net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotWindow.java Source code

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Here is the source code for net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotWindow.java

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/*
 * 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.intensityplot;

import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
import java.text.NumberFormat;
import java.util.logging.Logger;

import javax.swing.JFrame;
import javax.swing.JMenuBar;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.CategoryAxis;
import org.jfree.chart.axis.CategoryLabelPositions;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.labels.CategoryToolTipGenerator;
import org.jfree.chart.labels.XYToolTipGenerator;
import org.jfree.chart.plot.CategoryPlot;
import org.jfree.chart.plot.Plot;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.category.StatisticalLineAndShapeRenderer;
import org.jfree.chart.renderer.xy.XYErrorRenderer;
import org.jfree.chart.title.LegendTitle;
import org.jfree.chart.title.TextTitle;

import net.sf.mzmine.datamodel.PeakList;
import net.sf.mzmine.desktop.impl.WindowsMenu;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.parameters.ParameterSet;
import net.sf.mzmine.parameters.parametertypes.DoubleParameter;
import net.sf.mzmine.parameters.parametertypes.WindowSettingsParameter;

/**
 * 
 */
public class IntensityPlotWindow extends JFrame {

    /**
     * 
     */
    private static final long serialVersionUID = 1L;
    static final Font legendFont = new Font("SansSerif", Font.PLAIN, 10);
    static final Font titleFont = new Font("SansSerif", Font.PLAIN, 11);

    private Logger logger = Logger.getLogger(this.getClass().getName());

    private IntensityPlotDataset dataset;
    private JFreeChart chart;

    public IntensityPlotWindow(ParameterSet parameters) {

        PeakList peakList = parameters.getParameter(IntensityPlotParameters.peakList).getValue()
                .getMatchingPeakLists()[0];

        String title = "Intensity plot [" + peakList + "]";
        String xAxisLabel = parameters.getParameter(IntensityPlotParameters.xAxisValueSource).getValue().toString();
        String yAxisLabel = parameters.getParameter(IntensityPlotParameters.yAxisValueSource).getValue().toString();

        // create dataset
        dataset = new IntensityPlotDataset(parameters);

        // create new JFreeChart
        logger.finest("Creating new chart instance");
        Object xAxisValueSource = parameters.getParameter(IntensityPlotParameters.xAxisValueSource).getValue();
        boolean isCombo = (xAxisValueSource instanceof ParameterWrapper)
                && (!(((ParameterWrapper) xAxisValueSource).getParameter() instanceof DoubleParameter));
        if ((xAxisValueSource == IntensityPlotParameters.rawDataFilesOption) || isCombo) {

            chart = ChartFactory.createLineChart(title, xAxisLabel, yAxisLabel, dataset, PlotOrientation.VERTICAL,
                    true, true, false);

            CategoryPlot plot = (CategoryPlot) chart.getPlot();

            // set renderer
            StatisticalLineAndShapeRenderer renderer = new StatisticalLineAndShapeRenderer(false, true);
            renderer.setBaseStroke(new BasicStroke(2));
            plot.setRenderer(renderer);
            plot.setBackgroundPaint(Color.white);

            // set tooltip generator
            CategoryToolTipGenerator toolTipGenerator = new IntensityPlotTooltipGenerator();
            renderer.setBaseToolTipGenerator(toolTipGenerator);

            CategoryAxis xAxis = (CategoryAxis) plot.getDomainAxis();
            xAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);

        } else {

            chart = ChartFactory.createXYLineChart(title, xAxisLabel, yAxisLabel, dataset, PlotOrientation.VERTICAL,
                    true, true, false);

            XYPlot plot = (XYPlot) chart.getPlot();

            XYErrorRenderer renderer = new XYErrorRenderer();
            renderer.setBaseStroke(new BasicStroke(2));
            plot.setRenderer(renderer);
            plot.setBackgroundPaint(Color.white);

            // set tooltip generator
            XYToolTipGenerator toolTipGenerator = new IntensityPlotTooltipGenerator();
            renderer.setBaseToolTipGenerator(toolTipGenerator);

        }

        chart.setBackgroundPaint(Color.white);

        // create chart JPanel
        ChartPanel chartPanel = new ChartPanel(chart);
        add(chartPanel, BorderLayout.CENTER);

        IntensityPlotToolBar toolBar = new IntensityPlotToolBar(this);
        add(toolBar, BorderLayout.EAST);

        // disable maximum size (we don't want scaling)
        chartPanel.setMaximumDrawWidth(Integer.MAX_VALUE);
        chartPanel.setMaximumDrawHeight(Integer.MAX_VALUE);

        // set title properties
        TextTitle chartTitle = chart.getTitle();
        chartTitle.setMargin(5, 0, 0, 0);
        chartTitle.setFont(titleFont);

        LegendTitle legend = chart.getLegend();
        legend.setItemFont(legendFont);
        legend.setBorder(0, 0, 0, 0);

        Plot plot = chart.getPlot();

        // set shape provider
        IntensityPlotDrawingSupplier shapeSupplier = new IntensityPlotDrawingSupplier();
        plot.setDrawingSupplier(shapeSupplier);

        // set y axis properties
        NumberAxis yAxis;
        if (plot instanceof CategoryPlot)
            yAxis = (NumberAxis) ((CategoryPlot) plot).getRangeAxis();
        else
            yAxis = (NumberAxis) ((XYPlot) plot).getRangeAxis();
        NumberFormat yAxisFormat = MZmineCore.getConfiguration().getIntensityFormat();
        if (parameters.getParameter(IntensityPlotParameters.yAxisValueSource).getValue() == YAxisValueSource.RT)
            yAxisFormat = MZmineCore.getConfiguration().getRTFormat();
        yAxis.setNumberFormatOverride(yAxisFormat);

        setTitle(title);
        setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        setBackground(Color.white);

        // 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(IntensityPlotModule.class);
        WindowSettingsParameter settings = paramSet.getParameter(IntensityPlotParameters.windowSettings);

        // update the window and listen for changes
        settings.applySettingsToWindow(this);
        this.addComponentListener(settings);

    }

    JFreeChart getChart() {
        return chart;
    }

}