gui.DendrogramChart.java Source code

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Here is the source code for gui.DendrogramChart.java

Source

/* Copyright (c) 2005-2016 Biomathematics and Statistics Scotland
 * http://www.bioss.ac.uk/ 
 * 
 * This file is part of TetraploidMap.
 *
 *    TetraploidMap 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 3 of the License, or
 *    (at your option) any later version.
 *
 *    TetraploidMap 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 TetraploidMap.  If not, see <http://www.gnu.org/licenses/>.
 */

package gui;

import java.awt.CardLayout;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.RenderingHints;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.text.DecimalFormat;

import javax.swing.JPanel;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.LogarithmicAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.ValueAxis;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;

import data.Dendrogram;

class DendrogramChart extends JPanel implements Printable {
    static final long serialVersionUID = 5773262026713363L;
    private Dendrogram d;

    private CardLayout card;
    private ChartPanel panelNormal, panelLogged;

    private boolean isLogged = false;

    DendrogramChart(Dendrogram d, boolean log) {
        this.d = d;

        card = new CardLayout();
        setLayout(card);

        panelNormal = getChartPanel(d, false);
        panelLogged = getChartPanel(d, true);

        add("false", panelNormal);
        add("true", panelLogged);
    }

    ChartPanel getChartPanel(Dendrogram d, boolean log) {
        JFreeChart chart = ChartFactory.createXYLineChart(null, "Similarity", "No. of Groups", null,
                PlotOrientation.VERTICAL, true, true, false);

        setChartData(chart, log);

        RenderingHints rh = new RenderingHints(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
        chart.setRenderingHints(rh);
        chart.removeLegend();

        XYPlot plot = chart.getXYPlot();
        plot.setBackgroundPaint(new Color(255, 255, 220));
        plot.setDomainGridlinePaint(new Color(128, 128, 128));
        plot.setRangeGridlinePaint(new Color(128, 128, 128));
        if (log == false) {
            NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
            rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
            rangeAxis.setLowerBound(0);
            rangeAxis.setNumberFormatOverride(new DecimalFormat("0"));
            rangeAxis.setLabelFont(Prefs.labelFont);
        } else {
            // LogarithmicAxis logXAxis = new LogarithmicAxis("Similarity");
            // logXAxis.setAllowNegativesFlag(true);
            LogarithmicAxis logYAxis = new LogarithmicAxis("No. Of Groups");
            logYAxis.setAllowNegativesFlag(false);

            // plot.setDomainAxis(logXAxis);
            plot.setRangeAxis(logYAxis);
        }

        ChartPanel chartPanel = new ChartPanel(chart);
        // chartPanel.setPopupMenu(null);
        return chartPanel;
    }

    private void setChartData(JFreeChart chart, boolean log) {
        XYSeries series = new XYSeries("Similarity vs No. of Groups");

        double rSim = d.getRootSimilarity();
        double diff = 1 - rSim;

        // TODO: What causes this?
        if (diff == 0)
            return;

        for (double sim = rSim; sim <= 1.0; sim += (diff / 50)) {
            series.add(sim, d.getGroupCount(sim));
        }

        XYSeriesCollection data = new XYSeriesCollection(series);
        chart.getXYPlot().setDataset(data);
    }

    void setVisibleChart(boolean log) {
        card.show(this, "" + log);
        isLogged = log;
    }

    public int print(Graphics graphics, PageFormat pf, int pageIndex) {
        return getCurrentChartPanel().print(graphics, pf, pageIndex);
    }

    void setScaling(boolean autorange, double min, double max) {
        JFreeChart chart = ((ChartPanel) getComponent(0)).getChart();
        ValueAxis axis = chart.getXYPlot().getDomainAxis();

        axis.setAutoRange(autorange);
        if (!autorange) {
            axis.setLowerBound(min);
            axis.setUpperBound(max);
        }
    }

    private ChartPanel getCurrentChartPanel() {
        if (isLogged == false) {
            return ((ChartPanel) getComponent(0));
        } else {
            return ((ChartPanel) getComponent(1));
        }
    }
}