Examples with IdentificationFeaturesGenerator com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator used on opensource projects

Example 1 with IdentificationFeaturesGenerator

use of com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator in project peptide-shaker by compomics.

the class QCPanel method getProteinDataset.

/**
 * Returns the dataset to use for the protein QC plot.
 */
private void getProteinDataset() {
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getProteinIdentification().size());
    progressDialog.setValue(0);
    IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
    maxValue = Double.MIN_VALUE;
    validatedValues = new ArrayList<>();
    validatedDoubtfulValues = new ArrayList<>();
    nonValidatedValues = new ArrayList<>();
    validatedDecoyValues = new ArrayList<>();
    nonValidatedDecoyValues = new ArrayList<>();
    ProteinMatchesIterator proteinMatchesIterator = peptideShakerGUI.getIdentification().getProteinMatchesIterator(progressDialog);
    ProteinMatch proteinMatch;
    while ((proteinMatch = proteinMatchesIterator.next()) != null) {
        long proteinKey = proteinMatch.getKey();
        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 = peptideShakerGUI.getIdentificationFeaturesGenerator().getSequenceCoverage(proteinKey);
            Double sequenceCoverageConfident = 100 * sequenceCoverage.get(MatchValidationLevel.confident.getIndex());
            Double sequenceCoverageDoubtful = 100 * sequenceCoverage.get(MatchValidationLevel.doubtful.getIndex());
            value = sequenceCoverageConfident + sequenceCoverageDoubtful;
        } else if (proteinSequenceLengthJRadioButton.isSelected()) {
            String proteinSequence = peptideShakerGUI.getSequenceProvider().getSequence(proteinMatch.getLeadingAccession());
            value = proteinSequence.length();
        }
        PSParameter proteinParameter = (PSParameter) proteinMatch.getUrParam(PSParameter.dummy);
        if (!proteinParameter.getHidden()) {
            if (value > maxValue) {
                maxValue = value;
            }
            if (!proteinMatch.isDecoy()) {
                if (proteinParameter.getMatchValidationLevel().isValidated()) {
                    if (proteinParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                        validatedValues.add(value);
                    } else {
                        validatedDoubtfulValues.add(value);
                    }
                } else {
                    nonValidatedValues.add(value);
                }
            }
        }
        progressDialog.increasePrimaryProgressCounter();
    }
}

Example 2 with IdentificationFeaturesGenerator

use of com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator in project peptide-shaker by compomics.

the class OverviewPanel method updateSequenceCoverage.

/**
 * Updates the sequence coverage panel.
 *
 * @param proteinAccession the protein accession
 * @param updateProtein if true, force a complete recreation of the plot
 */
private void updateSequenceCoverage(long proteinKey, String proteinAccession, boolean updateProtein) {
    // @TODO: should be in a separate thread that is possible to cancel if the selection changes
    try {
        // only need to redo this if the protein changes
        if (updateProtein || !proteinAccession.equalsIgnoreCase(currentProteinAccession) || coverage == null) {
            updateProteinSequenceCoveragePanelTitle(proteinAccession);
            updatePtmCoveragePlot(proteinAccession);
            updatePeptideVariationsCoveragePlot(proteinAccession);
        }
        currentProteinAccession = proteinAccession;
        SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
        ArrayList<Integer> selectedPeptideStart = new ArrayList<>();
        int selectionLength = 0;
        if (peptideTable.getSelectedRow() != -1) {
            SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) peptideTable.getModel();
            int peptideIndex = tableModel.getViewIndex(peptideTable.getSelectedRow());
            long peptideKey = peptideKeys[peptideIndex];
            PeptideMatch peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);
            String peptideSequence = peptideMatch.getPeptide().getSequence();
            selectionLength = peptideSequence.length();
            try {
                for (int startIndex : peptideMatch.getPeptide().getProteinMapping().get(currentProteinAccession)) {
                    selectedPeptideStart.add(startIndex);
                }
            } catch (Exception e) {
            // ignore errors due to the user switching too quickly between rows. seems to solve themselves anyway
            }
        }
        IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
        int[] validationCoverage;
        if (coverageShowAllPeptidesJRadioButtonMenuItem.isSelected()) {
            validationCoverage = identificationFeaturesGenerator.getAACoverage(proteinKey);
        } else {
            validationCoverage = identificationFeaturesGenerator.estimateAACoverage(proteinKey, coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.isSelected());
        }
        double minHeight = 0.2, maxHeight = 1;
        NonSymmetricalNormalDistribution peptideLengthDistribution = peptideShakerGUI.getMetrics().getPeptideLengthDistribution();
        if (peptideLengthDistribution != null) {
            double medianLength = peptideLengthDistribution.getMean();
            maxHeight = (1 - minHeight) * peptideLengthDistribution.getProbabilityAt(medianLength);
        }
        double[] coverageLikelihood = identificationFeaturesGenerator.getCoverableAA(proteinKey);
        double[] coverageHeight = new double[coverageLikelihood.length];
        for (int i = 0; i < coverageLikelihood.length; i++) {
            double p = coverageLikelihood[i];
            coverageHeight[i] = minHeight + p / maxHeight;
        }
        HashMap<Integer, Color> colors = new HashMap<>();
        colors.put(MatchValidationLevel.confident.getIndex(), peptideShakerGUI.getSparklineColor());
        colors.put(MatchValidationLevel.doubtful.getIndex(), peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorDoubtful());
        colors.put(MatchValidationLevel.not_validated.getIndex(), peptideShakerGUI.getSparklineColorNonValidated());
        colors.put(MatchValidationLevel.none.getIndex(), peptideShakerGUI.getSparklineColorNotFound());
        int userSelectionIndex = 0;
        while (colors.containsKey(userSelectionIndex)) {
            userSelectionIndex++;
        }
        // @TODO: use non hard coded value
        colors.put(userSelectionIndex, Color.blue);
        int[] coverageColor = validationCoverage.clone();
        for (int aaStart : selectedPeptideStart) {
            for (int aa = aaStart; aa < aaStart + selectionLength; aa++) {
                coverageColor[aa] = userSelectionIndex;
            }
        }
        // Dirty fix until the width of the sparkline can change
        int transparentIndex = userSelectionIndex + 1;
        colors.put(userSelectionIndex + 1, new Color(0, 0, 0, 0));
        for (int aa = 0; aa < coverageHeight.length; aa++) {
            if (coverageColor[aa] == MatchValidationLevel.none.getIndex()) {
                if (coverageLikelihood[aa] < 0.01 || !coverageShowPossiblePeptidesJCheckBoxMenuItem.isSelected()) {
                    // NOTE: if the fix is removed, make sure that this line is kept!!!
                    coverageColor[aa] = transparentIndex;
                }
            }
        }
        // create the coverage plot
        ArrayList<JSparklinesDataSeries> sparkLineDataSeriesCoverage = ProteinSequencePanel.getSparkLineDataSeriesCoverage(coverageHeight, coverageColor, colors);
        HashMap<Integer, ArrayList<ResidueAnnotation>> proteinTooltips = peptideShakerGUI.getDisplayFeaturesGenerator().getResidueAnnotation(proteinKey, peptideShakerGUI.getIdentificationParameters().getSequenceMatchingParameters(), identificationFeaturesGenerator, peptideShakerGUI.getMetrics(), peptideShakerGUI.getIdentification(), coverageShowAllPeptidesJRadioButtonMenuItem.isSelected(), searchParameters, coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.isSelected());
        // Dirty fix for a bloc-level annotation
        HashMap<Integer, ArrayList<ResidueAnnotation>> blocTooltips = new HashMap<>();
        int aaCpt = 0, blocCpt = 0;
        for (JSparklinesDataSeries jSparklinesDataSeries : sparkLineDataSeriesCoverage) {
            double sparkLineLength = jSparklinesDataSeries.getData().get(0);
            ArrayList<ResidueAnnotation> blocAnnotation = new ArrayList<>();
            for (int j = 0; j < sparkLineLength; j++, aaCpt++) {
                ArrayList<ResidueAnnotation> aaAnnotation = proteinTooltips.get(aaCpt);
                if (aaAnnotation != null) {
                    for (ResidueAnnotation residueAnnotation : aaAnnotation) {
                        if (!blocAnnotation.contains(residueAnnotation)) {
                            blocAnnotation.add(residueAnnotation);
                        }
                    }
                }
            }
            blocTooltips.put(blocCpt, blocAnnotation);
            blocCpt++;
        }
        proteinSequencePanel = new ProteinSequencePanel(Color.WHITE);
        coverageChart = proteinSequencePanel.getSequencePlot(this, new JSparklinesDataset(sparkLineDataSeriesCoverage), blocTooltips, true, true);
        // make sure that the range is the same for all the sequence annotation charts
        coverageChart.getChart().addChangeListener(new ChartChangeListener() {

            @Override
            public void chartChanged(ChartChangeEvent cce) {
                if (ptmChart != null) {
                    Range range = ((CategoryPlot) coverageChart.getChart().getPlot()).getRangeAxis().getRange();
                    ((CategoryPlot) ptmChart.getChart().getPlot()).getRangeAxis().setRange(range);
                    ptmChart.revalidate();
                    ptmChart.repaint();
                }
                if (peptideVariationsChart != null) {
                    Range range = ((CategoryPlot) coverageChart.getChart().getPlot()).getRangeAxis().getRange();
                    ((CategoryPlot) peptideVariationsChart.getChart().getPlot()).getRangeAxis().setRange(range);
                    peptideVariationsChart.revalidate();
                    peptideVariationsChart.repaint();
                }
            }
        });
        sequenceCoverageInnerPanel.removeAll();
        sequenceCoverageInnerPanel.add(coverageChart);
        sequenceCoverageInnerPanel.revalidate();
        sequenceCoverageInnerPanel.repaint();
    } catch (ClassCastException e) {
    // ignore   @TODO: this should not happen, but can happen if the table does not update fast enough for the filtering
    }
}

Example 3 with IdentificationFeaturesGenerator

use of com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator in project peptide-shaker by compomics.

the class OverviewPanel method updatePeptideSelection.

/**
 * Updates the peptide selection according to the currently selected
 * protein.
 *
 * @param row the row index of the protein
 */
private void updatePeptideSelection(int proteinIndex) {
    if (proteinIndex != -1) {
        this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
        Identification identification = peptideShakerGUI.getIdentification();
        IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
        long proteinMatchKey = proteinKeys[proteinIndex];
        ProteinMatch proteinMatch = identification.getProteinMatch(proteinMatchKey);
        String accession = proteinMatch.getLeadingAccession();
        peptideKeys = identificationFeaturesGenerator.getSortedPeptideKeys(proteinMatchKey);
        // update the table model
        if (peptideTable.getModel() instanceof PeptideTableModel && ((PeptideTableModel) peptideTable.getModel()).isInstantiated()) {
            ((PeptideTableModel) peptideTable.getModel()).updateDataModel(identification, identificationFeaturesGenerator, peptideShakerGUI.getDisplayFeaturesGenerator(), accession, peptideKeys);
            ((PeptideTableModel) peptideTable.getModel()).setSelfUpdating(true);
            ((PeptideTableModel) peptideTable.getModel()).resetSorting(new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true));
        } else {
            PeptideTableModel peptideTableModel = new PeptideTableModel(identification, identificationFeaturesGenerator, peptideShakerGUI.getDisplayFeaturesGenerator(), accession, peptideKeys, peptideShakerGUI.getDisplayParameters().showScores(), peptideShakerGUI.getExceptionHandler());
            peptideTable.setModel(peptideTableModel);
        }
        setPeptideTableProperties();
        showSparkLines(peptideShakerGUI.showSparklines());
        ((DefaultTableModel) peptideTable.getModel()).fireTableDataChanged();
        int maxPeptideSpectra = peptideShakerGUI.getIdentificationFeaturesGenerator().getMaxNSpectra();
        ((JSparklinesArrayListBarChartTableCellRenderer) peptideTable.getColumn("#Spectra").getCellRenderer()).setMaxValue(maxPeptideSpectra);
        String tempSequence = peptideShakerGUI.getSequenceProvider().getSequence(proteinMatch.getLeadingAccession());
        peptideTable.getColumn("Start").setCellRenderer(new JSparklinesMultiIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, (double) tempSequence.length(), ((double) tempSequence.length()) / 50, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesMultiIntervalChartTableCellRenderer) peptideTable.getColumn("Start").getCellRenderer()).showReferenceLine(true, 0.02, Color.BLACK);
        ((JSparklinesMultiIntervalChartTableCellRenderer) peptideTable.getColumn("Start").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 10);
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                try {
                    updateSelection(true);
                    updatePeptidePanelTitle();
                } catch (Exception e) {
                    // Exception generally thrown at startup
                    e.printStackTrace();
                }
            }
        });
        this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
    }
}

Example 4 with IdentificationFeaturesGenerator

use of com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator in project peptide-shaker by compomics.

the class OverviewPanel method updatePsmPanelTitle.

/**
 * Updates the PSM panel title with the number of validated/confident
 */
public void updatePsmPanelTitle() {
    SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) peptideTable.getModel();
    IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
    int peptideIndex = tableModel.getViewIndex(peptideTable.getSelectedRow());
    long peptideKey = peptideKeys[peptideIndex];
    int nValidatedPsms = identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideKey);
    int nConfidentPsms = identificationFeaturesGenerator.getNConfidentSpectraForPeptide(peptideKey);
    int nPsms = psmTable.getRowCount();
    String title = PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Peptide Spectrum Matches (";
    if (nConfidentPsms > 0) {
        title += nValidatedPsms + "/" + nPsms + " - " + nConfidentPsms + " confident, " + (nValidatedPsms - nConfidentPsms) + " doubtful";
    } else {
        title += nValidatedPsms + "/" + nPsms;
    }
    title += ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING;
    ((TitledBorder) psmsPanel.getBorder()).setTitle(title);
    psmsPanel.repaint();
}

Example 5 with IdentificationFeaturesGenerator

use of com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator in project peptide-shaker by compomics.

the class FollowUpExportDialog method exportFasta.

/**
 * Export proteins.
 *
 * @param accessionsOnly if true, only accession numbers are exported
 */
private void exportFasta(boolean accessionsOnly) {
    // get the file to send the output to
    final File selectedFile;
    if (accessionsOnly) {
        selectedFile = peptideShakerGUI.getUserSelectedFile("proteins.txt", ".txt", "Supported formats: text format (.txt)", "Select Destination File", false);
    } else {
        selectedFile = peptideShakerGUI.getUserSelectedFile("proteins.fasta", ".fasta", "Supported formats: FASTA format (.fasta)", "Select Destination File", false);
    }
    final boolean finalAccessionsOnly = accessionsOnly;
    if (selectedFile != null) {
        progressDialog = new ProgressDialogX(this, peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
        progressDialog.setPrimaryProgressCounterIndeterminate(true);
        progressDialog.setTitle("Exporting. Please Wait...");
        new Thread(new Runnable() {

            public void run() {
                try {
                    progressDialog.setVisible(true);
                } catch (IndexOutOfBoundsException e) {
                // ignore
                }
            }
        }, "ProgressDialog").start();
        new Thread("ExportThread") {

            @Override
            public void run() {
                try {
                    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
                    FastaExport.ExportType exportType = finalAccessionsOnly ? FastaExport.ExportType.getTypeFromIndex(proteinExportCmb1.getSelectedIndex()) : FastaExport.ExportType.getTypeFromIndex(proteinExportCmb2.getSelectedIndex());
                    IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
                    progressDialog.setPrimaryProgressCounterIndeterminate(false);
                    if (exportType == FastaExport.ExportType.non_validated) {
                        progressDialog.setMaxPrimaryProgressCounter(sequenceProvider.getAccessions().size());
                    } else {
                        progressDialog.setMaxPrimaryProgressCounter(identificationFeaturesGenerator.getNValidatedProteins());
                    }
                    FastaExport.export(selectedFile, sequenceProvider, peptideShakerGUI.getIdentification(), exportType, progressDialog, finalAccessionsOnly);
                    boolean processCancelled = progressDialog.isRunCanceled();
                    progressDialog.setRunFinished();
                    if (!processCancelled) {
                        JOptionPane.showMessageDialog(FollowUpExportDialog.this, "Identified proteins exported to " + selectedFile.getPath() + ".", "Export Complete", JOptionPane.INFORMATION_MESSAGE);
                    }
                } catch (Exception e) {
                    progressDialog.setRunFinished();
                    e.printStackTrace();
                    JOptionPane.showMessageDialog(FollowUpExportDialog.this, "An error occurred when exporting the data.", "Export Failed", JOptionPane.ERROR_MESSAGE);
                }
            }
        }.start();
    }
}