/** {@inheritDoc} */
public boolean addAll(Collection<? extends Byte> collection) {
boolean changed = false;
for (Byte element : collection) {
byte e = element.byteValue();
if (add(e)) {
changed = true;
}
}
return changed;
}
Record rdataFromString(Name name, short dclass, int ttl, MyStringTokenizer st, Name origin)
throws TextParseException {
SIGRecord rec = new SIGRecord(name, dclass, ttl);
rec.covered = Type.value(st.nextToken());
rec.alg = Byte.parseByte(st.nextToken());
rec.labels = Byte.parseByte(st.nextToken());
rec.origttl = TTL.parseTTL(st.nextToken());
rec.expire = parseDate(st.nextToken());
rec.timeSigned = parseDate(st.nextToken());
rec.footprint = (short) Integer.parseInt(st.nextToken());
rec.signer = Name.fromString(st.nextToken(), origin);
if (st.hasMoreTokens()) rec.signature = base64.fromString(st.remainingTokens());
return rec;
}
// Gets a property and converts it into byte.
static byte getByteProperty(String propName, byte defaultValue) {
String temp = getConfigValue(propName);
byte result = defaultValue;
if (temp != null) {
result = Byte.parseByte(temp);
Logger.info("{DB}-" + propName + ":" + result);
} else {
result = Byte.parseByte(properties.getProperty(propName, Byte.toString(defaultValue)).trim());
Logger.info("{FILE}-" + propName + ":" + result);
}
return result;
}
/**
* Convert a byte array to a hex string
*
* @param bytes byte array to convert to a hex string
* @return return a String in hex representing the byte array
*/
public String toHexString(byte[] bytes) {
StringBuffer result = new StringBuffer("0x");
for (int i = 0; i < bytes.length; i++) {
Byte aByte = new Byte(bytes[i]);
Integer anInt = new Integer(aByte.intValue());
String hexVal = Integer.toHexString(anInt.intValue());
if (hexVal.length() > SIZE) hexVal = hexVal.substring(hexVal.length() - SIZE);
result.append(
(SIZE > hexVal.length() ? ZEROS.substring(0, SIZE - hexVal.length()) : "") + hexVal);
}
return (result.toString());
}
/**
* Parses the arguments table from the GATK Report and creates a RAC object with the proper
* initialization values
*
* @param table the GATKReportTable containing the arguments and its corresponding values
* @return a RAC object properly initialized with all the objects in the table
*/
private RecalibrationArgumentCollection initializeArgumentCollectionTable(GATKReportTable table) {
final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
for (int i = 0; i < table.getNumRows(); i++) {
final String argument = table.get(i, "Argument").toString();
Object value = table.get(i, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
if (value.equals("null"))
value =
null; // generic translation of null values that were printed out as strings | todo --
// add this capability to the GATKReport
if (argument.equals("covariate") && value != null)
RAC.COVARIATES = value.toString().split(",");
else if (argument.equals("standard_covs"))
RAC.DO_NOT_USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value);
else if (argument.equals("solid_recal_mode"))
RAC.SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.recalModeFromString((String) value);
else if (argument.equals("solid_nocall_strategy"))
RAC.SOLID_NOCALL_STRATEGY =
RecalUtils.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value);
else if (argument.equals("mismatches_context_size"))
RAC.MISMATCHES_CONTEXT_SIZE = Integer.parseInt((String) value);
else if (argument.equals("indels_context_size"))
RAC.INDELS_CONTEXT_SIZE = Integer.parseInt((String) value);
else if (argument.equals("mismatches_default_quality"))
RAC.MISMATCHES_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("insertions_default_quality"))
RAC.INSERTIONS_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("deletions_default_quality"))
RAC.DELETIONS_DEFAULT_QUALITY = Byte.parseByte((String) value);
else if (argument.equals("maximum_cycle_value"))
RAC.MAXIMUM_CYCLE_VALUE = Integer.parseInt((String) value);
else if (argument.equals("low_quality_tail"))
RAC.LOW_QUAL_TAIL = Byte.parseByte((String) value);
else if (argument.equals("default_platform")) RAC.DEFAULT_PLATFORM = (String) value;
else if (argument.equals("force_platform")) RAC.FORCE_PLATFORM = (String) value;
else if (argument.equals("quantizing_levels"))
RAC.QUANTIZING_LEVELS = Integer.parseInt((String) value);
else if (argument.equals("recalibration_report"))
RAC.existingRecalibrationReport = (value == null) ? null : new File((String) value);
else if (argument.equals("binary_tag_name"))
RAC.BINARY_TAG_NAME = (value == null) ? null : (String) value;
else if (argument.equals("sort_by_all_columns"))
RAC.SORT_BY_ALL_COLUMNS = Boolean.parseBoolean((String) value);
}
return RAC;
}
private RecalDatum getRecalDatum(
final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) {
final long nObservations =
asLong(reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME));
final double nErrors = asDouble(reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME));
// final double empiricalQuality = asDouble(reportTable.get(row,
// RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME));
// the estimatedQreported column only exists in the ReadGroup table
final double estimatedQReported =
hasEstimatedQReportedColumn
? (Double) reportTable.get(row, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME)
: // we get it if we are in the read group table
Byte.parseByte(
(String)
reportTable.get(
row,
RecalUtils
.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we
// are in any other table
final RecalDatum datum = new RecalDatum(nObservations, nErrors, (byte) 1);
datum.setEstimatedQReported(estimatedQReported);
// datum.setEmpiricalQuality(empiricalQuality); // don't set the value here because we will want
// to recompute with a different conditional Q score prior value
return datum;
}
/**
* Applies a list of transformation on a block, if the block is not protected.
*
* @param toTransform the Bukkit block object to transform
* @param transformations the list if transformations to apply
*/
public static void transform(Block toTransform, List<List<String>> transformations) {
if (isBlockProtected(toTransform)) {
return;
}
for (List<String> toCheck : transformations) {
ArrayList<String[]> stateIndex = new ArrayList<String[]>();
for (int i = 0; i != 2; ++i) {
String got = toCheck.get(i);
if (got.contains(":")) { // Check for data _ appended.
stateIndex.add(got.split(":"));
} else {
stateIndex.add(new String[] {got, "0"});
}
}
String[] curState = stateIndex.get(0), toState = stateIndex.get(1);
if (Integer.valueOf(curState[0]) == toTransform.getTypeId()
&& Integer.valueOf(curState[1]) == toTransform.getData()) {
toTransform.setTypeIdAndData(Integer.valueOf(toState[0]), Byte.parseByte(toState[1]), true);
return;
}
}
}
private boolean compare_Byte(int operation, byte byteval, Object value2) {
if (operation == SUBSTRING) {
return false;
}
byte byteval2;
try {
byteval2 = Byte.parseByte(((String) value2).trim());
} catch (IllegalArgumentException e) {
return false;
}
switch (operation) {
case APPROX:
case EQUAL:
{
return byteval == byteval2;
}
case GREATER:
{
return byteval >= byteval2;
}
case LESS:
{
return byteval <= byteval2;
}
}
return false;
}
@Override
public Response debug(Debug debug) throws TException {
Set<Byte> partitions;
if (debug.getType() == DebugCommands.POPULATE_FILE.getId()) {
partitions = oracle.partitionsOf("/");
} else {
partitions = new HashSet<>();
partitions.add(Byte.valueOf(Byte.parseByte(debug.getData().get("partition"))));
}
Command cmd = newCommand(CommandType.DEBUG, partitions, null);
cmd.setDebug(debug);
replica.submitCommand(cmd);
Response r = new Response(replica.getInstanceMap());
return r;
}
/**
* Helper method used to get default value for wrappers used for primitive types (0 for Integer
* etc)
*
* @since 1.6.1
*/
public static Object defaultValue(Class<?> cls) {
if (cls == Integer.TYPE) {
return Integer.valueOf(0);
}
if (cls == Long.TYPE) {
return Long.valueOf(0L);
}
if (cls == Boolean.TYPE) {
return Boolean.FALSE;
}
if (cls == Double.TYPE) {
return Double.valueOf(0.0);
}
if (cls == Float.TYPE) {
return Float.valueOf(0.0f);
}
if (cls == Byte.TYPE) {
return Byte.valueOf((byte) 0);
}
if (cls == Short.TYPE) {
return Short.valueOf((short) 0);
}
if (cls == Character.TYPE) {
return '\0';
}
throw new IllegalArgumentException("Class " + cls.getName() + " is not a primitive type");
}
/**
* Check for byte
*
* @param input
* @return
*/
public static boolean isByte(String input) {
try {
Byte.parseByte(input);
return true;
} catch (Exception ex) {
return false;
}
}
public static List readWatchableObjects(DataInputStream par0DataInputStream) throws IOException {
ArrayList arraylist = null;
for (byte byte0 = par0DataInputStream.readByte();
byte0 != 127;
byte0 = par0DataInputStream.readByte()) {
if (arraylist == null) {
arraylist = new ArrayList();
}
int i = (byte0 & 0xe0) >> 5;
int j = byte0 & 0x1f;
WatchableObject watchableobject = null;
switch (i) {
case 0:
watchableobject = new WatchableObject(i, j, Byte.valueOf(par0DataInputStream.readByte()));
break;
case 1:
watchableobject =
new WatchableObject(i, j, Short.valueOf(par0DataInputStream.readShort()));
break;
case 2:
watchableobject =
new WatchableObject(i, j, Integer.valueOf(par0DataInputStream.readInt()));
break;
case 3:
watchableobject =
new WatchableObject(i, j, Float.valueOf(par0DataInputStream.readFloat()));
break;
case 4:
watchableobject = new WatchableObject(i, j, Packet.readString(par0DataInputStream, 64));
break;
case 5:
short word0 = par0DataInputStream.readShort();
byte byte1 = par0DataInputStream.readByte();
short word1 = par0DataInputStream.readShort();
watchableobject = new WatchableObject(i, j, new ItemStack(word0, byte1, word1));
break;
case 6:
int k = par0DataInputStream.readInt();
int l = par0DataInputStream.readInt();
int i1 = par0DataInputStream.readInt();
watchableobject = new WatchableObject(i, j, new ChunkCoordinates(k, l, i1));
break;
}
arraylist.add(watchableobject);
}
return arraylist;
}
private static byte getByteData(String byte1Str) throws Exception {
byte data_LC;
byte byte1 = Byte.parseByte(byte1Str);
// byte byte2 = Byte.parseByte(byte2Str);
data_LC = byte1;
// data_LC[1] = byte2;
return data_LC;
}
public static Number toWrapper(int i) {
if (i >= Byte.MIN_VALUE && i <= Byte.MAX_VALUE) {
return Byte.valueOf((byte) i);
} else if (i >= Short.MIN_VALUE && i <= Short.MAX_VALUE) {
return Short.valueOf((short) i);
} else {
return Integer.valueOf(i);
}
}
public static void main(String[] args) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
// For each test
StringBuffer sb = new StringBuffer();
for (byte T = Byte.parseByte(br.readLine()); T > 0; --T) {
// INPUT
byte N = Byte.parseByte(br.readLine());
int[] A = new int[N];
N = 0;
for (String s : br.readLine().split(" ")) {
A[N++] = Integer.parseInt(s);
}
sb.append(solve(A, N) ? YES : NO);
}
System.out.print(sb);
}
/** {@inheritDoc} */
@SuppressWarnings({"SuspiciousMethodCalls"})
public boolean retainAll(Collection<?> collection) {
boolean modified = false;
TByteIterator iter = iterator();
while (iter.hasNext()) {
if (!collection.contains(Byte.valueOf(iter.next()))) {
iter.remove();
modified = true;
}
}
return modified;
}
/** Loads dependencies and initializes data structures. */
@Override
public void init(FloodlightModuleContext context) throws FloodlightModuleException {
log.info(String.format("Initializing %s...", MODULE_NAME));
Map<String, String> config = context.getConfigParams(this);
table = Byte.parseByte(config.get("table"));
this.floodlightProv = context.getServiceImpl(IFloodlightProviderService.class);
this.linkDiscProv = context.getServiceImpl(ILinkDiscoveryService.class);
this.deviceProv = context.getServiceImpl(IDeviceService.class);
this.knownHosts = new ConcurrentHashMap<IDevice, Host>();
}
public Object getFieldValue(_Fields field) {
switch (field) {
case ID:
return Long.valueOf(getId());
case FLAGS:
return Integer.valueOf(getFlags());
case PARTITION:
return Byte.valueOf(getPartition());
}
throw new IllegalStateException();
}
/*
* Read a single pair of (X,Y) values from the ADXL202EVB board.
* TODO: Better return value, or declare as throwing exception for errs
*/
public static double[] chipRead() {
double[] retval = {0.0, 0.0};
byte[] rawBuf = {0, 0, 0, 0};
int[] vals = {0, 0};
try {
// Read is triggered by sending 'G' to board
outputStream.write('G');
// Wait for all 4 result bytes to arrive
// TODO: Finite wait w/error return if data never arrives
while (inputStream.available() < 4) {
Thread.sleep(1);
}
inputStream.read(rawBuf, 0, 4);
// Convert from raw bytes to 16-bit signed integers, carefully
Byte bTmp = new Byte(rawBuf[0]);
vals[0] = bTmp.intValue() * 256;
bTmp = new Byte(rawBuf[1]);
vals[0] += bTmp.intValue();
bTmp = new Byte(rawBuf[2]);
vals[1] = bTmp.intValue() * 256;
bTmp = new Byte(rawBuf[3]);
vals[1] += bTmp.intValue();
// See ADXL202EVB specs for details on conversion
retval[0] = (((vals[0] / 100.0) - 50.0) / 12.5);
retval[1] = (((vals[1] / 100.0) - 50.0) / 12.5);
System.out.println("X: " + retval[0] + " Y: " + retval[1]);
} catch (Exception ioe) {
System.out.println("Error on data transmission");
}
return (retval);
}
public byte getParameter(String key, byte defaultValue) {
Number n = getNumbers().get(key);
if (n != null) {
return n.byteValue();
}
String value = getParameter(key);
if (value == null || value.length() == 0) {
return defaultValue;
}
byte b = Byte.parseByte(value);
getNumbers().put(key, b);
return b;
}
@Override
public Response readlink(String path, Map<Byte, Long> instanceMap) throws TException {
path = makePathAbsolute(path);
// can be sent to ANY partition that replicates the path - we send it to the first returned by
// the oracle
Set<Byte> parts = Sets.newHashSet(Byte.valueOf(partition));
Command cmd = newCommand(CommandType.READLINK, parts, instanceMap);
ReadlinkCmd readlink = new ReadlinkCmd(path, parts);
cmd.setReadlink(readlink);
String result = (String) replica.submitCommand(cmd);
Response r = new Response(replica.getInstanceMap());
r.setReadlink(result);
return r;
}
@Override
public Response getattr(String path, Map<Byte, Long> instanceMap) throws TException {
// can be sent to ANY partition that replicates the path - we send it to the first returned by
// the oracle
path = makePathAbsolute(path);
Set<Byte> parts = Sets.newHashSet(Byte.valueOf(partition));
Command cmd = newCommand(CommandType.ATTR, parts, instanceMap);
AttrCmd attr = new AttrCmd(path, parts);
cmd.setAttr(attr);
Attr result = (Attr) replica.submitCommand(cmd);
Response r = new Response(replica.getInstanceMap());
r.setGetattr(result);
return r;
}
public byte getMethodParameter(String method, String key, byte defaultValue) {
String methodKey = method + "." + key;
Number n = getNumbers().get(methodKey);
if (n != null) {
return n.byteValue();
}
String value = getMethodParameter(method, key);
if (value == null || value.length() == 0) {
return defaultValue;
}
byte b = Byte.parseByte(value);
getNumbers().put(methodKey, b);
return b;
}
/**
* Parses the quantization table from the GATK Report and turns it into a map of original =>
* quantized quality scores
*
* @param table the GATKReportTable containing the quantization mappings
* @return an ArrayList with the quantization mappings from 0 to MAX_SAM_QUAL_SCORE
*/
private QuantizationInfo initializeQuantizationTable(GATKReportTable table) {
final Byte[] quals = new Byte[QualityUtils.MAX_SAM_QUAL_SCORE + 1];
final Long[] counts = new Long[QualityUtils.MAX_SAM_QUAL_SCORE + 1];
for (int i = 0; i < table.getNumRows(); i++) {
final byte originalQual = (byte) i;
final Object quantizedObject = table.get(i, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME);
final Object countObject = table.get(i, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME);
final byte quantizedQual = Byte.parseByte(quantizedObject.toString());
final long quantizedCount = Long.parseLong(countObject.toString());
quals[originalQual] = quantizedQual;
counts[originalQual] = quantizedCount;
}
return new QuantizationInfo(Arrays.asList(quals), Arrays.asList(counts));
}
@Override
public Response readBlocks(
String path, FileHandle fh, long offset, long bytes, Map<Byte, Long> instanceMap)
throws TException {
path = makePathAbsolute(path);
// assuming this replica replicates the file, send to own partition
Set<Byte> parts = Sets.newHashSet(Byte.valueOf(partition));
Command cmd = newCommand(CommandType.READ_BLOCKS, parts, instanceMap);
ReadBlocksCmd read = new ReadBlocksCmd(path, fh, offset, bytes, parts);
cmd.setRead(read);
ReadResult readResult = (ReadResult) replica.submitCommand(cmd);
Response r = new Response(replica.getInstanceMap());
r.setReadBlocks(readResult);
return r;
}
@Override
public Response getdir(String path, Map<Byte, Long> instanceMap) throws TException {
// can be sent to ANY partition that replicates the path - we send it to the first returned by
// the oracle
path = makePathAbsolute(path);
Set<Byte> parts = Sets.newHashSet(Byte.valueOf(partition));
Command cmd = newCommand(CommandType.GETDIR, parts, instanceMap);
GetdirCmd getdir = new GetdirCmd(path, parts);
cmd.setGetdir(getdir);
@SuppressWarnings("unchecked")
List<DirEntry> entries = (List<DirEntry>) replica.submitCommand(cmd);
Response r = new Response(replica.getInstanceMap());
r.setGetdir(entries);
return r;
}
// Usage example
public static void main(String[] args) throws Exception {
FileInputStream fs = new FileInputStream("src/Lzw.java");
byte[] data = new byte[1_000_000];
int len = fs.read(data, 0, data.length);
data = Arrays.copyOf(data, len);
char[] buffer = new char[len];
for (int i = 0; i < len; i++) buffer[i] = (char) (Byte.toUnsignedInt(data[i]));
String s = new String(buffer, 0, len);
int[] encoded = lzwEncoding(s);
String s2 = lzwDecoding(encoded);
byte[] data2 = new byte[len];
for (int i = 0; i < len; i++) data2[i] = (byte) s2.charAt(i);
System.out.println(Arrays.equals(data, data2));
Locale.setDefault(Locale.US);
System.out.printf("%d -> %.0f\n", s.length(), optimalCompressedLength(encoded));
}
// Deserialize object into a row for the table
@Override
public Object deserialize(Writable blob) throws SerDeException {
Text rowText = (Text) blob;
String[] values = rowText.toString().split("\t");
String queryString = values[1];
if (LOG.isDebugEnabled()) {
LOG.debug("Deserialize row: " + queryString);
}
// create a map from log string
Map<String, String> map = getQueryMap(queryString);
map.put("key", values[0]);
// Loop over columns in table and set values
String colName;
Object value;
for (int c = 0; c < numColumns; c++) {
colName = columnNames.get(c).toLowerCase();
TypeInfo ti = columnTypes.get(c);
if (!map.containsKey(colName)) {
value = null;
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.DOUBLE_TYPE_NAME)) {
value = Double.parseDouble(map.get(colName));
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.BIGINT_TYPE_NAME)) {
value = Long.parseLong(map.get(colName));
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.INT_TYPE_NAME)) {
value = Integer.parseInt(map.get(colName));
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.TINYINT_TYPE_NAME)) {
value = Byte.parseByte(map.get(colName));
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.FLOAT_TYPE_NAME)) {
value = Float.parseFloat(map.get(colName));
} else if (ti.getTypeName().equalsIgnoreCase(serdeConstants.BOOLEAN_TYPE_NAME)) {
value = Boolean.parseBoolean(map.get(colName));
} else {
value = decode(map.get(colName));
}
row.set(c, value);
}
return row;
}
@SuppressWarnings("UnnecessaryBoxing")
private static Object box(final Object value) {
Object newBoxedValue;
if (value instanceof Integer) {
newBoxedValue = Integer.valueOf(((Integer) value).intValue());
} else if (value instanceof Byte) {
newBoxedValue = Byte.valueOf(((Byte) value).byteValue());
} else if (value instanceof Short) {
newBoxedValue = Short.valueOf(((Short) value).shortValue());
} else if (value instanceof Long) {
newBoxedValue = Long.valueOf(((Long) value).longValue());
} else if (value instanceof Boolean) {
newBoxedValue = Boolean.valueOf(((Boolean) value).booleanValue());
} else if (value instanceof Character) {
newBoxedValue = Character.valueOf(((Character) value).charValue());
} else {
return new Object();
}
return newBoxedValue;
}
@Override
public <T> T next(InstanceType<T> instanceType, FixtureContract fixture) {
try {
if (instanceType.isCompatibleWith(Integer.class)) {
return (T) Integer.valueOf(this.getNextRandom().intValue());
} else if (instanceType.isCompatibleWith(Short.class)) {
return (T) Short.valueOf(getNextRandom().shortValue());
} else if (instanceType.isCompatibleWith(Long.class)) {
return (T) getNextRandom();
} else if (instanceType.isCompatibleWith(Byte.class)) {
return (T) Byte.valueOf(getNextRandom().byteValue());
} else if (instanceType.isCompatibleWith(Character.class)) {
return (T)
Character.valueOf(new String(new byte[] {getNextRandom().byteValue()}).charAt(0));
}
return (T) this.getNextRandom();
} catch (Exception e) {
throw new ObjectCreationException(instanceType, e);
}
}
