Examples of eu.isas.peptideshaker.scoring.ProteinMap

eu.isas.peptideshaker.scoring.ProteinMap
This map will be used to score protein matches and solve protein inference problems @author Marc Vaudel

                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    ProteinMap proteinMap = psMaps.getProteinMap();
                    double pmin = 0;
                    int nMax = proteinMap.getTargetDecoyMap().getnMax();
                    if (nMax != 0) {
                        pmin = 100.0 / nMax;
                    }
                    writer.write(Util.roundDouble(pmin, 2) + " %");
                    writer.newLine();
                    line++;
                    break;
                case protein_confidence:
                    if (indexes) {
                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    double result = proteinMap.getTargetDecoyMap().getTargetDecoyResults().getConfidenceLimit();
                    writer.write(Util.roundDouble(result, 2) + " %");
                    writer.newLine();
                    line++;
                    break;
                case protein_fdr:
                    if (indexes) {
                        writer.write(line + "");
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    result = proteinMap.getTargetDecoyMap().getTargetDecoyResults().getFdrLimit();
                    writer.write(Util.roundDouble(result, 2) + " %");
                    writer.newLine();
                    line++;
                    break;
                case protein_fnr:
                    if (indexes) {
                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    result = proteinMap.getTargetDecoyMap().getTargetDecoyResults().getFnrLimit();
                    writer.write(Util.roundDouble(result, 2) + " %");
                    writer.newLine();
                    line++;
                    break;
                case protein_pep:
                    if (indexes) {
                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    result = 100 - proteinMap.getTargetDecoyMap().getTargetDecoyResults().getConfidenceLimit();
                    writer.write(Util.roundDouble(result, 2) + " %");
                    writer.newLine();
                    line++;
                    break;
                case total_protein:
                    if (indexes) {
                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    result = proteinMap.getTargetDecoyMap().getTargetDecoyResults().getnTPTotal();
                    writer.write(Util.roundDouble(result, 2) + "");
                    writer.newLine();
                    line++;
                    break;
                case validated_protein:
                    if (indexes) {
                        writer.write(line + "");
                        writer.addSeparator();
                    }
                    writer.write(validationFeature.getTitle());
                    writer.addSeparator();
                    proteinMap = psMaps.getProteinMap();
                    result = proteinMap.getTargetDecoyMap().getTargetDecoyResults().getN();
                    writer.write(Util.roundDouble(result, 0) + "");
                    writer.newLine();
                    line++;
                    break;
                case psm_accuracy:

View Full Code Here

            progressDialog.setTitle("Creating PRIDE XML File. Please Wait...  (Part 2 of 2: Exporting IDs)");
            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 {
                            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) {
                    e.printStackTrace(); // @TODO: add better error handling
                }
                MatchValidationLevel matchValidationLevel = psmProbabilities.getMatchValidationLevel();
                if (matchValidationLevel == MatchValidationLevel.doubtful && !proteinProbabilities.getReasonDoubtful().equals("")) {
                    br.write(getCurrentTabSpace() + "<userParam name=\"Protein Validation\" value=\"" + matchValidationLevel + " (" + StringEscapeUtils.escapeHtml4(proteinProbabilities.getReasonDoubtful()) + ")" + "\" />" + System.getProperty("line.separator"));
                } else {
                    br.write(getCurrentTabSpace() + "<userParam name=\"Protein Validation\" value=\"" + matchValidationLevel + "\" />" + System.getProperty("line.separator"));
                }
                String otherProteins = "";
                boolean first = true;
                for (String otherAccession : proteinMatch.getTheoreticProteinsAccessions()) {
                    if (!otherAccession.equals(proteinMatch.getMainMatch())) {
                        if (first) {
                            first = false;
                        } else {
                            otherAccession += ", ";
                        }
                        otherProteins += otherAccession;
                    }
                }
                if (!otherProteins.equals("")) {
                    br.write(getCurrentTabSpace() + "<userParam name=\"Secondary proteins\" value=\"" + otherProteins + "\" />" + System.getProperty("line.separator"));
                }
                tabCounter--;
                br.write(getCurrentTabSpace() + "</additional>" + System.getProperty("line.separator"));


                // protein score
                br.write(getCurrentTabSpace() + "<Score>" + Util.roundDouble(proteinProbabilities.getProteinConfidence(), CONFIDENCE_DECIMALS) + "</Score>" + System.getProperty("line.separator"));


                // protein threshold
                confidenceThreshold = proteinTargetDecoyMap.getTargetDecoyMap().getTargetDecoyResults().getConfidenceLimit();
                br.write(getCurrentTabSpace() + "<Threshold>" + Util.roundDouble(confidenceThreshold, CONFIDENCE_DECIMALS) + "</Threshold>" + System.getProperty("line.separator"));


                // the search engines used
                br.write(getCurrentTabSpace() + "<SearchEngine>" + searchEngineReport + "</SearchEngine>" + System.getProperty("line.separator"));

View Full Code Here

                } else if (type == Type.PEPTIDE) {


                    identification.updatePeptideMatchParameter(matchKey, psParameter);
                    PSMaps pSMaps = new PSMaps();
                    pSMaps = (PSMaps) identification.getUrParam(pSMaps);
                    ProteinMap proteinMap = pSMaps.getProteinMap();
                    PeptideMatch peptideMatch = identification.getPeptideMatch(matchKey);


                    for (String accession : peptideMatch.getTheoreticPeptide().getParentProteins(sequenceMatchingPreferences)) {


                        ArrayList<String> proteinMatches = identification.getProteinMap().get(accession);


                        if (proteinMatches != null) {


                            identification.loadProteinMatchParameters(proteinMatches, psParameter, null);


                            for (String proteinMatchKey : proteinMatches) {


                                identificationFeaturesGenerator.updateNConfidentPeptides(proteinMatchKey);
                                PSParameter proteinPSParameter = (PSParameter) identification.getProteinMatchParameter(proteinMatchKey, psParameter);
                                MatchValidationLevel proteinValidation = proteinPSParameter.getMatchValidationLevel();


                                if (proteinValidation.isValidated()) {


                                    MatchesValidator.updateProteinMatchValidationLevel(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, proteinMap, proteinMatchKey);
                                    proteinPSParameter = (PSParameter) identification.getProteinMatchParameter(proteinMatchKey, proteinPSParameter);
                                    MatchValidationLevel newValidation = proteinPSParameter.getMatchValidationLevel();


                                    if (newValidation == MatchValidationLevel.confident && proteinValidation == MatchValidationLevel.doubtful) {
                                        metrics.setnConfidentProteins(metrics.getnConfidentProteins() + 1);
                                    } else if (newValidation == MatchValidationLevel.doubtful && proteinValidation == MatchValidationLevel.confident) {
                                        metrics.setnConfidentProteins(metrics.getnConfidentProteins() - 1);
                                    }
                                }
                            }
                        }
                    }
                } else if (type == Type.PSM) {


                    PSMaps pSMaps = new PSMaps();
                    pSMaps = (PSMaps) identification.getUrParam(pSMaps);
                    PeptideSpecificMap peptideMap = pSMaps.getPeptideSpecificMap();
                    ProteinMap proteinMap = pSMaps.getProteinMap();
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(matchKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        String peptideKey = peptide.getMatchingKey(sequenceMatchingPreferences);
                        identificationFeaturesGenerator.updateNConfidentSpectraForPeptide(peptideKey);

View Full Code Here

        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();

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Related Classes of eu.isas.peptideshaker.scoring.ProteinMap

eu.isas.peptideshaker.export.MzIdentMLExport

eu.isas.peptideshaker.export.PrideXmlExport

eu.isas.peptideshaker.export.sections.PsValidationSection

eu.isas.peptideshaker.filtering.ProteinFilter

eu.isas.peptideshaker.gui.MatchValidationDialog

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