Examples of PeptideMatch

com.compomics.util.experiment.identification.matches.PeptideMatch

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinMatchKey);
        int cpt = 0;


        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);
        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
            PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
            if (identification.isUnique(peptideMatch.getTheoreticPeptide())) {
                cpt++;
            }
        }
        return cpt;
    }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

    private int estimateNSpectra(String proteinMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {


        int result = 0;


        ProteinMatch proteinMatch = identification.getProteinMatch(proteinMatchKey);
        PeptideMatch peptideMatch;
        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);
        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
            peptideMatch = identification.getPeptideMatch(peptideKey);
            result += peptideMatch.getSpectrumCount();
        }


        return result;
    }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinMatchKey);
        PSParameter psParameter = new PSParameter();


        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);
        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
            PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
            identification.loadSpectrumMatchParameters(peptideMatch.getSpectrumMatches(), psParameter, null);
            for (String spectrumKey : peptideMatch.getSpectrumMatches()) {
                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                if (psParameter.getMatchValidationLevel().isValidated()) {
                    result++;
                }
            }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinMatchKey);
        PSParameter psParameter = new PSParameter();


        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);
        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
            PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
            identification.loadSpectrumMatchParameters(peptideMatch.getSpectrumMatches(), psParameter, null);
            for (String spectrumKey : peptideMatch.getSpectrumMatches()) {
                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                if (psParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                    result++;
                }
            }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

     */
    private int estimateNConfidentSpectraForPeptide(String peptideMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {


        int nValidated = 0;


        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideMatchKey);
        PSParameter psParameter = new PSParameter();


        identification.loadSpectrumMatchParameters(peptideMatch.getSpectrumMatches(), psParameter, null);
        for (String spectrumKey : peptideMatch.getSpectrumMatches()) {
            psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
            if (psParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                nValidated++;
            }
        }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

     */
    private int estimateNValidatedSpectraForPeptide(String peptideMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {


        int nValidated = 0;


        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideMatchKey);
        PSParameter psParameter = new PSParameter();


        identification.loadSpectrumMatchParameters(peptideMatch.getSpectrumMatches(), psParameter, null);
        for (String spectrumKey : peptideMatch.getSpectrumMatches()) {
            psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
            if (psParameter.getMatchValidationLevel().isValidated()) {
                nValidated++;
            }
        }

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

                    double peptideProbabilityScore = probabilities.getPeptideProbabilityScore();


                    if (!peptideMap.containsKey(peptideProbabilityScore)) {
                        peptideMap.put(peptideProbabilityScore, new HashMap<Integer, ArrayList<String>>());
                    }
                    PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
                    int spectrumCount = -peptideMatch.getSpectrumCount();
                    if (peptideMatch.getSpectrumCount() > maxSpectrumCount) {
                        maxSpectrumCount = peptideMatch.getSpectrumCount();
                    }
                    if (!peptideMap.get(peptideProbabilityScore).containsKey(spectrumCount)) {
                        peptideMap.get(peptideProbabilityScore).put(spectrumCount, new ArrayList<String>());
                    }
                    peptideMap.get(peptideProbabilityScore).get(spectrumCount).add(peptideKey);

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

     * @throws InterruptedException
     */
    public ArrayList<String> getSortedPsmKeys(String peptideKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException {
        if (!peptideKey.equals(identificationFeaturesCache.getCurrentPeptideKey()) || identificationFeaturesCache.getPsmList() == null) {


            PeptideMatch currentPeptideMatch = identification.getPeptideMatch(peptideKey);
            HashMap<Integer, HashMap<Double, ArrayList<String>>> orderingMap = new HashMap<Integer, HashMap<Double, ArrayList<String>>>();
            boolean hasRT = true;
            double rt = -1;
            PSParameter psParameter = new PSParameter();
            int nValidatedPsms = 0;


            identification.loadSpectrumMatchParameters(currentPeptideMatch.getSpectrumMatches(), psParameter, null);
            identification.loadSpectrumMatches(currentPeptideMatch.getSpectrumMatches(), null);
            for (String spectrumKey : currentPeptideMatch.getSpectrumMatches()) {


                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);


                if (!psParameter.isHidden()) {
                    if (psParameter.getMatchValidationLevel().isValidated()) {

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

                    }
                }
                result += " - " + description;
                return result;
            case PEPTIDE:
                PeptideMatch peptideMatch = identification.getPeptideMatch(key);
                return peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(peptideMatch, true, true, true);
            case SPECTRUM:
                return Spectrum.getSpectrumTitle(key) + " (" + Spectrum.getSpectrumFile(key) + ")";
            default:
                return "Unknown";

View Full Code Here

Examples of com.compomics.util.experiment.identification.matches.PeptideMatch

                                        // pre-caching
                                        peptideShakerGUI.getIdentification().loadPeptideMatches(null);


                                        for (String secondaryCandidate : secondaryCandidates) {
                                            try {
                                                PeptideMatch peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(secondaryCandidate);
                                                ArrayList<String> proteins = peptideMatch.getTheoreticPeptide().getParentProteinsNoRemapping(); // we don't have time to remap proteins here
                                                if (proteins != null) {
                                                    for (String protein : proteins) {
                                                        if (!ProteinMatch.isDecoy(protein)) {
                                                            possibilities.get(jumpType).add(secondaryCandidate);
                                                            types.get(jumpType).add(Type.PEPTIDE);

View Full Code Here

0 1 2 3

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.