/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * 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 2
 * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import jalview.datamodel.*;

import java.awt.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class FeatureRenderer
{
    AlignViewport av;
    SequenceGroup currentSequenceGroup = null;
    SequenceGroup[] allGroups = null;
    Color resBoxColour;
    Graphics graphics;

    /**
     * Creates a new FeatureRenderer object.
     *
     * @param av DOCUMENT ME!
     */
    public FeatureRenderer(AlignViewport av)
    {
        this.av = av;
    }

    /**
     * DOCUMENT ME!
     *
     * @param g DOCUMENT ME!
     * @param seq DOCUMENT ME!
     * @param sg DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     * @param x1 DOCUMENT ME!
     * @param y1 DOCUMENT ME!
     * @param width DOCUMENT ME!
     * @param height DOCUMENT ME!
     */
    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
        int start, int end, int x1, int y1, int width, int height)
    {
        Vector features = seq.getSequenceFeatures();
        Enumeration e = features.elements();

        while (e.hasMoreElements())
        {
            SequenceFeature sf = (SequenceFeature) e.nextElement();

            if (sf.getStart() > seq.getEnd())
            {
                continue;
            }

            int fstart = seq.findIndex(sf.getStart()) - 1;
            int fend = seq.findIndex(sf.getEnd()) - 1;

            if (((fstart <= end) && (fend >= start)))
            {
                if (fstart < start)
                { // fix for if the feature we have starts before the sequence start,
                    fstart = start; // but the feature end is still valid!!
                }

                if (fend >= end)
                {
                    fend = end;
                }

                if (fstart == fend)
                {
                    g.setColor(Color.red);
                    g.fillRoundRect((fstart - start) * width, y1, width,
                        height, 4, 4);
                    g.setColor(Color.white);

                    char s = seq.getSequence().charAt(fstart);
                    FontMetrics fm = g.getFontMetrics();
                    int charOffset = (width - fm.charWidth(s)) / 2;
                    int pady = height / 5;
                    g.drawString(String.valueOf(s),
                        charOffset + x1 + (width * (fstart - start)),
                        (y1 + height) - pady);
                }
                else
                {
                    for (int i = fstart; i <= fend; i++)
                    {
                        char s = seq.getSequence().charAt(i);

                        if (jalview.util.Comparison.isGap(s))
                        {
                            continue;
                        }

                        g.setColor(Color.blue);
                        g.fillRect((i - start) * width, y1, width, height);

                        g.setColor(Color.white);

                        FontMetrics fm = g.getFontMetrics();
                        int charOffset = (width - fm.charWidth(s)) / 2;
                        int pady = height / 5;
                        g.drawString(String.valueOf(s),
                            charOffset + x1 + (width * (i - start)),
                            (y1 + height) - pady);
                    }
                }
            }
        }
    }
}