Examples with Feature net.sf.mzmine.datamodel.Feature used on opensource projects

Example 46 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class CombinedXICComponent method paint.

public void paint(Graphics g) {
    super.paint(g);
    // use Graphics2D for antialiasing
    Graphics2D g2 = (Graphics2D) g;
    // turn on antialiasing
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    // get canvas size
    Dimension size = getSize();
    int colorIndex = 0;
    for (Feature peak : peaks) {
        // set color for current XIC
        g2.setColor(plotColors[colorIndex]);
        colorIndex = (colorIndex + 1) % plotColors.length;
        // if we have no data, just return
        if ((peak == null) || (peak.getScanNumbers().length == 0))
            continue;
        // get scan numbers, one data point per each scan
        int[] scanNumbers = peak.getScanNumbers();
        // for each datapoint, find [X:Y] coordinates of its point in
        // painted image
        int[] xValues = new int[scanNumbers.length + 2];
        int[] yValues = new int[scanNumbers.length + 2];
        // find one datapoint with maximum intensity in each scan
        for (int i = 0; i < scanNumbers.length; i++) {
            double dataPointIntensity = 0;
            DataPoint dataPoint = peak.getDataPoint(scanNumbers[i]);
            if (dataPoint != null)
                dataPointIntensity = dataPoint.getIntensity();
            // get retention time (X value)
            double retentionTime = peak.getDataFile().getScan(scanNumbers[i]).getRetentionTime();
            // calculate [X:Y] coordinates
            xValues[i + 1] = (int) Math.floor((retentionTime - rtRange.lowerEndpoint()) / (rtRange.upperEndpoint() - rtRange.lowerEndpoint()) * (size.width - 1));
            yValues[i + 1] = size.height - (int) Math.floor(dataPointIntensity / maxIntensity * (size.height - 1));
        }
        // add first point
        xValues[0] = xValues[1];
        yValues[0] = size.height - 1;
        // add terminal point
        xValues[xValues.length - 1] = xValues[xValues.length - 2];
        yValues[yValues.length - 1] = size.height - 1;
        // draw the peak shape
        g2.drawPolyline(xValues, yValues, xValues.length);
    }
}

Example 47 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class SingleRowPredictionTask method checkConstraints.

private void checkConstraints(IMolecularFormula cdkFormula) {
    // Check elemental ratios
    if (checkRatios) {
        boolean check = ElementalHeuristicChecker.checkFormula(cdkFormula, ratiosParameters);
        if (!check)
            return;
    }
    Double rdbeValue = RDBERestrictionChecker.calculateRDBE(cdkFormula);
    // Check RDBE condition
    if (checkRDBE && (rdbeValue != null)) {
        boolean check = RDBERestrictionChecker.checkRDBE(rdbeValue, rdbeParameters);
        if (!check)
            return;
    }
    // Calculate isotope similarity score
    final IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    final String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
    final String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
    final double isotopeNoiseLevel = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
    // Fixed min abundance
    final double minPredictedAbundance = 0.00001;
    final IsotopePattern predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
    Double isotopeScore = null;
    if ((checkIsotopes) && (detectedPattern != null)) {
        isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern, predictedIsotopePattern, isotopeParameters);
        final double minScore = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopePatternScoreThreshold).getValue();
        if (isotopeScore < minScore)
            return;
    }
    // MS/MS evaluation is slowest, so let's do it last
    Double msmsScore = null;
    Feature bestPeak = peakListRow.getBestPeak();
    RawDataFile dataFile = bestPeak.getDataFile();
    Map<DataPoint, String> msmsAnnotations = null;
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if ((checkMSMS) && (msmsScanNumber > 0)) {
        Scan msmsScan = dataFile.getScan(msmsScanNumber);
        String massListName = msmsParameters.getParameter(MSMSScoreParameters.massList).getValue();
        MassList ms2MassList = msmsScan.getMassList(massListName);
        if (ms2MassList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("The MS/MS scan #" + msmsScanNumber + " in file " + dataFile.getName() + " does not have a mass list called '" + massListName + "'");
            return;
        }
        MSMSScore score = MSMSScoreCalculator.evaluateMSMS(cdkFormula, msmsScan, msmsParameters);
        double minMSMSScore = msmsParameters.getParameter(MSMSScoreParameters.msmsMinScore).getValue();
        if (score != null) {
            msmsScore = score.getScore();
            msmsAnnotations = score.getAnnotation();
            // Check the MS/MS condition
            if (msmsScore < minMSMSScore)
                return;
        }
    }
    // Create a new formula entry
    final ResultFormula resultEntry = new ResultFormula(cdkFormula, predictedIsotopePattern, rdbeValue, isotopeScore, msmsScore, msmsAnnotations);
    // Add the new formula entry
    resultWindow.addNewListItem(resultEntry);
    foundFormulas++;
}

Example 48 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class PeakListIdentificationTask method retrieveIdentification.

/**
 * Search the database for the peak's identity.
 *
 * @param row the feature list row.
 * @throws IOException if there are i/o problems.
 */
private void retrieveIdentification(final PeakListRow row) throws IOException {
    currentRow = row;
    // Determine peak charge.
    final Feature bestPeak = row.getBestPeak();
    int charge = bestPeak.getCharge();
    if (charge <= 0) {
        charge = 1;
    }
    // Calculate mass value.
    final double massValue = row.getAverageMZ() * (double) charge - ionType.getAddedMass();
    // Isotope pattern.
    final IsotopePattern rowIsotopePattern = bestPeak.getIsotopePattern();
    // Process each one of the result ID's.
    final String[] findCompounds = gateway.findCompounds(massValue, mzTolerance, numOfResults, db.getParameterSet());
    for (int i = 0; !isCanceled() && i < findCompounds.length; i++) {
        final DBCompound compound = gateway.getCompound(findCompounds[i], db.getParameterSet());
        // In case we failed to retrieve data, skip this compound
        if (compound == null)
            continue;
        final String formula = compound.getPropertyValue(PeakIdentity.PROPERTY_FORMULA);
        // If required, check isotope score.
        if (isotopeFilter && rowIsotopePattern != null && formula != null) {
            // First modify the formula according to ionization.
            final String adjustedFormula = FormulaUtils.ionizeFormula(formula, ionType, charge);
            LOG.finest("Calculating isotope pattern for compound formula " + formula + " adjusted to " + adjustedFormula);
            // Generate IsotopePattern for this compound
            final IsotopePattern compoundIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, MIN_ABUNDANCE, charge, ionType.getPolarity());
            // Check isotope pattern match
            boolean check = IsotopePatternScoreCalculator.checkMatch(rowIsotopePattern, compoundIsotopePattern, isotopeFilterParameters);
            if (!check)
                continue;
        }
        // Add the retrieved identity to the feature list row
        row.addPeakIdentity(compound, false);
        // Notify the GUI about the change in the project
        MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
        // Repaint the window to reflect the change in the feature list
        Desktop desktop = MZmineCore.getDesktop();
        if (!(desktop instanceof HeadLessDesktop))
            desktop.getMainWindow().repaint();
    }
}

Example 49 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class ResultWindow method actionPerformed.

public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("ADD")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to add as compound identity");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        peakListRow.addPeakIdentity(listElementModel.getCompoundAt(index), false);
        // Notify the GUI about the change in the project
        MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(peakListRow, false);
        // Repaint the window to reflect the change in the feature list
        MZmineCore.getDesktop().getMainWindow().repaint();
        dispose();
    }
    if (command.equals("VIEWER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to display molecule structure");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        DBCompound compound = listElementModel.getCompoundAt(index);
        URL url2D = compound.get2DStructureURL();
        URL url3D = compound.get3DStructureURL();
        String name = compound.getName() + " (" + compound.getPropertyValue(PeakIdentity.PROPERTY_ID) + ")";
        MolStructureViewer viewer = new MolStructureViewer(name, url2D, url3D);
        viewer.setVisible(true);
    }
    if (command.equals("ISOTOPE_VIEWER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to display the isotope pattern");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        final IsotopePattern predictedPattern = listElementModel.getCompoundAt(index).getIsotopePattern();
        if (predictedPattern == null)
            return;
        Feature peak = peakListRow.getBestPeak();
        RawDataFile dataFile = peak.getDataFile();
        int scanNumber = peak.getRepresentativeScanNumber();
        SpectraVisualizerModule.showNewSpectrumWindow(dataFile, scanNumber, null, peak.getIsotopePattern(), predictedPattern);
    }
    if (command.equals("BROWSER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one compound to display in a web browser");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        logger.finest("Launching default browser to display compound details");
        java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
        DBCompound compound = listElementModel.getCompoundAt(index);
        String urlString = compound.getPropertyValue(PeakIdentity.PROPERTY_URL);
        if ((urlString == null) || (urlString.length() == 0))
            return;
        try {
            URL compoundURL = new URL(urlString);
            desktop.browse(compoundURL.toURI());
        } catch (Exception ex) {
            logger.severe("Error trying to launch default browser: " + ex.getMessage());
        }
    }
}

Example 50 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class Ms2SearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting MS2 similarity search between " + peakList1 + " and " + peakList2 + " with mz tolerance:" + mzTolerance.getPpmTolerance());
    Ms2SearchResult searchResult;
    PeakListRow[] rows1 = peakList1.getRows();
    PeakListRow[] rows2 = peakList2.getRows();
    int rows1Length = rows1.length;
    int rows2Length = rows2.length;
    totalRows = rows1Length;
    for (int i = 0; i < rows1Length; i++) {
        for (int j = 0; j < rows2Length; j++) {
            Feature featureA = rows1[i].getBestPeak();
            Feature featureB = rows2[j].getBestPeak();
            // Complication. The "best" peak, may not have the "best" fragmentation
            Scan scanA = rows1[i].getBestFragmentation();
            Scan scanB = rows2[j].getBestFragmentation();
            searchResult = simpleMS2similarity(scanA, scanB, intensityThreshold, mzTolerance, massListName);
            // Report the final score to the peaklist identity
            if (searchResult != null && searchResult.getScore() > scoreThreshold && searchResult.getNumIonsMatched() >= minimumIonsMatched)
                this.addMS2Identity(rows1[i], featureA, featureB, searchResult);
            if (isCanceled())
                return;
        }
        // Update progress bar
        finishedRows++;
    }
    // Add task description to peakList
    ((SimplePeakList) peakList1).addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of similar MS2s", parameters));
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished MS2 similarity search for " + peakList1 + "against" + peakList2);
}