Java Code Examples for java.util.BitSet#size()

/**
 *
 * @param startValues fixed parameter values (if no parameters are fixed this is completely ignored)
 * @param transforms Array of ParameterLimitsTransform (which can be the NullTransform which does NOT transform the parameter) which transform
 *   a constrained function parameter (e.g. must be between -1 and 1) to a unconstrained fit parameter.
 * @param fixed BitSet with an element set to <b>true</b> if that parameter is fixed
 */
public UncoupledParameterTransforms(DoubleArray startValues, ParameterLimitsTransform[] transforms, BitSet fixed) {
  ArgChecker.notNull(startValues, "null start values");
  ArgChecker.notEmpty(transforms, "must specify transforms");
  ArgChecker.notNull(fixed, "must specify what is fixed (even if none)");
  _nMP = startValues.size();
  ArgChecker.isTrue(_nMP == transforms.length, "Have {}-dimensional start value but {} transforms", _nMP, transforms.length);
  _freeParameters = new boolean[_nMP];
  for (int i = 0; i < _nMP; i++) {
    if (i < fixed.size()) {
      _freeParameters[i] = !fixed.get(i);
    } else {
      _freeParameters[i] = true;
    }
  }
  int count = fixed.cardinality();
  ArgChecker.isTrue(count < _nMP, "all parameters are fixed");
  _nFP = _nMP - count;
  _startValues = startValues;
  _transforms = transforms;
}
 

/**
     *
     * @param Molecule1 BitSet
     * @param Molecule2 BitSet
     * @return <B>Similarity <U>Tanimoto, Jaccard</U> </B>
     * <B>c/(a+b-c)></B>
     * @throws java.lang.Exception
     */
    public static synchronized float getTanimotoSimilarity(BitSet Molecule1, BitSet Molecule2) throws Exception {
        BitSet bitset1 = (BitSet) Molecule1.clone();
        BitSet bitset2 = (BitSet) Molecule2.clone();

        float _bitset1_cardinality = bitset1.cardinality();
        float _bitset2_cardinality = bitset2.cardinality();

//        System.out.println("bitset1: "+ bitset1.size() + " " + " bitset2" + bitset2.size());
        if (bitset1.size() != bitset2.size()) {
            throw new Exception("BitSets must have the same bit length");
        }
        BitSet one_and_two = (BitSet) bitset1.clone();
        one_and_two.and(bitset2);
        float _common_bit_count = one_and_two.cardinality();
        return _common_bit_count / (_bitset1_cardinality + _bitset2_cardinality - _common_bit_count);
    }
 

/**
 *
 * @param Molecule1
 * @param Molecule2
 * @return <B>Similarity <U>Cosine,Ochiai,Carbo</U></B>
 * <B>c/sqrt(a*b)</B>
 * @throws Exception
 */
public static synchronized double getCosineSimilarity(BitSet Molecule1, BitSet Molecule2) throws Exception {
    BitSet bitset1 = (BitSet) Molecule1.clone();
    BitSet bitset2 = (BitSet) Molecule2.clone();

    float _bitset1_cardinality = bitset1.cardinality();
    float _bitset2_cardinality = bitset2.cardinality();

    if (bitset1.size() != bitset2.size()) {
        throw new Exception("Bisets must have the same bit length");
    }
    BitSet one_and_two = (BitSet) bitset1.clone();
    one_and_two.and(bitset2);
    float _common_bit_count = one_and_two.cardinality();

    return _common_bit_count / (sqrt(_bitset1_cardinality * _bitset2_cardinality));
}
 

public void reset(long[] ticks, long[] locations, long[] elevations, BitSet values, int size) throws IOException {
  
  int n = ticks.length;
  
  if (n != values.size() || (null != locations && n != locations.length) || (null != elevations && n != elevations.length)) {
    throw new IOException("Incoherent array lengths");
  }
  
  this.ticks = ticks;
  this.locations = locations;
  this.elevations = elevations;
  this.doubleValues = null;
  this.longValues = null;
  this.booleanValues = values;
  this.stringValues = null;
  this.sorted = false;
  this.values = size;
  this.sizehint = n;
  
  this.type = TYPE.BOOLEAN;    
}
 

public int findStartIdx(BitSet blocksMap, int requiredBlocks) {
  int startIdx = -1, blocks = 0, idx = 0;
  for (idx = 0; idx < blocksMap.size(); ++idx) {
    if (!blocksMap.get(idx)) {
       blocks++;
    } else {
       blocks = 0;
    }
    if (blocks == requiredBlocks) {
      break;
    }
  }
  if (blocks == requiredBlocks) {
    startIdx = idx - blocks + 1;
  }
  return startIdx;
}
 

protected static byte[] a(BitSet bitset)
{
    byte abyte0[] = new byte[bitset.size() / 8];
    int i = 0;
    while (i < bitset.size()) 
    {
        int j = i / 8;
        int k = 7 - i % 8;
        byte byte0 = abyte0[j];
        int l;
        if (bitset.get(i))
        {
            l = 1;
        } else
        {
            l = 0;
        }
        abyte0[j] = (byte)(byte0 | l << k);
        i++;
    }
    return abyte0;
}
 

/**
 *
 * @param Molecule1 BitSet
 * @param Molecule2 BitSet
 * <B>Note:</B> Can be Normalized to the range 1 to 0 if all attributes are
 * normalized to this range and the result is divided in N
 * @return <B>Distance (Dissimilarity) <U>Euclidean</U></B>
 * <B>sqrt(a+b-2c)</B>
 * <B>sqrt(OnA+OnB-2*c)</B>
 * @throws java.lang.Exception
 */
public static double getEuclideanDistance(BitSet Molecule1, BitSet Molecule2) throws Exception {

    A = (BitSet) Molecule1.clone();
    B = (BitSet) Molecule2.clone();

    float _bitset1_cardinality = A.cardinality();
    float _bitset2_cardinality = B.cardinality();

    if (A.size() != B.size()) {
        throw new Exception("Bisets must have the same bit length");
    }
    BitSet one_and_two = (BitSet) A.clone();
    one_and_two.and(B);
    float _common_bit_count = one_and_two.cardinality();
    double Val = sqrt((_bitset1_cardinality + _bitset2_cardinality - _common_bit_count) - _common_bit_count);

    return Val;
}
 

/**
 * 求素数 有无限个。一个大于1的自然数，如果除了1和它本身外，不能被其他自然数整除(除0以外）的数称之为素数(质数） 否则称为合数
 */
public static void computePrime() {
	BitSet sieve = new BitSet(1024);
	int size = sieve.size();
	for (int i = 2; i < size; i++)
		sieve.set(i);
	int finalBit = (int) Math.sqrt(sieve.size());

	for (int i = 2; i < finalBit; i++)
		if (sieve.get(i))
			for (int j = 2 * i; j < size; j += i)
				sieve.clear(j);

	int counter = 0;
	for (int i = 1; i < size; i++) {
		if (sieve.get(i)) {
			System.out.printf("%5d", i);
			if (++counter % 15 == 0)
				System.out.println();
		}
	}
	System.out.println();
}
 

/**
	 * 由bitset生成对应的bytebuf
	 * @param bitSet 
	 * @param bitSetSize bitset实际大小
	 * @return bytebuf
	 */
	private ByteBuf bitSetToResult(BitSet bitSet, int bitSetSize) {
		// 测试
//		if (bitSet.size() != bitSetSize) {
//			LOG.debug("bitSet.size() = " + bitSet.size());
//			LOG.debug("bitSetSize = " + bitSetSize);
//		}
		// 计算ret所需大小
		int retSize = (bitSet.size() / 8) + Integer.BYTES;
		LOG.debug("retSize = " + retSize);
		// 分配bytebuf
		ByteBuf ret = PooledByteBufAllocator.DEFAULT.buffer(retSize);
		// 先将bytebuf填充满
		ret.writerIndex(retSize);
		// 将bitset中的数据映射到bytebuf中
		for (int i = 0; i < bitSet.size(); i++) {
			int index = i / 8;
			int offset = 7 - i % 8;
			byte b = ret.getByte(index);
			b |= (bitSet.get(i) ? 1 : 0) << offset;
			ret.setByte(index, b);
		}
		// 将bitset大小信息添加到最后
		ret.setInt((bitSet.size() / 8), bitSetSize);
		return ret;
	}
 

/**
 *
 * @param Molecule1
 * @param Molecule2
 * @return <B>Distance (Dissimilarity)<U> Soergel</U></B>
 * <B>1-c/[a+b-c]=[a+b-2*c]/[a+b-c]</B>
 * @throws Exception
 */
public static double getSoergelDistance(BitSet Molecule1, BitSet Molecule2) throws Exception {

    A = (BitSet) Molecule1.clone();
    B = (BitSet) Molecule2.clone();

    float _bitset1_cardinality = A.cardinality();
    float _bitset2_cardinality = B.cardinality();

    if (A.size() != B.size()) {
        throw new Exception("Bisets must have the same bit length");
    }
    BitSet one_and_two = (BitSet) A.clone();
    one_and_two.and(B);
    float _common_bit_count = one_and_two.cardinality();
    double Val = (_bitset1_cardinality + _bitset2_cardinality - _common_bit_count) / _common_bit_count;

    return Val;

}
 

/**
 *
 * @param molSet
 * @throws CDKException
 */
private static IPatternFingerprinter getSumOfFingerprints(IAtomContainerSet molSet) throws CDKException, Exception {
    FingerprintGenerator molFingerprint = new FingerprintGenerator();
    IPatternFingerprinter fp = new PatternFingerprinter(getFingerprinterSize());
    for (IAtomContainer mol : molSet.atomContainers()) {
        BitSet booleanArray = molFingerprint.getFingerprint(mol);
        for (int i = 0; i < booleanArray.size(); i++) {
            if (booleanArray.get(i)) {
                fp.add(new Feature(valueOf(i), 1.0));
            }
        }
    }
    return fp;
}
 

private static <T> List <T> generateOne(List <T> elements, BitSet bs) {
    List <T> entry = new ArrayList <T> (bs.size()); 
    for (int i = 0; i < bs.size(); ++i) {
        if (bs.get(i)) {
            entry.add(elements.get(i));
        }
    }
    return entry;
}
 

protected static Date firstDate(DatePattern dp, int dayCode) {
   	if (dp == null) return null;
   	BitSet weekCode = dp.getPatternBitSet();
   	if (weekCode.isEmpty()) return null;
   	Calendar cal = Calendar.getInstance(Locale.US); cal.setLenient(true);
   	Date dpFirstDate = DateUtils.getDate(1, dp.getSession().getPatternStartMonth(), dp.getSession().getSessionStartYear());
   	cal.setTime(dpFirstDate);
   	int idx = weekCode.nextSetBit(0);
   	cal.add(Calendar.DAY_OF_YEAR, idx);
   	while (idx < weekCode.size()) {
   		if (weekCode.get(idx)) {
       		int dow = cal.get(Calendar.DAY_OF_WEEK);
       		switch (dow) {
       		case Calendar.MONDAY:
       			if ((dayCode & DayCode.MON.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.TUESDAY:
       			if ((dayCode & DayCode.TUE.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.WEDNESDAY:
       			if ((dayCode & DayCode.WED.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.THURSDAY:
       			if ((dayCode & DayCode.THU.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.FRIDAY:
       			if ((dayCode & DayCode.FRI.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.SATURDAY:
       			if ((dayCode & DayCode.SAT.getCode()) != 0) return cal.getTime();
       			break;
       		case Calendar.SUNDAY:
       			if ((dayCode & DayCode.SUN.getCode()) != 0) return cal.getTime();
       			break;
       		}
       	}
   		cal.add(Calendar.DAY_OF_YEAR, 1); idx++;
   	}
   	return null;
}
 

/**
 * Returns <code>true</code> iff any bit in the given set is 
 * <code>true</code>.
 */
private boolean anyValueSet(BitSet set) {
    for (int i = 0; i < set.size(); i++) {
        if (set.get(i)) {
            return true;
        }
    }
    return false;
}
 

public static byte[] toByteArray_bak(BitSet bitSet) {
    ByteArrayOutputStream baos = new ByteArrayOutputStream(bitSet.size());
    try {
        ObjectOutputStream oos = new ObjectOutputStream(baos);
        oos.writeObject(bitSet);
    } catch (IOException ex) {
        ex.printStackTrace();
    }
    return baos.toByteArray();
}
 

public byte[] toByteArray(BitSet bs) {
    if (bs.size() == 0) {
        return new byte[0];
    }

    // Find highest bit
    int hiBit = -1;
    for (int i = 0; i < bs.size(); i++) {
        if (bs.get(i)) {
            hiBit = i;
        }
    }

    int n = (hiBit + 8) / 8;
    byte[] bytes = new byte[n];
    if (n == 0) {
        return bytes;
    }

    Arrays.fill(bytes, (byte) 0);
    for (int i = 0; i < n * 8; i++) {
        if (bs.get(i)) {
            setBit(i, bytes);
        }
    }

    return bytes;
}
 

public FindPartitionConditions(BitSet dirs, RexBuilder builder) {
  // go deep
  super(true);
  this.dirs = dirs;
  this.builder = builder;
  this.referencedDirs = new BitSet(dirs.size());
}
 

private <V extends Number> ClusterAffinityDistribution<V> evaluateSimilarity(ValueFactory<V> valueFactory, ComparisonMeasure comparisonMeasure, List<ClusteringField> clusteringFields, List<FieldValue> values){
	ClusteringModel clusteringModel = getModel();

	List<Cluster> clusters = clusteringModel.getClusters();

	ClusterAffinityDistribution<V> result = createClusterAffinityDistribution(Classification.Type.SIMILARITY, clusters);

	BitSet flags = MeasureUtil.toBitSet(values);

	for(Cluster cluster : clusters){
		BitSet clusterFlags = CacheUtil.getValue(cluster, ClusteringModelEvaluator.clusterFlagCache);

		if(flags.size() != clusterFlags.size()){
			throw new InvalidElementException(cluster);
		}

		Value<V> similarity = MeasureUtil.evaluateSimilarity(valueFactory, comparisonMeasure, clusteringFields, flags, clusterFlags);

		result.put(cluster, similarity);
	}

	return result;
}
 

private synchronized void set(BitSet bitset) {
    arrayFingerprint = new boolean[bitset.size()];
    for (int i = 0; i < bitset.length(); i++) {
        arrayFingerprint[i] = (bitset.get(i));
    }
}
 

public FindPartitionConditions(BitSet dirs) {
  // go deep
  super(true);
  this.dirs = dirs;
  this.referencedDirs = new BitSet(dirs.size());
}