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.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.geom.Ellipse2D; import javax.swing.JFrame; import javax.swing.JMenuBar; import org.jfree.chart.LegendItem; import org.jfree.chart.LegendItemCollection; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.desktop.impl.WindowsMenu; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule; import net.sf.mzmine.modules.visualization.tic.CursorPosition; import net.sf.mzmine.parameters.Parameter; import net.sf.mzmine.parameters.ParameterSet; import net.sf.mzmine.parameters.impl.SimpleParameterSet; import net.sf.mzmine.parameters.parametertypes.BooleanParameter; import net.sf.mzmine.parameters.parametertypes.ComboParameter; import net.sf.mzmine.parameters.parametertypes.DoubleParameter; import net.sf.mzmine.parameters.parametertypes.WindowSettingsParameter; import net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance; import net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter; import net.sf.mzmine.util.ExitCode; import net.sf.mzmine.util.dialogs.AxesSetupDialog; import com.google.common.collect.Range; /** * IDA visualizer using JFreeChart library */ public class IDAVisualizerWindow extends JFrame implements ActionListener { private static final long serialVersionUID = 1L; private IDAToolBar toolBar; private IDAPlot IDAPlot; private IDABottomPanel bottomPanel; private IDADataSet dataset; private RawDataFile dataFile; private boolean tooltipMode; public IDAVisualizerWindow(RawDataFile dataFile, Range<Double> rtRange, Range<Double> mzRange, IntensityType intensityType, NormalizationType normalizationType, Double minPeakInt, ParameterSet parameters) { super("IDA visualizer: [" + dataFile.getName() + "]"); setDefaultCloseOperation(DISPOSE_ON_CLOSE); setBackground(Color.white); this.dataFile = dataFile; this.tooltipMode = true; dataset = new IDADataSet(dataFile, rtRange, mzRange, intensityType, normalizationType, minPeakInt, this); toolBar = new IDAToolBar(this); add(toolBar, BorderLayout.EAST); IDAPlot = new IDAPlot(this, dataFile, this, dataset, rtRange, mzRange); add(IDAPlot, BorderLayout.CENTER); bottomPanel = new IDABottomPanel(this, dataFile, parameters); add(bottomPanel, BorderLayout.SOUTH); updateTitle(); // After we have constructed everything, load the peak lists into the // bottom panel bottomPanel.rebuildPeakListSelector(); MZmineCore.getDesktop().addPeakListTreeListener(bottomPanel); // Add the Windows menu JMenuBar menuBar = new JMenuBar(); menuBar.add(new WindowsMenu()); setJMenuBar(menuBar); pack(); // get the window settings parameter ParameterSet paramSet = MZmineCore.getConfiguration().getModuleParameters(IDAVisualizerModule.class); WindowSettingsParameter settings = paramSet.getParameter(IDAParameters.windowSettings); // update the window and listen for changes settings.applySettingsToWindow(this); this.addComponentListener(settings); } public void dispose() { super.dispose(); MZmineCore.getDesktop().removePeakListTreeListener(bottomPanel); } void updateTitle() { StringBuffer title = new StringBuffer(); title.append("Time vs. m/z for IDA dependent precursor ions\n"); title.append(dataFile.getName()); IDAPlot.setTitle(title.toString()); } /** * @return current cursor position */ public CursorPosition getCursorPosition() { double selectedRT = (double) IDAPlot.getXYPlot().getDomainCrosshairValue(); double selectedMZ = (double) IDAPlot.getXYPlot().getRangeCrosshairValue(); int index = dataset.getIndex(selectedRT, selectedMZ); if (index >= 0) { double intensity = (double) dataset.getZ(0, index); CursorPosition pos = new CursorPosition(selectedRT, selectedMZ, intensity, dataset.getDataFile(), dataset.getScanNumber(index)); return pos; } return null; } /** * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent) */ public void actionPerformed(ActionEvent event) { String command = event.getActionCommand(); if (command.equals("SHOW_SPECTRUM")) { CursorPosition pos = getCursorPosition(); if (pos != null) { SpectraVisualizerModule.showNewSpectrumWindow(pos.getDataFile(), pos.getScanNumber()); } } if (command.equals("SETUP_AXES")) { AxesSetupDialog dialog = new AxesSetupDialog(this, IDAPlot.getXYPlot()); dialog.setVisible(true); } if (command.equals("SHOW_DATA_POINTS")) { IDAPlot.switchDataPointsVisible(); } if (command.equals("SWITCH_TOOLTIPS")) { if (tooltipMode) { IDAPlot.showPeaksTooltips(false); toolBar.setTooltipButton(false); tooltipMode = false; } else { IDAPlot.showPeaksTooltips(true); toolBar.setTooltipButton(true); tooltipMode = true; } } if (command.equals("FIND_SPECTRA")) { // Parameters final DoubleParameter inputMZ = new DoubleParameter("Ion m/z", "m/z value of ion to search for."); final MZToleranceParameter inputMZTolerance = new MZToleranceParameter(); final DoubleParameter inputIntensity = new DoubleParameter("Min. ion intensity", "Only ions with intensities above this value will be searched for."); final BooleanParameter inputNL = new BooleanParameter("Neutral Loss", "If selected, the ion to be searched for will be a neutral loss ion.\nIn this case, only ions above the min. intensity will be examined.", false); final ComboParameter<Colors> inputColors = new ComboParameter<Colors>("Color", "The color which the data points will be marked with.", Colors.values()); Parameter<?>[] parameters = new Parameter<?>[5]; parameters[0] = inputMZ; parameters[1] = inputMZTolerance; parameters[2] = inputIntensity; parameters[3] = inputNL; parameters[4] = inputColors; final ParameterSet parametersSearch = new SimpleParameterSet(parameters); ExitCode exitCode = parametersSearch.showSetupDialog(this, true); if (exitCode != ExitCode.OK) return; double searchMZ = parametersSearch.getParameter(inputMZ).getValue(); MZTolerance searchMZTolerance = parametersSearch.getParameter(inputMZTolerance).getValue(); double minIntensity = parametersSearch.getParameter(inputIntensity).getValue(); boolean neutralLoss = parametersSearch.getParameter(inputNL).getValue(); Color highligtColor = Color.red; ; if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.green)) { highligtColor = Color.green; } if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.blue)) { highligtColor = Color.blue; } // Find and highlight spectra with specific ion dataset.highlightSpectra(searchMZ, searchMZTolerance, minIntensity, neutralLoss, highligtColor); // Add legend entry LegendItemCollection chartLegend = IDAPlot.getXYPlot().getLegendItems(); chartLegend.add(new LegendItem("Ion: " + searchMZ, "", "MS/MS spectra which contain the " + searchMZ + " ion\nTolerance: " + searchMZTolerance.toString() + "\nMin intensity: " + minIntensity, "", new Ellipse2D.Double(0, 0, 7, 7), highligtColor)); IDAPlot.getXYPlot().setFixedLegendItems(chartLegend); } } IDAPlot getPlot() { return IDAPlot; } }