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

        }


        int totalNumberOfSpectra = 0, totalPeptideShakerIds = 0;


        int fileCounter = 1;
        PSParameter probabilities = new PSParameter();


        numberOfValidatedPsmsMap = new HashMap<String, Integer>();


        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(identification.getSpectrumIdentificationSize());
        progressDialog.setValue(0);


        ArrayList<String> spectrumFiles = identification.getSpectrumFiles();
        for (String fileName : spectrumFiles) {


            int numberOfValidatedPsms = 0;
            totalNumberOfSpectra += spectrumFactory.getNSpectra(fileName);


            progressDialog.setTitle("Loading Spectrum Information. Please Wait... (" + fileCounter + "/" + spectrumFiles.size() + ")");
            identification.loadSpectrumMatchParameters(fileName, probabilities, progressDialog);
            progressDialog.setTitle("Loading Spectrum Matches. Please Wait... (" + fileCounter + "/" + spectrumFiles.size() + ")");
            identification.loadSpectrumMatches(fileName, progressDialog);
            progressDialog.setTitle("Loading Data. Please Wait... (" + fileCounter++ + "/" + spectrumFiles.size() + ") ");


            for (String spectrumKey : identification.getSpectrumIdentification(fileName)) {
                if (progressDialog.isRunCanceled()) {
                    break;
                }


                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);


                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    ArrayList<Integer> currentAdvocates = new ArrayList<Integer>();
                    probabilities = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, probabilities);


                    if (probabilities.getMatchValidationLevel().isValidated()) {


                        totalPeptideShakerIds++;
                        numberOfValidatedPsms++;


                        for (Integer tempAdvocate : advocatesUsed) {

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Examples of eu.isas.peptideshaker.myparameters.PSParameter


                fileSelected = (String) fileNamesCmb.getSelectedItem();
                double maxMz = spectrumFactory.getMaxMz(fileSelected);
                try {
                    progressDialog.setTitle("Loading Spectrum Information for " + fileSelected + ". Please Wait..."); // @TODO: problem with progress bar??
                    identification.loadSpectrumMatchParameters(fileSelected, new PSParameter(), progressDialog);
                    identification.loadSpectrumMatches(fileSelected, progressDialog);
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                }
                progressDialog.setPrimaryProgressCounterIndeterminate(true);

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

                String key = getSelectedSpectrumKey();


                if (identification.matchExists(key)) {


                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(key);
                    PSParameter probabilities = new PSParameter();
                    probabilities = (PSParameter) identification.getSpectrumMatchParameter(key, probabilities);


                    // fill peptide shaker table
                    DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                    String proteins = "";
                    String sequence;
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        proteins = displayFeaturesGenerator.addDatabaseLinks(spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences()));
                        sequence = displayFeaturesGenerator.getTaggedPeptideSequence(spectrumMatch, true, true, true);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getPeptideModificationTooltipAsHtml(spectrumMatch);
                    } else if (spectrumMatch.getBestTagAssumption() != null) {
                        sequence = spectrumMatch.getBestTagAssumption().getTag().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), true, true, true, false, false);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getTagModificationTooltipAsHtml(spectrumMatch.getBestTagAssumption().getTag());
                    } else {
                        throw new IllegalArgumentException("No best hit found for spectrum " + spectrumMatch.getKey());
                    }
                    ((DefaultTableModel) peptideShakerJTable.getModel()).addRow(new Object[]{
                        1,
                        isBestPsmEqualForAllIdSoftware(spectrumMatch, peptideShakerGUI.getSequenceMatchingPreferences()),
                        sequence,
                        proteins,
                        probabilities.getPsmConfidence(),
                        probabilities.getMatchValidationLevel().getIndex()
                    });


                    currentAssumptionsList = new ArrayList<SpectrumIdentificationAssumption>();


                    // add the search results

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

     * @param software the identification software as indexed in the Advocate
     * class
     */
    private void addIdResultsToTable(SpectrumIdentificationAssumption currentAssumption, PSParameter aProbabilities, Integer software) {


        PSParameter probabilities = (PSParameter) currentAssumption.getUrParam(aProbabilities);
        Double confidence = probabilities.getSearchEngineConfidence();
        int currentRowNumber = 0;
        boolean addRowAtBottom = true;


        // find the correct row to insert the match
        if (searchResultsTable.getRowCount() > 0) {
            for (int i = 0; i < searchResultsTable.getRowCount(); i++) {
                if (confidence > (Double) searchResultsTable.getValueAt(i, 5)) {
                    currentRowNumber = i;
                    addRowAtBottom = false;
                    break;
                }
            }
        }


        Integer validationType = probabilities.getMatchValidationLevel().getIndex();


        String sequence;
        if (currentAssumption instanceof PeptideAssumption) {
            SearchParameters searchParameters = peptideShakerGUI.getSearchParameters();
            ModificationProfile modificationProfile = searchParameters.getModificationProfile();

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

                            }
                        }
                        return null;
                    case 9:
                        if (identification.matchExists(spectrumKey)) {
                            PSParameter pSParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                            if (pSParameter != null) {
                                return pSParameter.getPsmConfidence();
                            } else {
                                return null;
                            }
                        } else {
                            return null;
                        }
                    case 10:
                        if (identification.matchExists(spectrumKey)) {
                            PSParameter pSParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                            if (pSParameter != null) {
                                return pSParameter.getMatchValidationLevel().getIndex();
                            } else {
                                return null;
                            }
                        } else {
                            return null;

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

                                try {
                                    progressDialog.setTitle("Importing GO (1/3). Please Wait...");
                                    geneFactory.initialize(geneMappingsFile, null);
                                    goFactory.initialize(goMappingsFile, progressDialog);


                                    PSParameter psParameter = new PSParameter();


                                    Identification identification = peptideShakerGUI.getIdentification();
                                    identification.loadProteinMatchParameters(psParameter, null);


                                    progressDialog.setTitle("Getting GO Mappings (2/3). Please Wait...");
                                    progressDialog.setPrimaryProgressCounterIndeterminate(false);
                                    progressDialog.setMaxPrimaryProgressCounter(identification.getProteinIdentification().size());
                                    progressDialog.setValue(0);
                                    int totalNumberOfGoMappedProteinsInProject = 0;


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


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


                                        if (psParameter.getMatchValidationLevel().isValidated() && !ProteinMatch.isDecoy(proteinKey) && !psParameter.isHidden()) {
                                            ArrayList<String> goTerms = goFactory.getProteinGoAccessions(proteinKey);
                                            if (!goTerms.isEmpty()) {
                                                totalNumberOfGoMappedProteinsInProject++;
                                                for (String goTerm : goTerms) {
                                                    Integer usage = datasetGoTermUsage.get(goTerm);

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

                                }
                            }
                        }


                        identification.loadProteinMatches(proteinKeys, null);
                        identification.loadProteinMatchParameters(proteinKeys, new PSParameter(), null);


                        // update the table
                        if (proteinTable.getModel() instanceof ProteinGoTableModel) {
                            ((ProteinGoTableModel) proteinTable.getModel()).updateDataModel(peptideShakerGUI, proteinKeys);
                        } else {
                            ProteinGoTableModel proteinTableModel = new ProteinGoTableModel(peptideShakerGUI, proteinKeys);
                            proteinTable.setModel(proteinTableModel);
                        }


                        setProteinGoTableProperties();
                        ((DefaultTableModel) proteinTable.getModel()).fireTableDataChanged();


                        if (proteinTable.getRowCount() > 0) {


                            // get the number of confident and doubtful matches
                            int nConfident = 0;
                            int nDoubtful = 0;
                            PSParameter psParameter = new PSParameter();


                            for (String proteinKey : proteinKeys) {
                                psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, psParameter);
                                MatchValidationLevel level = psParameter.getMatchValidationLevel();


                                if (level == MatchValidationLevel.confident) {
                                    nConfident++;
                                } else if (level == MatchValidationLevel.doubtful) {
                                    nDoubtful++;

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

            spectrumChartJPanel.revalidate();
            spectrumChartJPanel.repaint();


            try {
                HashMap<Double, ArrayList<String>> scoreToPeptideMap = new HashMap<Double, ArrayList<String>>();
                PSParameter probabilities = new PSParameter();


                progressDialog.setPrimaryProgressCounterIndeterminate(false);
                progressDialog.setValue(0);
                progressDialog.setMaxPrimaryProgressCounter(peptideMap.get((String) ptmJTable.getValueAt(ptmJTable.getSelectedRow(), ptmJTable.getColumn("PTM").getModelIndex())).size());


                for (String peptideKey : peptideMap.get((String) ptmJTable.getValueAt(ptmJTable.getSelectedRow(), ptmJTable.getColumn("PTM").getModelIndex()))) {


                    progressDialog.increasePrimaryProgressCounter();


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


                    PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);


                    if (!peptideMatch.getTheoreticPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {


                        probabilities = (PSParameter) identification.getPeptideMatchParameter(peptideKey, probabilities);
                        double p = probabilities.getPeptideProbability();


                        if (!probabilities.isHidden()) {


                            if (!scoreToPeptideMap.containsKey(p)) {
                                scoreToPeptideMap.put(p, new ArrayList<String>());
                            }

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

    public void updateRelatedPeptidesTable(ProgressDialogX progressDialog) {


        HashMap<Double, ArrayList<String>> scoreToKeyMap = new HashMap<Double, ArrayList<String>>();
        String peptideKey = displayedPeptides.get((Integer) peptidesTable.getValueAt(peptidesTable.getSelectedRow(), 0) - 1);
        String currentSequence, referenceSequence = Peptide.getSequence(peptideKey);
        PSParameter probabilities = new PSParameter();


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


        for (String newKey : identification.getPeptideIdentification()) {


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


            progressDialog.increasePrimaryProgressCounter();


            currentSequence = Peptide.getSequence(newKey);


            if (currentSequence.contains(referenceSequence) || referenceSequence.contains(currentSequence)) {


                if (!newKey.equals(peptideKey)) {
                    try {
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(newKey, probabilities);
                    } catch (Exception e) {
                        peptideShakerGUI.catchException(e);
                    }
                    double p = probabilities.getPeptideProbability();


                    if (!probabilities.isHidden()) {


                        if (!scoreToKeyMap.containsKey(p)) {
                            scoreToKeyMap.put(p, new ArrayList<String>());
                        }

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Examples of eu.isas.peptideshaker.myparameters.PSParameter

        public Object getValueAt(int row, int column) {
            try {
                if (row >= displayedPeptides.size()) {
                    return "";
                }
                PSParameter probabilities;
                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(displayedPeptides.get(row), probabilities);
                        return probabilities.isStarred();
                    case 2:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(displayedPeptides.get(row), probabilities);
                        return probabilities.getProteinInferenceClass();
                    case 3:
                        String peptideKey = displayedPeptides.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(displayedPeptides.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(displayedPeptides.get(row), probabilities);
                        return probabilities.getPeptideConfidence();
                    case 6:
                        probabilities = new PSParameter();
                        probabilities = (PSParameter) identification.getPeptideMatchParameter(displayedPeptides.get(row), probabilities);
                        return probabilities.getMatchValidationLevel().getIndex();
                    default:
                        return "";
                }
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);

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