Examples of eu.isas.peptideshaker.scoring.PsmSpecificMap

eu.isas.peptideshaker.scoring.PsmSpecificMap
This map will store target decoy informations about the psms grouped according to their precursor charge. @author Marc Vaudel

                        String title = PeptideSpecificMap.getKeyName(peptideShakerGUI.getSearchParameters().getModificationProfile(), peptideKey);
                        ((DefaultTableModel) groupSelectionTable.getModel()).addRow(new Object[]{cpt + 1, title + " Peptides"});
                    }
                }


                PsmSpecificMap psmSpecificMap = pSMaps.getPsmSpecificMap();
                ArrayList<Integer> foundCharges = new ArrayList<Integer>();
                HashMap<Integer, ArrayList<Integer>> groupedCharges = new HashMap<Integer, ArrayList<Integer>>();
                for (Integer charge : psmSpecificMap.getPossibleCharges()) {
                    for (String file : psmSpecificMap.getFilesAtCharge(charge)) {
                        if (!psmSpecificMap.isFileGrouped(charge, file)) {
                            foundCharges.add(charge);
                            if (progressDialog.isRunCanceled()) {
                                break;
                            }
                            HashMap<Integer, String> psmKey = new HashMap<Integer, String>();
                            psmKey.put(charge, file);
                            psmMap.put(++cpt, psmKey);
                            modifiedMaps.put(cpt, false);
                            targetDecoyMap = pSMaps.getPsmSpecificMap().getTargetDecoyMap(charge, file);
                            targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
                            originalThresholdTypes.put(cpt, targetDecoyResults.getInputType());
                            originalThresholds.put(cpt, targetDecoyResults.getUserInput());
                        }
                    }
                }
                for (int charge : psmSpecificMap.getChargesFromGroupedFiles()) {
                    int correctedCharge = psmSpecificMap.getCorrectedCharge(charge);
                    if (correctedCharge == charge) {
                        HashMap<Integer, String> psmKey = new HashMap<Integer, String>();
                        psmKey.put(charge, null);
                        psmMap.put(++cpt, psmKey);
                        modifiedMaps.put(cpt, false);

View Full Code Here

            long increment = totalProgress / (2 * identification.getProteinIdentification().size());


            PSMaps pSMaps = new PSMaps();
            pSMaps = (PSMaps) identification.getUrParam(pSMaps);
            ProteinMap proteinTargetDecoyMap = pSMaps.getProteinMap();
            PsmSpecificMap psmTargetDecoyMap = pSMaps.getPsmSpecificMap();
            PeptideSpecificMap peptideTargetDecoyMap = pSMaps.getPeptideSpecificMap();


            // get the list of algorithms used
            String searchEngineReport;
            ArrayList<Integer> seList = projectDetails.getIdentificationAlgorithms();
            Collections.sort(seList);
            searchEngineReport = Advocate.getAdvocate(seList.get(0)).getName();


            for (int i = 1; i < seList.size(); i++) {


                if (i == seList.size() - 1) {
                    searchEngineReport += " and ";
                } else {
                    searchEngineReport += ", ";
                }


                searchEngineReport += Advocate.getAdvocate(seList.get(i)).getName();
            }


            searchEngineReport += " post-processed by PeptideShaker v" + peptideShakerVersion;


            for (String spectrumFile : identification.getSpectrumFiles()) {
                identification.loadSpectrumMatches(spectrumFile, null);
            }
            identification.loadPeptideMatches(null);
            identification.loadProteinMatches(null);
            for (String spectrumFile : identification.getSpectrumFiles()) {
                identification.loadSpectrumMatchParameters(spectrumFile, psmProbabilities, null);
            }
            identification.loadPeptideMatchParameters(peptideProbabilities, null);
            identification.loadProteinMatchParameters(proteinProbabilities, null);


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


                if (waitingHandler.isRunCanceled()) {
                    break;
                }
                ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
                proteinProbabilities = (PSParameter) identification.getProteinMatchParameter(proteinKey, proteinProbabilities);
                double confidenceThreshold;


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


                // protein accession and database
                br.write(getCurrentTabSpace() + "<Accession>" + proteinMatch.getMainMatch() + "</Accession>" + System.getProperty("line.separator"));
                br.write(getCurrentTabSpace() + "<Database>" + sequenceFactory.getHeader(proteinMatch.getMainMatch()).getDatabaseType() + "</Database>" + System.getProperty("line.separator"));


                identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null); // @TODO: should use the progress dialog here, but this messes up the overall progress bar...
                identification.loadPeptideMatchParameters(proteinMatch.getPeptideMatchesKeys(), peptideProbabilities, null);


                for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {


                    if (waitingHandler.isRunCanceled()) {
                        break;
                    }


                    PeptideMatch currentMatch = identification.getPeptideMatch(peptideKey);
                    peptideProbabilities = (PSParameter) identification.getPeptideMatchParameter(peptideKey, peptideProbabilities);


                    identification.loadSpectrumMatches(currentMatch.getSpectrumMatches(), null); // @TODO: should use the progress dialog here, but this messes up the overall progress bar...
                    identification.loadSpectrumMatchParameters(currentMatch.getSpectrumMatches(), psmProbabilities, null);


                    for (String spectrumKey : currentMatch.getSpectrumMatches()) {


                        if (waitingHandler.isRunCanceled()) {
                            break;
                        }


                        psmProbabilities = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psmProbabilities);
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        PeptideAssumption bestAssumption = spectrumMatch.getBestPeptideAssumption();
                        Peptide tempPeptide = bestAssumption.getPeptide();


                        // the peptide
                        br.write(getCurrentTabSpace() + "<PeptideItem>" + System.getProperty("line.separator"));
                        tabCounter++;


                        // peptide sequence
                        br.write(getCurrentTabSpace() + "<Sequence>" + tempPeptide.getSequence() + "</Sequence>" + System.getProperty("line.separator"));


                        // peptide start and end
                        String proteinAccession = proteinMatch.getMainMatch();
                        String proteinSequence = sequenceFactory.getProtein(proteinAccession).getSequence();
                        int peptideStart = proteinSequence.lastIndexOf(tempPeptide.getSequence()) + 1; // @TODO: lastIndexOf should be avoided!!
                        br.write(getCurrentTabSpace() + "<Start>" + peptideStart + "</Start>" + System.getProperty("line.separator"));
                        br.write(getCurrentTabSpace() + "<End>" + (peptideStart + tempPeptide.getSequence().length() - 1) + "</End>" + System.getProperty("line.separator"));


                        // spectrum index reference
                        br.write(getCurrentTabSpace() + "<SpectrumReference>" + spectrumIndexes.get(spectrumMatch.getKey()) + "</SpectrumReference>" + System.getProperty("line.separator"));


                        // modifications
                        writePtms(tempPeptide);


                        // fragment ions
                        writeFragmentIons(spectrumMatch);


                        // Get scores
                        HashMap<Integer, Double> eValues = new HashMap<Integer, Double>();
                        Double mascotScore = null, msAmandaScore = null;
                        for (int se : spectrumMatch.getAdvocates()) {
                            for (double eValue : spectrumMatch.getAllAssumptions(se).keySet()) {
                                for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(se).get(eValue)) {
                                    if (assumption instanceof PeptideAssumption) {
                                        PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                        if (peptideAssumption.getPeptide().isSameSequenceAndModificationStatus(bestAssumption.getPeptide(), sequenceMatchingPreferences)) {
                                            if (!eValues.containsKey(se) || eValues.get(se) > eValue) {
                                                eValues.put(se, eValue);
                                                if (se == Advocate.mascot.getIndex()) {
                                                    mascotScore = ((MascotScore) assumption.getUrParam(new MascotScore(0))).getScore();
                                                } else if (se == Advocate.msAmanda.getIndex()
                                                        && peptideAssumption.getUrParam(new MsAmandaScore()) != null) {
                                                    msAmandaScore = ((MsAmandaScore) assumption.getUrParam(new MsAmandaScore())).getScore();
                                                }
                                            }
                                        }
                                    }
                                }
                            }
                        }


                        // PTM scores
                        ArrayList<String> modifications = new ArrayList<String>();


                        for (ModificationMatch modificationMatch : bestAssumption.getPeptide().getModificationMatches()) {
                            if (modificationMatch.isVariable()) {
                                if (!modifications.contains(modificationMatch.getTheoreticPtm())) {
                                    modifications.add(modificationMatch.getTheoreticPtm());
                                }
                            }
                        }


                        StringBuilder dScore = new StringBuilder();
                        Collections.sort(modifications);
                        PSPtmScores ptmScores = new PSPtmScores();


                        for (String mod : modifications) {


                            if (spectrumMatch.getUrParam(ptmScores) != null) {


                                if (dScore.length() > 0) {
                                    dScore.append(", ");
                                }


                                ptmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());
                                dScore.append(mod).append(" (");


                                if (ptmScores != null && ptmScores.getPtmScoring(mod) != null) {
                                    PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                                    boolean firstSite = true;
                                    ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getDSites());
                                    Collections.sort(sites);
                                    for (int site : sites) {
                                        if (firstSite) {
                                            firstSite = false;
                                        } else {
                                            dScore.append(", ");
                                        }
                                        dScore.append(site).append(": ").append(ptmScoring.getDeltaScore(site));
                                    }
                                } else {
                                    dScore.append("Not Scored");
                                }
                                dScore.append(")");
                            }
                        }


                        StringBuilder probabilisticScore = new StringBuilder();


                        if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {


                            for (String mod : modifications) {


                                if (spectrumMatch.getUrParam(ptmScores) != null) {


                                    if (probabilisticScore.length() > 0) {
                                        probabilisticScore.append(", ");
                                    }


                                    ptmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());
                                    probabilisticScore.append(mod).append(" (");


                                    if (ptmScores != null && ptmScores.getPtmScoring(mod) != null) {
                                        PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                                        boolean firstSite = true;
                                        ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites());
                                        Collections.sort(sites);
                                        for (int site : sites) {
                                            if (firstSite) {
                                                firstSite = false;
                                            } else {
                                                probabilisticScore.append(", ");
                                            }
                                            probabilisticScore.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site));
                                        }
                                    } else {
                                        probabilisticScore.append("Not Scored");
                                    }


                                    probabilisticScore.append(")");
                                }
                            }
                        }


                        // @TODO: the line below uses the protein tree, which has to be rebuilt if not available...
                        ArrayList<String> peptideParentProteins = tempPeptide.getParentProteins(sequenceMatchingPreferences);
                        String peptideProteins = "";
                        for (String accession : peptideParentProteins) {
                            if (!peptideProteins.equals("")) {
                                peptideProteins += ", ";
                            }
                            peptideProteins += accession;
                        }


                        // 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 {

View Full Code Here

                    writer.write(Util.roundDouble(result, 0) + "");
                    writer.newLine();
                    line++;
                    break;
                case psm_accuracy:
                    PsmSpecificMap psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                pmin = 0;
                                nMax = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getnMax();
                                if (nMax != 0) {
                                    pmin = 100.0 / nMax;
                                }
                                writer.write(Util.roundDouble(pmin, 2) + " %");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        pmin = 0;
                        nMax = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getnMax();
                        if (nMax != 0) {
                            pmin = 100.0 / nMax;
                        }
                        writer.write(Util.roundDouble(pmin, 2) + " %");
                        writer.newLine();
                        line++;
                    }
                    break;
                case psm_confidence:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getConfidenceLimit();
                                writer.write(Util.roundDouble(result, 2) + " %");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getConfidenceLimit();
                        writer.write(Util.roundDouble(result, 2) + " %");
                        writer.newLine();
                        line++;
                    }
                    break;
                case psm_fdr:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getFdrLimit();
                                writer.write(Util.roundDouble(result, 2) + " %");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getFdrLimit();
                        writer.write(Util.roundDouble(result, 2) + " %");
                        writer.newLine();
                        line++;
                    }
                    break;
                case psm_fnr:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getFnrLimit();
                                writer.write(Util.roundDouble(result, 2) + " %");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getFnrLimit();
                        writer.write(Util.roundDouble(result, 2) + " %");
                        writer.newLine();
                        line++;
                    }
                    break;
                case psm_pep:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = 100 - psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getConfidenceLimit();
                                writer.write(Util.roundDouble(result, 2) + " %");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = 100 - psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getConfidenceLimit();
                        writer.write(Util.roundDouble(result, 2) + " %");
                        writer.newLine();
                        line++;
                    }
                    break;
                case total_psm:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getnTPTotal();
                                writer.write(Util.roundDouble(result, 2) + "");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getnTPTotal();
                        writer.write(Util.roundDouble(result, 2) + "");
                        writer.newLine();
                        line++;
                    }
                    break;
                case validated_psm:
                    psmTargetDecoyMap = psMaps.getPsmSpecificMap();
                    for (int charge : psmTargetDecoyMap.getPossibleCharges()) {
                        for (String file : psmTargetDecoyMap.getFilesAtCharge(charge)) {
                            if (!psmTargetDecoyMap.isFileGrouped(charge, file)) {
                                if (indexes) {
                                    writer.write(line + "");
                                    writer.addSeparator();
                                }
                                writer.write(validationFeature.getTitle());
                                writer.addSeparator();
                                result = psmTargetDecoyMap.getTargetDecoyMap(charge, file).getTargetDecoyResults().getN();
                                writer.write(Util.roundDouble(result, 0) + "");
                                writer.newLine();
                                line++;
                            }
                        }
                    }
                    for (int charge : psmTargetDecoyMap.getGroupedCharges()) {
                        if (indexes) {
                            writer.write(line + "");
                            writer.addSeparator();
                        }
                        writer.write(validationFeature.getTitle());
                        writer.addSeparator();
                        result = psmTargetDecoyMap.getTargetDecoyMap(charge, null).getTargetDecoyResults().getN();
                        writer.write(Util.roundDouble(result, 0) + "");
                        writer.newLine();
                        line++;
                    }
                    break;

View Full Code Here

        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()) {

View Full Code Here

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