Examples with MessagePackSerialization org.rcsb.mmtf.serialization.MessagePackSerialization used on opensource projects

Example 1 with MessagePackSerialization

use of org.rcsb.mmtf.serialization.MessagePackSerialization in project mmtf-spark by sbl-sdsc.

the class MmtfReader method readMmtfFiles.

/**
 * Reads uncompressed and compressed MMTF files recursively from
 * a given directory.
 * This methods reads files with the mmtf or mmtf.gz extension.
 *
 * @param path Path to MMTF files
 * @param sc Spark context
 * @return structure data as keyword/value pairs
 */
public static JavaPairRDD<String, StructureDataInterface> readMmtfFiles(String path, JavaSparkContext sc) {
    return sc.parallelize(getFiles(path)).mapToPair(new PairFunction<File, String, StructureDataInterface>() {

        private static final long serialVersionUID = 9018971417443154996L;

        public Tuple2<String, StructureDataInterface> call(File f) throws Exception {
            try {
                if (f.toString().contains(".mmtf.gz")) {
                    InputStream in = new FileInputStream(f);
                    MmtfStructure mmtf = new MessagePackSerialization().deserialize(new GZIPInputStream(in));
                    return new Tuple2<String, StructureDataInterface>(f.getName().substring(0, f.getName().indexOf(".mmtf")), new GenericDecoder(mmtf));
                } else if (f.toString().contains(".mmtf")) {
                    InputStream in = new FileInputStream(f);
                    MmtfStructure mmtf = new MessagePackSerialization().deserialize(in);
                    return new Tuple2<String, StructureDataInterface>(f.getName().substring(0, f.getName().indexOf(".mmtf")), new GenericDecoder(mmtf));
                } else
                    return null;
            } catch (Exception e) {
                System.out.println(e);
                return null;
            }
        }
    }).filter(t -> t != null);
}

Example 2 with MessagePackSerialization

use of org.rcsb.mmtf.serialization.MessagePackSerialization in project mmtf-spark by sbl-sdsc.

the class MmtfWriter method toByteArray.

/**
 * Returns an MMTF-encoded byte array with optional gzip compression.
 * @return MMTF encoded and optionally gzipped structure data
 * @throws IOException
 */
private static byte[] toByteArray(StructureDataInterface structure, boolean compressed) throws IOException {
    GenericEncoder genericEncoder = new GenericEncoder(structure);
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    MessagePackSerialization serializer = new MessagePackSerialization();
    serializer.serialize(genericEncoder.getMmtfEncodedStructure(), bos);
    if (compressed) {
        return WriterUtils.gzipCompress(bos.toByteArray());
    } else {
        return bos.toByteArray();
    }
}