Example usage for java.io DataInput readShort

Introduction

In this page you can find the example usage for java.io DataInput readShort.

Prototype

short readShort() throws IOException;

Source Link

Document

Reads two input bytes and returns a short value.

Usage

From source file:backup.store.BackupUtil.java

public static String readShortString(DataInput in) throws IOException {
    byte[] buf = new byte[in.readShort()];
    in.readFully(buf);/*w  w  w . j ava  2  s . c  o  m*/
    return new String(buf);
}

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From source file:hivemall.fm.FFMPredictionModel.java

@Nonnull
private static void readEntry(@Nonnull final DataInput in, final int factors, @Nonnull final float[] Vf,
        @Nonnull Entry dst) throws IOException {
    final byte type = in.readByte();
    switch (type) {
    case HALF_FLOAT_ENTRY: {
        float W = HalfFloat.halfFloatToFloat(in.readShort());
        dst.setW(W);//w  ww  .j a va 2  s  .  co  m
        for (int i = 0; i < factors; i++) {
            Vf[i] = HalfFloat.halfFloatToFloat(in.readShort());
        }
        dst.setV(Vf);
        break;
    }
    case W_ONLY_HALF_FLOAT_ENTRY: {
        float W = HalfFloat.halfFloatToFloat(in.readShort());
        dst.setW(W);
        break;
    }
    case FLOAT_ENTRY: {
        float W = in.readFloat();
        dst.setW(W);
        IOUtils.readFloats(in, Vf);
        dst.setV(Vf);
        break;
    }
    case W_ONLY_FLOAT_ENTRY: {
        float W = in.readFloat();
        dst.setW(W);
        break;
    }
    default:
        throw new IOException("Unexpected Entry type: " + type);
    }
}

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From source file:com.buaa.cfs.fs.permission.FsPermission.java

@Override
public void readFields(DataInput in) throws IOException {
    fromShort(in.readShort());
}

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From source file:libra.common.hadoop.io.datatypes.CompressedIntArrayWritable.java

@Override
public void readFields(DataInput in) throws IOException {
    byte flag = in.readByte();
    int count = 0;
    if ((flag & 0x0f) == 0x00) {
        count = in.readByte();// ww  w .  j a  v  a  2 s .com
    } else if ((flag & 0x0f) == 0x01) {
        count = in.readShort();
    } else if ((flag & 0x0f) == 0x02) {
        count = in.readInt();
    } else {
        throw new IOException("unhandled flag");
    }

    this.positiveEntries = 0;
    this.negativeEntries = 0;

    int[] arr = new int[count];
    if ((flag & 0xf0) == 0x00) {
        for (int i = 0; i < count; i++) {
            arr[i] = in.readByte();
            if (arr[i] >= 0) {
                this.positiveEntries++;
            } else {
                this.negativeEntries++;
            }
        }
    } else if ((flag & 0xf0) == 0x10) {
        for (int i = 0; i < count; i++) {
            arr[i] = in.readShort();
            if (arr[i] >= 0) {
                this.positiveEntries++;
            } else {
                this.negativeEntries++;
            }
        }
    } else if ((flag & 0xf0) == 0x20) {
        for (int i = 0; i < count; i++) {
            arr[i] = in.readInt();
            if (arr[i] >= 0) {
                this.positiveEntries++;
            } else {
                this.negativeEntries++;
            }
        }
    } else {
        throw new IOException("unhandled flag");
    }

    this.intArray = arr;
    this.prevBytes = null;
}

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From source file:edu.msu.cme.rdp.readseq.readers.core.SFFCore.java

public ReadBlock readReadBlock() throws IOException {
    try {/*from w  w w.  j a v a  2s .  c o m*/
        DataInput seqFile = super.getDataInput();

        ReadBlock ret = new ReadBlock();

        /*
         * READ BLOCK HEADER
         */

        ret.headerLength = seqFile.readShort();
        ret.nameLength = seqFile.readShort();

        int tmp = (ret.headerLength << 16) | ret.nameLength;
        if (tmp == mftMagicNumber) { //We ended up in the index...certainly possible
            return null;
        }

        ret.numBases = seqFile.readInt();
        ret.clipQualLeft = seqFile.readUnsignedShort();
        ret.clipQualRight = seqFile.readUnsignedShort();
        ret.clipAdapterLeft = seqFile.readUnsignedShort();
        ret.clipAdapterRight = seqFile.readUnsignedShort();

        byte[] readName = new byte[ret.nameLength];
        super.read(readName);

        int dataOffset = ret.headerLength - (ret.nameLength + READ_BLOCK_STATIC_SIZE);
        if (dataOffset < 0) {
            throw new IOException("Illegal ReadBlock header length (" + ret.headerLength
                    + "), it would have me seek back in to the readblock");
        }

        seqFile.skipBytes(dataOffset);

        /*
         * READ BLOCK DATA
         */

        byte[] flowgramIndex = new byte[ret.numBases];
        byte[] bases = new byte[ret.numBases];
        byte[] quality = new byte[ret.numBases];

        byte[] homopolymerStretchEstimates = new byte[(commonHeader.flowLength) * 2];

        super.read(homopolymerStretchEstimates);
        super.read(flowgramIndex);
        super.read(bases);
        super.read(quality);

        DataInputStream flowgramStream = new DataInputStream(
                new ByteArrayInputStream(homopolymerStretchEstimates));

        short[] flowgrams = new short[commonHeader.flowLength];
        for (int index = 0; index < commonHeader.flowLength; index++) {
            flowgrams[index] = flowgramStream.readShort();
        }
        flowgramStream.close();

        ret.name = new String(readName);
        ret.flowgrams = flowgrams;
        ret.flowIndex = flowgramIndex;
        ret.seq = new String(bases);
        ret.qual = quality;
        int bytesRead = homopolymerStretchEstimates.length + flowgramIndex.length + bases.length
                + quality.length;

        alignToBoundary(bytesRead);

        return ret;
    } catch (EOFException e) {
        return null;
    }
}

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From source file:edu.msu.cme.rdp.readseq.readers.core.SFFCore.java

private void parseCommonHeader() throws IOException {
    if (commonHeader != null) {
        throw new IOException("Common header already initialized");
    }/*from   w  ww  .  ja  v  a2  s  .  c  om*/
    commonHeader = new CommonHeader();

    DataInput seqFile = super.getDataInput();

    commonHeader.magicNumber = seqFile.readInt();

    if (commonHeader.magicNumber != SeqUtils.SFF_MAGIC_NUMBER) {
        throw new IOException("Not an SFF File");
    }

    commonHeader.version = seqFile.readInt();

    if (commonHeader.version != 1) {
        throw new IOException("Cannot parse v" + commonHeader.version + " sff files");
    }

    commonHeader.indexOffset = seqFile.readLong();
    commonHeader.indexLength = seqFile.readInt();
    commonHeader.numReads = seqFile.readInt();
    commonHeader.headerLength = seqFile.readShort();
    commonHeader.keyLength = seqFile.readShort();
    commonHeader.flowLength = seqFile.readShort();
    commonHeader.flowgramFormat = seqFile.readByte();

    byte[] flow = new byte[commonHeader.flowLength];
    super.read(flow);
    commonHeader.flow = new String(flow);

    byte[] key = new byte[commonHeader.keyLength];
    super.read(key);
    commonHeader.key = new String(key);

    int readBytes = COMMON_HEADER_STATIC_SIZE + flow.length + key.length;

    alignToBoundary(readBytes);

    if (super.isSeekable() && commonHeader.indexOffset > commonHeader.headerLength) {
        readIndex();
    }
}

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From source file:de.hpi.fgis.hdrs.Triple.java

@Override
public void readFields(DataInput in) throws IOException {
    // read header
    Slen = in.readShort();
    Plen = in.readShort();/*from  ww  w . j ava2 s.  c o m*/
    Olen = in.readInt();
    multiplicity = in.readInt();
    // read data
    //int size = Slen + (int) Plen + Olen;
    int size = bufferSize();
    buffer = new byte[size];
    in.readFully(buffer, 0, size);
}

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From source file:dk.statsbiblioteket.util.LineReaderTest.java

public void testSample(String type, DataInput in) throws Exception {
    assertEquals("Int 1 should work for " + type, 12345, in.readInt());
    assertEquals("Int 2 should work for " + type, -87, in.readInt());
    assertEquals("Long should work for " + type, 123456789L, in.readLong());
    assertEquals("String 1 should work for " + type, "Hello World!", in.readLine());
    assertEquals("String 2 should work for " + type, "Another world", in.readLine());
    assertEquals("Float should work for " + type, 0.5f, in.readFloat());
    assertEquals("Boolean 1 should work for " + type, true, in.readBoolean());
    assertEquals("Boolean 2 should work for " + type, false, in.readBoolean());
    assertEquals("Byte 1 should work for " + type, (byte) 12, in.readByte());
    assertEquals("Byte 2 should work for " + type, (byte) -12, in.readByte());
    assertEquals("Unsigned byte should work for " + type, 129, in.readUnsignedByte());
    assertEquals("Short should work for " + type, -4567, in.readShort());
    byte[] loaded = new byte[5];
    byte[] expected = new byte[] { (byte) 'A', (byte) 'S', (byte) 'C', (byte) 'I', (byte) 'I' };
    in.readFully(loaded);//  w  ww  .  j a  v  a2 s .  c o  m
    for (int i = 0; i < loaded.length; i++) {
        assertEquals("Byte-stored string should be equal at byte " + i + " for " + type, expected[i],
                loaded[i]);
    }
}

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From source file:org.ambud.marauder.source.ids.pcap.layer3.ARP.java

@Override
public void decode(DataInput di, EtherFrame parent) throws IOException {
    this.parent = parent;
    this.hardType = di.readShort();
    this.protoType = di.readShort();
    this.hardSize = di.readByte();
    this.protoAddrSize = di.readByte();
    this.opCode = di.readShort();
    di.readFully(senderEthAddr);//from   w w w. j a va 2  s.co  m
    this.senderIP = di.readInt();
    di.readFully(targetEthAddr);
    this.targetIP = di.readInt();
}

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From source file:org.apache.carbondata.core.indexstore.blockletindex.BlockletDataMap.java

/**
 * Read column schema from binary/*from w  ww . j  a  va  2 s  . c o  m*/
 * @param schemaArray
 * @throws IOException
 */
public List<ColumnSchema> readColumnSchema(byte[] schemaArray) throws IOException {
    // uncompress it.
    schemaArray = Snappy.uncompress(schemaArray);
    ByteArrayInputStream schemaStream = new ByteArrayInputStream(schemaArray);
    DataInput schemaInput = new DataInputStream(schemaStream);
    List<ColumnSchema> columnSchemas = new ArrayList<>();
    int size = schemaInput.readShort();
    for (int i = 0; i < size; i++) {
        ColumnSchema columnSchema = new ColumnSchema();
        columnSchema.readFields(schemaInput);
        columnSchemas.add(columnSchema);
    }
    return columnSchemas;
}

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