Java tutorial
/* * Copyright 2006-2015 The MZmine 2 Development Team * * This file is part of MZmine 2. * * MZmine 2 is free software; you can redistribute it and/or modify it under the * terms of the GNU General Public License as published by the Free Software * Foundation; either version 2 of the License, or (at your option) any later * version. * * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR * A PARTICULAR PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin * St, Fifth Floor, Boston, MA 02110-1301 USA */ package net.sf.mzmine.modules.visualization.ida; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.text.NumberFormat; import javax.swing.JFileChooser; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; import javax.swing.filechooser.FileNameExtensionFilter; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.util.GUIUtils; import net.sf.mzmine.util.SaveImage; import net.sf.mzmine.util.SaveImage.FileType; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.plot.DatasetRenderingOrder; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.SeriesRenderingOrder; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.title.TextTitle; import org.jfree.data.general.DatasetUtilities; import org.jfree.data.xy.XYDataset; import org.jfree.ui.RectangleInsets; import com.google.common.collect.Range; /** * */ class IDAPlot extends ChartPanel implements MouseWheelListener { private static final long serialVersionUID = 1L; private RawDataFile rawDataFile; private Range<Double> rtRange, mzRange; private JFreeChart chart; private XYPlot plot; // Zoom factor. private static final double ZOOM_FACTOR = 1.2; // VisualizerWindow visualizer. private final ActionListener visualizer; private PeakDataRenderer peakDataRenderer; // grid color private static final Color gridColor = Color.lightGray; // Renderers private IDAPlotRenderer mainRenderer; // crosshair (selection) color private static final Color crossHairColor = Color.gray; // crosshair stroke private static final BasicStroke crossHairStroke = new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 1.0f, new float[] { 5, 3 }, 0); // title font private static final Font titleFont = new Font("SansSerif", Font.BOLD, 12); private static final Font subTitleFont = new Font("SansSerif", Font.PLAIN, 11); private TextTitle chartTitle, chartSubTitle; private NumberAxis xAxis, yAxis; private NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat(); private NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat(); IDAPlot(final ActionListener listener, RawDataFile rawDataFile, IDAVisualizerWindow visualizer, IDADataSet dataset, Range<Double> rtRange, Range<Double> mzRange) { super(null, true); this.visualizer = visualizer; this.rawDataFile = rawDataFile; this.rtRange = rtRange; this.mzRange = mzRange; // initialize the chart by default time series chart from factory chart = ChartFactory.createXYLineChart("", // title "", // x-axis label "", // y-axis label null, // data set PlotOrientation.VERTICAL, // orientation true, // create legend false, // generate tooltips false // generate URLs ); chart.setBackgroundPaint(Color.white); setChart(chart); // disable maximum size (we don't want scaling) setMaximumDrawWidth(Integer.MAX_VALUE); setMaximumDrawHeight(Integer.MAX_VALUE); // set the plot properties plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD); plot.setDomainGridlinePaint(gridColor); plot.setRangeGridlinePaint(gridColor); // Set the domain log axis xAxis = new NumberAxis("Retention time (min)"); xAxis.setAutoRangeIncludesZero(false); xAxis.setNumberFormatOverride(rtFormat); xAxis.setUpperMargin(0.01); xAxis.setLowerMargin(0.01); plot.setDomainAxis(xAxis); // Set the range log axis yAxis = new NumberAxis("Precursor m/z"); yAxis.setAutoRangeIncludesZero(false); yAxis.setNumberFormatOverride(mzFormat); yAxis.setUpperMargin(0.1); yAxis.setLowerMargin(0.1); plot.setRangeAxis(yAxis); // Set crosshair properties plot.setDomainCrosshairVisible(true); plot.setRangeCrosshairVisible(true); plot.setDomainCrosshairPaint(crossHairColor); plot.setRangeCrosshairPaint(crossHairColor); plot.setDomainCrosshairStroke(crossHairStroke); plot.setRangeCrosshairStroke(crossHairStroke); // Create renderers mainRenderer = new IDAPlotRenderer(); plot.setRenderer(0, mainRenderer); // title chartTitle = chart.getTitle(); chartTitle.setMargin(5, 0, 0, 0); chartTitle.setFont(titleFont); chartSubTitle = new TextTitle(); chartSubTitle.setFont(subTitleFont); chartSubTitle.setMargin(5, 0, 0, 0); chart.addSubtitle(chartSubTitle); // Add data sets; plot.setDataset(0, dataset); // set rendering order plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); peakDataRenderer = new PeakDataRenderer(); // Add EMF and EPS options to the save as menu JPopupMenu popupMenu = getPopupMenu(); JMenuItem saveAsMenu = (JMenuItem) popupMenu.getComponent(3); GUIUtils.addMenuItem(saveAsMenu, "EMF...", this, "SAVE_EMF"); GUIUtils.addMenuItem(saveAsMenu, "EPS...", this, "SAVE_EPS"); // Register for mouse-wheel events addMouseWheelListener(this); } @Override public void actionPerformed(final ActionEvent event) { super.actionPerformed(event); final String command = event.getActionCommand(); if ("SAVE_EMF".equals(command)) { JFileChooser chooser = new JFileChooser(); FileNameExtensionFilter filter = new FileNameExtensionFilter("EMF Image", "EMF"); chooser.setFileFilter(filter); int returnVal = chooser.showSaveDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { String file = chooser.getSelectedFile().getPath(); if (!file.toLowerCase().endsWith(".emf")) file += ".emf"; int width = (int) this.getSize().getWidth(); int height = (int) this.getSize().getHeight(); // Save image SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EMF); new Thread(SI).start(); } } if ("SAVE_EPS".equals(command)) { JFileChooser chooser = new JFileChooser(); FileNameExtensionFilter filter = new FileNameExtensionFilter("EPS Image", "EPS"); chooser.setFileFilter(filter); int returnVal = chooser.showSaveDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { String file = chooser.getSelectedFile().getPath(); if (!file.toLowerCase().endsWith(".eps")) file += ".eps"; int width = (int) this.getSize().getWidth(); int height = (int) this.getSize().getHeight(); // Save image SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EPS); new Thread(SI).start(); } } } XYPlot getXYPlot() { return plot; } void setTitle(String title) { chartTitle.setText(title); } void loadPeakList(PeakList peakList) { PeakDataSet peaksDataSet = new PeakDataSet(rawDataFile, peakList, rtRange, mzRange); plot.setDataset(1, peaksDataSet); plot.setRenderer(1, peakDataRenderer); } void switchDataPointsVisible() { boolean dataPointsVisible = peakDataRenderer.getBaseShapesVisible(); peakDataRenderer.setBaseShapesVisible(!dataPointsVisible); } public void showPeaksTooltips(boolean mode) { if (mode) { PeakToolTipGenerator toolTipGenerator = new PeakToolTipGenerator(); this.peakDataRenderer.setBaseToolTipGenerator(toolTipGenerator); } else { this.peakDataRenderer.setBaseToolTipGenerator(null); } } public void mouseWheelMoved(MouseWheelEvent event) { int notches = event.getWheelRotation(); if (notches < 0) { getXYPlot().getDomainAxis().resizeRange(1.0 / ZOOM_FACTOR); } else { getXYPlot().getDomainAxis().resizeRange(ZOOM_FACTOR); } } @Override public void mouseClicked(final MouseEvent event) { // Let the parent handle the event (selection etc.) super.mouseClicked(event); if (event.getX() < 70) { // User clicked on Y-axis if (event.getClickCount() == 2) { // Reset zoom on Y-axis XYDataset data = ((XYPlot) getChart().getPlot()).getDataset(); Number maximum = DatasetUtilities.findMaximumRangeValue(data); getXYPlot().getRangeAxis().setRange(0, 1.05 * maximum.floatValue()); } else if (event.getClickCount() == 1) { // Auto range on Y-axis getXYPlot().getRangeAxis().setAutoTickUnitSelection(true); getXYPlot().getRangeAxis().setAutoRange(true); } } else if (event.getY() > this.getChartRenderingInfo().getPlotInfo().getPlotArea().getMaxY() - 41 && event.getClickCount() == 2) { // Reset zoom on X-axis getXYPlot().getDomainAxis().setAutoTickUnitSelection(true); restoreAutoDomainBounds(); } else if (event.getClickCount() == 2) { visualizer.actionPerformed( new ActionEvent(event.getSource(), ActionEvent.ACTION_PERFORMED, "SHOW_SPECTRUM")); } } }