Examples of PSParameter

eu.isas.peptideshaker.myparameters.PSParameter
PeptideShaker compomics utilities experiment customizable parameter. This parameter will be added to spectrum, peptide and protein matches to score them, indicate the estimated posterior error probability associated and flag whether they have been validated or not. @author Marc Vaudel

Examples of eu.isas.peptideshaker.myparameters.PSParameter

     */
    private void writePsms(ProgressDialogX progressDialog) throws IOException, MzMLUnmarshallerException {


        try {
            SequenceFactory sequenceFactory = SequenceFactory.getInstance();
            PSParameter proteinProbabilities = new PSParameter();
            PSParameter peptideProbabilities = new PSParameter();
            PSParameter psmProbabilities = new PSParameter();


            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"));
                }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


        @Override
        public Object getValueAt(int row, int column) {
            try {
                String proteinKey = identification.getProteinIdentification().get(row);
                PSParameter psParameter;
                ProteinMatch proteinMatch;


                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, new PSParameter());
                        return psParameter.isStarred();
                    case 2:
                        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, new PSParameter());
                        return psParameter.isHidden();
                    case 3:
                        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, new PSParameter());
                        return psParameter.getProteinInferenceClass();
                    case 4:
                        proteinMatch = identification.getProteinMatch(proteinKey);
                        return proteinMatch.getMainMatch();
                    case 5:
                        String otherAccessions = "";
                        proteinMatch = identification.getProteinMatch(proteinKey);
                        for (String accession : ProteinMatch.getAccessions(proteinKey)) {
                            if (!accession.equals(proteinMatch.getMainMatch())) {
                                otherAccessions += accession + " ";
                            }
                        }
                        return otherAccessions;
                    case 6:
                        proteinMatch = identification.getProteinMatch(proteinKey);
                        return sequenceFactory.getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription().toLowerCase();
                    case 7:
                        Double coverage;
                        try {
                            HashMap<Integer, Double> sequenceCoverage;
                            try {
                                sequenceCoverage = peptideShakerGUI.getIdentificationFeaturesGenerator().getSequenceCoverage(proteinKey);
                            } catch (Exception e) {
                                peptideShakerGUI.catchException(e);
                                sequenceCoverage = new HashMap<Integer, Double>();
                            }
                            Double sequenceCoverageConfident = 100 * sequenceCoverage.get(MatchValidationLevel.confident.getIndex());
                            Double sequenceCoverageDoubtful = 100 * sequenceCoverage.get(MatchValidationLevel.doubtful.getIndex());
                            coverage = sequenceCoverageConfident + sequenceCoverageDoubtful;
                        } catch (Exception e) {
                            peptideShakerGUI.catchException(e);
                            coverage = Double.NaN;
                        }
                        return coverage;
                    case 8:
                        proteinMatch = identification.getProteinMatch(proteinKey);
                        return proteinMatch.getPeptideCount();
                    case 9:
                        proteinMatch = identification.getProteinMatch(proteinKey);
                        int cpt = 0;
                        PeptideMatch peptideMatch;
                        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);
                        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
                            peptideMatch = identification.getPeptideMatch(peptideKey);
                            cpt += peptideMatch.getSpectrumCount();
                        }
                        return cpt;
                    case 10:
                        try {
                            return peptideShakerGUI.getIdentificationFeaturesGenerator().getSpectrumCounting(proteinKey);
                        } catch (Exception e) {
                            peptideShakerGUI.catchException(e);
                            return Double.NaN;
                        }
                    case 11:
                        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, new PSParameter());
                        return psParameter.getProteinScore();
                    case 12:
                        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, new PSParameter());
                        return psParameter.getProteinConfidence();
                    default:
                        return "";
                }
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


        @Override
        public Object getValueAt(int row, int column) {
            try {
                String peptideKey = identification.getPeptideIdentification().get(row);
                PSParameter psParameter;
                PeptideMatch peptideMatch;
                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, new PSParameter());
                        return psParameter.isStarred();
                    case 2:
                        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, new PSParameter());
                        return psParameter.isHidden();
                    case 3:
                        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, new PSParameter());
                        return psParameter.getProteinInferenceClass();
                    case 4:
                        peptideMatch = identification.getPeptideMatch(peptideKey);
                        String accessions = "";
                        for (String accession : peptideMatch.getTheoreticPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences())) {
                            accessions += accession + " ";
                        }
                        return accessions;
                    case 5:
                        peptideMatch = identification.getPeptideMatch(peptideKey);
                        String descriptions = "";
                        for (String accession : peptideMatch.getTheoreticPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences())) {
                            descriptions += sequenceFactory.getHeader(accession).getSimpleProteinDescription() + " ";
                        }
                        return descriptions;
                    case 6:
                        peptideMatch = identification.getPeptideMatch(peptideKey);
                        return peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(peptideMatch, true, true, true);
                    case 7:
                        peptideMatch = identification.getPeptideMatch(peptideKey);
                        return peptideMatch.getSpectrumCount();
                    case 8:
                        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, new PSParameter());
                        return psParameter.getPeptideScore();
                    case 9:
                        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, new PSParameter());
                        return psParameter.getPeptideConfidence();
                    case 10:
                        return peptideKey;
                    default:
                        return "";
                }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

            try {
                String spectrumKey = getSpectrumKey(row);
                if (spectrumKey == null) {
                    return "";
                }
                PSParameter psParameter;
                SpectrumMatch spectrumMatch;
                Precursor precursor;
                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                        return psParameter.isStarred();
                    case 2:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                        return psParameter.isHidden();
                    case 3:
                        return Spectrum.getSpectrumFile(spectrumKey);
                    case 4:
                        return Spectrum.getSpectrumTitle(spectrumKey);
                    case 5:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        return precursor.getRt();
                    case 6:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        return precursor.getMz();
                    case 7:
                        spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return spectrumMatch.getBestTagAssumption().getIdentificationCharge().value;
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + spectrumKey + ".");
                        }
                    case 8:
                        spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestPeptideAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestTagAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + spectrumKey + ".");
                        }
                    case 9:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                        return psParameter.getPsmConfidence();
                    default:
                        return "";
                }
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


            for (String fileName : peptideShakerGUI.getIdentification().getOrderedSpectrumFileNames()) {
                fileNames.add(fileName);
            }


            PSParameter psParameter = new PSParameter();
            DefaultCategoryDataset peptidePlotDataset = new DefaultCategoryDataset();
            DefaultCategoryDataset spectrumPlotDataset = new DefaultCategoryDataset();
            DefaultCategoryDataset intensityPlotDataset = new DefaultCategoryDataset();


            int[] selectedRows = proteinTable.getSelectedRows();


            // disable the coverage tab if more than one protein is selected
            plotsTabbedPane.setEnabledAt(2, selectedRows.length == 1);


            if (selectedRows.length > 1 && plotsTabbedPane.getSelectedIndex() == 2) {
                plotsTabbedPane.setSelectedIndex(5);
            }


            for (int row = 0; row < selectedRows.length; row++) {


                int currentRow = selectedRows[row];
                SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) proteinTable.getModel();
                int proteinIndex = tableModel.getViewIndex(currentRow);
                String proteinKey = proteinKeys.get(proteinIndex);
                ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);


                try {
                    peptideKeys = peptideShakerGUI.getIdentificationFeaturesGenerator().getSortedPeptideKeys(proteinKey);
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    try {
                        // Let's try without order
                        peptideKeys = proteinMatch.getPeptideMatchesKeys();
                    } catch (Exception e1) {
                        peptideShakerGUI.catchException(e1);
                        // ok you are really unlucky... Just hope the GUI holds...
                        peptideKeys = new ArrayList<String>();
                    }
                }


                // get the current protein and protein sequence
                Protein currentProtein = sequenceFactory.getProtein(proteinMatch.getMainMatch());
                String currentProteinSequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();


                int[][] coverage = new int[fileNames.size()][currentProteinSequence.length() + 1];


                // get the chart data
                for (int i = 0; i < fileNames.size(); i++) {


                    String fraction = fileNames.get(i);


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


                        String peptideKey = peptideKeys.get(j);


                        try {
                            psParameter = (PSParameter) peptideShakerGUI.getIdentification().getPeptideMatchParameter(peptideKey, psParameter);


                            if (psParameter.getFractions() != null && psParameter.getFractions().contains(fraction)) {
                                if (psParameter.getMatchValidationLevel().isValidated()) {


                                    String peptideSequence = Peptide.getSequence(peptideKey);


                                    boolean includePeptide = false;


                                    if (coverageShowAllPeptidesJRadioButtonMenuItem.isSelected()) {
                                        includePeptide = true;
                                    } else if (coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.isSelected()) {
                                        includePeptide = currentProtein.isEnzymaticPeptide(peptideSequence,
                                                peptideShakerGUI.getSearchParameters().getEnzyme(),
                                                peptideShakerGUI.getSequenceMatchingPreferences());
                                    } else if (coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem.isSelected()) {
                                        includePeptide = !currentProtein.isEnzymaticPeptide(peptideSequence,
                                                peptideShakerGUI.getSearchParameters().getEnzyme(),
                                                peptideShakerGUI.getSequenceMatchingPreferences());
                                    }


                                    if (includePeptide && selectedRows.length == 1) {


                                        AminoAcidPattern aminoAcidPattern = new AminoAcidPattern(peptideSequence);
                                        for (int startIndex : aminoAcidPattern.getIndexes(currentProteinSequence, peptideShakerGUI.getSequenceMatchingPreferences())) {
                                            int peptideTempStart = startIndex -1;
                                            int peptideTempEnd = peptideTempStart + peptideSequence.length();
                                            for (int k = peptideTempStart; k < peptideTempEnd; k++) {
                                                coverage[i][k]++;
                                            }
                                        }
                                    }
                                }
                            }
                        } catch (Exception e) {
                            peptideShakerGUI.catchException(e);
                        }
                    }
                }


                psParameter = new PSParameter();
                psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(proteinKey, psParameter);


                for (int i = 0; i < fileNames.size(); i++) {
                    String fraction = fileNames.get(i);
                    psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(proteinKey, psParameter);


                    if (selectedRows.length == 1) {
                        peptidePlotDataset.addValue(psParameter.getFractionValidatedPeptides(fraction), "Validated Peptides", "" + (i + 1));
                    } else {
                        peptidePlotDataset.addValue(psParameter.getFractionValidatedPeptides(fraction), proteinMatch.getMainMatch()
                                + ": " + sequenceFactory.getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription(), "" + (i + 1));
                    }
                }


                double longestFileName = "Fraction".length();


                // update the coverage table
                if (selectedRows.length == 1) {


                    DefaultTableModel coverageTableModel = (DefaultTableModel) coverageTable.getModel();
                    coverageTableModel.getDataVector().removeAllElements();


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


                        // create the coverage plot
                        ArrayList<JSparklinesDataSeries> sparkLineDataSeriesCoverage = new ArrayList<JSparklinesDataSeries>();


                        for (int j = 0; j < currentProteinSequence.length(); j++) {


                            boolean covered = coverage[i][j] > 0;


                            int sequenceCounter = 1;


                            if (covered) {
                                while (j + 1 < coverage[0].length && coverage[i][j + 1] > 0) {
                                    sequenceCounter++;
                                    j++;
                                }
                            } else {
                                while (j + 1 < coverage[0].length && coverage[i][j + 1] == 0) {
                                    sequenceCounter++;
                                    j++;
                                }
                            }


                            ArrayList<Double> data = new ArrayList<Double>();
                            data.add(new Double(sequenceCounter));


                            JSparklinesDataSeries sparklineDataseries;


                            if (covered) {
                                sparklineDataseries = new JSparklinesDataSeries(data, peptideShakerGUI.getSparklineColor(), null);
                            } else {
                                sparklineDataseries = new JSparklinesDataSeries(data, new Color(0, 0, 0, 0), null);
                            }


                            sparkLineDataSeriesCoverage.add(sparklineDataseries);
                        }


                        ChartPanel coverageChart = new ProteinSequencePanel(Color.WHITE).getSequencePlot(this, new JSparklinesDataset(sparkLineDataSeriesCoverage),
                                new HashMap<Integer, ArrayList<ResidueAnnotation>>(), true, true);


                        ((DefaultTableModel) coverageTable.getModel()).addRow(new Object[]{(i + 1), fileNames.get(i), coverageChart});


                        if (fileNames.get(i).length() > longestFileName) {
                            longestFileName = fileNames.get(i).length();
                        }
                    }
                }


                // set the preferred size of the fraction name column in the coverage table
                Integer width = peptideShakerGUI.getPreferredColumnWidth(coverageTable, coverageTable.getColumn("Fraction").getModelIndex(), 6);


                if (width != null) {
                    coverageTable.getColumn("Fraction").setMinWidth(width);
                    coverageTable.getColumn("Fraction").setMaxWidth(width);
                } else {
                    coverageTable.getColumn("Fraction").setMinWidth(15);
                    coverageTable.getColumn("Fraction").setMaxWidth(Integer.MAX_VALUE);
                }


                // get the psms per fraction
                for (int i = 0; i < fileNames.size(); i++) {
                    String fraction = fileNames.get(i);
                    psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(proteinKey, psParameter);


                    if (selectedRows.length == 1) {
                        spectrumPlotDataset.addValue(psParameter.getFractionValidatedSpectra(fraction), "Validated Spectra", "" + (i + 1));
                        intensityPlotDataset.addValue(psParameter.getPrecursorIntensitySummedPerFraction(fraction), "Summed Intensity", "" + (i + 1));
                    } else {
                        spectrumPlotDataset.addValue(psParameter.getFractionValidatedSpectra(fraction), proteinMatch.getMainMatch()
                                + ": " + sequenceFactory.getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription(), "" + (i + 1));
                        intensityPlotDataset.addValue(psParameter.getPrecursorIntensitySummedPerFraction(fraction), proteinMatch.getMainMatch()
                                + ": " + sequenceFactory.getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription(), "" + (i + 1));
                    }
                }
            }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


                String proteinMatchKey = proteinKeys.get(proteinIndex);
                ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinMatchKey);
                peptideTableMap = new HashMap<Integer, String>();


                PSParameter probabilities = new PSParameter();
                int index = 0;


                ArrayList<String> peptideKeys;
                try {
                    peptideKeys = peptideShakerGUI.getIdentificationFeaturesGenerator().getSortedPeptideKeys(proteinMatchKey);
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    try {
                        // Let's try without order
                        peptideKeys = proteinMatch.getPeptideMatchesKeys();
                    } catch (Exception e1) {
                        peptideShakerGUI.catchException(e1);
                        // ok you are really unlucky... Just hope the GUI holds...
                        peptideKeys = new ArrayList<String>();
                    }
                }


                for (String peptideKey : peptideKeys) {
                    PeptideMatch currentMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);
                    probabilities = (PSParameter) peptideShakerGUI.getIdentification().getPeptideMatchParameter(peptideKey, probabilities);


                    if (!probabilities.isHidden()) {


                        // find and add the peptide start and end indexes
                        int peptideStart = 0;
                        String peptideSequence = currentMatch.getTheoreticPeptide().getSequence();


                        try {
                            String proteinAccession = proteinMatch.getMainMatch();
                            String tempProteinSequence = sequenceFactory.getProtein(proteinAccession).getSequence();
                            peptideStart = tempProteinSequence.lastIndexOf(peptideSequence) + 1; //@TODO: allow multiple start indexes and use amino acid matching
                        } catch (Exception e) {
                            peptideShakerGUI.catchException(e);
                            e.printStackTrace();
                        }
                        int proteinInferenceType = probabilities.getProteinInferenceClass();


                        // @TODO: should be replaced by a table model!!!
                        ((DefaultTableModel) peptideTable.getModel()).addRow(new Object[]{
                            index + 1,
                            probabilities.isStarred(),
                            proteinInferenceType,
                            peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(currentMatch, true, true, true),
                            peptideStart,
                            false,
                            probabilities.getMatchValidationLevel().getIndex()
                        });


                        peptideTableMap.put(index + 1, currentMatch.getKey());
                        index++;
                    }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


                this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));


                if (column == proteinTable.getColumn("  ").getModelIndex()) {
                    try {
                        PSParameter psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(proteinKey, new PSParameter());
                        if (!psParameter.isStarred()) {
                            peptideShakerGUI.getStarHider().starProtein(proteinKey);
                        } else {
                            peptideShakerGUI.getStarHider().unStarProtein(proteinKey);
                        }
                    } catch (Exception e) {

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

    private void selectAllMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_selectAllMenuItemActionPerformed
        for (int i = 0; i < proteinTable.getRowCount(); i++) {
            proteinTable.setValueAt(true, i, proteinTable.getColumn("  ").getModelIndex());


            String key = proteinKeys.get(i);
            PSParameter psParameter = new PSParameter();
            try {
                psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(key, psParameter);
                psParameter.setStarred(true);
                peptideShakerGUI.getIdentification().updateProteinMatchParameter(key, psParameter);
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);
            }
        }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

    private void deselectAllMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_deselectAllMenuItemActionPerformed
        for (int i = 0; i < proteinTable.getRowCount(); i++) {
            proteinTable.setValueAt(false, i, proteinTable.getColumn("  ").getModelIndex());


            String proteinKey = proteinKeys.get(i);
            PSParameter psParameter = new PSParameter();
            try {
                psParameter = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(proteinKey, psParameter);
                psParameter.setStarred(false);
                peptideShakerGUI.getIdentification().updateProteinMatchParameter(proteinKey, psParameter);
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);
            }
        }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

        super(parent, true);
        initComponents();
        setUpGui();


        this.matchKey = proteinMatchKey;
        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinMatchKey, new PSParameter());
        this.exceptionHandler = exceptionHandler;
        this.identification = identification;
        this.identificationFeaturesGenerator = identificationFeaturesGenerator;
        this.searchParameters = searchParameters;
        this.annotationPreferences = annotationPreferences;

View Full Code Here

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