Package com.compomics.util.experiment.identification.matches

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

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     * @throws IOException
     * @throws ClassNotFoundException
     */
    private int estimateNUniquePeptides(String proteinMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        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++;
            }
        }
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     */
    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;
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     */
    private int estimateNValidatedSpectra(String proteinMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        int result = 0;

        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()) {
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     */
    private int estimateNConfidentSpectra(String proteinMatchKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        int result = 0;

        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) {
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     * @throws ClassNotFoundException
     */
    public String getConfidentPtmSites(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        StringBuilder result = new StringBuilder();
        boolean firstPtm = true;
        ArrayList<String> ptms = psPtmScores.getConfidentlyLocalizedPtms();
        Collections.sort(ptms);
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     * @throws ClassNotFoundException
     */
    public String getConfidentPtmSites(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        StringBuilder result = new StringBuilder();

        Collections.sort(targetedPtms);
        ArrayList<Integer> sites = new ArrayList<Integer>();
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     * @throws ClassNotFoundException
     */
    public String getConfidentPtmSitesNumber(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        StringBuilder result = new StringBuilder();
        boolean firstPtm = true;
        ArrayList<String> ptms = psPtmScores.getConfidentlyLocalizedPtms();
        Collections.sort(ptms);
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     * @throws ClassNotFoundException
     */
    public String getConfidentPtmSitesNumber(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        ArrayList<Integer> sites = new ArrayList<Integer>();
        for (String ptm : targetedPtms) {
            for (Integer site : psPtmScores.getConfidentSitesForPtm(ptm)) {
                if (!sites.contains(site)) {
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     * @throws ClassNotFoundException
     */
    public String getAmbiguousPtmSites(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        StringBuilder result = new StringBuilder();
        ArrayList<String> ptms = psPtmScores.getAmbiguouslyLocalizedPtms();
        Collections.sort(ptms);
        for (String ptmName : ptms) {
            if (result.length() > 0) {
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     * @throws ClassNotFoundException
     */
    public String getAmbiguousPtmSites(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        HashMap<Integer, ArrayList<String>> reportPerSite = new HashMap<Integer, ArrayList<String>>();

        for (String ptmName : targetedPtms) {

            HashMap<Integer, ArrayList<Integer>> sites = psPtmScores.getAmbiguousModificationsSites(ptmName);
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