Examples with ChartGroup net.sf.mzmine.chartbasics.chartgroups.ChartGroup used on opensource projects

Example 1 with ChartGroup

use of net.sf.mzmine.chartbasics.chartgroups.ChartGroup in project mzmine2 by mzmine.

the class MSMSLibrarySubmissionWindow method updateAllChartSelectors.

/**
 * Create new scan selector panels
 */
public void updateAllChartSelectors() {
    group = new ChartGroup(showCrosshair, showCrosshair, true, false);
    pnCharts.removeAll();
    GridLayout layout = new GridLayout(0, 1);
    pnCharts.setLayout(layout);
    if (checkInput()) {
        Integer minSignals = paramSubmit.getParameter(LibrarySubmitParameters.minSignals).getValue();
        Double noiseLevel = paramSubmit.getParameter(LibrarySubmitParameters.noiseLevel).getValue();
        String massListName = paramSubmit.getParameter(LibrarySubmitParameters.massList).getValue();
        if (minSignals != null && noiseLevel != null && massListName != null) {
            ScanSortMode sort = (ScanSortMode) getComboSortMode().getSelectedItem();
            if (rows != null) {
                // create MS2 of all rows
                for (int i = 0; i < rows.length; i++) {
                    PeakListRow row = rows[i];
                    ScanSelectPanel pn = new ScanSelectPanel(row, sort, noiseLevel, minSignals, massListName);
                    pnScanSelect[i] = pn;
                    pn.addChartChangedListener(chart -> regroupCharts());
                    pnCharts.add(pn);
                    // add to group
                    EChartPanel c = pn.getChart();
                    if (c != null) {
                        group.add(new ChartViewWrapper(c));
                    }
                }
            } else if (scanList != null) {
                // all selectors of scanlist
                for (int i = 0; i < scanList.size(); i++) {
                    Scan[] scansEntry = scanList.get(i);
                    ScanSelectPanel pn = new ScanSelectPanel(scansEntry, sort, noiseLevel, minSignals, massListName);
                    pnScanSelect[i] = pn;
                    pn.addChartChangedListener(chart -> regroupCharts());
                    pnCharts.add(pn);
                    // add to group
                    EChartPanel c = pn.getChart();
                    if (c != null) {
                        group.add(new ChartViewWrapper(c));
                    }
                }
            }
        }
        streamSelection().forEach(pn -> {
            pn.setFragmentScan(isFragmentScan);
            // only show exclude/check button if more than 1 entry
            pn.setShowExcludeButton(pnScanSelect.length > 1);
        });
    }
    pnCharts.revalidate();
    pnCharts.repaint();
}

Example 2 with ChartGroup

use of net.sf.mzmine.chartbasics.chartgroups.ChartGroup in project mzmine2 by mzmine.

the class MultiMSMSWindow method updateAllCharts.

/**
 * Create new charts
 */
public void updateAllCharts() {
    msone = null;
    group = new ChartGroup(showCrosshair, showCrosshair, true, false);
    // MS1
    if (createMS1) {
        Scan scan = null;
        Feature best = null;
        for (PeakListRow r : rows) {
            Feature f = raw == null ? r.getBestPeak() : r.getPeak(raw);
            if (f != null && (best == null || f.getHeight() > best.getHeight())) {
                best = f;
            }
        }
        if (best != null) {
            scan = best.getDataFile().getScan(best.getRepresentativeScanNumber());
            EChartPanel cp = SpectrumChartFactory.createScanChartPanel(scan, showTitle, showLegend);
            if (cp != null)
                msone = new ChartViewWrapper(cp);
        }
    } else {
        // pseudo MS1 from all rows and isotope pattern
        EChartPanel cp = PseudoSpectrum.createChartPanel(rows, raw, false, "pseudo");
        if (cp != null) {
            cp.getChart().getLegend().setVisible(showLegend);
            cp.getChart().getTitle().setVisible(showTitle);
            msone = new ChartViewWrapper(cp);
        }
    }
    if (msone != null)
        group.add(msone);
    // MS2 of all rows
    for (PeakListRow row : rows) {
        EChartPanel c = SpectrumChartFactory.createMSMSChartPanel(row, raw, showTitle, showLegend, alwaysShowBest, useBestForMissingRaw);
        if (c != null) {
            group.add(new ChartViewWrapper(c));
        }
    }
    renewCharts(group);
}