// Path: scala/org/broad/igv/StringUtils.java
// public class StringUtils {
// 
// 
//     public static List<String> breakQuotedString(String string, char splitToken) {
// 
//         ArrayList<String> strings = new ArrayList();
//         if (string.length() == 0) {
//             return strings;
//         }
// 
//         char[] characters = string.toCharArray();
//         char c = characters[0];
// 
//         boolean isQuoted = false;
//         StringBuffer buff = new StringBuffer(100);
//         for (int i = 0; i < characters.length; i++) {
//             c = characters[i];
//             if (isQuoted) {
//                 if (c == '"') {
//                     isQuoted = false;
//                 }
//                 buff.append(c);
//             } else if (c == '"') {
//                 isQuoted = true;
//                 buff.append(c);
//             } else {
//                 if (c == splitToken) {
//                     strings.add(buff.toString().trim());
//                     buff.setLength(0);
//                 } else {
//                     buff.append(c);
//                 }
//             }
//         }
//         if (buff.length() > 0) {
//             strings.add(buff.toString().trim());
//         }
//         return strings;
// 
//     }
// 
// 
//     public static short genoToShort(String genotype) {
//         byte[] bytes = genotype.getBytes();
//         return (short) ((bytes[0] & 0xff) << 8 | (bytes[1] & 0xff));
//     }
//     
//     public static String readString(ByteBuffer byteBuffer) throws IOException {
//         ByteArrayOutputStream bytes = new ByteArrayOutputStream();
//         byte b = -1;
//         while ((b = byteBuffer.get()) != 0) {
//             bytes.write(b);
//         }
//         return new String(bytes.toByteArray());
//     }
// 
//     public static void main(String[] args) {
// 
//         String genotype = "AC";
//         short genoShort = genoToShort(genotype);
// 
//         char allel1 = (char) ((genoShort >>> 8) & 0xFF);
//         char allel2 = (char) ((genoShort >>> 0) & 0xFF);
// 
//         System.out.println("Allele1: " + allel1);
//         System.out.println("Allele2: " + allel2);
// 
//     }
// }


import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import org.broad.igv.StringUtils;
/*
 * 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;




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

    public static TDFTile createTile(byte[] buffer, int nSamples) throws IOException {

        ByteBuffer byteBuffer = ByteBuffer.wrap(buffer);
        byteBuffer.order(ByteOrder.LITTLE_ENDIAN);

// Path: scala/org/broad/igv/StringUtils.java
// public class StringUtils {
// 
// 
//     public static List<String> breakQuotedString(String string, char splitToken) {
// 
//         ArrayList<String> strings = new ArrayList();
//         if (string.length() == 0) {
//             return strings;
//         }
// 
//         char[] characters = string.toCharArray();
//         char c = characters[0];
// 
//         boolean isQuoted = false;
//         StringBuffer buff = new StringBuffer(100);
//         for (int i = 0; i < characters.length; i++) {
//             c = characters[i];
//             if (isQuoted) {
//                 if (c == '"') {
//                     isQuoted = false;
//                 }
//                 buff.append(c);
//             } else if (c == '"') {
//                 isQuoted = true;
//                 buff.append(c);
//             } else {
//                 if (c == splitToken) {
//                     strings.add(buff.toString().trim());
//                     buff.setLength(0);
//                 } else {
//                     buff.append(c);
//                 }
//             }
//         }
//         if (buff.length() > 0) {
//             strings.add(buff.toString().trim());
//         }
//         return strings;
// 
//     }
// 
// 
//     public static short genoToShort(String genotype) {
//         byte[] bytes = genotype.getBytes();
//         return (short) ((bytes[0] & 0xff) << 8 | (bytes[1] & 0xff));
//     }
//     
//     public static String readString(ByteBuffer byteBuffer) throws IOException {
//         ByteArrayOutputStream bytes = new ByteArrayOutputStream();
//         byte b = -1;
//         while ((b = byteBuffer.get()) != 0) {
//             bytes.write(b);
//         }
//         return new String(bytes.toByteArray());
//     }
// 
//     public static void main(String[] args) {
// 
//         String genotype = "AC";
//         short genoShort = genoToShort(genotype);
// 
//         char allel1 = (char) ((genoShort >>> 8) & 0xFF);
//         char allel2 = (char) ((genoShort >>> 0) & 0xFF);
// 
//         System.out.println("Allele1: " + allel1);
//         System.out.println("Allele2: " + allel2);
// 
//     }
// }


// Path: scala/org/broad/igv/TileFactory.java
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import org.broad.igv.StringUtils;

/*
 * 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;




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

    public static TDFTile createTile(byte[] buffer, int nSamples) throws IOException {

        ByteBuffer byteBuffer = ByteBuffer.wrap(buffer);
        byteBuffer.order(ByteOrder.LITTLE_ENDIAN);

        String typeString = StringUtils.readString(byteBuffer);