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;
}
/**
* 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;
}
/**
* 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 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;
}
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;
}
/**
* Check for byte
*
* @param input
* @return
*/
public static boolean isByte(String input) {
try {
Byte.parseByte(input);
return true;
} catch (Exception ex) {
return false;
}
}
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 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);
}
/** 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 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;
}
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 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;
}
// 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;
}
/**
* Notifies this instance that the dynamic payload types of the associated {@link MediaStream}
* have changed.
*/
public void onDynamicPayloadTypesChanged() {
rtxPayloadType = -1;
rtxAssociatedPayloadType = -1;
MediaStream mediaStream = channel.getStream();
Map<Byte, MediaFormat> mediaFormatMap = mediaStream.getDynamicRTPPayloadTypes();
Iterator<Map.Entry<Byte, MediaFormat>> it = mediaFormatMap.entrySet().iterator();
while (it.hasNext() && rtxPayloadType == -1) {
Map.Entry<Byte, MediaFormat> entry = it.next();
MediaFormat format = entry.getValue();
if (!Constants.RTX.equalsIgnoreCase(format.getEncoding())) {
continue;
}
// XXX(gp) we freak out if multiple codecs with RTX support are
// present.
rtxPayloadType = entry.getKey();
rtxAssociatedPayloadType = Byte.parseByte(format.getFormatParameters().get("apt"));
}
}
@SuppressWarnings("unchecked")
public static Object directBind(
String name, Annotation[] annotations, String value, Class<?> clazz, Type type)
throws Exception {
Logger.trace(
"directBind: value ["
+ value
+ "] annotation ["
+ Utils.join(annotations, " ")
+ "] Class ["
+ clazz
+ "]");
boolean nullOrEmpty = value == null || value.trim().length() == 0;
if (annotations != null) {
for (Annotation annotation : annotations) {
if (annotation.annotationType().equals(As.class)) {
Class<? extends TypeBinder<?>> toInstanciate = ((As) annotation).binder();
if (!(toInstanciate.equals(As.DEFAULT.class))) {
// Instantiate the binder
TypeBinder<?> myInstance = toInstanciate.newInstance();
return myInstance.bind(name, annotations, value, clazz, type);
}
}
}
}
// custom types
for (Class<?> c : supportedTypes.keySet()) {
Logger.trace("directBind: value [" + value + "] c [" + c + "] Class [" + clazz + "]");
if (c.isAssignableFrom(clazz)) {
Logger.trace("directBind: isAssignableFrom is true");
return supportedTypes.get(c).bind(name, annotations, value, clazz, type);
}
}
// application custom types
for (Class<TypeBinder<?>> c : Play.classloader.getAssignableClasses(TypeBinder.class)) {
if (c.isAnnotationPresent(Global.class)) {
Class<?> forType =
(Class) ((ParameterizedType) c.getGenericInterfaces()[0]).getActualTypeArguments()[0];
if (forType.isAssignableFrom(clazz)) {
return c.newInstance().bind(name, annotations, value, clazz, type);
}
}
}
// raw String
if (clazz.equals(String.class)) {
return value;
}
// Enums
if (Enum.class.isAssignableFrom(clazz)) {
if (nullOrEmpty) {
return null;
}
return Enum.valueOf((Class<Enum>) clazz, value);
}
// int or Integer binding
if (clazz.getName().equals("int") || clazz.equals(Integer.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? 0 : null;
}
return Integer.parseInt(value.contains(".") ? value.substring(0, value.indexOf(".")) : value);
}
// long or Long binding
if (clazz.getName().equals("long") || clazz.equals(Long.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? 0l : null;
}
return Long.parseLong(value.contains(".") ? value.substring(0, value.indexOf(".")) : value);
}
// byte or Byte binding
if (clazz.getName().equals("byte") || clazz.equals(Byte.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? (byte) 0 : null;
}
return Byte.parseByte(value.contains(".") ? value.substring(0, value.indexOf(".")) : value);
}
// short or Short binding
if (clazz.getName().equals("short") || clazz.equals(Short.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? (short) 0 : null;
}
return Short.parseShort(value.contains(".") ? value.substring(0, value.indexOf(".")) : value);
}
// float or Float binding
if (clazz.getName().equals("float") || clazz.equals(Float.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? 0f : null;
}
return Float.parseFloat(value);
}
// double or Double binding
if (clazz.getName().equals("double") || clazz.equals(Double.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? 0d : null;
}
return Double.parseDouble(value);
}
// BigDecimal binding
if (clazz.equals(BigDecimal.class)) {
if (nullOrEmpty) {
return null;
}
return new BigDecimal(value);
}
// boolean or Boolean binding
if (clazz.getName().equals("boolean") || clazz.equals(Boolean.class)) {
if (nullOrEmpty) {
return clazz.isPrimitive() ? false : null;
}
if (value.equals("1")
|| value.toLowerCase().equals("on")
|| value.toLowerCase().equals("yes")) {
return true;
}
return Boolean.parseBoolean(value);
}
return null;
}
// Get property value as a byte
public byte getByte(String key) {
return (properties.containsKey(key)) ? Byte.parseByte(properties.get(key).toString()) : 0;
}
