List of usage examples for java.nio ByteOrder BIG_ENDIAN
ByteOrder BIG_ENDIAN
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From source file:com.inductiveautomation.xopc.drivers.modbus2.requests.WriteSingleRegisterRequest.java
private short getRegisterValue(ModbusAddress address, Variant variant) { ModbusDataType modbusType = address.getModbusDataType(); switch (modbusType) { case BCD16:/* w w w . j a va 2 s . c om*/ short bcd16 = (Short) TypeUtilities.coerce(variant.getValue(), Short.class); byte[] bcdBytes = BCDByteUtilities.get(ByteOrder.BIG_ENDIAN).fromShort(bcd16, 0xFFFF); return ByteUtilities.get(ByteOrder.BIG_ENDIAN).getShort(bcdBytes, 0); case String: // This is copypasta from WriteMultipleRegistersRequest... yuck. String s = TypeUtilities.toString(variant.getValue()); int addressLength = address.getStringLength(); if (s.length() > addressLength) { s = s.substring(0, addressLength); } byte[] padding = new byte[addressLength - s.length()]; Arrays.fill(padding, (byte) ' '); byte[] stringBytes = rightJustifyStrings ? ArrayUtils.addAll(padding, s.getBytes()) : ArrayUtils.addAll(s.getBytes(), padding); if (reverseStringByteOrder) { byte[] reversed = new byte[stringBytes.length]; for (int i = 0; i < stringBytes.length; i += 2) { byte[] swapped = ByteUtilities.swapBytes(stringBytes, i); System.arraycopy(swapped, 0, reversed, i, swapped.length); } stringBytes = reversed; } return ByteUtilities.get(ByteOrder.BIG_ENDIAN).getShort(stringBytes, 0); default: return (Short) TypeUtilities.coerce(variant.getValue(), Short.class); } }
From source file:org.openhab.binding.modbus.internal.ModbusBinding.java
private DecimalType extractStateFromRegisters(InputRegister[] registers, int index, String type) { if (type.equals(ModbusBindingProvider.VALUE_TYPE_BIT)) { return new DecimalType((registers[index / 16].toUnsignedShort() >> (index % 16)) & 1); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_INT8)) { return new DecimalType(registers[index / 2].toBytes()[1 - (index % 2)]); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_UINT8)) { return new DecimalType((registers[index / 2].toUnsignedShort() >> (8 * (index % 2))) & 0xff); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_INT16)) { ByteBuffer buff = ByteBuffer.allocate(2); buff.put(registers[index].toBytes()); return new DecimalType(buff.order(ByteOrder.BIG_ENDIAN).getShort(0)); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_UINT16)) { return new DecimalType(registers[index].toUnsignedShort()); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_INT32)) { ByteBuffer buff = ByteBuffer.allocate(4); buff.put(registers[index * 2 + 0].toBytes()); buff.put(registers[index * 2 + 1].toBytes()); return new DecimalType(buff.order(ByteOrder.BIG_ENDIAN).getInt(0)); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_UINT32)) { ByteBuffer buff = ByteBuffer.allocate(8); buff.position(4);/* w w w . j a v a2s . c o m*/ buff.put(registers[index * 2 + 0].toBytes()); buff.put(registers[index * 2 + 1].toBytes()); return new DecimalType(buff.order(ByteOrder.BIG_ENDIAN).getLong(0)); } else if (type.equals(ModbusBindingProvider.VALUE_TYPE_FLOAT32)) { ByteBuffer buff = ByteBuffer.allocate(4); buff.put(registers[index * 2 + 0].toBytes()); buff.put(registers[index * 2 + 1].toBytes()); return new DecimalType(buff.order(ByteOrder.BIG_ENDIAN).getFloat(0)); } else { throw new IllegalArgumentException(); } }
From source file:org.xenei.compressedgraph.SerializableNode.java
public static byte[] getRawIdx(int i) { byte[] retval = new byte[4]; ByteBuffer.wrap(retval).order(ByteOrder.BIG_ENDIAN).putInt(i); return retval; }
From source file:ffx.xray.MTZFilter.java
/** * {@inheritDoc}//from w ww . j a v a2 s . co m */ @Override public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) { ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } } catch (EOFException eof) { System.out.println("EOF reached "); } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return null; } // column identifiers foString = sigfoString = rfreeString = null; if (properties != null) { foString = properties.getString("fostring", null); sigfoString = properties.getString("sigfostring", null); rfreeString = properties.getString("rfreestring", null); } h = k = l = fo = sigfo = rfree = -1; fplus = sigfplus = fminus = sigfminus = rfreeplus = rfreeminus = -1; fc = phic = -1; boolean print = false; parseColumns(print); parseFcColumns(print); if (fo < 0 && fplus < 0 && sigfo < 0 && sigfplus < 0 && fc < 0 && phic < 0) { logger.info( " The MTZ header contains insufficient information to generate the reflection list.\n For non-default column labels set fostring/sigfostring in the properties file."); return null; } Column c; if (fo > 0) { c = (Column) columns.get(fo); } else if (fplus > 0) { c = (Column) columns.get(fplus); } else { c = (Column) columns.get(fc); } Dataset d = (Dataset) datasets.get(c.id - dsetoffset); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\n Reading %s\n\n", mtzFile.getName())); sb.append(String.format(" Setting up reflection list based on MTZ file.\n")); sb.append(String.format(" Space group number: %d (name: %s)\n", sgnum, SpaceGroup.spaceGroupNames[sgnum - 1])); sb.append(String.format(" Resolution: %8.3f\n", 0.999999 * resHigh)); sb.append(String.format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5])); logger.info(sb.toString()); } Crystal crystal = new Crystal(d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5], SpaceGroup.spaceGroupNames[sgnum - 1]); double sampling = 0.6; if (properties != null) { sampling = properties.getDouble("sampling", 0.6); } Resolution resolution = new Resolution(0.999999 * resHigh, sampling); return new ReflectionList(crystal, resolution, properties); }
From source file:org.openspaces.memcached.protocol.binary.MemcachedBinaryResponseEncoder.java
@Override public void messageReceived(ChannelHandlerContext channelHandlerContext, MessageEvent messageEvent) throws Exception { ResponseMessage command = (ResponseMessage) messageEvent.getMessage(); Object additional = messageEvent.getMessage(); MemcachedBinaryCommandDecoder.BinaryOp bcmd = MemcachedBinaryCommandDecoder.BinaryOp .forCommandMessage(command.cmd); // write extras == flags & expiry ChannelBuffer extrasBuffer = null;//from ww w . j av a 2 s. co m // write key if there is one ChannelBuffer keyBuffer = null; if (bcmd.isAddKeyToResponse() && command.cmd.keys != null && command.cmd.keys.size() != 0) { keyBuffer = ChannelBuffers.wrappedBuffer(command.cmd.keys.get(0).bytes); } // write value if there is one ChannelBuffer valueBuffer = null; if (command.elements != null) { extrasBuffer = ChannelBuffers.buffer(ByteOrder.BIG_ENDIAN, 4); LocalCacheElement element = command.elements[0]; extrasBuffer.writeShort((short) (element != null ? element.getExpire() : 0)); extrasBuffer.writeShort((short) (element != null ? element.getFlags() : 0)); if ((command.cmd.op == Op.GET || command.cmd.op == Op.GETS)) { if (element != null) { valueBuffer = ChannelBuffers.wrappedBuffer(ByteOrder.BIG_ENDIAN, element.getData()); } else { valueBuffer = ChannelBuffers.buffer(0); } } else if (command.cmd.op == Op.INCR || command.cmd.op == Op.DECR) { valueBuffer = ChannelBuffers.buffer(ByteOrder.BIG_ENDIAN, 8); valueBuffer.writeLong(command.incrDecrResponse); } } else if (command.cmd.op == Op.INCR || command.cmd.op == Op.DECR) { valueBuffer = ChannelBuffers.buffer(ByteOrder.BIG_ENDIAN, 8); valueBuffer.writeLong(command.incrDecrResponse); } long casUnique = 0; if (command.elements != null && command.elements.length != 0 && command.elements[0] != null) { casUnique = command.elements[0].getCasUnique(); } // stats is special -- with it, we write N times, one for each stat, then an empty payload if (command.cmd.op == Op.STATS) { // first uncork any corked buffers if (corkedBuffers.containsKey(command.cmd.opaque)) uncork(command.cmd.opaque, messageEvent.getChannel()); for (Map.Entry<String, Set<String>> statsEntries : command.stats.entrySet()) { for (String stat : statsEntries.getValue()) { // Move to use this in Java 6 // keyBuffer = ChannelBuffers.wrappedBuffer(ByteOrder.BIG_ENDIAN, statsEntries.getKey().getBytes(MemcachedBinaryCommandDecoder.USASCII.toString())); // valueBuffer = ChannelBuffers.wrappedBuffer(ByteOrder.BIG_ENDIAN, stat.getBytes(MemcachedBinaryCommandDecoder.USASCII)); keyBuffer = ChannelBuffers.wrappedBuffer(ByteOrder.BIG_ENDIAN, statsEntries.getKey().getBytes("US-ASCII")); valueBuffer = ChannelBuffers.wrappedBuffer(ByteOrder.BIG_ENDIAN, stat.getBytes("US-ASCII")); ChannelBuffer headerBuffer = constructHeader(bcmd, extrasBuffer, keyBuffer, valueBuffer, getStatusCode(command).code, command.cmd.opaque, casUnique); writePayload(messageEvent, extrasBuffer, keyBuffer, valueBuffer, headerBuffer); } } keyBuffer = null; valueBuffer = null; ChannelBuffer headerBuffer = constructHeader(bcmd, extrasBuffer, keyBuffer, valueBuffer, getStatusCode(command).code, command.cmd.opaque, casUnique); writePayload(messageEvent, extrasBuffer, keyBuffer, valueBuffer, headerBuffer); } else { ChannelBuffer headerBuffer = constructHeader(bcmd, extrasBuffer, keyBuffer, valueBuffer, getStatusCode(command).code, command.cmd.opaque, casUnique); // write everything // is the command 'quiet?' if so, then we append to our 'corked' buffer until a non-corked command comes along if (bcmd.isNoreply()) { int totalCapacity = headerBuffer.capacity() + (extrasBuffer != null ? extrasBuffer.capacity() : 0) + (keyBuffer != null ? keyBuffer.capacity() : 0) + (valueBuffer != null ? valueBuffer.capacity() : 0); ChannelBuffer corkedResponse = cork(command.cmd.opaque, totalCapacity); corkedResponse.writeBytes(headerBuffer); if (extrasBuffer != null) corkedResponse.writeBytes(extrasBuffer); if (keyBuffer != null) corkedResponse.writeBytes(keyBuffer); if (valueBuffer != null) corkedResponse.writeBytes(valueBuffer); } else { // first write out any corked responses if (corkedBuffers.containsKey(command.cmd.opaque)) uncork(command.cmd.opaque, messageEvent.getChannel()); writePayload(messageEvent, extrasBuffer, keyBuffer, valueBuffer, headerBuffer); } } }
From source file:com.inductiveautomation.xopc.drivers.modbus2.requests.WriteMultipleRegistersRequest.java
private byte[] getValue(WriteItem item, ModbusAddress address) { ModbusDataType modbusType = address.getModbusDataType(); Variant variant = item.getWriteValue(); switch (modbusType) { case BCD16://from w w w.j a v a 2 s . com short bcd16 = (Short) TypeUtilities.coerce(variant.getValue(), Short.class); return BCDByteUtilities.get(ByteOrder.BIG_ENDIAN).fromShort(bcd16, 0xFFFF); case BCD32: int bcd32 = (Integer) TypeUtilities.coerce(variant.getValue(), Integer.class); byte[] bcd32bs = BCDByteUtilities.get(ByteOrder.BIG_ENDIAN).fromInt(bcd32, 0xFFFFFFFF); if (swapWords) { return ByteUtilities.swapWords(bcd32bs, 0); } return bcd32bs; case Int16: case UInt16: return UAByteUtilities.fromVariant(variant, ByteOrder.BIG_ENDIAN); case Int32: case UInt32: case Float: byte[] bs = UAByteUtilities.fromVariant(variant, ByteOrder.BIG_ENDIAN); if (swapWords) { return ByteUtilities.swapWords(bs, 0); } return bs; case Int64: case UInt64: case Double: byte[] bs64 = UAByteUtilities.fromVariant(variant, ByteOrder.BIG_ENDIAN); if (swapWords) { byte[] h1 = ByteUtilities.swapWords(bs64, 0); byte[] h2 = ByteUtilities.swapWords(bs64, 4); System.arraycopy(h2, 0, bs64, 0, 4); System.arraycopy(h1, 0, bs64, 4, 4); } return bs64; case String: String s = TypeUtilities.toString(variant.getValue()); int addressLength = address.getStringLength(); if (s.length() > addressLength) { s = s.substring(0, addressLength); } byte[] padding = new byte[addressLength - s.length()]; Arrays.fill(padding, (byte) ' '); byte[] stringBytes = rightJustifyStrings ? ArrayUtils.addAll(padding, s.getBytes()) : ArrayUtils.addAll(s.getBytes(), padding); if (reverseStringByteOrder) { byte[] reversed = new byte[stringBytes.length]; for (int i = 0; i < stringBytes.length; i += 2) { byte[] swapped = ByteUtilities.swapBytes(stringBytes, i); System.arraycopy(swapped, 0, reversed, i, swapped.length); } stringBytes = reversed; } return stringBytes; case Boolean: throw new RuntimeException(String.format("Writing %s to %s not allowed.", modbusType, address)); default: throw new RuntimeException(String.format("Case for %s not defined.", modbusType)); } }
From source file:ome.io.bioformats.BfPyramidPixelBuffer.java
private synchronized void initializeReader() throws IOException, FormatException { if (isLockedByOthers()) { throw new LockTimeout(String.format("%s is locked by others", readerFile.getAbsolutePath()), 15 * 1000, 0);/*from w w w.j a v a 2 s. c o m*/ } reader = new OmeroPixelsPyramidReader(); delegate = new BfPixelBuffer(readerFile.getAbsolutePath(), reader); byteOrder = delegate.isLittleEndian() ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN; }
From source file:ffx.xray.CCP4MapFilter.java
/** * {@inheritDoc}/*from ww w .j av a2s . c om*/ */ @Override public boolean readFile(String filename, RealSpaceRefinementData refinementdata, CompositeConfiguration properties) { int imapdata; double cella, cellb, cellc, cellalpha, cellbeta, cellgamma; String stampstr; ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; double min = Double.POSITIVE_INFINITY; double max = Double.NEGATIVE_INFINITY; double mean = 0.0; double sd = 0.0; double rmsd = 0.0; // first determine byte order of file versus system try { fis = new FileInputStream(filename); dis = new DataInputStream(fis); dis.skipBytes(212); byte bytes[] = new byte[4]; dis.read(bytes, 0, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); imapdata = bb.order(ByteOrder.BIG_ENDIAN).getInt(); stampstr = Integer.toHexString(imapdata); // System.out.println("stamp: " + stampstr); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\nOpening CCP4 map: %s\n", filename)); sb.append(String.format("file type (machine stamp): %s\n", stampstr)); logger.info(sb.toString()); } fis.close(); } catch (Exception e) { String message = "Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); System.exit(-1); } try { fis = new FileInputStream(filename); dis = new DataInputStream(fis); byte bytes[] = new byte[2048]; dis.read(bytes, 0, 1024); ByteBuffer bb = ByteBuffer.wrap(bytes); int ext[] = new int[3]; ext[0] = bb.order(b).getInt(); ext[1] = bb.order(b).getInt(); ext[2] = bb.order(b).getInt(); // mode (2 = reals, only one we accept) int mode = bb.order(b).getInt(); int ori[] = new int[3]; ori[0] = bb.order(b).getInt(); ori[1] = bb.order(b).getInt(); ori[2] = bb.order(b).getInt(); int ni[] = new int[3]; ni[0] = bb.order(b).getInt(); ni[1] = bb.order(b).getInt(); ni[2] = bb.order(b).getInt(); cella = bb.order(b).getFloat(); cellb = bb.order(b).getFloat(); cellc = bb.order(b).getFloat(); cellalpha = bb.order(b).getFloat(); cellbeta = bb.order(b).getFloat(); cellgamma = bb.order(b).getFloat(); int axisi[] = new int[3]; for (int i = 0; i < 3; i++) { int axis = bb.order(b).getInt(); switch (axis) { case 1: axisi[0] = i; break; case 2: axisi[1] = i; break; case 3: axisi[2] = i; break; } } min = bb.order(b).getFloat(); max = bb.order(b).getFloat(); mean = bb.order(b).getFloat(); int sg = bb.order(b).getInt(); int nsymb = bb.order(b).getInt(); int skew = bb.order(b).getInt(); for (int i = 0; i < 12; i++) { bb.order(b).getFloat(); } for (int i = 0; i < 15; i++) { bb.order(b).getInt(); } byte word[] = new byte[2048]; bb.order(b).get(word, 0, 4); String mapstr = new String(word); // System.out.println("MAP?: " + mapstr); sd = bb.order(b).getFloat(); rmsd = bb.order(b).getFloat(); /* System.out.println("col: " + ori[0] + " " + ext[0] + " " + ni[0]); System.out.println("row: " + ori[1] + " " + ext[1] + " " + ni[1]); System.out.println("sec: " + ori[2] + " " + ext[2] + " " + ni[2]); System.out.println("order: " + axisi[0] + " " + axisi[1] + " " + axisi[2]); System.out.println("min: " + min + " max: " + max + " mean: " + mean); System.out.println("sd: " + sd + " rmsd: " + rmsd); System.out.println("sg: " + sg); System.out.println("a: " + cella + " b: " + cellb + " c: " + cellc + " alpha: " + cellalpha + " beta: " + cellbeta + " gamma: " + cellgamma); */ if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format(" column origin: %d extent: %d\n", ori[0], ext[0])); sb.append(String.format(" row origin: %d extent: %d\n", ori[1], ext[1])); sb.append(String.format(" section origin: %d extent: %d\n", ori[2], ext[2])); sb.append(String.format(" axis order: %d %d %d\n", axisi[0], axisi[1], axisi[2])); sb.append(String.format(" number of X, Y, Z columns: %d %d %d\n", ni[0], ni[1], ni[2])); sb.append(String.format(" spacegroup #: %d (name: %s)\n", sg, SpaceGroup.spaceGroupNames[sg - 1])); sb.append(String.format(" cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", cella, cellb, cellc, cellalpha, cellbeta, cellgamma)); logger.info(sb.toString()); } int nlabel = bb.order(b).getInt(); // System.out.println("nsymb: " + nsymb + " nlabel: " + nlabel); for (int i = 0; i < 10; i++) { bb.order(b).get(word, 0, 80); mapstr = new String(word); // System.out.println("label " + i + " : " + mapstr); } if (nsymb > 0) { bb.rewind(); dis.read(bytes, 0, nsymb); for (int i = 0; i < nsymb / 80; i += 80) { bb.order(b).get(word, 0, 80); mapstr = new String(word); // System.out.println("symm: " + mapstr); } } bb.rewind(); dis.read(bytes, 0, 2048); refinementdata.data = new double[ext[0] * ext[1] * ext[2]]; int ijk[] = new int[3]; int index, x, y, z; refinementdata.ori[0] = ori[axisi[0]]; refinementdata.ori[1] = ori[axisi[1]]; refinementdata.ori[2] = ori[axisi[2]]; int nx = ext[axisi[0]]; int ny = ext[axisi[1]]; int nz = ext[axisi[2]]; refinementdata.ext[0] = nx; refinementdata.ext[1] = ny; refinementdata.ext[2] = nz; refinementdata.ni[0] = ni[0]; refinementdata.ni[1] = ni[1]; refinementdata.ni[2] = ni[2]; for (ijk[2] = 0; ijk[2] < ext[2]; ijk[2]++) { for (ijk[1] = 0; ijk[1] < ext[1]; ijk[1]++) { for (ijk[0] = 0; ijk[0] < ext[0]; ijk[0]++) { x = ijk[axisi[0]]; y = ijk[axisi[1]]; z = ijk[axisi[2]]; index = x + nx * (y + ny * z); refinementdata.data[index] = bb.order(b).getFloat(); if (!bb.hasRemaining()) { bb.rewind(); dis.read(bytes, 0, 2048); } } } } fis.close(); } catch (Exception e) { String message = "Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); System.exit(-1); } return true; }
From source file:com.sanlq.common.IPIP.java
private void loadToTree() { FileInputStream fin = null;// w ww. j a va 2 s . c o m lock.lock(); try { if (IPDB_FILE_CONTENT == null) { IPDB_FILE_CONTENT = readHDFSFile("/data/lib/ipip/ipdb.dat"); } if (IPDB_FILE_CONTENT != null) { dataBuffer = ByteBuffer.allocate(Long.valueOf(IPDB_FILE_CONTENT.length).intValue()); dataBuffer.put(IPDB_FILE_CONTENT); dataBuffer.position(0); int indexLength = dataBuffer.getInt(); byte[] indexBytes = new byte[indexLength]; dataBuffer.get(indexBytes, 0, indexLength - 4); indexBuffer = ByteBuffer.wrap(indexBytes); indexBuffer.order(ByteOrder.LITTLE_ENDIAN); offset = indexLength; int loop = 0; while (loop++ < 256) { index[loop - 1] = indexBuffer.getInt(); } indexBuffer.order(ByteOrder.BIG_ENDIAN); } } finally { lock.unlock(); } }
From source file:ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor.java
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public Date parseGenericCCHeader(DataInputStream str) throws IOException {
/*/*from w ww . j a v a2 s. c o m*/
* acquisition data, intensity data etc. Usually "intensity data" for the first header.
*/
String datatypeIdentifier = this.readString(str);
AffyScanDateExtractor.log.debug(datatypeIdentifier);
String guid = this.readString(str);
AffyScanDateExtractor.log.debug(guid);
@SuppressWarnings("unused")
String createDate = this.readUnicodeString(str); // blank?
@SuppressWarnings("unused")
String locale = this.readUnicodeString(str); // e.g. en-US
int numKeyValuePairs = this.readIntBigEndian(str); // e.g. 55
Date result = null;
for (int i = 0; i < numKeyValuePairs; i++) {
String name = this.readUnicodeString(str);
byte[] value = this.readBytes(str);
String type = this.readUnicodeString(str);
Object v;
switch (type) {
case "text/x-calvin-float": {
FloatBuffer intBuf = ByteBuffer.wrap(value).order(ByteOrder.BIG_ENDIAN).asFloatBuffer();
float[] array = new float[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/plain":
case "text/ascii":
// text/ascii is undocumented, but needed.
v = new String(value, "US-ASCII");
if (name.equals("affymetrix-scan-date")) {
result = this.parseISO8601(new String(((String) v).getBytes(), "UTF-16"));
AffyScanDateExtractor.log.info("Scan date = " + result);
}
if (name.equals("affymetrix-Hyb-Start-Time")) {
// We don't use this but I'm curious to start looking at it.
AffyScanDateExtractor.log
.info("Hyb start date = " + new String(((String) v).getBytes(), "UTF-16"));
}
break;
case "text-x-calvin-unsigned-integer-8": {
ShortBuffer intBuf = ByteBuffer.wrap(value).asShortBuffer();
short[] array = new short[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/x-calvin-integer-16": {
IntBuffer intBuf = ByteBuffer.wrap(value).order(ByteOrder.BIG_ENDIAN).asIntBuffer(); // wrong?
int[] array = new int[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/x-calvin-integer-32": {
IntBuffer intBuf = ByteBuffer.wrap(value).order(ByteOrder.BIG_ENDIAN).asIntBuffer();
int[] array = new int[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/x-calvin-unsigned-integer-8": {
ShortBuffer intBuf = ByteBuffer.wrap(value).asShortBuffer();
short[] array = new short[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/x-calvin-unsigned-integer-16": {
IntBuffer intBuf = ByteBuffer.wrap(value).order(ByteOrder.BIG_ENDIAN).asIntBuffer();// wrong?
int[] array = new int[intBuf.remaining()];
intBuf.get(array);
break;
}
case "text/x-calvin-unsigned-integer-32": {
IntBuffer intBuf = ByteBuffer.wrap(value).order(ByteOrder.BIG_ENDIAN).asIntBuffer();
int[] array = new int[intBuf.remaining()];
intBuf.get(array);
break;
}
default:
throw new IOException("Unknown mime type:" + type);
}
}
@SuppressWarnings("unused")
int numParentHeaders = this.readIntBigEndian(str);
return result;
}