peakmlviewer.widgets.IPeakIntensityGraph.java Source code

Introduction

Here is the source code for peakmlviewer.widgets.IPeakIntensityGraph.java

Source

/* Copyright (C) 2008, Groningen Bioinformatics Centre (http://gbic.biol.rug.nl/)
 * This file is part of mzmatch.
 * 
 * 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.
 * 
 * mzmatch 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 peakmlviewer.widgets;

// java
import java.util.*;

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

// jfreechart
import org.jfree.chart.*;
import org.jfree.chart.axis.*;
import org.jfree.chart.plot.*;
import org.jfree.chart.renderer.category.*;

import org.jfree.data.category.*;

// libraries

// metabolome
import peakml.*;
import peakml.io.*;

// peakmlviewer

/**
* 
*/
public class IPeakIntensityGraph extends Composite {
    // constructor(s)
    @SuppressWarnings("deprecation")
    public IPeakIntensityGraph(Composite parent, int style) {
        super(parent, style | SWT.EMBEDDED);

        // create the components
        linechart = ChartFactory.createLineChart(null, "", "Intensity", dataset, PlotOrientation.VERTICAL, false, // legend
                false, // tooltips
                false // urls
        );

        CategoryPlot plot = (CategoryPlot) linechart.getPlot();
        CategoryAxis axis = (CategoryAxis) plot.getDomainAxis();
        axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
        LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer();

        renderer.setShapesFilled(true);
        renderer.setShapesVisible(true);

        linechart.setBackgroundPaint(java.awt.Color.WHITE);
        linechart.setBorderVisible(false);
        linechart.setAntiAlias(true);

        plot.setBackgroundPaint(java.awt.Color.WHITE);
        plot.setDomainGridlinesVisible(true);
        plot.setRangeGridlinesVisible(true);

        // add the components
        // --------------------------------------------------------------------------------
        // This uses the SWT-trick for embedding AWT-controls in an SWT-Composite.
        try {
            System.setProperty("sun.awt.noerasebackground", "true");
        } catch (NoSuchMethodError error) {
            ;
        }

        // create a new ChartPanel, without the popup-menu (5x false)
        java.awt.Frame frame = org.eclipse.swt.awt.SWT_AWT.new_Frame(this);
        frame.add(new ChartPanel(linechart, false, false, false, false, false));
        // --------------------------------------------------------------------------------
    }

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

    @SuppressWarnings("unchecked")
    public void setPeak(Header header, IPeak peak, String id) {
        if (IPeakSet.class.equals(peak.getClass())) {
            IPeakSet<IPeak> peakset = (IPeakSet<IPeak>) peak;

            java.util.Collections.sort(peakset.getPeaks(), IPeak.sort_profileid_ascending);
            for (IPeak p : peakset)
                dataset.addValue(p.getIntensity(), id,
                        header.getSetInfoForMeasurementID(p.getMeasurementID()).getID());
        } else {

        }
    }

    public void setPeaks(Header headers[], IPeak peaks[]) {
        if (headers.length != peaks.length)
            throw new RuntimeException(
                    "setPeaks requires both the headers and the peaks vectors to be of the same size.");

        int size = headers.length;
        for (int i = 0; i < size; ++i)
            setPeak(headers[i], peaks[i], Integer.toString(i));
    }

    public void setPeaks(Vector<Header> headers, Vector<IPeak> peaks) {
        setPeaks((Header[]) headers.toArray(), (IPeak[]) peaks.toArray());
    }

    // data
    protected JFreeChart linechart = null;
    protected DefaultCategoryDataset dataset = new DefaultCategoryDataset();
}