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;
}
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;
}
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);
}
public static void main(String[] args) throws IOException {
StringBuffer sb = new StringBuffer();
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
// For each test case
for (byte T = Byte.parseByte(br.readLine()); T > 0; --T) {
// Solve
sb.append(getMinDeletions(br.readLine().toCharArray()) + "\n");
}
System.out.print(sb);
}
/**
* 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));
}
public static void main(String[] args) throws IOException {
StringBuffer sb = new StringBuffer();
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
// INPUT
for (byte T = Byte.parseByte(br.readLine()); T > 0; --T) {
String[] input = br.readLine().split(" ");
int A = Integer.parseInt(input[0]);
int B = Integer.parseInt(input[1]);
// SOLVE
int C = (int) (Math.floor(Math.sqrt(B)) - Math.ceil(Math.sqrt(A)) + 1);
sb.append(C + "\n");
}
// OUTPUT
System.out.print(sb);
}
// Get property value as a byte
public byte getByte(String key) {
return (properties.containsKey(key)) ? Byte.parseByte(properties.get(key).toString()) : 0;
}
private void parseMobFile(String strStore, RandomAccessFile rafFile) {
try {
if (strStore.equalsIgnoreCase("skill")) {
strStore = rafFile.readLine();
int value = Byte.parseByte(rafFile.readLine());
addToSkill(strStore, value);
engGame.log.printMessage(Log.DEBUG, strStore + "=" + value);
return;
}
if (strStore.equalsIgnoreCase("condition")) {
Condition cndStore = engGame.getCondition(rafFile.readLine());
cndStore.intTicksPast = Integer.parseInt(rafFile.readLine());
cndStore.intDuration = Integer.parseInt(rafFile.readLine());
addCondition(cndStore);
engGame.log.printMessage(Log.DEBUG, "condition \"" + cndStore.strName + "\"");
return;
}
if (strStore.equalsIgnoreCase("giveitem")) {
String strItem = rafFile.readLine();
double dblChance = Double.valueOf(rafFile.readLine()).doubleValue();
vctGiveItems.addElement(new GiveItem(strItem, dblChance));
engGame.log.printMessage(
Log.DEBUG,
strName + " gives a \"" + strItem + "\" " + (100 * dblChance) + "% of the time.");
return;
}
if (strStore.equalsIgnoreCase("item")) {
Item itmStore = engGame.getItem(rafFile.readLine());
if (itmStore != null) {
itmStore.lngDurability = Long.parseLong(rafFile.readLine());
itmStore.intUses = Integer.parseInt(rafFile.readLine());
vctItems.addElement(itmStore);
}
return;
}
if (strStore.equalsIgnoreCase("clan")) {
strClan = rafFile.readLine();
return;
}
if (strStore.equalsIgnoreCase("race")) {
strRace = rafFile.readLine();
return;
}
if (strStore.equalsIgnoreCase("title")) {
strTitle = rafFile.readLine();
return;
}
if (strStore.equalsIgnoreCase("description")) {
strDescription = rafFile.readLine();
return;
}
if (strStore.equalsIgnoreCase("x")) {
intLocX = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("y")) {
intLocY = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("maxhp")) {
maxhp = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("maxmp")) {
maxmp = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("stre")) {
stre = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("inte")) {
inte = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("dext")) {
dext = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equals("cons")) {
cons = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("wisd")) {
wisd = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("image")) {
intImage = Integer.parseInt(rafFile.readLine());
return;
}
if (strStore.equalsIgnoreCase("bravery")) {
dblBravery = Double.valueOf(rafFile.readLine()).doubleValue();
return;
}
if (strStore.equalsIgnoreCase("grouprelation")) {
dblGroupRelation = Double.valueOf(rafFile.readLine()).doubleValue();
return;
}
if (strStore.equalsIgnoreCase("wield")) {
equWorn.wield = engGame.getItem(rafFile.readLine());
if (equWorn.wield != null) {
equWorn.wield.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.wield.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.wield);
return;
}
if (strStore.equalsIgnoreCase("arms")) {
equWorn.arms = engGame.getItem(rafFile.readLine());
if (equWorn.arms != null) {
equWorn.arms.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.arms.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.arms);
return;
}
if (strStore.equalsIgnoreCase("legs")) {
equWorn.legs = engGame.getItem(rafFile.readLine());
if (equWorn.legs != null) {
equWorn.legs.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.legs.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.legs);
return;
}
if (strStore.equalsIgnoreCase("torso")) {
equWorn.torso = engGame.getItem(rafFile.readLine());
if (equWorn.torso != null) {
equWorn.torso.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.torso.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.torso);
return;
}
if (strStore.equalsIgnoreCase("waist")) {
equWorn.waist = engGame.getItem(rafFile.readLine());
if (equWorn.waist != null) {
equWorn.waist.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.waist.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.waist);
return;
}
if (strStore.equalsIgnoreCase("neck")) {
equWorn.neck = engGame.getItem(rafFile.readLine());
if (equWorn.neck != null) {
equWorn.neck.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.neck.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.neck);
return;
}
if (strStore.equalsIgnoreCase("skull")) {
equWorn.skull = engGame.getItem(rafFile.readLine());
if (equWorn.skull != null) {
equWorn.skull.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.skull.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.skull);
return;
}
if (strStore.equalsIgnoreCase("eyes")) {
equWorn.eyes = engGame.getItem(rafFile.readLine());
if (equWorn.eyes != null) {
equWorn.eyes.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.eyes.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.eyes);
return;
}
if (strStore.equalsIgnoreCase("hands")) {
equWorn.hands = engGame.getItem(rafFile.readLine());
if (equWorn.hands != null) {
equWorn.hands.lngDurability = Long.parseLong(rafFile.readLine());
equWorn.hands.intUses = Integer.parseInt(rafFile.readLine());
}
runWearScript(equWorn.hands);
return;
}
if (strStore.equalsIgnoreCase("faction")) {
String strFaction = rafFile.readLine();
fctFaction = engGame.getFaction(strFaction);
if (fctFaction != null) {
engGame.log.printMessage(Log.DEBUG, "faction=\"" + fctFaction.strName + "\"");
} else {
engGame.log.printMessage(Log.DEBUG, "no faction found for \"" + strFaction + "\"");
}
return;
}
if (strStore.equalsIgnoreCase("onBattle")) {
strOnBattle = rafFile.readLine();
return;
}
if (strStore.equalsIgnoreCase("nofollow")) {
noFollow = true;
return;
}
} catch (Exception e) {
engGame.log.printError(
"parseMobFile():Parsing \"" + strStore + "\" from " + strName + "'s file", e);
}
}
// ========================================================================//
// ============================ PRIVATE METHODS ===========================//
// ========================================================================//
// Gets a property and converts it into byte.
static byte getByteProperty(String propName, byte defaultValue) {
return Byte.parseByte(properties.getProperty(propName, Byte.toString(defaultValue)).trim());
}