/*
 * 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.
 */

package org.broad.igv.track.tribble;

import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.Exon;
import org.broad.igv.feature.Strand;
import org.broad.igv.util.ParsingUtils;
import org.broad.tribble.Feature;

/**
 * @author jrobinso
 * @date Aug 5, 2010
 */
public class PSLCodec extends UCSCCodec {

    public Feature decode(String line) {

        BasicFeature f = null;
        try {
            if (line.trim().length() == 0 || line.startsWith("#") || line.startsWith("track") ||
                    line.startsWith("browser")) {
                return null;
            }

            int nTokens = ParsingUtils.splitWhitespace(line, tokens);
            if (nTokens < 21) {
                // log.info("Skipping line ")
                return null;
            }
            int tSize = Integer.parseInt(tokens[14]);
            String chr = tokens[13];
            int start = Integer.parseInt(tokens[15]); // IS PSL 1 or ZERO based,  closed or open?

            String strandString = tokens[8];
            Strand strand = strandString.startsWith("+") ? Strand.POSITIVE : Strand.NEGATIVE;

            boolean gNeg = false;
            if (strandString.length() > 1) {
                gNeg = strandString.charAt(1) == '-';
            }

            f = new BasicFeature();
            f.setName(tokens[9]);
            f.setChr(chr);
            f.setStart(start);
            f.setEnd(Integer.parseInt(tokens[16]));
            f.setStrand(strand);

            int exonCount = Integer.parseInt(tokens[17]);
            String[] exonSizes = tokens[18].split(",");
            String[] startsBuffer = tokens[20].split(",");

            if (startsBuffer.length == exonSizes.length && exonCount == startsBuffer.length) {
                for (int i = 0; i < startsBuffer.length; i++) {
                    int exonSize = Integer.parseInt(exonSizes[i]);
                    int exonStart = Integer.parseInt(startsBuffer[i]);
                    if (gNeg) {
                        exonStart = tSize - exonStart - exonSize;
                    }
                    int exonEnd = exonStart + exonSize;
                    Exon exon = new Exon(chr, exonStart, exonEnd, strand);
                    f.addExon(exon);
                }
            } else {
                // TODO -- warn
            }
        } catch (NumberFormatException e) {
            return null;
        }


        return f;   
    }
}
