de.julielab.genemapper.resources.MultiStreamBZip2InputStream Maven / Gradle / Ivy

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This project assembles code and files required to build the dictionaries and indexes used by the JCoRe Gene Mapper.

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package de.julielab.genemapper.resources;

import org.apache.commons.compress.compressors.CompressorInputStream;
import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;

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

/**
 * Handle multistream BZip2 files.
 * From https://chaosinmotion.com/2011/07/29/and-another-curiosity-multi-stream-bzip2-files/
 */
public class MultiStreamBZip2InputStream extends CompressorInputStream {
    private final InputStream fInputStream;
    private BZip2CompressorInputStream fBZip2;

    public MultiStreamBZip2InputStream(InputStream in) throws IOException {
        fInputStream = in;
        fBZip2 = new BZip2CompressorInputStream(in);
    }

    @Override
    public int read() throws IOException {
        int ch = fBZip2.read();
        if (ch == -1) {
            /*
             * If this is a multistream file, there will be more data that
             * follows that is a valid compressor input stream. Restart the
             * decompressor engine on the new segment of the data.
             */
            if (fInputStream.available() > 0) {
                // Make use of the fact that if we hit EOF, the data for
                // the old compressor was deleted already, so we don't need
                // to close.
                fBZip2 = new BZip2CompressorInputStream(fInputStream);
                ch = fBZip2.read();
            }
        }
        return ch;
    }

    /**
     * Read the data from read(). This makes sure we funnel through read so
     * we can do our multistream magic.
     */
    public int read(byte[] dest, int off, int len) throws IOException {
        if ((off < 0) || (len < 0) || (off + len > dest.length)) {
            throw new IndexOutOfBoundsException("Reading " + len + " bytes from offset " + off + " which sums to " + off + len + " but there are only " + dest.length + " bytes.");
        }

        int i = 1;
        int c = read();
        if (c == -1) return -1;
        dest[off++] = (byte) c;
        while (i < len) {
            c = read();
            if (c == -1) break;
            dest[off++] = (byte) c;
            ++i;
        }
        return i;
    }

    public void close() throws IOException {
        fBZip2.close();
        fInputStream.close();
    }
}