Examples with AxesSetupDialog net.sf.mzmine.util.dialogs.AxesSetupDialog used on opensource projects

Example 1 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class RTMZAnalyzerWindow method actionPerformed.

public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, plot.getChart().getXYPlot());
        dialog.setVisible(true);
    }
    if (command.equals("SETUP_COLORS")) {
        InterpolatingLookupPaintScaleSetupDialog colorDialog = new InterpolatingLookupPaintScaleSetupDialog(this, plot.getPaintScale());
        colorDialog.setVisible(true);
        if (colorDialog.getExitCode() == ExitCode.OK)
            plot.setPaintScale(colorDialog.getPaintScale());
    }
}

Example 2 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class ProjectionPlotWindow method actionPerformed.

public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, plot.getChart().getXYPlot());
        dialog.setVisible(true);
    }
    if (command.equals("TOGGLE_LABELS")) {
        /*
       * XYItemRenderer rend = plot.getChart().getXYPlot().getRenderer();
       * rend.setBaseItemLabelsVisible(!rend.getBaseItemLabelsVisible());
       */
        plot.cycleItemLabelMode();
    }
}

Example 3 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class TwoDVisualizerWindow method actionPerformed.

/**
 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
 */
public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("SWITCH_PALETTE")) {
        twoDPlot.getXYPlot().switchPalette();
    }
    if (command.equals("SHOW_DATA_POINTS")) {
        twoDPlot.switchDataPointsVisible();
    }
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, twoDPlot.getXYPlot());
        dialog.setVisible(true);
    }
    if (command.equals("SWITCH_PLOTMODE")) {
        if (twoDPlot.getPlotMode() == PlotMode.CENTROID) {
            toolBar.setCentroidButton(true);
            twoDPlot.setPlotMode(PlotMode.CONTINUOUS);
        } else {
            toolBar.setCentroidButton(false);
            twoDPlot.setPlotMode(PlotMode.CENTROID);
        }
    }
    if (command.equals("SWITCH_TOOLTIPS")) {
        if (tooltipMode) {
            twoDPlot.showPeaksTooltips(false);
            toolBar.setTooltipButton(false);
            tooltipMode = false;
        } else {
            twoDPlot.showPeaksTooltips(true);
            toolBar.setTooltipButton(true);
            tooltipMode = true;
        }
    }
    if (command.equals("SWITCH_LOG_SCALE")) {
        if (twoDPlot != null) {
            logScale = !logScale;
            twoDPlot.setLogScale(logScale);
        }
    }
    if ("PEAKLIST_CHANGE".equals(command)) {
        final PeakList selectedPeakList = bottomPanel.getSelectedPeakList();
        if (selectedPeakList != null) {
            logger.finest("Loading a feature list " + selectedPeakList + " to a 2D view of " + dataFile);
            twoDPlot.loadPeakList(selectedPeakList);
        }
    }
}

Example 4 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class IntensityPlotToolBar method actionPerformed.

public void actionPerformed(ActionEvent e) {
    Object src = e.getSource();
    if (src == linesVisibleButton) {
        Plot plot = window.getChart().getPlot();
        Boolean linesVisible;
        if (plot instanceof CategoryPlot) {
            LineAndShapeRenderer renderer = (LineAndShapeRenderer) ((CategoryPlot) plot).getRenderer();
            linesVisible = renderer.getDefaultLinesVisible();
        } else {
            XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) ((XYPlot) plot).getRenderer();
            linesVisible = renderer.getDefaultLinesVisible();
            renderer.setDrawSeriesLineAsPath(true);
        }
        // check for null value
        if (linesVisible == null)
            linesVisible = false;
        // update the icon
        if (linesVisible) {
            linesVisibleButton.setIcon(linesIcon);
        } else {
            linesVisibleButton.setIcon(pointsIcon);
        }
        // switch the button
        linesVisible = !linesVisible;
        if (plot instanceof CategoryPlot) {
            LineAndShapeRenderer renderer = (LineAndShapeRenderer) ((CategoryPlot) plot).getRenderer();
            renderer.setDefaultLinesVisible(linesVisible);
        } else {
            XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) ((XYPlot) plot).getRenderer();
            renderer.setDefaultLinesVisible(linesVisible);
            renderer.setDrawSeriesLineAsPath(true);
        }
    }
    if (src == setupAxesButton) {
        AxesSetupDialog dialog = new AxesSetupDialog(window, window.getChart().getXYPlot());
        dialog.setVisible(true);
    }
}

Example 5 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class SpectraVisualizerWindow method actionPerformed.

@Override
public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("PEAKLIST_CHANGE")) {
        // If no scan is loaded yet, ignore
        if (currentScan == null)
            return;
        PeakList selectedPeakList = bottomPanel.getSelectedPeakList();
        loadPeaks(selectedPeakList);
    }
    if (command.equals("PREVIOUS_SCAN")) {
        if (dataFile == null)
            return;
        int msLevel = currentScan.getMSLevel();
        int[] scanNumbers = dataFile.getScanNumbers(msLevel);
        int scanIndex = Arrays.binarySearch(scanNumbers, currentScan.getScanNumber());
        if (scanIndex > 0) {
            final int prevScanIndex = scanNumbers[scanIndex - 1];
            Runnable newThreadRunnable = new Runnable() {

                @Override
                public void run() {
                    loadRawData(dataFile.getScan(prevScanIndex));
                }
            };
            Thread newThread = new Thread(newThreadRunnable);
            newThread.start();
        }
    }
    if (command.equals("NEXT_SCAN")) {
        if (dataFile == null)
            return;
        int msLevel = currentScan.getMSLevel();
        int[] scanNumbers = dataFile.getScanNumbers(msLevel);
        int scanIndex = Arrays.binarySearch(scanNumbers, currentScan.getScanNumber());
        if (scanIndex < (scanNumbers.length - 1)) {
            final int nextScanIndex = scanNumbers[scanIndex + 1];
            Runnable newThreadRunnable = new Runnable() {

                @Override
                public void run() {
                    loadRawData(dataFile.getScan(nextScanIndex));
                }
            };
            Thread newThread = new Thread(newThreadRunnable);
            newThread.start();
        }
    }
    if (command.equals("SHOW_MSMS")) {
        String selectedScanString = (String) bottomPanel.getMSMSSelector().getSelectedItem();
        if (selectedScanString == null)
            return;
        int sharpIndex = selectedScanString.indexOf('#');
        int commaIndex = selectedScanString.indexOf(',');
        selectedScanString = selectedScanString.substring(sharpIndex + 1, commaIndex);
        int selectedScan = Integer.valueOf(selectedScanString);
        SpectraVisualizerModule.showNewSpectrumWindow(dataFile, selectedScan);
    }
    if (command.equals("TOGGLE_PLOT_MODE")) {
        if (spectrumPlot.getPlotMode() == MassSpectrumType.CENTROIDED) {
            spectrumPlot.setPlotMode(MassSpectrumType.PROFILE);
            toolBar.setCentroidButton(MassSpectrumType.PROFILE);
        } else {
            spectrumPlot.setPlotMode(MassSpectrumType.CENTROIDED);
            toolBar.setCentroidButton(MassSpectrumType.CENTROIDED);
        }
    }
    if (command.equals("SHOW_DATA_POINTS")) {
        spectrumPlot.switchDataPointsVisible();
    }
    if (command.equals("SHOW_ANNOTATIONS")) {
        spectrumPlot.switchItemLabelsVisible();
    }
    if (command.equals("SHOW_PICKED_PEAKS")) {
        spectrumPlot.switchPickedPeaksVisible();
    }
    if (command.equals("SHOW_ISOTOPE_PEAKS")) {
        spectrumPlot.switchIsotopePeaksVisible();
    }
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, spectrumPlot.getXYPlot());
        dialog.setVisible(true);
    }
    // library entry creation
    if (command.equals("CREATE_LIBRARY_ENTRY")) {
        // open window with all selected rows
        MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
        libraryWindow.setData(currentScan);
        libraryWindow.setVisible(true);
    }
    if (command.equals("EXPORT_SPECTRA")) {
        ExportScansModule.showSetupDialog(currentScan);
    }
    if (command.equals("ADD_ISOTOPE_PATTERN")) {
        IsotopePattern newPattern = IsotopePatternCalculator.showIsotopePredictionDialog(this, true);
        if (newPattern == null)
            return;
        loadIsotopes(newPattern);
    }
    if ((command.equals("ZOOM_IN")) || (command.equals("ZOOM_IN_BOTH_COMMAND"))) {
        spectrumPlot.getXYPlot().getDomainAxis().resizeRange(1 / zoomCoefficient);
    }
    if ((command.equals("ZOOM_OUT")) || (command.equals("ZOOM_OUT_BOTH_COMMAND"))) {
        spectrumPlot.getXYPlot().getDomainAxis().resizeRange(zoomCoefficient);
    }
    if (command.equals("SET_SAME_RANGE")) {
        // Get current axes range
        NumberAxis xAxis = (NumberAxis) spectrumPlot.getXYPlot().getDomainAxis();
        NumberAxis yAxis = (NumberAxis) spectrumPlot.getXYPlot().getRangeAxis();
        double xMin = xAxis.getRange().getLowerBound();
        double xMax = xAxis.getRange().getUpperBound();
        double xTick = xAxis.getTickUnit().getSize();
        double yMin = yAxis.getRange().getLowerBound();
        double yMax = yAxis.getRange().getUpperBound();
        double yTick = yAxis.getTickUnit().getSize();
        // Get all frames of my class
        Window[] spectraFrames = JFrame.getWindows();
        // Set the range of these frames
        for (Window frame : spectraFrames) {
            if (!(frame instanceof SpectraVisualizerWindow))
                continue;
            SpectraVisualizerWindow spectraFrame = (SpectraVisualizerWindow) frame;
            spectraFrame.setAxesRange(xMin, xMax, xTick, yMin, yMax, yTick);
        }
    }
    if (command.equals("ONLINEDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                OnlineDBSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("CUSTOMDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                CustomDBSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("LIPIDSEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                LipidSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SUMFORMULA")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                SumFormulaSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SPECTRALDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                SpectraIdentificationSpectralDatabaseModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SET_PROCESSING_PARAMETERS")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                if (!dppmWindowOpen) {
                    dppmWindowOpen = true;
                    ExitCode exitCode = DataPointProcessingManager.getInst().getParameters().showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
                    dppmWindowOpen = false;
                    if (exitCode == ExitCode.OK && DataPointProcessingManager.getInst().isEnabled()) {
                        // if processing was run before, this removes the previous results.
                        getSpectrumPlot().removeDataPointProcessingResultDataSets();
                        getSpectrumPlot().checkAndRunController();
                    }
                }
            }
        });
    }
    if (command.equals("ENABLE_PROCESSING")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                DataPointProcessingManager inst = DataPointProcessingManager.getInst();
                inst.setEnabled(!inst.isEnabled());
                bottomPanel.updateProcessingButton();
                getSpectrumPlot().checkAndRunController();
                // if the tick is removed, set the data back to default
                if (!inst.isEnabled()) {
                    getSpectrumPlot().removeDataPointProcessingResultDataSets();
                // loadRawData(currentScan);
                }
            }
        });
    }
}