Package com.compomics.util.pride

Examples of com.compomics.util.pride.CvTerm

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        // add species
        if (speciesJComboBox.getSelectedIndex() > 0
                && speciesJComboBox.getSelectedIndex() < speciesJComboBox.getItemCount() - 1) {

            if (!((String) speciesJComboBox.getSelectedItem()).equalsIgnoreCase(comboboxSeparator)) {
                cvTerms.add(new CvTerm(
                        "NEWT",
                        speciesMap.get((String) speciesJComboBox.getSelectedItem()),
                        (String) speciesJComboBox.getSelectedItem(),
                        null));
            }
        }

        // add tissue type
        if (tissueJComboBox.getSelectedIndex() > 0
                && tissueJComboBox.getSelectedIndex() < tissueJComboBox.getItemCount() - 1) {

            if (!((String) tissueJComboBox.getSelectedItem()).equalsIgnoreCase(comboboxSeparator)) {
                cvTerms.add(new CvTerm(
                        "BTO",
                        tissueMap.get((String) tissueJComboBox.getSelectedItem()),
                        (String) tissueJComboBox.getSelectedItem(),
                        null));
            }
        }

        // add cell type
        if (cellTypeJComboBox.getSelectedIndex() > 0
                && cellTypeJComboBox.getSelectedIndex() < cellTypeJComboBox.getItemCount() - 1) {

            if (!((String) cellTypeJComboBox.getSelectedItem()).equalsIgnoreCase(comboboxSeparator)) {
                cvTerms.add(new CvTerm(
                        "CL",
                        cellTypeMap.get((String) cellTypeJComboBox.getSelectedItem()),
                        (String) cellTypeJComboBox.getSelectedItem(),
                        null));
            }
        }

        // add additional cv terms
        for (int i = 0; i < sampleCvTermsJTable.getRowCount(); i++) {
            cvTerms.add(new CvTerm(
                    (String) sampleCvTermsJTable.getValueAt(i, 1),
                    (String) sampleCvTermsJTable.getValueAt(i, 2),
                    (String) sampleCvTermsJTable.getValueAt(i, 3),
                    (String) sampleCvTermsJTable.getValueAt(i, 4)));
        }
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                        // additional peptide id parameters
                        br.write(getCurrentTabSpace() + "<additional>" + System.getProperty("line.separator"));
                        tabCounter++;
                        br.write(getCurrentTabSpace() + "<userParam name=\"Spectrum File\" value=\"" + Spectrum.getSpectrumFile(spectrumKey) + "\" />" + System.getProperty("line.separator"));
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1000796", "Spectrum Title", "" + StringEscapeUtils.escapeHtml4(Spectrum.getSpectrumTitle(spectrumKey))));
                        br.write(getCurrentTabSpace() + "<userParam name=\"Protein Inference\" value=\"" + peptideProteins + "\" />" + System.getProperty("line.separator"));
                        br.write(getCurrentTabSpace() + "<userParam name=\"Peptide Confidence\" value=\"" + Util.roundDouble(peptideProbabilities.getPeptideConfidence(), CONFIDENCE_DECIMALS) + "\" />" + System.getProperty("line.separator"));
                        confidenceThreshold = peptideTargetDecoyMap.getTargetDecoyMap(peptideTargetDecoyMap.getCorrectedKey(peptideProbabilities.getSpecificMapKey())).getTargetDecoyResults().getConfidenceLimit();
                        br.write(getCurrentTabSpace() + "<userParam name=\"Peptide Confidence Threshold\" value=\"" + Util.roundDouble(confidenceThreshold, CONFIDENCE_DECIMALS) + "\" />" + System.getProperty("line.separator"));
                        MatchValidationLevel matchValidationLevel = peptideProbabilities.getMatchValidationLevel();
                        if (matchValidationLevel == MatchValidationLevel.doubtful && !peptideProbabilities.getReasonDoubtful().equals("")) {
                            br.write(getCurrentTabSpace() + "<userParam name=\"Peptide Validation\" value=\"" + matchValidationLevel + " (" + StringEscapeUtils.escapeHtml4(peptideProbabilities.getReasonDoubtful()) + ")" + "\" />" + System.getProperty("line.separator"));
                        } else {
                            br.write(getCurrentTabSpace() + "<userParam name=\"Peptide Validation\" value=\"" + matchValidationLevel + "\" />" + System.getProperty("line.separator"));
                        }
                        br.write(getCurrentTabSpace() + "<userParam name=\"PSM Confidence\" value=\"" + Util.roundDouble(psmProbabilities.getPsmConfidence(), CONFIDENCE_DECIMALS) + "\" />" + System.getProperty("line.separator"));
                        Integer charge = new Integer(psmProbabilities.getSpecificMapKey());
                        String fileName = Spectrum.getSpectrumFile(spectrumKey);
                        confidenceThreshold = psmTargetDecoyMap.getTargetDecoyMap(charge, fileName).getTargetDecoyResults().getConfidenceLimit();
                        br.write(getCurrentTabSpace() + "<userParam name=\"PSM Confidence Threshold\" value=\"" + Util.roundDouble(confidenceThreshold, CONFIDENCE_DECIMALS) + "\" />" + System.getProperty("line.separator"));
                        matchValidationLevel = psmProbabilities.getMatchValidationLevel();
                        if (matchValidationLevel == MatchValidationLevel.doubtful && !psmProbabilities.getReasonDoubtful().equals("")) {
                            br.write(getCurrentTabSpace() + "<userParam name=\"PSM Validation\" value=\"" + matchValidationLevel + " (" + StringEscapeUtils.escapeHtml4(psmProbabilities.getReasonDoubtful()) + ")" + "\" />" + System.getProperty("line.separator"));
                        } else {
                            br.write(getCurrentTabSpace() + "<userParam name=\"PSM Validation\" value=\"" + matchValidationLevel + "\" />" + System.getProperty("line.separator"));
                        }

                        writeCvTerm(new CvTerm("PSI-MS", "MS:1000041", "Charge State", "" + bestAssumption.getIdentificationCharge().value)); // @TODO: is 2+ etc supported?
                        //br.write(getCurrentTabSpace() + "<userParam name=\"Identified Charge\" value=\"" + bestAssumption.getIdentificationCharge().value + "\" />" + System.getProperty("line.separator"));

                        // search engine specific parameters
                        ArrayList<Integer> searchEngines = new ArrayList<Integer>(eValues.keySet());
                        Collections.sort(searchEngines);

                        // add the search engine e-values
                        ArrayList<Integer> algorithms = new ArrayList<Integer>(eValues.keySet());
                        Collections.sort(algorithms);
                        for (int tempAdvocate : algorithms) {
                            double eValue = eValues.get(tempAdvocate);
                            if (tempAdvocate == Advocate.msgf.getIndex()) {
                                writeCvTerm(new CvTerm("PSI-MS", "MS:1002052", "MS-GF:SpecEValue", Double.toString(eValue)));
                            } else if (tempAdvocate == Advocate.mascot.getIndex()) {
                                writeCvTerm(new CvTerm("PSI-MS", "MS:1001172", "Mascot:expectation value", Double.toString(eValue)));
                            } else if (tempAdvocate == Advocate.omssa.getIndex()) {
                                writeCvTerm(new CvTerm("PSI-MS", "MS:1001328", "OMSSA:evalue", Double.toString(eValue)));
                            } else if (tempAdvocate == Advocate.xtandem.getIndex()) {
                                writeCvTerm(new CvTerm("PSI-MS", "MS:1001330", "X!Tandem:expect", Double.toString(eValue)));
                            } else if (tempAdvocate == Advocate.comet.getIndex()) {
                                writeCvTerm(new CvTerm("PSI-MS", "MS:1002257", "Comet:expectation value", Double.toString(eValue)));
                            } else {
                                br.write(getCurrentTabSpace() + "<userParam name=\"" + Advocate.getAdvocate(tempAdvocate).getName()
                                        + " e-value\" value=\"" + eValue + "\" />" + System.getProperty("line.separator"));  // @TODO: add cv params for the other new advocates
                            }
                           
                            // @TODO: add scores for MyriMatch!

                            // @TODO: add generic e-value for user algorithms?
                        }

                        // add the additional search engine scores
                        if (mascotScore != null) {
                            writeCvTerm(new CvTerm("PSI-MS", "MS:1001171", "Mascot:score", "" + mascotScore));
                        }
                        if (msAmandaScore != null) {
                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002319", "Amanda:AmandaScore", "" + msAmandaScore));
                        }

                        // @TODO: add additional scores for OMSSA and X!Tandem as well
                        // "MS:1001329", "OMSSA:pvalue"
                        // "PRIDE:0000182","X|Tandem Z score"
                        // "MS:1001331", "X!Tandem:hyperscore"
                        // PTM scoring
                        if (dScore.length() > 0) {
                            br.write(getCurrentTabSpace() + "<userParam name=\"PTM D-score\" value=\"" + dScore + "\" />" + System.getProperty("line.separator"));
                        }
                        if (ptmScoringPreferences.isProbabilitsticScoreCalculation() && probabilisticScore.length() > 0) {
                            br.write(getCurrentTabSpace() + "<userParam name=\"PTM "
                                    + ptmScoringPreferences.getSelectedProbabilisticScore().getName()
                                    + "\" value=\"" + probabilisticScore + "\" />" + System.getProperty("line.separator"));
                        }
                        tabCounter--;
                        br.write(getCurrentTabSpace() + "</additional>" + System.getProperty("line.separator"));
                        tabCounter--;
                        br.write(getCurrentTabSpace() + "</PeptideItem>" + System.getProperty("line.separator"));
                    }
                }

                // additional protein id parameters
                br.write(getCurrentTabSpace() + "<additional>" + System.getProperty("line.separator"));
                tabCounter++;
                if (ProteinMatch.isDecoy(proteinKey)) {
                    br.write(getCurrentTabSpace() + "<userParam name=\"Decoy\" value=\"1\" />" + System.getProperty("line.separator"));
                } else {
                    br.write(getCurrentTabSpace() + "<userParam name=\"Decoy\" value=\"0\" />" + System.getProperty("line.separator"));
                }
                try {
                    if (spectrumCountingPreferences.getSelectedMethod() == SpectrumCountingPreferences.SpectralCountingMethod.EMPAI) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1001905", "emPAI value", "" + identificationFeaturesGenerator.getSpectrumCounting(proteinKey)));
                    } else {
                        br.write(getCurrentTabSpace() + "<userParam name=\"NSAF+\" value=\""
                                + identificationFeaturesGenerator.getSpectrumCounting(proteinKey) + "\" />" + System.getProperty("line.separator"));
                    }
                } catch (Exception e) {
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    private void writeFragmentIon(IonMatch ionMatch) throws IOException {

        // @TODO: to add neutral losses with more than one loss we need to create new CV terms!!
        // @TODO: to add phospho neutral losses we need to create new CV terms!!
        // @TODO: implement reporter ions! (required cv terms not found)
        CvTerm fragmentIonTerm = ionMatch.ion.getPrideCvTerm();

        if (fragmentIonTerm != null) {
            if (ionMatch.ion.getType() == IonType.PEPTIDE_FRAGMENT_ION
                    || ionMatch.ion.getType() == IonType.IMMONIUM_ION
                    || ionMatch.ion.getType() == IonType.PRECURSOR_ION
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            ModificationMatch modMatch = peptide.getModificationMatches().get(i);
            String modName = modMatch.getTheoreticPtm();
            PTM ptm = ptmFactory.getPTM(modName);

            CvTerm cvTerm = ptmToPrideMap.getCVTerm(modName);

            if (cvTerm == null) {
                cvTerm = PtmToPrideMap.getDefaultCVTerm(ptm.getName());
            }

            String cvTermName;
            String ptmMass;

            if (cvTerm == null) {
                cvTermName = modName;
                ptmMass = "" + ptm.getMass();
            } else {
                cvTermName = cvTerm.getName();
                ptmMass = cvTerm.getValue();

                // two extra tests to guard against problems with the cv terms, better to have a valid ptm than no ptm at all...
                if (cvTermName == null) {
                    cvTermName = modName;
                }
                if (ptmMass == null) {
                    ptmMass = "" + ptm.getMass();
                }
            }

            // get the modification location
            int modLocation = modMatch.getModificationSite();

            // have to handle terminal ptms separatly
            if (ptm.isNTerm()) {
                modLocation = 0;
            } else if (ptm.isCTerm()) {
                modLocation = peptide.getSequence().length() + 1;
            }

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

            if (cvTerm == null) {
                br.write(getCurrentTabSpace() + "<ModAccession>" + cvTermName + "</ModAccession>" + System.getProperty("line.separator"));
                br.write(getCurrentTabSpace() + "<ModDatabase>" + "PSI-MS" + "</ModDatabase>" + System.getProperty("line.separator"));
            } else {
                br.write(getCurrentTabSpace() + "<ModAccession>" + cvTerm.getAccession() + "</ModAccession>" + System.getProperty("line.separator"));
                br.write(getCurrentTabSpace() + "<ModDatabase>" + "UNIMOD" + "</ModDatabase>" + System.getProperty("line.separator"));
            }

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

            br.write(getCurrentTabSpace() + "<additional>" + System.getProperty("line.separator"));
            tabCounter++;
            if (cvTerm == null) {
                br.write(getCurrentTabSpace() + "<cvParam cvLabel=\"MS\" accession=\"MS:1001460\" name=\"" + cvTermName + "\" value=\"" + ptmMass + "\" />" + System.getProperty("line.separator"));
            } else {
                br.write(getCurrentTabSpace() + "<cvParam cvLabel=\"UNIMOD\" accession=\"" + cvTerm.getAccession() + "\" name=\"" + cvTermName + "\" value=\"" + ptmMass + "\" />" + System.getProperty("line.separator"));
            }
            tabCounter--;
            br.write(getCurrentTabSpace() + "</additional>" + System.getProperty("line.separator"));

            tabCounter--;
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    private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed

        ArrayList<CvTerm> cvTerms = new ArrayList<CvTerm>();

        for (int i = 0; i < protocolCvTermsJTable.getRowCount(); i++) {
            cvTerms.add(new CvTerm(
                    (String) protocolCvTermsJTable.getValueAt(i, 1),
                    (String) protocolCvTermsJTable.getValueAt(i, 2),
                    (String) protocolCvTermsJTable.getValueAt(i, 3),
                    (String) protocolCvTermsJTable.getValueAt(i, 4)));
        }
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    private void okJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okJButtonActionPerformed

        ArrayList<CvTerm> cvTerms = new ArrayList<CvTerm>();

        for (int i = 0; i < analyzerCvTermsJTable.getRowCount(); i++) {
            cvTerms.add(new CvTerm(
                    (String) analyzerCvTermsJTable.getValueAt(i, 1),
                    (String) analyzerCvTermsJTable.getValueAt(i, 2),
                    (String) analyzerCvTermsJTable.getValueAt(i, 3),
                    (String) analyzerCvTermsJTable.getValueAt(i, 4)));
        }

        String tempSource = instrumentSourceJTextField.getText();
        String termSource = tempSource.substring(0, tempSource.lastIndexOf("[") - 1);
        String accessionSource = tempSource.substring(tempSource.lastIndexOf("[") + 1, tempSource.lastIndexOf("]"));
        String ontologySource = ProjectExportDialog.getOntologyFromCvTerm(accessionSource);

        String tempDetector = instrumentDetectorJTextField.getText();
        String termDetector = tempDetector.substring(0, tempDetector.lastIndexOf("[") - 1);
        String accessionDetector = tempDetector.substring(tempDetector.lastIndexOf("[") + 1, tempDetector.lastIndexOf("]"));
        String ontologyDetector = ProjectExportDialog.getOntologyFromCvTerm(accessionDetector);

        prideExportDialog.setInstrument(new Instrument(nameJTextField.getText(),
                new CvTerm(ontologySource, accessionSource, termSource, null),
                new CvTerm(ontologyDetector, accessionDetector, termDetector, null),
                cvTerms));
        dispose();
    }//GEN-LAST:event_okJButtonActionPerformed
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        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"));
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        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"));
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                + "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"));
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            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--;
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