/*
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  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
 * WARRANTES 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.feature.genome;

import org.broad.igv.util.ParsingUtils;
import org.broad.tribble.util.SeekableStream;
import org.broad.tribble.util.SeekableStreamFactory;

import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Set;

/**
 * Implementation of Sequence backed by an indexed fasta file
 *
 * @author jrobinso
 * @date 8/7/11
 */
public class FastaIndexedSequence implements Sequence {

    FastaIndex index;
    String path;
    long contentLength;

    public FastaIndexedSequence(String path) throws IOException {

        this.path = path;

        contentLength = ParsingUtils.getContentLength(path);

        // TODO -- check for existence path & index
        String indexPath = path + ".fai";
        index = new FastaIndex(indexPath);
    }


    /**
     * Return the sequence for the query interval as a byte array.  Coordinates are "ucsc" style (0 based)
     * <p/>
     * Example:  5 bases per line, 6 bytes per line
     * <p/>
     * Bases    0 1 2 3 4 * | 5 6 7 8  9 * | 10 11 12 13 14 *  etc
     * Offset   0 1 2 3 4     0 1 2 3  4      0  1  2  3  4
     * Bytes    0 1 2 3 4 5 | 6 7 8 9 10   | 11 12 13 14 15 16
     * <p/>
     * query 9 - 13
     * start line = 1
     * base0      = 1*5 = 5
     * offset     = (9 - 5) = 4
     * start byte = (1*6) + 3 = 10
     * end   line = 2
     *
     * @param chr
     * @param qstart
     * @param qend
     * @return
     */

    public byte[] readSequence(String chr, int qstart, int qend) {

        FastaIndex.FastaSequenceIndexEntry idxEntry = index.getIndexEntry(chr);
        if (idxEntry == null) {
            return null;
        }

        try {

            final int start = Math.max(0, qstart);    // qstart should never be < 0
            final int end = Math.min((int) idxEntry.getSize(), qend);

            final int bytesPerLine = idxEntry.getBytesPerLine();
            final int basesPerLine = idxEntry.getBasesPerLine();
            int nEndBytes = bytesPerLine - basesPerLine;

            int startLine = start / basesPerLine;
            int endLine = end / basesPerLine;

            int base0 = startLine * basesPerLine;   // Base at beginning of start line

            int offset = start - base0;
            final long position = idxEntry.getPosition();
            long startByte = position + startLine * bytesPerLine + offset;

            int base1 = endLine * basesPerLine;
            int offset1 = end - base1;
            long endByte = Math.min(contentLength, position + endLine * bytesPerLine + offset1);

            if (startByte >= endByte) {
                return null;
            }

            // Read all the bytes in the range.  This will include endline characters
            byte[] allBytes = readBytes(startByte, endByte);

            // Create the array for the sequence -- this will be "allBytes" without the endline characters.
            ByteArrayOutputStream bos = new ByteArrayOutputStream(end - start);

            int srcPos = 0;
            int desPos = 0;
            // Copy first line
            final int allBytesLength = allBytes.length;
            if (offset > 0) {
                int nBases = Math.min(end - start, basesPerLine - offset);
                bos.write(allBytes, srcPos, nBases);
                srcPos += (nBases + nEndBytes);
                desPos += nBases;
            }

            while (srcPos < allBytesLength) {
                int nBases = Math.min(basesPerLine, allBytesLength - srcPos);
                bos.write(allBytes, srcPos, nBases);
                srcPos += (nBases + nEndBytes);
                desPos += nBases;
            }


            return bos.toByteArray();

        } catch (IOException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.

            return null;
        }


    }


    /**
     * Read the bytes between file position posStart and posEnd
     *
     * @throws IOException
     */
    private byte[] readBytes(long posStart, long posEnd) throws IOException {

        SeekableStream ss = null;
        try {
            ss = SeekableStreamFactory.getStreamFor(path);
            int nBytes = (int) (posEnd - posStart);
            byte[] bytes = new byte[nBytes];
            ss.seek(posStart);
            ss.readFully(bytes);
            return bytes;
        } finally {
            if (ss != null) {
                ss.close();
            }
        }
    }

    public Set<String> getChromosomeNames() {
        return index.getSequenceNames();
    }

    public int getChromosomeLength(String chrname) {
        return index.getSequenceSize(chrname);
    }
}
