peakmlviewer.dialog.peakinformation.Graph.java Source code

Introduction

Here is the source code for peakmlviewer.dialog.peakinformation.Graph.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.dialog.peakinformation;

// java
import java.awt.Color;
import java.awt.BasicStroke;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;

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

// peakml
import peakml.*;
import peakml.chemistry.*;

// peakmlviewer
import peakmlviewer.*;

/**
 * 
 */
public class Graph extends Composite {
    // constructor(s)
    public Graph(Composite parent) {
        super(parent, SWT.EMBEDDED);

        setLayout(new FillLayout());

        // create the chart
        linechart = ChartFactory.createLineChart(null, "", "Abundance", dataset_intensity, PlotOrientation.VERTICAL,
                false, // legend
                false, // tooltips
                false // urls
        );

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

        // make the labels for the xaxis 45 degrees
        CategoryAxis xaxis = (CategoryAxis) plot.getDomainAxis();
        xaxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);

        // add the mass accuracy yaxis
        NumberAxis yaxis_massacc = new NumberAxis("Mass accuracy (ppm)");
        plot.setRangeAxis(1, yaxis_massacc);
        plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_RIGHT);

        // create the mass accuracy dataset
        dataset_ppm = new DefaultCategoryDataset();
        plot.setDataset(1, dataset_ppm);
        plot.mapDatasetToRangeAxis(1, 1);

        // create the renderer for the mass accuracy dataset
        LineAndShapeRenderer renderer_ppm = new LineAndShapeRenderer();
        renderer_ppm.setBaseShapesFilled(true);
        renderer_ppm.setBaseShapesVisible(true);
        renderer_ppm.setBaseStroke(
                new BasicStroke(1, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, 1, new float[] { 5, 5 }, 0));
        plot.setRenderer(1, renderer_ppm);

        // setup the renderer for the intensity dataset
        LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer();
        renderer.setBaseShapesFilled(true);
        renderer.setBaseShapesVisible(true);

        // general properties
        linechart.setBackgroundPaint(Color.WHITE);
        linechart.setBorderVisible(false);
        linechart.setAntiAlias(true);

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

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

        java.awt.Frame frame = org.eclipse.swt.awt.SWT_AWT.new_Frame(this);

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

    // access
    @SuppressWarnings("unchecked")
    public void setPeak(IPeak peak, Document document, MolecularFormula formula) {
        if (peak == null)
            return;

        for (String setname : document.getSetNames()) {
            dataset_intensity.addValue(0, "INTENSITY", setname);
            dataset_ppm.addValue(0, "PPM", setname);
        }

        // fill the graph with the appropriate data
        Class<? extends IPeak> c = peak.getClass();
        if (c.equals(IPeakSet.class)) {
            IPeakSet<? extends IPeak> peakset = (IPeakSet<? extends IPeak>) peak;
            double mass = peakset.getMeanMass();
            if (formula != null)
                mass = formula.getMass(Mass.MONOISOTOPIC);

            java.util.Collections.sort(peakset.getPeaks(), IPeak.sort_profileid_ascending);
            for (IPeak p : peakset) {
                dataset_ppm.addValue(PeriodicTable.PPMNr(mass, mass - p.getMass()), "PPM", document.getSetName(p));
                dataset_intensity.addValue(p.getIntensity(), "INTENSITY", document.getSetName(p));
            }
        } else {
            dataset_ppm.addValue(0, "", document.getSetName(peak));
            dataset_intensity.addValue(peak.getIntensity(), "", document.getSetName(peak));
        }
    }

    public BufferedImage getGraphImage(int width, int height) {
        BufferedImage img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
        Graphics2D g = img.createGraphics();
        g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);

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

        return img;
    }

    // data
    protected JFreeChart linechart = null;

    protected DefaultCategoryDataset dataset_ppm = new DefaultCategoryDataset();
    protected DefaultCategoryDataset dataset_intensity = new DefaultCategoryDataset();
}