/*
 * 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.track.TrackProperties;
import org.broad.igv.track.TrackType;
import org.broad.igv.util.ParsingUtils;
import org.broad.tribble.Feature;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.util.LineReader;

import java.awt.*;
import java.io.IOException;

/**
 * Created by IntelliJ IDEA.
 * User: jrobinso
 * Date: Dec 20, 2009
 * Time: 10:15:49 PM
 * To change this template use File | Settings | File Templates.
 */
public class BEDCodec implements org.broad.tribble.FeatureCodec {

    // Declare a static array once, to be reused.
    static String[] tokens = new String[15];
    int startBase = 0;
    FeatureFileHeader header;

    public Object readHeader(LineReader reader) {
        String nextLine;
        header = new FeatureFileHeader();
        int nLines = 0;

        try {
            while ((nextLine = reader.readLine()) != null &&
                    (nextLine.startsWith("#") || nextLine.startsWith("track")) ||
                    nextLine.startsWith("browser")) {
                nLines++;
                if (nextLine.startsWith("#type")) {
                    String[] tokens = nextLine.split("=");
                    if (tokens.length > 1) {
                        try {
                            header.setTrackType(TrackType.valueOf(tokens[1]));
                        } catch (Exception e) {
                            // log.error("Error converting track type: " + tokens[1]);
                        }
                    }
                } else if (nextLine.startsWith("track")) {
                    TrackProperties tp = new TrackProperties();
                    ParsingUtils.parseTrackLine(nextLine, tp);
                    header.setTrackProperties(tp);
                }
            }
            return header;
        }
        catch (IOException e) {
            throw new CodecLineParsingException("Error parsing header", e);
        }
    }

    public Feature decodeLoc(String line) {
        return decode(line);  //To change body of implemented methods use File | Settings | File Templates.
    }

    public BasicFeature decode(String nextLine) {

        if (nextLine.trim().length() == 0 || nextLine.startsWith("#") || nextLine.startsWith("track") ||
                nextLine.startsWith("browser")) {
            return null;
        }

        int tokenCount = ParsingUtils.splitWhitespace(nextLine, tokens);

        // The first 3 columns are non optional for BED.  We will relax this
        // and only require 2.

        if (tokenCount < 2) {
            return null;
        }

        String chr = tokens[0];  //genome == null ? tokens[0] : genome.getChromosomeAlias(tokens[0]);
        int start = Integer.parseInt(tokens[1]) - startBase;

        int end = start + 1;
        if (tokenCount > 2) {
            end = Integer.parseInt(tokens[2]) - startBase;
        }

        BasicFeature feature = new BasicFeature(chr, start, end);

        // The rest of the columns are optional.  Stop parsing upon encountering
        // a non-expected value

        // Name
        if (tokenCount > 3) {
            String name = tokens[3].replaceAll("\"", "");
            feature.setName(name);
            feature.setIdentifier(name);
        }

        // Score
        if (tokenCount > 4) {
            try {
                float score = Float.parseFloat(tokens[4]);
                feature.setScore(score);
            } catch (NumberFormatException numberFormatException) {

                // Unexpected, but does not invalidate the previous values.
                // Stop parsing the line here but keep the feature
                // Don't log, would just slow parsing down.
                return feature;
            }
        }

        // Strand
        if (tokenCount > 5) {
            String strandString = tokens[5].trim();
            char strand = (strandString.length() == 0)
                    ? ' ' : strandString.charAt(0);

            if (strand == '-') {
                feature.setStrand(Strand.NEGATIVE);
            } else if (strand == '+') {
                feature.setStrand(Strand.POSITIVE);
            } else {
                feature.setStrand(Strand.NONE);
            }
        }

        if (tokenCount > 8) {
            String colorString = tokens[8];
            feature.setColor(parseColor(colorString));
        }

        // Coding information is optional
        if (tokenCount > 11) {
            createExons(start, tokens, feature, chr, feature.getStrand());
        }

        return feature;
    }


    public Class getFeatureType() {
        return BasicFeature.class;  //To change body of implemented methods use File | Settings | File Templates.
    }

    private void createExons(int start, String[] tokens, BasicFeature gene, String chr,
                             Strand strand) throws NumberFormatException {

        int cdStart = Integer.parseInt(tokens[6]);
        int cdEnd = Integer.parseInt(tokens[7]);

        int exonCount = Integer.parseInt(tokens[9]);
        String[] exonSizes = new String[exonCount];
        String[] startsBuffer = new String[exonCount];
        ParsingUtils.split(tokens[10], exonSizes, ',');
        ParsingUtils.split(tokens[11], startsBuffer, ',');

        int exonNumber = (strand == Strand.NEGATIVE ? exonCount : 1);

        if (startsBuffer.length == exonSizes.length) {
            for (int i = 0; i < startsBuffer.length; i++) {
                int exonStart = start + Integer.parseInt(startsBuffer[i]);
                int exonEnd = exonStart + Integer.parseInt(exonSizes[i]);
                Exon exon = new Exon(chr, exonStart, exonEnd, strand);
                exon.setCodingStart(cdStart);
                exon.setCodingEnd(cdEnd);
                exon.setNumber(exonNumber);
                gene.addExon(exon);

                if (strand == Strand.NEGATIVE) {
                    exonNumber--;
                } else {
                    exonNumber++;
                }
            }
        }
    }


    /**
     * TODO -- move this to a utility class
     *
     * @param colorString
     * @return
     */
    private Color parseColor(String colorString) {
        String[] rgb = new String[3];
        int nTokens = ParsingUtils.split(tokens[8].replaceAll("\"", ""), rgb, ',');

        try {
            if (nTokens < 3) {
                // TODO -- is this the right constructor to use?
                return new Color(Integer.parseInt(rgb[0]));
            } else {
                return new Color(Integer.parseInt(rgb[0]), Integer.parseInt(rgb[1]),
                        Integer.parseInt(rgb[2]));
            }
        } catch (NumberFormatException numberFormatException) {
            //log.error("Error parsing color from rgb string: " + rgb[0] + rgb[1] + rgb[2]);
            return null;
        }
    }


}