es.uvigo.darwin.jmodeltest.io.RFHistogram.java Source code

Introduction

Here is the source code for es.uvigo.darwin.jmodeltest.io.RFHistogram.java

Source

/*
Copyright (C) 2011  Diego Darriba, David Posada
    
This program 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.
    
This program 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 this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 */
package es.uvigo.darwin.jmodeltest.io;

import java.util.List;
import java.util.Random;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.data.statistics.HistogramDataset;
import org.jfree.data.statistics.HistogramType;

import pal.tree.Tree;
import es.uvigo.darwin.jmodeltest.model.Model;
import es.uvigo.darwin.jmodeltest.selection.InformationCriterion;
import es.uvigo.darwin.jmodeltest.tree.TreeDistancesCache;
import es.uvigo.darwin.jmodeltest.tree.TreeEuclideanDistancesCache;
import es.uvigo.darwin.jmodeltest.tree.TreeRFDistancesCache;

public class RFHistogram {

    private static JFreeChart buildHistogram(double[] values, int steps, String plotTitle, String xAxis,
            String yAxis) {
        HistogramDataset hds = new HistogramDataset();
        hds.setType(HistogramType.RELATIVE_FREQUENCY);
        hds.addSeries(1, values, steps);
        PlotOrientation orientation = PlotOrientation.VERTICAL;
        boolean show = false;
        boolean toolTips = false;
        boolean urls = false;
        JFreeChart chart = ChartFactory.createHistogram(plotTitle, xAxis, yAxis, hds, orientation, show, toolTips,
                urls);
        return chart;
    }

    public static JFreeChart buildDistancesHistogram(InformationCriterion ic, TreeDistancesCache distances,
            String plotTitle) {
        List<Model> models = ic.getConfidenceModels();

        Tree bestTree = ic.getMinModel().getTree();
        int maxRF = 2 * (bestTree.getIdCount() - 3);
        double values[] = new double[models.size() - 1];
        int i = 0;
        for (Model model : models) {
            if (!model.equals(ic.getMinModel())) {
                double distance = distances.getDistance(bestTree, model.getTree());
                /* make relative RF distance */
                values[i] = 1.0 * distance / maxRF;
                i++;
            }
        }
        String xaxis = "distance";
        String yaxis = "count";
        int steps = 10;
        JFreeChart chart = buildHistogram(values, steps, plotTitle, xaxis, yaxis);

        return chart;
    }

    public static JFreeChart buildRFHistogram(InformationCriterion ic) {
        return buildDistancesHistogram(ic, TreeRFDistancesCache.getInstance(), ic + " RF distances histogram");
    }

    public static JFreeChart buildEuclideanHistogram(InformationCriterion ic) {
        return buildDistancesHistogram(ic, TreeEuclideanDistancesCache.getInstance(),
                ic + " euclidean distances histogram");
    }

    public static JFreeChart buildRandomHistogram() {
        Random generator = new Random();
        double[] value = new double[100];
        for (int i = 1; i < 100; i++) {
            value[i] = generator.nextDouble();
        }
        int number = 10;
        String plotTitle = "Histogram";
        String xaxis = "number";
        String yaxis = "value";
        JFreeChart chart = buildHistogram(value, number, plotTitle, xaxis, yaxis);
        return chart;
    }
}