com.mugarov.neview.view.GraphPanel.java Source code

Introduction

Here is the source code for com.mugarov.neview.view.GraphPanel.java

Source

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package com.mugarov.neview.view;

import com.mugarov.neview.model.elements.Coordinates;
import com.mugarov.neview.model.elements.Dot;
import com.mugarov.neview.model.elements.DotBag;
import com.mugarov.neview.model.elements.Median;
import com.mugarov.neview.view.datarepresentation.CoordinateSeries;
import com.mugarov.neview.view.datarepresentation.CoordinateSeriesCollection;
import com.mugarov.neview.view.datarepresentation.ExpAxis;
import java.awt.BorderLayout;
import java.awt.Color;
import java.text.AttributedString;
import java.text.NumberFormat;
import java.util.ArrayList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.LogAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.labels.XYToolTipGenerator;

import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.data.xy.XYDataset;

/**
 *
 * @author mugarov
 */
public class GraphPanel extends JPanel {

    private final JScrollPane scroll;
    private final JPanel content;
    private final ArrayList<CoordinateSeries> dotSeries;
    private final ArrayList<CoordinateSeries> lineSeries;
    private final ArrayList<Coordinates> coordinates;
    private CoordinateSeriesCollection seriesCollection;
    private JFreeChart chart;
    private ChartPanel chartPanel;
    private final ColorGenerator colorGen;

    public static final String XAxis = "Length";
    public static final String YAxis = "Reads";

    public GraphPanel() {
        super(new BorderLayout());
        super.setBackground(Color.blue);

        this.colorGen = new ColorGenerator();

        this.content = new JPanel(new BorderLayout());
        this.scroll = new JScrollPane(this.content);

        this.add(this.scroll, BorderLayout.CENTER);
        this.dotSeries = new ArrayList<>();
        this.lineSeries = new ArrayList<>();
        this.coordinates = new ArrayList<>();
    }

    public void setValues(ArrayList<DotBag> dotBags, ArrayList<Median> lines, String name) {

        CoordinateSeries ser;
        for (DotBag db : dotBags) {

            ser = new CoordinateSeries(db.getName());
            for (Dot d : db) {

                ser.add(d.getCoordinates(), d.getName(), d.getScaffoldName());
                //                System.out.println("New dot:"+d.getLogX()+", "+d.getLogY());
            }

            this.dotSeries.add(ser);
        }

        for (Median med : lines) {
            ser = new CoordinateSeries(med.getName());

            ser.add(med.getStart(), med.getName(), null);
            ser.add(med.getEnd(), med.getName(), null);
            //            System.out.println("New line from " + med.getStart().getX()+","+ med.getStart().getY()+" to "+med.getEnd().getX()+","+ med.getEnd().getY());
            this.lineSeries.add(ser);
        }

        this.seriesCollection = new CoordinateSeriesCollection();

        for (CoordinateSeries dotSeries : this.dotSeries) {
            this.seriesCollection.addSeries(dotSeries);
        }
        for (CoordinateSeries line : this.lineSeries) {
            this.seriesCollection.addSeries(line);
        }

        this.chart = ChartFactory.createXYLineChart(name, GraphPanel.XAxis, GraphPanel.YAxis, this.seriesCollection,
                PlotOrientation.VERTICAL, true, true, false);
        this.chart.setBackgroundPaint(Color.white);

        XYPlot plot = chart.getXYPlot();

        ExpAxis x1Axis = new ExpAxis(GraphPanel.XAxis);
        ExpAxis y1Axis = new ExpAxis(GraphPanel.YAxis);

        NumberAxis x2Axis = new NumberAxis("Proportion to max of " + GraphPanel.XAxis);
        NumberAxis y2Axis = new NumberAxis("Proportion to max of " + GraphPanel.YAxis);

        plot.setDomainAxis(0, x1Axis);
        plot.setDomainAxis(1, x2Axis);
        plot.setRangeAxis(0, y1Axis);
        plot.setRangeAxis(1, y2Axis);
        //        plot.setDomainAxis(1, yAxis);

        XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();

        for (int i = 0; i < this.dotSeries.size(); i++) {
            renderer.setSeriesLinesVisible(i, false);
            renderer.setSeriesPaint(i, this.colorGen.get(i));
        }

        for (int i = this.dotSeries.size(); i < this.lineSeries.size() + this.dotSeries.size(); i++) {
            renderer.setSeriesShapesVisible(i, false);
            //             renderer.setSeriesPaint(i, Color.black);
            renderer.setSeriesPaint(i, this.colorGen.get(i - this.dotSeries.size()));
        }

        renderer.setBaseToolTipGenerator(new ItemGenerator());

        plot.setRenderer(renderer);
        plot.setBackgroundPaint(Color.white);

        plot.setDomainGridlinePaint(Color.MAGENTA);
        plot.setRangeGridlinePaint(Color.MAGENTA);

        boolean add = (this.chartPanel == null);
        this.chartPanel = new ChartPanel(chart);

        if (add) {
            this.content.add(this.chartPanel, BorderLayout.CENTER);
            this.scroll.setViewportView(this.chartPanel);
        }

        this.setBackground(Color.green);
        this.chartPanel.setBackground(Color.MAGENTA);
        this.updateUI();
    }

    private class ItemGenerator implements XYToolTipGenerator {

        public ItemGenerator() {

        }

        @Override
        public String generateToolTip(XYDataset dataset, int series, int category) {
            String name = ((CoordinateSeries) seriesCollection.getSeries(series)).getName(category);
            int v1 = (int) ((CoordinateSeries) seriesCollection.getSeries(series)).getXValue(category);
            int v2 = (int) ((CoordinateSeries) seriesCollection.getSeries(series)).getYValue(category);
            String scaffold = ((CoordinateSeries) seriesCollection.getSeries(series)).getScaffold(category);

            return "\t" + name + ": " + GraphPanel.XAxis + ": " + v1 + ", " + GraphPanel.YAxis + ":" + v2 + "  \t "
                    + scaffold;
        }

    }

}