : runMzDeviation.getPrecursorRTList()) {


                    debugWriter.write(rtKey + "\nm/z");


                    for (double mzKey : runMzDeviation.getFragmentMZList(rtKey)) {


                        debugWriter.write("\t" + mzKey);


                    }
                    debugWriter.newLine();
                    debugWriter.write("Error");


                    for (double mzKey : runMzDeviation.getFragmentMZList(rtKey)) {


                        debugWriter.write("\t" + runMzDeviation.getFragmentMzError(rtKey, mzKey));


                    }


                    debugWriter.newLine();
                }
                debugWriter.flush();
                debugWriter.close();
                // End of debug part
            }


            if (waitingHandler != null && waitingHandler.isRunCanceled()) {
                return;
            }


            File file = new File(folder, getRecalibratedFileName(fileName));
            BufferedWriter writer = new BufferedWriter(new FileWriter(file));
            if (waitingHandler != null) {
                waitingHandler.setWaitingText("Recalibrating Spectra. Writing Spectra. Please Wait... (" + progress + "/" + spectrumFactory.getMgfFileNames().size() + ")");
                waitingHandler.resetSecondaryProgressCounter();
                waitingHandler.setMaxSecondaryProgressCounter(spectrumFactory.getNSpectra(fileName));
            }


            for (String spectrumTitle : spectrumFactory.getSpectrumTitles(fileName)) {


                if (debug) {
                    //System.out.println(new Date() + " recalibrating " + spectrumTitle + "\n");
                }


                MSnSpectrum recalibratedSpectrum = spectrumRecalibrator.recalibrateSpectrum(fileName, spectrumTitle, recalibratePrecursors, recalibrateFragmentIons);
                recalibratedSpectrum.writeMgf(writer);
                writer.flush();


                if (waitingHandler != null) {
                    if (waitingHandler.isRunCanceled()) {
                        break;
                    }
                    waitingHandler.increasePrimaryProgressCounter();
                }
            }


            spectrumRecalibrator.clearErrors(fileName);
            writer.close();
        }
    }

View Full Code Here

TOP

Related Classes of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator

com.compomics.util.experiment.massspectrometry.MSnSpectrum

com.compomics.util.experiment.massspectrometry.Precursor

eu.isas.peptideshaker.followup.RecalibrationExporter

eu.isas.peptideshaker.followup.TrainingExport

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.