/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package org.broad.igv.sam;

import org.broad.igv.track.RenderContext;

import java.awt.*;
import java.util.List;
import java.util.Map;

/**
 * @author jrobinso
 */
public class BedRenderer implements FeatureRenderer {

    public void renderAlignments(List<Alignment> alignments, RenderContext context,
                                 Rectangle rect, AlignmentTrack.RenderOptions renderOptions, boolean leaveMargin,
                                 Map<String, Color> selectedReadNames) {

        double origin = context.getOrigin();
        double locScale = context.getScale();

        if ((alignments != null) && (alignments.size() > 0)) {


            for (Alignment alignment : alignments) {

                // Compute the start and dend of the alignment in pixels
                double pixelStart = ((alignment.getStart() - origin) / locScale);
                double pixelEnd = ((alignment.getEnd() - origin) / locScale);

                // If the any part of the feature fits in the track rectangle draw  it
                if ((pixelEnd >= rect.getX()) && (pixelStart <= rect.getMaxX())) {

                    Graphics2D g = context.getGraphic2DForColor(Color.GRAY);

                    // If the alignment is 3 pixels or less,  draw alignment as posA single block,
                    // further detail would not be seen and just add to drawing overhead
                    int w = Math.max(1, (int) (pixelEnd - pixelStart));
                    int h = (int) Math.max(1, rect.getHeight() - 2);
                    int y = (int) (rect.getY() + (rect.getHeight() - h) / 2);
                    g.fillRect((int) pixelStart, y, w, h);


                }
            }

        }

    }
}
