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Apache Commons Imaging (previously Sanselan) is a pure-Java image library.
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/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.commons.imaging.common.itu_t4;

import java.io.IOException;
import java.io.InputStream;

/**
 * Input stream that allows reading up to 32 bits
 * across byte boundaries in most significant
 * bit first order.
 */
class BitInputStreamFlexible extends InputStream {
    // TODO should be byte order conscious, ie TIFF for reading
    // samples size<8 - shuoldn't that effect their order within byte?
    private final InputStream is;
    private int cache;
    private int cacheBitsRemaining;
    private long bytesRead;

    public BitInputStreamFlexible(final InputStream is) {
        this.is = is;
        // super(is);
    }

    @Override
    public int read() throws IOException {
        if (cacheBitsRemaining > 0) {
            throw new IOException("BitInputStream: incomplete bit read");
        }
        return is.read();
    }

    public final int readBits(int count) throws IOException {

        if (count <= 32)  {
            // catch-all
            int result = 0;
            // int done = 0;

            if (cacheBitsRemaining > 0) {
                if (count >= cacheBitsRemaining) {
                    result = ((1 << cacheBitsRemaining) - 1) & cache;
                    count -= cacheBitsRemaining;
                    cacheBitsRemaining = 0;
                } else {
                    // cache >>= count;
                    cacheBitsRemaining -= count;
                    result = ((1 << count) - 1) & (cache >> cacheBitsRemaining);
                    count = 0;
                }
            }
            while (count >= 8) {
                cache = is.read();
                if (cache < 0) {
                    throw new IOException("couldn't read bits");
                }
                // System.out.println("cache 1: " + cache + " ("
                // + Integer.toHexString(cache) + ", "
                // + Integer.toBinaryString(cache) + ")");
                bytesRead++;
                result = (result << 8) | (0xff & cache);
                count -= 8;
            }
            if (count > 0) {
                cache = is.read();
                if (cache < 0) {
                    throw new IOException("couldn't read bits");
                }
                // System.out.println("cache 2: " + cache + " ("
                // + Integer.toHexString(cache) + ", "
                // + Integer.toBinaryString(cache) + ")");
                bytesRead++;
                cacheBitsRemaining = 8 - count;
                result = (result << count)
                        | (((1 << count) - 1) & (cache >> cacheBitsRemaining));
                count = 0;
            }

            return result;
        }

        throw new IOException("BitInputStream: unknown error");

    }

    public void flushCache() {
        cacheBitsRemaining = 0;
    }

    public long getBytesRead() {
        return bytesRead;
    }
}