peakml.util.swt.widget.IPeakGraph.java Source code

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Here is the source code for peakml.util.swt.widget.IPeakGraph.java

Source

/* Copyright (C) 2008, Groningen Bioinformatics Centre (http://gbic.biol.rug.nl/)
 * This file is part of PeakML.
 * 
 * PeakML is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation; either version 2.1 of the License, or
 * (at your option) any later version.
 * 
 * PeakML 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 Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with PeakML; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */

package peakml.util.swt.widget;

// java
import java.util.*;

// eclipse
import java.awt.Color;

import org.eclipse.swt.*;
import org.eclipse.swt.layout.*;
import org.eclipse.swt.widgets.*;

// jfreechart
import org.jfree.chart.*;

// peakml
import peakml.*;
import peakml.io.*;
import peakml.graphics.*;

import peakml.util.jfreechart.*;

/**
* 
*/
public class IPeakGraph extends Composite {
    // constructor(s)
    public IPeakGraph(Composite parent, int style) {
        super(parent, SWT.EMBEDDED | style);

        // layout
        setLayout(new FillLayout());

        // create the components
        timeplot = new FastTimePlot("retention time", "intensity");
        timeplot.setBackgroundPaint(Color.WHITE);
        linechart = new JFreeChart("", timeplot);
        linechart.setBackgroundPaint(Color.WHITE);

        //      org.jfree.experimental.chart.swt.ChartComposite c =
        //         new org.jfree.experimental.chart.swt.ChartComposite(this, SWT.NONE, linechart);
        //      
        //      c.setRangeZoomable(true);
        //      c.setDomainZoomable(true);

        // add the components
        // --------------------------------------------------------------------------------
        // This uses the SWT-trick for embedding AWT-controls in an SWT-Composite.
        // 2009-10-17: Tested the SWT setup in jfreechart.experimental - this is still better.
        try {
            System.setProperty("sun.awt.noerasebackground", "true");
        } catch (NoSuchMethodError error) {
            ;
        }

        java.awt.Frame frame = org.eclipse.swt.awt.SWT_AWT.new_Frame(this);
        ChartPanel panel = new ChartPanel(linechart, false, false, false, false, false);

        panel.setFillZoomRectangle(true);
        panel.setMouseZoomable(true, true);

        // create a new ChartPanel, without the popup-menu (5x false)
        frame.add(panel);
        // --------------------------------------------------------------------------------
    }

    // access
    public void clear() {
        timeplot.clear();
    }

    public void setPeak(IPeak peak, Header header, HashMap<String, Integer> colors) {
        if (peak == null) {
            timeplot.clear();
        } else {
            timeplot.clear();
            updateGraph(peak, header, colors);
        }
    }

    public java.awt.image.BufferedImage getGraphImage(int width, int height) {
        java.awt.image.BufferedImage img = new java.awt.image.BufferedImage(width, height,
                java.awt.image.BufferedImage.TYPE_INT_ARGB);
        java.awt.Graphics2D g = img.createGraphics();

        g.setRenderingHint(java.awt.RenderingHints.KEY_ANTIALIASING, java.awt.RenderingHints.VALUE_ANTIALIAS_ON);

        linechart.draw(g, new java.awt.Rectangle(0, 0, width, height));

        return img;
    }

    public JFreeChart getChart() {
        return linechart;
    }

    // helper
    @SuppressWarnings("unchecked")
    protected void updateGraph(IPeak peak, Header header, HashMap<String, Integer> colors) {
        if (peak == null)
            return;

        // fill the graph with the appropriate data
        Class<? extends IPeak> c = peak.getClass();
        if (c.equals(MassChromatogram.class) || c.equals(BackgroundIon.class)) {
            PeakData<Centroid> peakdata;
            if (c.equals(MassChromatogram.class))
                peakdata = ((MassChromatogram<Centroid>) peak).getPeakData();
            else
                peakdata = ((BackgroundIon<Centroid>) peak).getPeakData();

            MeasurementInfo measurementinfo = header.getMeasurementInfo(peak.getMeasurementID());
            if (measurementinfo != null && measurementinfo.getVisible() == false)
                return;
            SetInfo setinfo = null;
            if (measurementinfo != null)
                setinfo = header.getSetInfoForMeasurementID(measurementinfo.getID());

            int color = 0;
            if (colors != null && setinfo != null)
                color = colors.get(setinfo.getID());
            else if (setinfo != null)
                color = colormap.getColor(header.indexOfSetInfo(setinfo.getID()));

            FastTimePlot.Data data = new FastTimePlot.Data(
                    measurementinfo != null ? measurementinfo.getLabel() : "", peakdata.getRetentionTimes(),
                    peakdata.getIntensities(), color);
            timeplot.addData(data);
        } else if (c.equals(IPeakSet.class)) {
            IPeakSet<? extends IPeak> peakset = (IPeakSet<? extends IPeak>) peak;
            for (IPeak p : peakset)
                updateGraph(p, header, colors);
        }
    }

    // data
    protected JFreeChart linechart;
    protected FastTimePlot timeplot;

    protected boolean smooth;
    protected boolean smooth_show_original;

    protected static final Colormap colormap = new Colormap(Colormap.EXCEL);
}