* The class that takes care of converting the data to mzIdentML.

*

* @author Harald Barsnes

* @author Marc Vaudel

*/

    /**

     * The fileWriter.

     */

    private FileWriter r;

    /**

     * The buffered writer which will write the results in the desired file.

     */

    private BufferedWriter br;

    /**

     * Integer keeping track of the number of tabs to include at the beginning

     * of each line.

     */

    private int tabCounter = 0;

    /**

     * The spectrum factory.

     */

    private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();

    /**

     * The PTM factory.

     */

    private PTMFactory ptmFactory = PTMFactory.getInstance();

    /**

     * The sequence factory.

     */

    private SequenceFactory sequenceFactory = SequenceFactory.getInstance();

    /**

     * The PTM to mzIdentML map.

     */

    private PtmToPrideMap ptmToPrideMap; // @TODO: should be renamed!!!

    /**

     * The number of decimals to use for the confidence values.

     */

    private final int CONFIDENCE_DECIMALS = 2;

    /**

     * Write mzid 1.2? False, results in mzid 1.1.

     */

    private boolean mzidVersion1_2 = false;

    /**

     * The PeptideShaker version.

     */

    private String peptideShakerVersion;

    /**

     * The identifications object.

     */

    private Identification identification;

    /**

     * The project details.

     */

    private ProjectDetails projectDetails;

    /**

     * The processing preferences.

     */

    private ProcessingPreferences processingPreferences;

    /**

     * The search parameters.

     */

    private SearchParameters searchParameters;

    /**

     * The PTM scoring preferences.

     */

    private PTMScoringPreferences ptmScoringPreferences;

    /**

     * The spectrum counting preferences.

     */

    private SpectrumCountingPreferences spectrumCountingPreferences;

    /**

     * The identification feature generator.

     */

    private IdentificationFeaturesGenerator identificationFeaturesGenerator;

    /**

     * The peptide spectrum annotator.

     */

    private PeptideSpectrumAnnotator peptideSpectrumAnnotator;

    /**

     * The annotation preferences.

     */

    private AnnotationPreferences annotationPreferences;

    /**

     * The sequence matching preferences.

     */

    private SequenceMatchingPreferences sequenceMatchingPreferences;

    /**

     * The waiting handler.

     */

    private WaitingHandler waitingHandler;

    /**

     * The peptide evidence IDs.

     */

    private HashMap<String, String> pepEvidenceIds = new HashMap<String, String>();

    /**

     * The spectrum IDs.

     */

    private HashMap<String, String> spectrumIds = new HashMap<String, String>();

    /**

     * Constructor.

     *

     * @param peptideShakerVersion the PeptideShaker version

     * @param identification the identification object which can be used to retrieve identification matches and parameters

     * @param projectDetails the project details

     * @param processingPreferences the processing preferences

     * @param spectrumCountingPreferences the spectrum counting preferences

     * @param identificationFeaturesGenerator the identification features generator

     * @param searchParameters the search parameters

     * @param annotationPreferences the annotation preferences

     * @param ptmScoringPreferences the PTM scoring preferences

     * @param sequenceMatchingPreferences the sequence matching preferences

     * @param outputFile Output file

     * @param waitingHandler waiting handler used to display progress to the user and interrupt the process

     *

     * @throws FileNotFoundException Exception thrown whenever a file was not

     * found

     * @throws IOException Exception thrown whenever an error occurred while

     * reading/writing a file

     * @throws ClassNotFoundException Exception thrown whenever an error

     * occurred while deserializing a pride object

     */

    public MzIdentMLExport(String peptideShakerVersion, Identification identification, ProjectDetails projectDetails, ProcessingPreferences processingPreferences,

            SearchParameters searchParameters, PTMScoringPreferences ptmScoringPreferences, SpectrumCountingPreferences spectrumCountingPreferences,

            IdentificationFeaturesGenerator identificationFeaturesGenerator, AnnotationPreferences annotationPreferences, SequenceMatchingPreferences sequenceMatchingPreferences,

            File outputFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException, ClassNotFoundException {

        this.peptideShakerVersion = peptideShakerVersion;

        this.identification = identification;

        this.projectDetails = projectDetails;

        this.processingPreferences = processingPreferences;

        this.searchParameters = searchParameters;

        this.ptmScoringPreferences = ptmScoringPreferences;

        this.spectrumCountingPreferences = spectrumCountingPreferences;

        this.identificationFeaturesGenerator = identificationFeaturesGenerator;

        this.annotationPreferences = annotationPreferences;

        this.sequenceMatchingPreferences = sequenceMatchingPreferences;

        this.waitingHandler = waitingHandler;

        PrideObjectsFactory prideObjectsFactory = PrideObjectsFactory.getInstance(); // @TODO: should be renamed!!!

        ptmToPrideMap = prideObjectsFactory.getPtmToPrideMap();

        this.peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();

        r = new FileWriter(outputFile);

        br = new BufferedWriter(r);

    }

    /**

     * Creates the mzIdentML file.

     *

     * @param version12 if true, mzid 1.2 version information will be included

     *

     * @throws IOException exception thrown whenever a problem occurred while

     * reading/writing a file

     * @throws MzMLUnmarshallerException exception thrown whenever a problem

     * occurred while reading the mzML file

     * @throws ClassNotFoundException thrown of ClassNotFoundException occurs

     * @throws InterruptedException thrown if FileNotFoundException occurs

     * @throws SQLException thrown of SQLException occurs

     */

    public void createMzIdentMLFile(boolean version12) throws IOException, MzMLUnmarshallerException, IllegalArgumentException, ClassNotFoundException, InterruptedException, SQLException {

        mzidVersion1_2 = version12;

        // @TODO: use the waiting handler more (especially for command line mode)

        // the mzIdentML start tag

        writeMzIdentMLStartTag();

        // write the cv list

        writeCvList();

        // write the AnalysisSoftwareList

        writeAnalysisSoftwareList();

        // write the Provider details

        writeProviderDetails();

        // write the AuditCollection details

        writeAuditCollection();

        waitingHandler.setPrimaryProgressCounterIndeterminate(false);

        waitingHandler.resetPrimaryProgressCounter();

        waitingHandler.setMaxPrimaryProgressCounter(sequenceFactory.getNSequences() + identification.getSpectrumIdentificationSize() * 3 + identification.getProteinIdentification().size());

        // write the sequence collection

        writeSequenceCollection();

        // write the analyis collection

        writeAnalysisCollection();

        // write the analysis protocol

        writeAnalysisProtocol();

        // write the data collection

        writeDataCollection();

        if (waitingHandler.isRunCanceled()) {

            br.close();

            r.close();

            return;

        }

        // the experiment end tag

        writeMzIdentMLEndTag();

        br.close();

        r.close();

    }

    /**

     * Writes the CV list.

     *

     * @throws IOException exception thrown whenever a problem occurred while

     * reading/writing a file

     */

    private void writeCvList() throws IOException {

        br.write(getCurrentTabSpace() + "<cvList>" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace()

                + "<cv id=\"PSI-MS\" "

                + "uri=\"http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\" "

                + "version=\"2.25.0\" "

                + "fullName=\"PSI-MS\"/>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace()

                + "<cv id=\"UNIMOD\" "

                + "uri=\"http://www.unimod.org/obo/unimod.obo\" "

                + "fullName=\"UNIMOD\"/>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace()

                + "<cv id=\"UO\" "

                + "uri=\"http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo\" "

                + "fullName=\"UNIT-ONTOLOGY\"/>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace()

                + "<cv id=\"PRIDE\" "

                + "uri=\"http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo\" "

                + "fullName=\"PRIDE\"/>" + System.getProperty("line.separator"));

        // @TODO: add more? perhaps not hardcode?

        tabCounter--;

        br.write(getCurrentTabSpace() + "</cvList>" + System.getProperty("line.separator"));

    }

    /**

     * Write the software list.

     *

     * @throws IOException

     */

    private void writeAnalysisSoftwareList() throws IOException {

        br.write(getCurrentTabSpace() + "<AnalysisSoftwareList>" + System.getProperty("line.separator"));

        tabCounter++;

        // @TODO: also add SearchGUI and/or search engines used?

        br.write(getCurrentTabSpace() + "<AnalysisSoftware "

                + "name=\"PeptideShaker\" "

                + "version=\"" + peptideShakerVersion + "\" "

                + "id=\"ID_software\" "

                + "uri=\"http://peptide-shaker.googlecode.com\">"

                + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<ContactRole contact_ref=\"PS_DEV\">" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<Role>" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1001267", "software vendor", "CompOmics"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Role>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ContactRole>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace() + "<SoftwareName>" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1002458", "PeptideShaker", null));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SoftwareName>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace() + "<Customizations>No customisations</Customizations>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AnalysisSoftware>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AnalysisSoftwareList>" + System.getProperty("line.separator"));

    }

    /**

     * Write the provider details.

     *

     * @throws IOException

     */

    private void writeProviderDetails() throws IOException {

        br.write(getCurrentTabSpace() + "<Provider id=\"PROVIDER\">" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<ContactRole contact_ref=\"PROVIDER\">" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<Role>" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1001271", "researcher", null)); // @TODO: add the provider role here!!

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Role>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ContactRole>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Provider>" + System.getProperty("line.separator"));

    }

    /**

     * Write the audit collection.

     *

     * @throws IOException

     */

    private void writeAuditCollection() throws IOException {

        br.write(getCurrentTabSpace() + "<AuditCollection>" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<Person "

                + "firstName=\"" + projectDetails.getContactFirstName() + "\" "

                + "lastName=\"" + projectDetails.getContactLastName() + "\" "

                + "id=\"PROVIDER\">"

                + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000587", "contact address", projectDetails.getContactAddress()));

        if (projectDetails.getContactUrl() != null && !projectDetails.getContactUrl().isEmpty()) {

            writeCvTerm(new CvTerm("PSI-MS", "MS:1000588", "contact url", projectDetails.getContactUrl()));

        }

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000589", "contact email", projectDetails.getContactEmail()));

        br.write(getCurrentTabSpace() + "<Affiliation organization_ref=\"ORG_DOC_OWNER\"/>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Person>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace() + "<Organization name=\"" + projectDetails.getOrganizationName() + "\" id=\"ORG_DOC_OWNER\">" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000586", "contact name", projectDetails.getOrganizationName()));

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000587", "contact address", projectDetails.getOrganizationAddress()));

        if (projectDetails.getOrganizationUrl() != null && !projectDetails.getOrganizationUrl().isEmpty()) {

            writeCvTerm(new CvTerm("PSI-MS", "MS:1000588", "contact url", projectDetails.getOrganizationUrl()));

        }

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000589", "contact email", projectDetails.getOrganizationEmail()));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Organization>" + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace() + "<Organization name=\"PeptideShaker developers\" id=\"PS_DEV\">" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000586", "contact name", "PeptideShaker developers"));

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000587", "contact address", "Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"));

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000588", "contact url", "http://peptide-shaker.googlecode.com"));

        writeCvTerm(new CvTerm("PSI-MS", "MS:1000589", "contact email", "peptide-shaker@googlegroups.com"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Organization>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AuditCollection>" + System.getProperty("line.separator"));

    }

    /**

     * Write the sequence collection.

     *

     * @throws IOException

     * @throws IllegalArgumentException

     * @throws InterruptedException

     * @throws ClassNotFoundException

     * @throws SQLException

     */

    private void writeSequenceCollection() throws IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException, SQLException {

        br.write(getCurrentTabSpace() + "<SequenceCollection>" + System.getProperty("line.separator"));

        tabCounter++;

        // get the sequence database

        ProteinIterator iterator = sequenceFactory.getProteinIterator(false);

//        FastaIndex fastaIndex = sequenceFactory.getCurrentFastaIndex();

//        if (fastaIndex != null) {

//            dbType = Header.getDatabaseTypeAsString(fastaIndex.getDatabaseType());

//        }

        // iterate all the protein sequences

        while (iterator.hasNext()) {

            Protein currentProtein = iterator.getNextProtein();

            br.write(getCurrentTabSpace() + "<DBSequence id=\"" + currentProtein.getAccession() + "\" "

                    + "accession=\"" + currentProtein.getAccession() + "\" searchDatabase_ref=\"" + "SearchDB_1" + "\" >" + System.getProperty("line.separator"));

            tabCounter++;

            //br.write(getCurrentTabSpace() + "<Seq>" + currentProtein.getSequence() + "</Seq>" + System.getProperty("line.separator"));

            writeCvTerm(new CvTerm("PSI-MS", "MS:1001088", "protein description", StringEscapeUtils.escapeHtml4(sequenceFactory.getHeader(currentProtein.getAccession()).getDescription())));

            tabCounter--;

            br.write(getCurrentTabSpace() + "</DBSequence>" + System.getProperty("line.separator"));

            waitingHandler.increasePrimaryProgressCounter();

            if (waitingHandler.isRunCanceled()) {

                break;

            }

        }

        iterator.close();

        identification.loadPeptideMatches(null);

        identification.loadPeptideMatchParameters(new PSParameter(), null);

        // iterate all the peptides

        for (String peptideKey : identification.getPeptideIdentification()) {

            PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);

            Peptide peptide = peptideMatch.getTheoreticPeptide();

            String peptideSequence = peptide.getSequence();

            br.write(getCurrentTabSpace() + "<Peptide id=\"" + peptideKey + "\" >" + System.getProperty("line.separator"));

            tabCounter++;

            br.write(getCurrentTabSpace() + "<PeptideSequence>" + peptideSequence + "</PeptideSequence>" + System.getProperty("line.separator"));

            int modMatchIndex = 0;

            for (ModificationMatch modMatch : peptide.getModificationMatches()) {

                PTM currentPtm = ptmFactory.getPTM(modMatch.getTheoreticPtm());

                int ptmLocation = modMatch.getModificationSite();

                if (currentPtm.isNTerm()) {

                    ptmLocation = 0;

                } else if (currentPtm.isCTerm()) {

                    ptmLocation = peptideSequence.length() + 1;

                }

                br.write(getCurrentTabSpace() + "<Modification monoisotopicMassDelta=\"" + currentPtm.getMass() + "\" "

                        + "residues=\"" + peptideSequence.charAt(modMatch.getModificationSite() - 1) + "\" "

                        + "location=\"" + ptmLocation + "\" >" + System.getProperty("line.separator"));

                CvTerm ptmCvTerm = PtmToPrideMap.getDefaultCVTerm(currentPtm.getName());

                if (ptmCvTerm != null) {

                    tabCounter++;

                    writeCvTerm(ptmCvTerm);

                    if (mzidVersion1_2) {

                        writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "order", modMatchIndex + "")); // @TODO: add correct cv term!

                        modMatchIndex++;

                    }

                    tabCounter--;

                }

                // add cv/user params

                // @TODO: ptm validation

                // @TODO: ptm localization scores across possible sites: PhosphoRS, A-score, d-score, ms-score

                br.write(getCurrentTabSpace() + "</Modification>" + System.getProperty("line.separator"));

            }

            modMatchIndex = 0;

            for (ModificationMatch modMatch : peptideMatch.getTheoreticPeptide().getModificationMatches()) {

                CvTerm ptmCvTerm = PtmToPrideMap.getDefaultCVTerm(modMatch.getTheoreticPtm());

                if (ptmCvTerm != null) {

                    writeCvTerm(ptmCvTerm);

                    writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "peptide: order", modMatchIndex + ""));

                    modMatchIndex++;

                }

            }

            tabCounter--;

            br.write(getCurrentTabSpace() + "</Peptide>" + System.getProperty("line.separator"));

            waitingHandler.increasePrimaryProgressCounter();

            if (waitingHandler.isRunCanceled()) {

                break;

            }

        }

        int peptideEvidenceCounter = 0;

        // iterate the spectrum files

        for (String spectrumFileName : identification.getSpectrumFiles()) {

            identification.loadSpectrumMatches(spectrumFileName, null);

            identification.loadSpectrumMatchParameters(spectrumFileName, new PSParameter(), null);

            // iterate the psms

            for (String psmKey : identification.getSpectrumIdentification(spectrumFileName)) {

                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmKey);

                PeptideAssumption bestPeptideAssumption = spectrumMatch.getBestPeptideAssumption();

                if (bestPeptideAssumption != null) {

                    Peptide peptide = bestPeptideAssumption.getPeptide();

                    // get all the possible parent proteins

                    ArrayList<String> possibleProteins = peptide.getParentProteins(sequenceMatchingPreferences);

                    // iterate all the possible protein parents for each peptide

                    for (String tempProtein : possibleProteins) {

                        // get the start indexes and the surrounding

                        HashMap<Integer, String[]> aaSurrounding = sequenceFactory.getProtein(tempProtein).getSurroundingAA(

                                peptide.getSequence(), 1, sequenceMatchingPreferences);

                        ArrayList<Integer> indexes = new ArrayList<Integer>();

                        ArrayList<String> before = new ArrayList<String>();

                        ArrayList<String> after = new ArrayList<String>();

                        if (aaSurrounding.size() == 1) {

                            for (int index : aaSurrounding.keySet()) {

                                indexes.add(index);

                                before.add(aaSurrounding.get(index)[0]);

                                after.add(aaSurrounding.get(index)[1]);

                            }

                        } else {

                            ArrayList<Integer> tempIndexes = new ArrayList<Integer>(aaSurrounding.keySet());

                            Collections.sort(tempIndexes);

                            for (int index : tempIndexes) {

                                indexes.add(index);

                                before.add(aaSurrounding.get(index)[0]);

                                after.add(aaSurrounding.get(index)[1]);

                            }

                        }

                        for (int i = 0; i < indexes.size(); i++) {

                            String aaBefore = "-";

                            String aaAfter = "-";

                            if (!before.get(i).isEmpty()) {

                                aaBefore = before.get(i);

                            }

                            if (!after.get(i).isEmpty()) {

                                aaAfter = after.get(i);

                            }

                            int peptideStart = indexes.get(i);

                            int peptideEnd = (indexes.get(i) + peptide.getSequence().length() - 1);

                            String peptideKey = peptide.getMatchingKey(sequenceMatchingPreferences);

                            String pepEvidenceKey = tempProtein + "_" + peptideStart + "_" + peptideKey;

                            pepEvidenceIds.put(pepEvidenceKey, "PepEv_" + ++peptideEvidenceCounter);

                            String matchingPeptideKey = peptide.getMatchingKey(sequenceMatchingPreferences);

                            br.write(getCurrentTabSpace() + "<PeptideEvidence isDecoy=\"" + peptide.isDecoy(sequenceMatchingPreferences) + "\" "

                                    + "pre=\"" + aaBefore + "\" "

                                    + "post=\"" + aaAfter + "\" "

                                    + "start=\"" + peptideStart + "\" "

                                    + "end=\"" + peptideEnd + "\" "

                                    + "peptide_ref=\"" + matchingPeptideKey + "\" "

                                    + "dBSequence_ref=\"" + sequenceFactory.getProtein(tempProtein).getAccession() + "\" "

                                    + "id=\"" + pepEvidenceIds.get(pepEvidenceKey) + "\" "

                                    + "/>" + System.getProperty("line.separator"));

                        }

                    }

                    waitingHandler.increasePrimaryProgressCounter();

                    if (waitingHandler.isRunCanceled()) {

                        break;

                    }

                }

            }

            if (waitingHandler.isRunCanceled()) {

                break;

            }

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SequenceCollection>" + System.getProperty("line.separator"));

    }

    /**

     * Write the analysis collection.

     *

     * @throws IOException

     */

    private void writeAnalysisCollection() throws IOException {

        br.write(getCurrentTabSpace() + "<AnalysisCollection>" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<SpectrumIdentification "

                + "spectrumIdentificationList_ref=\"SIL_1\" " // @TODO: should not be hardcoded?

                + "spectrumIdentificationProtocol_ref=\"SearchProtocol_1\" " // @TODO: should not be hardcoded?

                + "id=\"SpecIdent_1\">" // @TODO: should not be hardcoded?

                + System.getProperty("line.separator"));

        tabCounter++;

        // iterate the spectrum files and add the file name refs

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

            br.write(getCurrentTabSpace() + "<InputSpectra spectraData_ref=\"" + mgfFileName + "\"/>" + System.getProperty("line.separator"));

        }

        br.write(getCurrentTabSpace() + "<SearchDatabaseRef searchDatabase_ref=\"SearchDB_1\"/>" + System.getProperty("line.separator")); // @TODO: should not be hardcoded?

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SpectrumIdentification>" + System.getProperty("line.separator"));

        // add protein detection

        br.write(getCurrentTabSpace() + "<ProteinDetection " // @TODO: add activityDate? example: activityDate="2011-03-25T13:33:51

                + "proteinDetectionProtocol_ref=\"PeptideShaker_1\" " // @TODO: should not be hardcoded?

                + "proteinDetectionList_ref=\"Protein_groups\" " // @TODO: should not be hardcoded?

                + "id=\"PD_1\">" // @TODO: should not be hardcoded?

                + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<InputSpectrumIdentifications spectrumIdentificationList_ref=\"SIL_1\"/>" + System.getProperty("line.separator")); // @TODO: should not be hardcoded?

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ProteinDetection>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AnalysisCollection>" + System.getProperty("line.separator"));

    }

    /**

     * Write the analysis protocol.

     *

     * @throws IOException

     */

    private void writeAnalysisProtocol() throws IOException {

        br.write(getCurrentTabSpace() + "<AnalysisProtocolCollection>" + System.getProperty("line.separator"));

        tabCounter++;

        // add spectrum identification protocol

        br.write(getCurrentTabSpace() + "<SpectrumIdentificationProtocol "

                + "analysisSoftware_ref=\"ID_software\" id=\"SearchProtocol_1\">" + System.getProperty("line.separator"));

        tabCounter++;

        // the search type

        br.write(getCurrentTabSpace() + "<SearchType>" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1001083", "ms-ms search", null));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SearchType>" + System.getProperty("line.separator"));

        // the search parameters

        br.write(getCurrentTabSpace() + "<AdditionalSearchParams>" + System.getProperty("line.separator"));

        tabCounter++;

        writeCvTerm(new CvTerm("PSI-MS", "MS:1001211", "parent mass type mono", null));

        writeCvTerm(new CvTerm("PSI-MS", "MS:1001256", "fragment mass type mono", null));

        if (mzidVersion1_2) {

            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "peptide-level scoring performed", null)); // @TODO: add correct cv term!

            writeCvTerm(new CvTerm("PSI-MS", "MS:1002497", "Group PSMs by distinct peptide sequence with taking modifications into account", null));

            writeCvTerm(new CvTerm("PSI-MS", "MS:1002489", "Modification localization scoring performed", null));

            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", ptmScoringPreferences.getSelectedProbabilisticScore().getName(), null)); // @TODO: add correct cv term!

            }

            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "D-score", null)); // @TODO: add correct cv term!

        }

        // @TODO: list all search parameters from the search engines used?

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AdditionalSearchParams>" + System.getProperty("line.separator"));

        // the modifications

        br.write(getCurrentTabSpace() + "<ModificationParams>" + System.getProperty("line.separator"));

        tabCounter++;

        // iterate and add the ptms

        for (String ptm : searchParameters.getModificationProfile().getAllModifications()) {

            PTM currentPtm = ptmFactory.getPTM(ptm);

            String aminoAcidsAtTarget = "";

            if (currentPtm.getType() == PTM.MODN

                    || currentPtm.getType() == PTM.MODNP

                    || currentPtm.getType() == PTM.MODC

                    || currentPtm.getType() == PTM.MODCP) {

                aminoAcidsAtTarget = ".";

            } else {

                for (Character aa : currentPtm.getPattern().getAminoAcidsAtTarget()) {

                    aminoAcidsAtTarget += aa;

                }

            }

            br.write(getCurrentTabSpace() + "<SearchModification residues=\"" + aminoAcidsAtTarget + "\" massDelta=\"" + currentPtm.getMass()

                    + "\" fixedMod= \"" + searchParameters.getModificationProfile().getFixedModifications().contains(ptm) + "\" >" + System.getProperty("line.separator"));

            tabCounter++;

            CvTerm cvTerm = ptmToPrideMap.getCVTerm(ptm);

            if (cvTerm != null) {

                writeCvTerm(cvTerm);

            } else {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1001460", "unknown modification", null));

            }

            // add modification specificity

            if (currentPtm.getType() == PTM.MODN

                    || currentPtm.getType() == PTM.MODNAA) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002057", "modification specificity protein N-term", null));

            } else if (currentPtm.getType() == PTM.MODNP

                    || currentPtm.getType() == PTM.MODNPAA) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1001189", "modification specificity peptide N-term", null));

            } else if (currentPtm.getType() == PTM.MODC

                    || currentPtm.getType() == PTM.MODCAA) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002058", "modification specificity protein C-term", null));

            } else if (currentPtm.getType() == PTM.MODCP

                    || currentPtm.getType() == PTM.MODCPAA) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1001190", "modification specificity peptide C-term", null));

            }

            tabCounter--;

            br.write(getCurrentTabSpace() + "</SearchModification>" + System.getProperty("line.separator"));

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ModificationParams>" + System.getProperty("line.separator"));

        // enzyme

        br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + System.getProperty("line.separator"));

        // note: if multiple enzymes are specified, independent is set to true if cleavage with different enzymes is performed independently

        tabCounter++;

        Enzyme enzyme = searchParameters.getEnzyme();

        br.write(getCurrentTabSpace() + "<Enzyme "

                + "missedCleavages=\"" + searchParameters.getnMissedCleavages() + "\" "

                + "semiSpecific=\"" + enzyme.isSemiSpecific() + "\" "

                //+ "cTermGain=\"OH\" " // Element formula gained at CTerm

                //+ "nTermGain=\"H\" " // Element formula gained at NTerm

                + "id=\"Enz1\" "

                + "name=\"" + enzyme.getName() + "\">"

                + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<EnzymeName>" + System.getProperty("line.separator"));

        tabCounter++;

        CvTerm enzymeCvTerm = EnzymeFactory.getEnzymeCvTerm(enzyme);

        if (enzymeCvTerm != null) {

            writeCvTerm(enzymeCvTerm);

        } else {

            writeUserParam(enzyme.getName());

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</EnzymeName>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Enzyme>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Enzymes>" + System.getProperty("line.separator"));

        // fragment tolerance

        br.write(getCurrentTabSpace() + "<FragmentTolerance>" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<cvParam "

                + "accession=\"MS:1001412\" "

                + "cvRef=\"PSI-MS\" "

                + "unitCvRef=\"UO\" "

                + "unitName=\"dalton\" "

                + "unitAccession=\"UO:0000221\" "

                + "value=\"" + searchParameters.getFragmentIonAccuracy() + "\" "

                + "name=\"search tolerance plus value\" />"

                + System.getProperty("line.separator"));

        br.write(getCurrentTabSpace() + "<cvParam "

                + "accession=\"MS:1001413\" "

                + "cvRef=\"PSI-MS\" "

                + "unitCvRef=\"UO\" "

                + "unitName=\"dalton\" "

                + "unitAccession=\"UO:0000221\" "

                + "value=\"" + searchParameters.getFragmentIonAccuracy() + "\" "

                + "name=\"search tolerance minus value\" />"

                + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</FragmentTolerance>" + System.getProperty("line.separator"));

        // precursor tolerance

        br.write(getCurrentTabSpace() + "<ParentTolerance>" + System.getProperty("line.separator"));

        tabCounter++;

        if (searchParameters.isPrecursorAccuracyTypePpm()) {

            br.write(getCurrentTabSpace() + "<cvParam "

                    + "accession=\"MS:1001412\" "

                    + "cvRef=\"PSI-MS\" "

                    + "unitCvRef=\"UO\" "

                    + "unitName=\"parts per million\" "

                    + "unitAccession=\"UO:0000169\" "

                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "

                    + "name=\"search tolerance plus value\" />"

                    + System.getProperty("line.separator"));

            br.write(getCurrentTabSpace() + "<cvParam "

                    + "accession=\"MS:1001413\" "

                    + "cvRef=\"PSI-MS\" "

                    + "unitCvRef=\"UO\" "

                    + "unitName=\"parts per million\" "

                    + "unitAccession=\"UO:0000169\" "

                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "

                    + "name=\"search tolerance minus value\" />"

                    + System.getProperty("line.separator"));

        } else {

            br.write(getCurrentTabSpace() + "<cvParam "

                    + "accession=\"MS:1001412\" "

                    + "cvRef=\"PSI-MS\" "

                    + "unitCvRef=\"UO\" "

                    + "unitName=\"dalton\" "

                    + "unitAccession=\"UO:0000221\" "

                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "

                    + "name=\"search tolerance plus value\" />"

                    + System.getProperty("line.separator"));

            br.write(getCurrentTabSpace() + "<cvParam "

                    + "accession=\"MS:1001413\" "

                    + "cvRef=\"PSI-MS\" "

                    + "unitCvRef=\"UO\" "

                    + "unitName=\"dalton\" "

                    + "unitAccession=\"UO:0000221\" "

                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "

                    + "name=\"search tolerance minus value\" />"

                    + System.getProperty("line.separator"));

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ParentTolerance>" + System.getProperty("line.separator"));

        // thresholds

        br.write(getCurrentTabSpace() + "<Threshold>" + System.getProperty("line.separator"));

        tabCounter++;

        boolean targetDecoy = sequenceFactory.concatenatedTargetDecoy();

        if (!targetDecoy) {

            writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));

        } else {

            // Initial global thresholds

            writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "distinct peptide-level global FDR", Double.toString(Util.roundDouble(processingPreferences.getPeptideFDR(), CONFIDENCE_DECIMALS))));

            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(processingPreferences.getPsmFDR(), CONFIDENCE_DECIMALS))));

            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", ptmScoringPreferences.getSelectedProbabilisticScore().getName() + " threshold", ptmScoringPreferences.getProbabilisticScoreThreshold() + ""));

            }

            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "D-score threshold", "95")); //@TODO: avoid this hard coded value

//            // peptideshaker maps

//            PSMaps psMaps = new PSMaps();

//            psMaps = (PSMaps) identification.getUrParam(psMaps);

//

//            // peptide level threshold

//            PeptideSpecificMap peptideSpecificMap = psMaps.getPeptideSpecificMap();

//            ArrayList<String> peptideGroupsKeys = peptideSpecificMap.getKeys();

//

//            for (String key : peptideGroupsKeys) { // @TODO: find a way of annotating all thresholds..?

//                TargetDecoyMap targetDecoyMap = peptideSpecificMap.getTargetDecoyMap(key);

//                TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();

//                double threshold = targetDecoyResults.getUserInput() / 100;

//                int thresholdType = targetDecoyResults.getInputType();

//                if (peptideGroupsKeys.size() > 1) {

//                    String peptideClass = PeptideSpecificMap.getKeyName(searchParameters.getModificationProfile(), key);

//                    // @TODO: somehow indicate the class of peptide thresholded?

//                }

//                if (thresholdType == 0) {

//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002463", "distinct peptide-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence

//                } else if (targetDecoyResults.getInputType() == 1) {

//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "distinct peptide-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR

//                } else if (targetDecoyResults.getInputType() == 2) {

//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002462", "distinct peptide-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR

//                }

//            }

//

//            // psm level threshold

//            ArrayList<Integer> chargesWithFileSpecificity = new ArrayList<Integer>();

//            PsmSpecificMap psmSpecificMap = psMaps.getPsmSpecificMap();

//

//            for (Integer charge : psmSpecificMap.getPossibleCharges()) {

//                for (String file : psmSpecificMap.getFilesAtCharge(charge)) {

//                    if (!psmSpecificMap.isFileGrouped(charge, file)) { // @TODO: find a way of annotating all thresholds..?

//                        chargesWithFileSpecificity.add(charge);

//                        TargetDecoyMap targetDecoyMap = psMaps.getPsmSpecificMap().getTargetDecoyMap(charge, file);

//                        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();

//                        double threshold = targetDecoyResults.getUserInput() / 100;

//                        int thresholdType = targetDecoyResults.getInputType();

//                        String psmClass = "Charge " + charge + " of file " + file; // @TODO: annotate class?

//                        if (thresholdType == 0) {

//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence

//                        } else if (targetDecoyResults.getInputType() == 1) {

//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR

//                        } else if (targetDecoyResults.getInputType() == 2) {

//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR

//                        }

//                    }

//                }

//            }

            //@TODO: set the PSM group label

//            for (int charge : psmSpecificMap.getChargesFromGroupedFiles()) {

//                int correctedCharge = psmSpecificMap.getCorrectedCharge(charge);

//                if (correctedCharge == charge) {

//                    TargetDecoyMap targetDecoyMap = pSMaps.getPsmSpecificMap().getTargetDecoyMap(charge, null);

//                    TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();

//                    double threshold = targetDecoyResults.getUserInput() / 100;

//                    int thresholdType = targetDecoyResults.getInputType();

//                    // @TODO: check the cv terms used!!!

//                    if (thresholdType == 0) {

//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence

//                    } else if (targetDecoyResults.getInputType() == 1) {

//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR

//                    } else if (targetDecoyResults.getInputType() == 2) {

//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR

//                    }

//                }

//            }

//

            // @TODO: re-add psm ptm thresholds

//            PsmPTMMap psmPTMMap = pSMaps.getPsmPTMMap();

//            if (psmPTMMap != null) { // backward compatibility: information only present in versions 0.28.2 and later

//                for (Double ptmMass : psmPTMMap.getModificationsScored()) {

//                    for (int mapKey : psmPTMMap.getKeys(ptmMass).keySet()) {

//                        TargetDecoyMap targetDecoyMap = psmPTMMap.getTargetDecoyMap(ptmMass, mapKey);

//                        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();

//                        double threshold = targetDecoyResults.getUserInput() / 100;

//                        int thresholdType = targetDecoyResults.getInputType(); // For now only FDR is implemented but others will follow after my next transatlantic flight :)

//                        String ptmClass = "Modification of mass " + ptmMass;

//                        //@TODO: find cv terms

//                    }

//                }

//            }

            // @TODO: one for ptm scores, one per ptm per charge state per file

            // match quality thresholds

            // @TODO: match quality thresholds?? some are per file...

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Threshold>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SpectrumIdentificationProtocol>" + System.getProperty("line.separator"));

        // add ProteinDetectionProtocol

        br.write(getCurrentTabSpace() + "<ProteinDetectionProtocol "

                + "analysisSoftware_ref=\"ID_software\" id=\"PeptideShaker_1\">" + System.getProperty("line.separator"));

        tabCounter++;

//        tabCounter++;

        // @TODO: add cv terms? (children of MS:1001302)

//        tabCounter--;

//        br.write(getCurrentTabSpace() + "</AnalysisParams>" + System.getProperty("line.separator"));

        // protein level threshold

        br.write(getCurrentTabSpace() + "<Threshold>" + System.getProperty("line.separator"));

        tabCounter++;

        if (!targetDecoy) {

            writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));

        } else {

            PSMaps psMaps = new PSMaps();

            psMaps = (PSMaps) identification.getUrParam(psMaps);

            ProteinMap proteinMap = psMaps.getProteinMap();

            TargetDecoyMap targetDecoyMap = proteinMap.getTargetDecoyMap();

            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();

            double threshold = targetDecoyResults.getUserInput() / 100;

            int thresholdType = targetDecoyResults.getInputType();

            if (thresholdType == 0) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002461", "protein group-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence

            } else if (targetDecoyResults.getInputType() == 1) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002369", "protein group-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR

            } else if (targetDecoyResults.getInputType() == 2) {

                writeCvTerm(new CvTerm("PSI-MS", "MS:1002460", "protein group-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR

            }

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</Threshold>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</ProteinDetectionProtocol>" + System.getProperty("line.separator"));

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AnalysisProtocolCollection>" + System.getProperty("line.separator"));

    }

    /**

     * Write the data collection.

     *

     * @throws IOException

     */

    private void writeDataCollection() throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {

        br.write(getCurrentTabSpace() + "<DataCollection>" + System.getProperty("line.separator"));

        tabCounter++;

        writeInputFileDetails();

        writeDataAnalysis();

        tabCounter--;

        br.write(getCurrentTabSpace() + "</DataCollection>" + System.getProperty("line.separator"));

    }

    /**

     * Write the data analysis section.

     *

     * @throws IOException

     */

    private void writeDataAnalysis() throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {

        br.write(getCurrentTabSpace() + "<AnalysisData>" + System.getProperty("line.separator"));

        tabCounter++;

        br.write(getCurrentTabSpace() + "<SpectrumIdentificationList id=\"SIL_1\">" + System.getProperty("line.separator"));

        tabCounter++;

        writeFragmentationTable();

        int psmCount = 0;

        // iterate the spectrum files

        for (String spectrumFileName : identification.getSpectrumFiles()) {

            identification.loadSpectrumMatches(spectrumFileName, null);

            identification.loadSpectrumMatchParameters(spectrumFileName, new PSParameter(), null);

            // iterate the psms

            for (String psmKey : identification.getSpectrumIdentification(spectrumFileName)) {

                writeSpectrumIdentificationResult(psmKey, ++psmCount);

                waitingHandler.increasePrimaryProgressCounter();

                if (waitingHandler.isRunCanceled()) {

                    break;

                }

            }

            if (waitingHandler.isRunCanceled()) {

                break;

            }

        }

        if (waitingHandler.isRunCanceled()) {

            return;

        }

        tabCounter--;

        br.write(getCurrentTabSpace() + "</SpectrumIdentificationList>" + System.getProperty("line.separator"));

        writeProteinDetectionList();

        tabCounter--;

        br.write(getCurrentTabSpace() + "</AnalysisData>" + System.getProperty("line.separator"));

    }

    /**

     * Write the protein groups.

     *

     * @throws IOException

     */

    private void writeProteinDetectionList() throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException {

        br.write(getCurrentTabSpace() + "<ProteinDetectionList id=\"Protein_groups\">" + System.getProperty("line.separator"));

        tabCounter++;

        identification.loadPeptideMatches(null);

        int groupCpt = 0;

        PSParameter psParameter = new PSParameter();

        identification.loadProteinMatches(null);

        identification.loadProteinMatchParameters(psParameter, null);

        for (String proteinGroupKey : identification.getProteinIdentification()) {

            String proteinGroupId = "PAG_" + groupCpt++;

            br.write(getCurrentTabSpace() + "<ProteinAmbiguityGroup id=\"" + proteinGroupId + "\">" + System.getProperty("line.separator"));

            tabCounter++;

            ProteinMatch proteinMatch = identification.getProteinMatch(proteinGroupKey);

            psParameter = (PSParameter) identification.getProteinMatchParameter(proteinGroupKey, psParameter);

            String mainAccession = proteinMatch.getMainMatch();

            for (int j = 0; j < proteinMatch.getTheoreticProteinsAccessions().size(); j++) {

                String accession = proteinMatch.getTheoreticProteinsAccessions().get(j);

                br.write(getCurrentTabSpace() + "<ProteinDetectionHypothesis id=\"" + proteinGroupId + "_" + (j + 1) + "\" dBSequence_ref=\"" + accession

                        + "\" passThreshold=\"" + psParameter.getMatchValidationLevel().isValidated() + "\">" + System.getProperty("line.separator"));