Examples with TICSumDataSet net.sf.mzmine.modules.visualization.tic.TICSumDataSet used on opensource projects

Example 1 with TICSumDataSet

use of net.sf.mzmine.modules.visualization.tic.TICSumDataSet in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method updateChart.

private void updateChart() {
    updateParameterSetFromComponents();
    if (selectedDataFile == null)
        return;
    try {
        // old charts axes ranges
        org.jfree.data.Range domainZoom = chart == null ? null : chart.getChart().getXYPlot().getDomainAxis().getRange();
        org.jfree.data.Range rangeZoom = chart == null ? null : chart.getChart().getXYPlot().getRangeAxis().getRange();
        Range<Double> rangeMZ = parameterSet.getParameter(KovatsIndexExtractionParameters.mzRange).getValue();
        Range<Double> rangeRT = parameterSet.getParameter(KovatsIndexExtractionParameters.rtRange).getValue();
        if (rangeMZ == null) {
            // set range to specific alkane fragment
            rangeMZ = Range.closed(56.6, 57.5);
            ((MZRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.mzRange)).setValue(rangeMZ);
        }
        if (rangeRT == null) {
            rangeRT = selectedDataFile[0].getDataRTRange();
            ((RTRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.rtRange)).setValue(rangeRT);
        }
        // create dataset
        TICSumDataSet data = new TICSumDataSet(selectedDataFile, rangeRT, rangeMZ, null, TICPlotType.BASEPEAK);
        chart = new TICPlot(this);
        chart.addTICDataset(data);
        if (domainZoom != null)
            chart.getChart().getXYPlot().getDomainAxis().setRange(domainZoom);
        if (rangeZoom != null)
            chart.getChart().getXYPlot().getRangeAxis().setRange(rangeZoom);
        // add control for markers
        chart.getGestureAdapter().addGestureHandler(new ChartGestureDragDiffHandler(Entity.PLOT, Button.BUTTON1, new Key[] { Key.NONE }, e -> handleMarkerDrag(e)));
        chart.getGestureAdapter().addGestureHandler(new ChartGestureHandler(new ChartGesture(Entity.PLOT, Event.RELEASED), e -> {
            if (chart != null)
                chart.setMouseZoomable(true);
            if (currentlyDraggedMarker != null) {
                // set value of current marker
                logger.info("Marker dragging ended at " + currentlyDraggedMarker.getValue());
                int index = markers.indexOf(currentlyDraggedMarker);
                double value = e.getCoordinates().getX();
                setValue(index, value);
                // 
                currentlyDraggedMarker = null;
            }
        }));
        kovatsValuesChanged();
        pnChart.removeAll();
        pnChart.add(chart, BorderLayout.CENTER);
        revalidate();
        repaint();
    } catch (Exception e) {
        logger.log(Level.WARNING, "Peak picking parameters incorrect");
    }
}