Examples of PrideXmlReader

        Double fragmentIonMassTolerance = null;
        Double peptideIonMassTolerance = null;
        Integer maxMissedCleavages = null;
        ArrayList<String> enzymes = new ArrayList<String>();


        PrideXmlReader prideXmlReader = new PrideXmlReader(currentPrideDataFile);


        Description description = prideXmlReader.getDescription();
        DataProcessing dataProcessing = description.getDataProcessing();


        if (dataProcessing != null && dataProcessing.getProcessingMethod() != null) {
            List<CvParam> processingMethods = dataProcessing.getProcessingMethod().getCvParam();


            for (CvParam cvParam : processingMethods) {
                if (cvParam.getAccession().equalsIgnoreCase("PRIDE:0000161")) { // fragment mass tolerance
                    String value = cvParam.getValue().trim();
                    if (value.indexOf(" ") != -1) { // escape Da or ppm
                        value = value.substring(0, value.indexOf(" "));
                    }
                    fragmentIonMassTolerance = new Double(value);
                } else if (cvParam.getAccession().equalsIgnoreCase("PRIDE:0000078")) { // peptide mass tolerance
                    String value = cvParam.getValue().trim();
                    if (value.indexOf(" ") != -1) { // escape Da or ppm
                        value = value.substring(0, value.indexOf(" "));
                    }
                    peptideIonMassTolerance = new Double(value);
                } else if (cvParam.getAccession().equalsIgnoreCase("PRIDE:0000162")) { // allowed missed cleavages
                    maxMissedCleavages = new Integer(cvParam.getValue());
                }
            }
        }


        if (prideXmlReader.getProtocol() != null && prideXmlReader.getProtocol().getProtocolSteps() != null) {


            List<Param> protocolStepDescription = prideXmlReader.getProtocol().getProtocolSteps().getStepDescription();


            for (Param stepDescription : protocolStepDescription) {
                List<CvParam> stepCvParams = stepDescription.getCvParam();


                for (CvParam stepCvParam : stepCvParams) {
                    if (stepCvParam.getAccession().equalsIgnoreCase("PRIDE:0000160") || stepCvParam.getAccession().equalsIgnoreCase("PRIDE:0000024")) { // enzyme
                        if (stepCvParam.getValue() != null) {
                            enzymes.add(stepCvParam.getValue());
                        }
                    }
                }
            }
        }


        HashMap<String, Integer> ionTypes = new HashMap<String, Integer>();
        HashMap<String, Integer> peptideLastResidues = new HashMap<String, Integer>();


        // get the fragment ion types used
        List<String> ids = prideXmlReader.getIdentIds();


        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(ids.size());
        progressDialog.setValue(0);


        // set the ion types
        for (String id : ids) {


            // @TODO: implement me!
            progressDialog.increasePrimaryProgressCounter();


            Identification identification = prideXmlReader.getIdentById(id);
            List<PeptideItem> peptides = identification.getPeptideItem();


            for (PeptideItem peptide : peptides) {
                String residue = peptide.getSequence().substring(peptide.getSequence().length() - 1);


        boolean conversionOk = true;


        try {
            progressDialog.setPrimaryProgressCounterIndeterminate(true);
            PrideXmlReader prideXmlReader = new PrideXmlReader(currentPrideDataFile);
            FileWriter w = new FileWriter(currentMgfFile);
            BufferedWriter bw = new BufferedWriter(w);
            List<String> spectra = prideXmlReader.getSpectrumIds();
            int spectraCount = spectra.size();


            if (spectraCount == 0) {
                bw.close();
                w.close();
                progressDialog.setRunFinished();
                JOptionPane.showMessageDialog(this, "The file " + currentPrideDataFile.getName() + " contains no valid spectra!"
                        + "\nConversion canceled.", "No Spectra Found", JOptionPane.WARNING_MESSAGE);
                return false;
            }


            progressDialog.setPrimaryProgressCounterIndeterminate(false);
            progressDialog.setMaxPrimaryProgressCounter(spectraCount);
            progressDialog.setValue(0);


            int validSpectrumCount = 0;


            for (String spectrumId : spectra) {


                if (progressDialog.isRunCanceled()) {
                    bw.close();
                    w.close();
                    progressDialog.setRunFinished();
                    return false;
                }


                Spectrum spectrum = prideXmlReader.getSpectrumById(spectrumId);
                boolean valid = asMgf(spectrum, bw);


                if (valid) {
                    validSpectrumCount++;
                }

Examples of PrideXmlReader

Examples of uk.ac.ebi.pride.jaxb.xml.PrideXmlReader

Examples of uk.ac.ebi.pride.jaxb.xml.PrideXmlReader