Java Code Examples for com.esotericsoftware.kryo.io.Input#readByte()

public ArrayMetaData<byte[]> read(Kryo kryo, Input input, Class<ArrayMetaData<byte[]>> type) {
    try {
        byte[] arrData = arrayMetaData.getArrData();
        thatArrMetaData = arrayMetaData.recv(input);
        int arrSegNum = thatArrMetaData.getSegNum();
        for (int i = 0; i < arrSegNum; i++) {
            int from = thatArrMetaData.getFrom(i);
            int to = thatArrMetaData.getTo(i);
            for (int j = from; j < to; j++) {
                arrData[j] = input.readByte();
            }
        }
        thatArrMetaData.setArrData(arrData);
    } catch (IOException e) {
        LOG.error("double array read exception", e);
        System.exit(1);
    }
    return thatArrMetaData;

}
 

@Override
public MapMetaData<Byte> read(Kryo kryo, Input input, Class<MapMetaData<Byte>> type) {
    try {
        thatMapMetaData = mapMetaData.recv(input);
        int thatMapSegNum = thatMapMetaData.getSegNum();
        List<Map<String, Byte>> mapDataList = new ArrayList<>(thatMapSegNum);
        thatMapMetaData.setMapDataList(mapDataList);

        for (int i = 0; i < thatMapSegNum; i++) {
            int dataNum = thatMapMetaData.getDataNum(i);
            Map<String, Byte> mapData = new HashMap<>(dataNum);
            mapDataList.add(mapData);
            for (int j = 0; j < dataNum; j++) {
                String key = input.readString();
                Byte val = input.readByte();
                mapData.put(key, val);
            }
        }
    } catch (IOException e) {
        LOG.error("double array read exception", e);
        System.exit(1);
    }
    return thatMapMetaData;
}
 

AlignedContig(final Kryo kryo, final Input input) {

        contigName = input.readString();

        final int nBases = input.readInt();
        contigSequence = new byte[nBases];
        for (int b = 0; b < nBases; ++b) {
            contigSequence[b] = input.readByte();
        }

        final int nAlignments = input.readInt();
        alignmentIntervals = new ArrayList<>(nAlignments);
        for (int i = 0; i < nAlignments; ++i) {
            alignmentIntervals.add(new AlignmentInterval(kryo, input));
        }
    }
 

public void read (Kryo kryo, Input input) {
	objectID = input.readInt(true);

	int methodClassID = input.readInt(true);
	Class methodClass = kryo.getRegistration(methodClassID).getType();
	byte methodIndex = input.readByte();
	CachedMethod cachedMethod;
	try {
		cachedMethod = getMethods(kryo, methodClass)[methodIndex];
	} catch (IndexOutOfBoundsException ex) {
		throw new KryoException("Invalid method index " + methodIndex + " for class: " + methodClass.getName());
	}
	method = cachedMethod.method;

	args = new Object[cachedMethod.serializers.length];
	for (int i = 0, n = args.length; i < n; i++) {
		Serializer serializer = cachedMethod.serializers[i];
		if (serializer != null)
			args[i] = kryo.readObjectOrNull(input, method.getParameterTypes()[i], serializer);
		else
			args[i] = kryo.readClassAndObject(input);
	}

	responseID = input.readByte();
}
 

public MapMetaData<Byte> read(Kryo kryo, Input input, Class<MapMetaData<Byte>> type) {
    try {
        thatMapMetaData = mapMetaData.recv(input);
        int thatMapSegNum = thatMapMetaData.getSegNum();
        List<Map<String, Byte>> thatMapListData = new ArrayList<>(thatMapSegNum);
        List<Integer> thatDataNums = new ArrayList<>(thatMapSegNum);
        for (int i = 0; i < thatMapSegNum; i++) {
            Map<String, Byte> thisMapData = mapMetaData.getMapDataList().get(i);
            int dataNum = thatMapMetaData.getDataNum(i);
            for (int j = 0; j < dataNum; j++) {
                String key = input.readString();
                Byte val = input.readByte();

                Byte thisVal = thisMapData.get(key);
                if (thisVal == null) {
                    thisMapData.put(key, val);
                } else {
                    thisMapData.put(key, operator.apply(thisVal, val));
                }
            }
            thatMapListData.add(thisMapData);
            thatDataNums.add(thisMapData.size());
        }

        thatMapMetaData.setMapDataList(thatMapListData);
        thatMapMetaData.setDataNums(thatDataNums);

    } catch (IOException e) {
        LOG.error("double array read exception", e);
        System.exit(1);
    }
    return thatMapMetaData;
}
 

protected NovelAdjacencyAndAltHaplotype(final Kryo kryo, final Input input) {
    final String contig1 = input.readString();
    final int start1 = input.readInt();
    final int end1 = input.readInt();
    this.leftJustifiedLeftRefLoc = new SimpleInterval(contig1, start1, end1);
    final String contig2 = input.readString();
    final int start2 = input.readInt();
    final int end2 = input.readInt();
    this.leftJustifiedRightRefLoc = new SimpleInterval(contig2, start2, end2);

    this.strandSwitch = StrandSwitch.values()[input.readInt()];

    this.complication = (BreakpointComplications) kryo.readClassAndObject(input);

    this.type = TypeInferredFromSimpleChimera.values()[ input.readInt() ];

    final boolean altSeqIsNull = input.readBoolean();
    if (altSeqIsNull) {
        altHaplotypeSequence = null;
    } else {
        final int arraySize = input.readInt();
        altHaplotypeSequence = new byte[arraySize];
        for (int i = 0 ; i < arraySize; ++i) {
            altHaplotypeSequence[i] = input.readByte();
        }
    }
}
 

/**
 * a technical constructor for use in Kryo (de-)serialization.
 * this creates an object by reading a Kryo-serialized stream.
 * it will be called by subclasses in their own constructors from Kryo streams (as super(kryo, input)).
 */
protected ReadEvidence( final Kryo kryo, final Input input ) {
    super(kryo, input);
    this.templateName = input.readString();
    this.fragmentOrdinal = TemplateFragmentOrdinal.values()[input.readByte()];
    this.forwardStrand = input.readBoolean();
    this.cigarString = input.readString();
    this.mappingQuality = input.readInt();
    this.templateSize = input.readInt();
    this.readGroup = input.readString();
}
 

public void read (Kryo kryo, Input input) {
	objectID = input.readInt(true);

	int methodClassID = input.readInt(true);
	Class methodClass = kryo.getRegistration(methodClassID).getType();

	byte methodIndex = input.readByte();
	try {
		cachedMethod = getMethods(kryo, methodClass)[methodIndex];
	} catch (IndexOutOfBoundsException ex) {
		throw new KryoException("Invalid method index " + methodIndex + " for class: " + methodClass.getName());
	}

	Serializer[] serializers = cachedMethod.serializers;
	Class[] parameterTypes = cachedMethod.method.getParameterTypes();
	Object[] args = new Object[serializers.length];
	this.args = args;
	for (int i = 0, n = args.length; i < n; i++) {
		Serializer serializer = serializers[i];
		if (serializer != null)
			args[i] = kryo.readObjectOrNull(input, parameterTypes[i], serializer);
		else
			args[i] = kryo.readClassAndObject(input);
	}

	responseData = input.readByte();
}
 

@Override
public Value read(final Kryo kryo, final Input input, final Class<Value> type) {
    switch (input.readByte()) {
        case 0:
            return new Value(null);
        case 1:
            return new Value(kryo.readClassAndObject(input));
        case 2:
            return new Value(kryo.readObject(input, UUID.class));
        default:
            throw new SynchronizeFXException("Received a Value message of an unknown type.");
    }
}
 

@Override
public Interpolation.Bounce read(Kryo kryo, Input input, Class<Interpolation.Bounce> type) {
	int widths = input.readByte();
	int heights = input.readByte();
	return new Interpolation.Bounce(input.readFloats(widths), input.readFloats(heights));
}
 

@Override
public Interpolation.BounceIn read(Kryo kryo, Input input, Class<Interpolation.BounceIn> type) {
	int widths = input.readByte();
	int heights = input.readByte();
	return new Interpolation.BounceIn(input.readFloats(widths), input.readFloats(heights));
}
 

@Override
public Interpolation.BounceOut read(Kryo kryo, Input input, Class<Interpolation.BounceOut> type) {
	int widths = input.readByte();
	int heights = input.readByte();
	return new Interpolation.BounceOut(input.readFloats(widths), input.readFloats(heights));
}