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

        }


        @Override
        public Object getValueAt(int row, int column) {
            try {
                PSParameter probabilities;


                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(relatedPeptides.get(row), probabilities);
                        return probabilities.isStarred();
                    case 2:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(relatedPeptides.get(row), probabilities);
                        return probabilities.getProteinInferenceClass();
                    case 3:
                        String peptideKey = relatedPeptides.get(row);
                        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
                        return peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(peptideMatch, true, true, true);
                    case 4:
                        PSPtmScores ptmScores = new PSPtmScores();
                        ptmScores = (PSPtmScores) identification.getPeptideMatch(relatedPeptides.get(row)).getUrParam(ptmScores);
                        if (ptmScores != null && ptmScores.getPtmScoring(getSelectedModification()) != null) {
                            PtmScoring ptmScoring = ptmScores.getPtmScoring(getSelectedModification());
                            return ptmScoring.getMinimalLocalizationConfidence();
                        } else {
                            return PtmScoring.NOT_FOUND;
                        }
                    case 5:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(relatedPeptides.get(row), probabilities);
                        return probabilities.getPeptideConfidence();
                    case 6:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(relatedPeptides.get(row), probabilities);
                        return probabilities.getMatchValidationLevel().getIndex();
                    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 spectrumKey;
                PSParameter probabilities = new PSParameter();
                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        probabilities = (PSParameter) peptideShakerGUI.getIdentification().getSpectrumMatchParameter(spectrumKey, probabilities);
                        return probabilities.isStarred();
                    case 2:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        return peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(identification.getSpectrumMatch(spectrumKey), true, true, true);
                    case 3:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        PSPtmScores ptmScores = new PSPtmScores();
                        ptmScores = (PSPtmScores) identification.getSpectrumMatch(spectrumKey).getUrParam(ptmScores);
                        if (ptmScores != null && ptmScores.getPtmScoring(getSelectedModification()) != null) {
                            PtmScoring ptmScoring = ptmScores.getPtmScoring(getSelectedModification());
                            return ptmScoring.getMinimalLocalizationConfidence();
                        } else {
                            return PtmScoring.NOT_FOUND;
                        }
                    case 4:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        return identification.getSpectrumMatch(spectrumKey).getBestPeptideAssumption().getIdentificationCharge().value;
                    case 5:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        try {
                            Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey); // @TODO: there is sometimes an IOException when closing the tool...


                            if (precursor != null) {
                                return precursor.getRt();
                            } else {
                                return null;
                            }
                        } catch (Exception e) {
                            e.printStackTrace();
                            return null;
                        }
                    case 6:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        probabilities = (PSParameter) peptideShakerGUI.getIdentification().getSpectrumMatchParameter(spectrumKey, probabilities);
                        return probabilities.getMatchValidationLevel().getIndex();
                    default:
                        return null;
                }
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

        try {


            Identification identification = peptideShakerGUI.getIdentification();
            IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();


            PSParameter proteinParameter = new PSParameter();
            maxValue = Double.MIN_VALUE;


            validatedValues = new ArrayList<Double>();
            validatedDoubtfulValues = new ArrayList<Double>();
            nonValidatedValues = new ArrayList<Double>();
            validatedDecoyValues = new ArrayList<Double>();
            nonValidatedDecoyValues = new ArrayList<Double>();


            for (String proteinKey : identification.getProteinIdentification()) {


                if (progressDialog.isRunCanceled()) {
                    break;
                }


                double value = 0;


                if (proteinNumberValidatedPeptidesJRadioButton.isSelected()) {
                    value = identificationFeaturesGenerator.getNValidatedPeptides(proteinKey);
                } else if (proteinSpectrumCountingScoreJRadioButton.isSelected()) {
                    value = identificationFeaturesGenerator.getSpectrumCounting(proteinKey);
                } else if (proteinSequenceCoverageJRadioButton.isSelected()) {
                        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());
                        value = sequenceCoverageConfident + sequenceCoverageDoubtful;
                } else if (proteinSequenceLengthJRadioButton.isSelected()) {
                    ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
                    Protein currentProtein = sequenceFactory.getProtein(proteinMatch.getMainMatch());
                    value = currentProtein.getSequence().length();
                }


                proteinParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, proteinParameter);


                if (!proteinParameter.isHidden()) {


                    if (value > maxValue) {
                        maxValue = value;
                    }
                    if (!ProteinMatch.isDecoy(proteinKey)) {
                        if (proteinParameter.getMatchValidationLevel().isValidated()) {
                            if (proteinParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                                validatedValues.add(value);
                            } else {
                                validatedDoubtfulValues.add(value);
                            }
                        } else {

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);


        try {
            PSParameter peptideParameter = new PSParameter();
            PSParameter spectrumParameter = new PSParameter();
            maxValue = Double.MIN_VALUE;


            if (peptideValidatedPsmsJRadioButton.isSelected()) {


                // Values for the number of validated PSMs
                validatedValues = new ArrayList<Double>();
                validatedDoubtfulValues = new ArrayList<Double>();
                nonValidatedValues = new ArrayList<Double>();
                validatedDecoyValues = new ArrayList<Double>();
                nonValidatedDecoyValues = new ArrayList<Double>();


                for (String peptideKey : peptideShakerGUI.getIdentification().getPeptideIdentification()) {


                    if (progressDialog.isRunCanceled()) {
                        break;
                    }


                    double value = 0;
                    PeptideMatch peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);


                    peptideShakerGUI.getIdentification().loadSpectrumMatchParameters(peptideMatch.getSpectrumMatches(), spectrumParameter, null);
                    for (String spectrumKey : peptideMatch.getSpectrumMatches()) {


                        if (progressDialog.isRunCanceled()) {
                            break;
                        }


                        spectrumParameter = (PSParameter) peptideShakerGUI.getIdentification().getSpectrumMatchParameter(spectrumKey, spectrumParameter);
                        if (spectrumParameter.getMatchValidationLevel().isValidated() && !spectrumParameter.isHidden()) {
                            value = value + 1;
                        }
                    }
                    if (value > maxValue) {
                        maxValue = value;

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getSpectrumIdentificationSize());
        progressDialog.setValue(0);


        try {
            PSParameter psmParameter = new PSParameter();
            maxValue = Double.MIN_VALUE;
            Identification identification = peptideShakerGUI.getIdentification();


            if (psmPrecursorMassErrorJRadioButton.isSelected()) {


                // Values for the precursor mass deviation
                validatedValues = new ArrayList<Double>();
                validatedDoubtfulValues = new ArrayList<Double>();
                nonValidatedValues = new ArrayList<Double>();
                validatedDecoyValues = new ArrayList<Double>();
                nonValidatedDecoyValues = new ArrayList<Double>();


                for (String spectrumFileName : identification.getSpectrumFiles()) {
                    identification.loadSpectrumMatches(spectrumFileName, progressDialog);
                    identification.loadSpectrumMatchParameters(spectrumFileName, psmParameter, progressDialog);
                    for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {


                        if (progressDialog.isRunCanceled()) {
                            break;
                        }


                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        psmParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psmParameter);


                        if (!psmParameter.isHidden() && spectrumMatch.getBestPeptideAssumption() != null) {


                            Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                            double value = spectrumMatch.getBestPeptideAssumption().getDeltaMass(
                                    precursor.getMz(),
                                    peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm());
                            if (value > maxValue) {
                                maxValue = value;
                            }


                            if (!spectrumMatch.getBestPeptideAssumption().getPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    if (psmParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                                        validatedValues.add(value);
                                    } else {
                                        validatedDoubtfulValues.add(value);
                                    }
                                } else {
                                    nonValidatedValues.add(value);
                                }
                            } else {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    validatedDecoyValues.add(value);
                                } else {
                                    nonValidatedDecoyValues.add(value);
                                }
                            }
                        }


                        progressDialog.increasePrimaryProgressCounter();
                    }
                }
            } else if (psmPrecursorChargeJRadioButton.isSelected()) {


                // Values for the precursor charge
                validatedValues = new ArrayList<Double>();
                validatedDoubtfulValues = new ArrayList<Double>();
                nonValidatedValues = new ArrayList<Double>();
                validatedDecoyValues = new ArrayList<Double>();
                nonValidatedDecoyValues = new ArrayList<Double>();


                for (String spectrumFileName : identification.getSpectrumFiles()) {
                    identification.loadSpectrumMatches(spectrumFileName, progressDialog);
                    identification.loadSpectrumMatchParameters(spectrumFileName, psmParameter, progressDialog);
                    for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {
                        if (progressDialog.isRunCanceled()) {
                            break;
                        }


                        SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                        psmParameter = (PSParameter) peptideShakerGUI.getIdentification().getSpectrumMatchParameter(spectrumKey, psmParameter);


                        if (!psmParameter.isHidden() && spectrumMatch.getBestPeptideAssumption() != null) {


                            double value = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                            if (value > maxValue) {
                                maxValue = value;
                            }


                            if (!spectrumMatch.getBestPeptideAssumption().getPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    if (psmParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                                        validatedValues.add(value);
                                    } else {
                                        validatedDoubtfulValues.add(value);
                                    }
                                } else {
                                    nonValidatedValues.add(value);
                                }
                            } else {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    validatedDecoyValues.add(value);
                                } else {
                                    nonValidatedDecoyValues.add(value);
                                }
                            }

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter

                }
                psmMap.get(fileName).add(key);
            }
        }


        PSParameter psParameter = new PSParameter();
        int line = 1;


        int totalSize = 0;


        for (String spectrumFile : psmMap.keySet()) {

View Full Code Here

Examples of eu.isas.peptideshaker.myparameters.PSParameter


        if (keys == null) {
            keys = identification.getPeptideIdentification();
        }


        PSParameter psParameter = new PSParameter();
        PeptideMatch peptideMatch;
        int line = 1;


        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Loading Peptides. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
        }
        identification.loadPeptideMatches(keys, waitingHandler);
        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Loading Peptide Details. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
        }
        identification.loadPeptideMatchParameters(keys, psParameter, waitingHandler);


        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Exporting. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
            waitingHandler.setMaxSecondaryProgressCounter(keys.size());
        }


        for (String peptideKey : keys) {


            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.increaseSecondaryProgressCounter();
            }


            psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);


            if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {


                peptideMatch = identification.getPeptideMatch(peptideKey);


                if (decoys || !peptideMatch.getTheoreticPeptide().isDecoy(sequenceMatchingPreferences)) {

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

                        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());


                        for (String peptideKey : peptideShakerGUI.getIdentification().getPeptideIdentification()) {


                            PeptideMatch peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);
                            PSParameter probabilities = new PSParameter();
                            probabilities = (PSParameter) peptideShakerGUI.getIdentification().getPeptideMatchParameter(peptideKey, probabilities);


                            // write the peptide node
                            if (((String) graphDatabaseFormat.getSelectedItem()).equalsIgnoreCase("Neo4j")) {
                                nodeWriter.write("create n={id:'" + peptideKey + "', name:'" + peptideMatch.getTheoreticPeptide().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), false, false, true, false) + "', type:'Peptide'};\n");
                            } else {
                                nodeWriter.write(peptideKey + "\t"
                                        + peptideMatch.getTheoreticPeptide().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), false, false, true, false)
                                        + "\tpeptide" + "\t" + probabilities.getMatchValidationLevel() + "\t" + peptideMatch.getTheoreticPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences()) + "\n"); // @TODO: add more information?
                            }


                            // write the peptide to protein edge and the protein nodes
                            for (String protein : peptideMatch.getTheoreticPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences())) {


                                // write the protein node
                                if (!proteinsAdded.contains(protein)) {
                                    proteinsAdded.add(protein);
                                    ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(protein);
                                    if (proteinMatch != null) {
                                        probabilities = (PSParameter) peptideShakerGUI.getIdentification().getProteinMatchParameter(protein, probabilities);


                                        if (((String) graphDatabaseFormat.getSelectedItem()).equalsIgnoreCase("Neo4j")) {
                                            nodeWriter.write("create n={id:'" + protein + "', name:'" + protein + "', type:'Protein'};\n");
                                        } else {
                                            nodeWriter.write(protein + "\t" + protein + "\tprotein" + "\t" + probabilities.getMatchValidationLevel() + "\t" + proteinMatch.isDecoy() + "\n"); // @TODO: add more information?
                                        }
                                    } else {
                                        if (((String) graphDatabaseFormat.getSelectedItem()).equalsIgnoreCase("Neo4j")) {
                                            nodeWriter.write("create n={id:'" + protein + "', name:'" + protein + "', type:'Protein'};\n");
                                        } else {

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Examples of eu.isas.peptideshaker.myparameters.PSParameter


                            if (assumption instanceof PeptideAssumption) {


                                PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                annotationPreferences.setCurrentSettings(peptideAssumption, true, sequenceMatchingPreferences);
                                PSParameter psParameter = new PSParameter();
                                MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);


                                for (int scoreIndex : processingPreferences.getScores(advocateIndex)) {


                                    Peptide peptide = peptideAssumption.getPeptide();
                                    boolean decoy = peptide.isDecoy(sequenceMatchingPreferences);
                                    double score;


                                    if (scoreIndex == PsmScores.native_score.index) {
                                        score = peptideAssumption.getScore();
                                    } else {
                                        score = PsmScores.getDecreasingScore(peptide, spectrum, iontypes, neutralLosses, charges,
                                                peptideAssumption.getIdentificationCharge().value, searchParameters, scoreIndex);
                                    }


                                    psParameter.setIntermediateScore(scoreIndex, score);
                                    inputMap.setIntermediateScore(spectrumFileName, advocateIndex, scoreIndex, score, decoy);


//                                    try {
//                                        BufferedWriter br = brs.get(scoreIndex);
//                                        if (br == null) {

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

            throws SQLException, IOException, InterruptedException, ClassNotFoundException, MzMLUnmarshallerException {


        waitingHandler.setSecondaryProgressCounterIndeterminate(false);
        waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());


        PSParameter psParameter = new PSParameter();


//        BufferedWriter br = new BufferedWriter(new FileWriter(new File("D:\\projects\\PeptideShaker\\rescoring", "combination.txt")));
//        br.write("Title\tPeptide\tScore\tDecoy");
//        br.newLine();
        for (String spectrumFileName : identification.getSpectrumFiles()) {


            // batch load the spectrum matches
            identification.loadSpectrumMatches(spectrumFileName, null);


            for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {


                waitingHandler.increaseSecondaryProgressCounter();


                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);


                for (int advocateIndex : spectrumMatch.getAdvocates()) {


                    for (double eValue : spectrumMatch.getAllAssumptions(advocateIndex).keySet()) {


                        for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(advocateIndex).get(eValue)) {


                            if (assumption instanceof PeptideAssumption) {


                                psParameter = (PSParameter) assumption.getUrParam(psParameter);


                                double score = 1;


                                ArrayList<Integer> scores = processingPreferences.getScores(advocateIndex);


                                if (scores.size() == 1 || !sequenceFactory.concatenatedTargetDecoy()) {
                                    score = psParameter.getIntermediateScore(scores.get(0));
                                } else {
                                    for (int scoreIndex : scores) {
                                        TargetDecoyMap targetDecoyMap = inputMap.getIntermediateScoreMap(spectrumFileName, advocateIndex, scoreIndex);
                                        Double intermediateScore = psParameter.getIntermediateScore(scoreIndex);
                                        if (intermediateScore != null) {
                                            double p = targetDecoyMap.getProbability(intermediateScore);
                                            score *= p;
                                        }
                                    }

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