Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Package eu.isas.peptideshaker.scoring.targetdecoy

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap
This map contains the information of a target/decoy strategy @author Marc Vaudel

        psParameter = (PSParameter) peptideAssumption.getUrParam(psParameter);
        psParameter.resetQcResults();


        if (sequenceFactory.concatenatedTargetDecoy()) {


            TargetDecoyMap targetDecoyMap = inputMap.getTargetDecoyMap(peptideAssumption.getAdvocate());
            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
            double seThreshold = targetDecoyResults.getScoreLimit();
            double confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();


            if (confidenceThreshold > 100) {
                confidenceThreshold = 100;
            }


            boolean noValidated = targetDecoyResults.noValidated();


            if (!noValidated && peptideAssumption.getScore() <= seThreshold) { //@TODO: include ascending/descending scores


                String reasonDoubtful = null;
                boolean filterPassed = true;


                for (AssumptionFilter filter : inputMap.getDoubtfulMatchesFilters()) {
                    boolean validated = filter.isValidated(spectrumKey, peptideAssumption, searchParameters, annotationPreferences, peptideSpectrumAnnotator);
                    psParameter.setQcResult(filter.getName(), validated);
                    if (!validated) {
                        filterPassed = false;
                        if (reasonDoubtful == null) {
                            reasonDoubtful = "";
                        } else {
                            reasonDoubtful += ", ";
                        }
                        reasonDoubtful += filter.getDescription();
                    }
                }


                boolean confidenceThresholdPassed = psParameter.getSearchEngineConfidence() >= confidenceThreshold; //@TODO: not sure whether we should include all 100% confidence hits by default?


                if (!confidenceThresholdPassed) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
                        reasonDoubtful += ", ";
                    }
                    reasonDoubtful += "Low confidence";
                }


                boolean enoughHits = targetDecoyMap.getnTargetOnly() > 100;


                if (!enoughHits) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {

View Full Code Here

            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();


            if (thresholdType == 0) {

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     * @throws java.lang.ClassNotFoundException
     */
    public void addPoint(double probabilityScore, PeptideMatch peptideMatch, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, SQLException, ClassNotFoundException {
        String key = getKey(peptideMatch);
        if (!peptideMaps.containsKey(key)) {
            peptideMaps.put(key, new TargetDecoyMap());
        }
        peptideMaps.get(key).put(probabilityScore, peptideMatch.getTheoreticPeptide().isDecoy(sequenceMatchingPreferences));
    }

View Full Code Here

     * This method puts all the small peptide groups in the dustbin to be
     * analyzed together.
     */
    public void clean() {
        if (peptideMaps.size() > 1) {
            peptideMaps.put(DUSTBIN, new TargetDecoyMap());
            for (String key : peptideMaps.keySet()) {
                if (!key.equals(DUSTBIN)) {
                    TargetDecoyMap peptideMap = peptideMaps.get(key);
                    if (peptideMap.getnMax() < 100 || peptideMap.getnTargetOnly() < 100) {
                        groupedMaps.add(key);
                        peptideMaps.get(DUSTBIN).addAll(peptideMap);
                    }
                }
            }

View Full Code Here

        ArrayList<MatchFilter> filters = new ArrayList<MatchFilter>();
        for (ProteinFilter proteinFilter : proteinMap.getDoubtfulMatchesFilters()) {
            filters.add(proteinFilter);
        }


        TargetDecoyMap targetDecoyMap = proteinMap.getTargetDecoyMap();
        populateGUI(identificationFeaturesGenerator, targetDecoyMap, filters, "Proteins");


        setTitle("Protein Group Validation Quality");


        setLocationRelativeTo(parent);

View Full Code Here

        for (PeptideFilter peptideFilter : peptideSpecificMap.getDoubtfulMatchesFilters()) {
            filters.add(peptideFilter);
        }


        String peptideGroupKey = psParameter.getSpecificMapKey();
        TargetDecoyMap targetDecoyMap = peptideSpecificMap.getTargetDecoyMap(peptideSpecificMap.getCorrectedKey(peptideGroupKey));
        String groupName = "";
        if (peptideSpecificMap.getKeys().size() > 1) {
            groupName += PeptideSpecificMap.getKeyName(searchParameters.getModificationProfile(), peptideGroupKey) + " ";
        }
        groupName += "Peptides";

View Full Code Here

        ArrayList<MatchFilter> filters = new ArrayList<MatchFilter>();
        for (PsmFilter psmFilter : psmSpecificMap.getDoubtfulMatchesFilters(charge, fileName)) {
            filters.add(psmFilter);
        }


        TargetDecoyMap targetDecoyMap = psmSpecificMap.getTargetDecoyMap(charge, fileName);
        String groupName = "Charge ";
        if (!psmSpecificMap.isFileGrouped(charge, fileName)) {
            groupName += charge + " in file " + fileName;
        } else {
            int correctedCharge = psmSpecificMap.getCorrectedCharge(charge);

View Full Code Here

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eu.isas.peptideshaker.export.MzIdentMLExport

eu.isas.peptideshaker.gui.MatchValidationDialog

eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

eu.isas.peptideshaker.gui.tabpanels.StatsPanel

eu.isas.peptideshaker.ptm.PtmScorer

eu.isas.peptideshaker.scoring.InputMap

eu.isas.peptideshaker.scoring.PeptideSpecificMap

eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer

eu.isas.peptideshaker.scoring.PsmPTMMap

eu.isas.peptideshaker.scoring.PsmSpecificMap

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