Examples with MZRangeComponent net.sf.mzmine.parameters.parametertypes.ranges.MZRangeComponent used on opensource projects

Example 1 with MZRangeComponent

use of net.sf.mzmine.parameters.parametertypes.ranges.MZRangeComponent in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method addDialogComponents.

@Override
protected void addDialogComponents() {
    super.addDialogComponents();
    mainPanel.removeAll();
    mainPanel.getParent().remove(mainPanel);
    ddlKovats = new DelayedDocumentListener(e -> updateKovatsList());
    DelayedDocumentListener ddlUpdateChart = new DelayedDocumentListener(e -> updateChart());
    newMainPanel = new JPanel(new MigLayout("fill", "[right][grow,fill]", ""));
    getContentPane().add(newMainPanel, BorderLayout.SOUTH);
    JPanel pnCenter = new JPanel(new BorderLayout());
    getContentPane().add(pnCenter, BorderLayout.CENTER);
    pnChart = new JPanel(new BorderLayout());
    pnCenter.add(pnChart, BorderLayout.CENTER);
    Box sizedummy = new Box(BoxLayout.X_AXIS);
    sizedummy.setMinimumSize(new Dimension(200, 450));
    sizedummy.setPreferredSize(new Dimension(200, 450));
    pnChart.add(sizedummy, BorderLayout.CENTER);
    // left: Kovats: min max and list
    JPanel west = new JPanel(new BorderLayout());
    newMainPanel.add(west);
    // add min max
    JPanel pnKovatsParam = new JPanel(new FlowLayout(FlowLayout.CENTER, 5, 5));
    west.add(pnKovatsParam, BorderLayout.NORTH);
    minc = (IntegerComponent) getComponentForParameter(KovatsIndexExtractionParameters.minKovats);
    maxc = (IntegerComponent) getComponentForParameter(KovatsIndexExtractionParameters.maxKovats);
    minc.addDocumentListener(ddlKovats);
    maxc.addDocumentListener(ddlKovats);
    pnKovatsParam.add(new JLabel("Min carbon:"));
    pnKovatsParam.add(minc);
    pnKovatsParam.add(new JLabel("Max carbon:"));
    pnKovatsParam.add(maxc);
    // kovats list
    JPanel pnKovatsSelect = new JPanel(new BorderLayout());
    west.add(pnKovatsSelect, BorderLayout.CENTER);
    comboKovats = (MultiChoiceComponent) getComponentForParameter(KovatsIndexExtractionParameters.kovats);
    comboKovats.addValueChangeListener(() -> handleKovatsSelectionChange());
    pnKovatsSelect.add(comboKovats, BorderLayout.CENTER);
    // center: Chart and parameters
    JPanel center = new JPanel(new BorderLayout());
    newMainPanel.add(center);
    // all parameters on peak pick panel
    JPanel pnSouth = new JPanel(new BorderLayout());
    center.add(pnSouth, BorderLayout.SOUTH);
    JPanel pnPeakPick = new JPanel(new MigLayout("", "[right][]", ""));
    pnSouth.add(pnPeakPick, BorderLayout.CENTER);
    valuesComponent = (StringComponent) getComponentForParameter(KovatsIndexExtractionParameters.pickedKovatsValues);
    MZRangeComponent mzc = (MZRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.mzRange);
    RTRangeComponent rtc = (RTRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.rtRange);
    DoubleComponent noisec = (DoubleComponent) getComponentForParameter(KovatsIndexExtractionParameters.noiseLevel);
    DoubleComponent edgeRatioC = (DoubleComponent) getComponentForParameter(KovatsIndexExtractionParameters.ratioTopEdge);
    valuesComponent.addDocumentListener(new DelayedDocumentListener(e -> kovatsValuesChanged()));
    valuesComponent.setLayout(new GridLayout(1, 1));
    pnCenter.add(valuesComponent, BorderLayout.SOUTH);
    JPanel pnButtonFlow = new JPanel();
    pnPeakPick.add(pnButtonFlow, "cell 0 0 2 1");
    JButton btnUpdateChart = new JButton("Update chart");
    btnUpdateChart.addActionListener(e -> updateChart());
    pnButtonFlow.add(btnUpdateChart);
    JButton btnPickRT = new JButton("Pick peaks");
    btnPickRT.addActionListener(e -> pickRetentionTimes());
    pnButtonFlow.add(btnPickRT);
    JButton btnSaveFile = new JButton("Save to file");
    btnSaveFile.setToolTipText("Save Kovats index file");
    btnSaveFile.addActionListener(e -> saveToFile());
    pnButtonFlow.add(btnSaveFile);
    JButton btnLoad = new JButton("Load");
    btnLoad.setToolTipText("Load Kovats index file");
    btnLoad.addActionListener(e -> loadFile());
    pnButtonFlow.add(btnLoad);
    JButton btnCombineFiles = new JButton("Combine files");
    btnCombineFiles.setToolTipText("Select multiple Kovats index files to be combined into one");
    btnCombineFiles.addActionListener(e -> combineFiles());
    pnButtonFlow.add(btnCombineFiles);
    // add combo for raw data file
    dataFiles = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
    comboDataFileName = new JComboBox<RawDataFile>(dataFiles);
    comboDataFileName2 = new JComboBox<RawDataFile>(dataFiles);
    cbSecondRaw = new JCheckBox();
    initRawDataFileSelection();
    pnPeakPick.add(new JLabel("Raw data file(s)"), "cell 0 1");
    pnPeakPick.add(comboDataFileName);
    cbSecondRaw.addItemListener(e -> useSecondDataFile(cbSecondRaw.isSelected()));
    pnPeakPick.add(cbSecondRaw, "cell 0 2");
    pnPeakPick.add(comboDataFileName2);
    // direct alkane selection < CxH2x+1 >
    JPanel pnAlkaneSelect = new JPanel();
    Dimension dim = new Dimension(SIZE, SIZE);
    JButton btnPrevAlkane = new JButton(iconPrev);
    btnPrevAlkane.addActionListener(e -> setMzRangeByAlkane(-1));
    btnPrevAlkane.setPreferredSize(dim);
    btnPrevAlkane.setMaximumSize(dim);
    JButton btnNextAlkane = new JButton(iconNext);
    btnNextAlkane.addActionListener(e -> setMzRangeByAlkane(1));
    btnNextAlkane.setPreferredSize(dim);
    btnNextAlkane.setMaximumSize(dim);
    lbCurrentAlkane = new JLabel("");
    cbCurrentAlkaneSubH = new JCheckBox("-H");
    cbCurrentAlkaneSubH.setSelected(true);
    cbCurrentAlkaneSubH.addItemListener(e -> setMzRangeByAlkane(0));
    pnAlkaneSelect.add(btnPrevAlkane);
    pnAlkaneSelect.add(lbCurrentAlkane);
    pnAlkaneSelect.add(btnNextAlkane);
    pnAlkaneSelect.add(cbCurrentAlkaneSubH);
    pnPeakPick.add(pnAlkaneSelect, "cell 1 3");
    pnPeakPick.add(new JLabel("m/z range"), "cell 0 4");
    pnPeakPick.add(mzc);
    pnPeakPick.add(new JLabel(KovatsIndexExtractionParameters.rtRange.getName()), "cell 0 5");
    pnPeakPick.add(rtc);
    pnPeakPick.add(new JLabel(KovatsIndexExtractionParameters.noiseLevel.getName()), "cell 0 6");
    pnPeakPick.add(noisec);
    pnPeakPick.add(new JLabel(KovatsIndexExtractionParameters.ratioTopEdge.getName()), "cell 0 7");
    pnPeakPick.add(edgeRatioC);
    // add listeners
    comboDataFileName.addItemListener(e -> updateChart());
    mzc.addDocumentListener(ddlUpdateChart);
    rtc.addDocumentListener(ddlUpdateChart);
    // show
    revalidate();
    updateMinimumSize();
    pack();
    updateChart();
}

Example 2 with MZRangeComponent

use of net.sf.mzmine.parameters.parametertypes.ranges.MZRangeComponent 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");
    }
}

Example 3 with MZRangeComponent

use of net.sf.mzmine.parameters.parametertypes.ranges.MZRangeComponent in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method setMzRangeByAlkane.

private void setMzRangeByAlkane(int diff) {
    if (currentAlkane == null) {
        currentAlkane = KovatsIndex.C4;
    } else {
        int index = currentAlkane.ordinal() + diff;
        index = Math.min(Math.max(index, 0), KovatsIndex.values().length);
        currentAlkane = KovatsIndex.values()[index];
    }
    String formula = currentAlkane.getFormula(cbCurrentAlkaneSubH.isSelected());
    lbCurrentAlkane.setText(formula);
    // set mz
    Range<Double> mzRange = MzRangeFormulaCalculatorModule.getMzRangeFromFormula(formula, IonizationType.POSITIVE, new MZTolerance(0.75, 0), 1);
    ((MZRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.mzRange)).setValue(mzRange);
}