/*
 * 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.tools;

import java.io.*;

/**
 * @author jrobinso
 */
public class UCSCUtils {


    public static void main(String[] args) {

        if (args.length < 3) {
            System.out.println("Usage convertWIGVile <txtFile> <wibFile> <wigFile> [trackLine options]");
            System.exit(-1);
        }
        File txtFile = new File(args[0]);
        File wibFile = new File(args[1]);
        File wigFile = new File(args[2]);
        String trackLine = null;
        if(args.length > 3) {
            trackLine = "track";
            for(int i=3; i<args.length; i++) {
                trackLine += (" " + args[i]);
            }
        }
        convertWIBFile(txtFile, wibFile, wigFile, trackLine);
    }

    /**
     * 0 bin smallint(5) unsigned not null,	# bin scheme for indexing
     * 1  chrom varchar(255) not null,        # Human chromosome or FPC contig
     * 2  chromStart int unsigned not null,   # Start position in chromosome
     * 3  chromEnd int unsigned not null,     # End position in chromosome
     * 4  name varchar(255) not null, 	# Name of item
     * 5  span int unsigned not null, 	# each value spans this many bases
     * 6  count int unsigned not null,        # number of values in this block
     * 7  offset int unsigned not null,       # offset in File to fetch data
     * 8  file varchar(255) not null, 	# path name to .wib data file
     * 9  lowerLimit double not null, 	# lowest data value in this block
     * 10 dataRange double not null,  	# lowerLimit + dataRange = upperLimit
     * 11 validCount int unsigned not null,   # number of valid data values in this block
     * 12 sumData double not null,    	# sum of the data points, for average and stddev calculation
     * 13sumSquares double not null, 	# sum of data points squared, used for stddev calculation
     * 14 INDEX(chrom(8),bin)
     * );
     * <p/>
     * <p/>
     * 0       1       2       3       4       5       6       7        8                              9       10      11
     * 607     chr1    3000000 3005120 chr1.0  5       1024    0       /gbdb/mm8/wib/gc5Base.wib       0       100     1024    37240   1866400
     * <p/>
     * variableStep chrom=chr1 span=5
     * 3000001 19.685
     *
     * @param txtFile
     * @param wibFile
     * @param wigFile
     */
    public static void convertWIBFile(File txtFile, File wibFile, File wigFile, String trackLine) {

        BufferedReader txtReader = null;
        FileInputStream dataInputStream = null;
        PrintWriter wigWriter = null;

        String lastChr = "";
        int lastSpan = -1;
        try {
            txtReader = new BufferedReader(new FileReader(txtFile));
            dataInputStream = new FileInputStream(wibFile);
            wigWriter = new PrintWriter(new BufferedWriter(new FileWriter(wigFile)));

            if (trackLine != null) {
                wigWriter.println(trackLine);
            }

            String nextLine;
            while ((nextLine = txtReader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                String chr = tokens[1];
                // .wig files are 1 based, database is 0 based
                int start = Integer.parseInt(tokens[2]) + 1;
                int span = Integer.parseInt(tokens[5]);

                if (!chr.equals(lastChr) || (span != lastSpan)) {
                    System.out.println("variableStep chrom=" + chr + " span=" + span);
                    wigWriter.println("variableStep chrom=" + chr + " span=" + span);
                    lastChr = chr;
                    lastSpan = span;

                }

                int count = Integer.parseInt(tokens[6]);
                byte[] data = new byte[count];

//seek to position "offset"
//read a block of "count" bytes into array: unsigned char data[]
//The first data byte corresponds to genome position "chromStart"
//The next data byte genome position is: "chromStart" + "span"
//data byte value of 128 indicates "NO DATA" at this position
//data byte values 0 to 127 are expanded to double types via:
                Integer offset = Integer.parseInt(tokens[7]);
                dataInputStream.getChannel().position(offset);
                DataInputStream dis = new DataInputStream(dataInputStream);
                dis.readFully(data);

                double lowerLimit = Double.parseDouble(tokens[9]);
                double dataRange = Double.parseDouble(tokens[10]);

                int chromPosition = start;
                for (int i = 0; i < count; ++i, chromPosition += span) {
                    if (data[i] < 128) {
                        double value = lowerLimit + (dataRange * ((double) data[i] / 127.0));
                        wigWriter.println(chromPosition + "\t" + value);
                    }
                }


            }

        } catch (IOException ex) {
            ex.printStackTrace();
        } finally {
            try {
                txtReader.close();
                dataInputStream.close();
                wigWriter.close();
            } catch (IOException ex) {
                ex.printStackTrace();
            }
        }
    }

}
