/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package org.broad.igv.util;

import java.io.ByteArrayOutputStream;
import java.io.EOFException;
import java.io.FilterInputStream;
import java.io.IOException;
import java.io.InputStream;

public class LittleEndianInputStream extends htsjdk.tribble.util.LittleEndianInputStream {
    byte[] buffer = new byte[8];

    public LittleEndianInputStream(InputStream in) {
        super(in);
    }

    public int readUShort() throws IOException {

        int byte1 = in.read();
        int byte2 = in.read();
        if(byte2 < 0) {
            throw new EOFException();
        } else {
            return ((byte2 << 24 >>> 16) + (byte1 << 24 >>> 24));
        }
    }

    public void readFully(byte[] b) throws IOException {
        readFully(b, 0, b.length);
    }

    public void readFully(byte[] b, int off, int len) throws IOException {
        if(len < 0) {
            throw new IndexOutOfBoundsException("len is negative");
        } else {
            int total;
            int result;
            for(total = 0; total < len; total += result) {
                result = in.read(b, off + total, len - total);
                if(result == -1) {
                    break;
                }
            }

        }
    }

    @Override
    public String readString() throws IOException {
        ByteArrayOutputStream bis = new ByteArrayOutputStream(1000);
        int b;
        while ((b = in.read()) != 0) {
            if(b < 0) {
                throw new EOFException();
            }
            bis.write((byte) b);
        }
        return new String(bis.toByteArray());
    }
}
