Package org.jmol.java

Class BS

  • All Implemented Interfaces:
    java.lang.Cloneable, javajs.api.JSONEncodable
    Direct Known Subclasses:
    BondSet, SmilesRing

    public class BS
    extends java.lang.Object
    implements java.lang.Cloneable, javajs.api.JSONEncodable
    a fast 64-bit BitSet optimized as 32-bit in Java2Script -- about 25 times faster than java.util.BitSet in JavaScript.
    Since:
    JDK1.0
    Author:
    Bob Hanson hansonr@stolaf.edu This class implements a 64-bit vector of bits that grows as needed. Each component of the bit set has a boolean value. The bits of a BitSet are indexed by nonnegative integers. Individual be used to modify the contents of another BitSet through logical AND, logical inclusive OR, and logical exclusive OR operations.

    By default, all bits in the set initially have the value false.

    Every bit set has a current size, which is the number of bits of space currently in use by the bit set. Note that the size is related to the implementation of a bit set, so it may change with implementation. The length of a bit set relates to logical length of a bit set and is defined independently of implementation.

    Unless otherwise noted, passing a null parameter to any of the methods in a BitSet will result in a NullPointerException.

    A BitSet is not safe for multithreaded use without external synchronization., Arthur van Hoff, Michael McCloskey, Martin Buchholz

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private static int ADDRESS_BITS_PER_WORD  
      private static int BITS_PER_WORD  
      private static long[] emptyBitmap  
      private boolean sizeIsSticky
      Whether the size of "words" is user-specified.
      private static long WORD_MASK  
      private long[] words
      The internal field corresponding to the serialField "bits".
      private int wordsInUse
      The number of words in the logical size of this BitSet.
    • Constructor Summary

      Constructors 
      Constructor Description
      BS()
      Creates a new bit set.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void and​(BS set)
      Performs a logical AND of this target bit set with the argument bit set.
      void andNot​(BS set)
      Clears all of the bits in this BitSet whose corresponding bit is set in the specified BitSet.
      int cardinality()
      Returns the number of bits set to true in this BitSet.
      int cardinalityN​(int max)  
      void clear​(int bitIndex)
      Sets the bit specified by the index to false.
      void clearAll()
      Sets all of the bits in this BitSet to false.
      void clearBits​(int fromIndex, int toIndex)
      Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to false.
      java.lang.Object clone()
      Cloning this BitSet produces a new BitSet that is equal to it.
      private void ensureCapacity​(int wordsRequired)
      Ensures that the BitSet can hold enough words.
      boolean equals​(java.lang.Object obj)
      Compares this object against the specified object.
      static java.lang.String escape​(BS bs, char chOpen, char chClose)  
      private void expandTo​(int wordIndex)
      Ensures that the BitSet can accommodate a given wordIndex, temporarily violating the invariants.
      boolean get​(int bitIndex)
      Returns the value of the bit with the specified index.
      int hashCode()
      Returns a hash code value for this bit set.
      private void init​(int nbits)  
      private void initWords​(int nbits)  
      boolean intersects​(BS set)
      Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
      boolean isEmpty()
      Returns true if this BitSet contains no bits that are set to true.
      int length()
      Returns the "logical size" of this BitSet: the index of the highest set bit in the BitSet plus one.
      static BS newN​(int nbits)
      Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
      int nextClearBit​(int fromIndex)
      Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
      int nextSetBit​(int fromIndex)
      Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
      void or​(BS set)
      Performs a logical OR of this bit set with the bit set argument.
      private void recalculateWordsInUse()
      Sets the field wordsInUse to the logical size in words of the bit set.
      void set​(int bitIndex)
      Sets the bit at the specified index to true.
      void setBits​(int fromIndex, int toIndex)
      Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true.
      void setBitTo​(int bitIndex, boolean value)
      Sets the bit at the specified index to the specified value.
      private void setLength​(int n)  
      int size()
      Returns the number of bits of space actually in use by this BitSet to represent bit values.
      java.lang.String toJSON()  
      java.lang.String toString()
      Returns a string representation of this bit set.
      static BS unescape​(java.lang.String str)
      ({ 1 2 3:5 }) or ({null}) or [{ 1 2 3:5 }]
      private static int wordIndex​(int bitIndex)
      Given a bit index, return word index containing it.
      void xor​(BS set)
      Performs a logical XOR of this bit set with the bit set argument.
      • Methods inherited from class java.lang.Object

        finalize, getClass, notify, notifyAll, wait, wait, wait
    • Field Detail

      • words

        private long[] words
        The internal field corresponding to the serialField "bits".
      • wordsInUse

        private transient int wordsInUse
        The number of words in the logical size of this BitSet.
      • sizeIsSticky

        private transient boolean sizeIsSticky
        Whether the size of "words" is user-specified. If so, we assume the user knows what he's doing and try harder to preserve it.
      • emptyBitmap

        private static final long[] emptyBitmap
    • Constructor Detail

      • BS

        public BS()
        Creates a new bit set. All bits are initially false.
    • Method Detail

      • wordIndex

        private static int wordIndex​(int bitIndex)
        Given a bit index, return word index containing it.
        Parameters:
        bitIndex -
        Returns:
        index
      • newN

        public static BS newN​(int nbits)
        Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1. All bits are initially false.
        Parameters:
        nbits - the initial size of the bit set
        Returns:
        bs
        Throws:
        java.lang.NegativeArraySizeException - if the specified initial size is negative
      • recalculateWordsInUse

        private void recalculateWordsInUse()
        Sets the field wordsInUse to the logical size in words of the bit set. WARNING:This method assumes that the number of words actually in use is less than or equal to the current value of wordsInUse!
      • init

        private void init​(int nbits)
      • initWords

        private void initWords​(int nbits)
      • ensureCapacity

        private void ensureCapacity​(int wordsRequired)
        Ensures that the BitSet can hold enough words.
        Parameters:
        wordsRequired - the minimum acceptable number of words.
      • expandTo

        private void expandTo​(int wordIndex)
        Ensures that the BitSet can accommodate a given wordIndex, temporarily violating the invariants. The caller must restore the invariants before returning to the user, possibly using recalculateWordsInUse().
        Parameters:
        wordIndex - the index to be accommodated.
      • set

        public void set​(int bitIndex)
        Sets the bit at the specified index to true.
        Parameters:
        bitIndex - a bit index
        Throws:
        java.lang.IndexOutOfBoundsException - if the specified index is negative
        Since:
        JDK1.0
      • setBitTo

        public void setBitTo​(int bitIndex,
                             boolean value)
        Sets the bit at the specified index to the specified value.
        Parameters:
        bitIndex - a bit index
        value - a boolean value to set
        Throws:
        java.lang.IndexOutOfBoundsException - if the specified index is negative
        Since:
        1.4
      • setBits

        public void setBits​(int fromIndex,
                            int toIndex)
        Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true.
        Parameters:
        fromIndex - index of the first bit to be set
        toIndex - index after the last bit to be set
        Throws:
        java.lang.IndexOutOfBoundsException - if fromIndex is negative, or toIndex is negative, or fromIndex is larger than toIndex
        Since:
        1.4
      • clear

        public void clear​(int bitIndex)
        Sets the bit specified by the index to false.
        Parameters:
        bitIndex - the index of the bit to be cleared
        Throws:
        java.lang.IndexOutOfBoundsException - if the specified index is negative
        Since:
        JDK1.0
      • clearBits

        public void clearBits​(int fromIndex,
                              int toIndex)
        Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to false.
        Parameters:
        fromIndex - index of the first bit to be cleared
        toIndex - index after the last bit to be cleared
        Throws:
        java.lang.IndexOutOfBoundsException - if fromIndex is negative, or toIndex is negative, or fromIndex is larger than toIndex
        Since:
        1.4
      • clearAll

        public void clearAll()
        Sets all of the bits in this BitSet to false.
        Since:
        1.4
      • get

        public boolean get​(int bitIndex)
        Returns the value of the bit with the specified index. The value is true if the bit with the index bitIndex is currently set in this BitSet; otherwise, the result is false.
        Parameters:
        bitIndex - the bit index
        Returns:
        the value of the bit with the specified index
        Throws:
        java.lang.IndexOutOfBoundsException - if the specified index is negative
      • nextSetBit

        public int nextSetBit​(int fromIndex)
        Returns the index of the first bit that is set to true that occurs on or after the specified starting index. If no such bit exists then -1 is returned.

        To iterate over the true bits in a BitSet, use the following loop:

      • nextClearBit

        public int nextClearBit​(int fromIndex)
        Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
        Parameters:
        fromIndex - the index to start checking from (inclusive)
        Returns:
        the index of the next clear bit
        Throws:
        java.lang.IndexOutOfBoundsException - if the specified index is negative
        Since:
        1.4
      • length

        public int length()
        Returns the "logical size" of this BitSet: the index of the highest set bit in the BitSet plus one. Returns zero if the BitSet contains no set bits.
        Returns:
        the logical size of this BitSet
        Since:
        1.2
      • isEmpty

        public boolean isEmpty()
        Returns true if this BitSet contains no bits that are set to true.
        Returns:
        boolean indicating whether this BitSet is empty
        Since:
        1.4
      • intersects

        public boolean intersects​(BS set)
        Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
        Parameters:
        set - BitSet to intersect with
        Returns:
        boolean indicating whether this BitSet intersects the specified BitSet
        Since:
        1.4
      • cardinality

        public int cardinality()
        Returns the number of bits set to true in this BitSet.
        Returns:
        the number of bits set to true in this BitSet
        Since:
        1.4
      • and

        public void and​(BS set)
        Performs a logical AND of this target bit set with the argument bit set. This bit set is modified so that each bit in it has the value true if and only if it both initially had the value true and the corresponding bit in the bit set argument also had the value true.
        Parameters:
        set - a bit set
      • or

        public void or​(BS set)
        Performs a logical OR of this bit set with the bit set argument. This bit set is modified so that a bit in it has the value true if and only if it either already had the value true or the corresponding bit in the bit set argument has the value true.
        Parameters:
        set - a bit set
      • xor

        public void xor​(BS set)
        Performs a logical XOR of this bit set with the bit set argument. This bit set is modified so that a bit in it has the value true if and only if one of the following statements holds:
        • The bit initially has the value true, and the corresponding bit in the argument has the value false.
        • The bit initially has the value false, and the corresponding bit in the argument has the value true.
        Parameters:
        set - a bit set
      • andNot

        public void andNot​(BS set)
        Clears all of the bits in this BitSet whose corresponding bit is set in the specified BitSet.
        Parameters:
        set - the BitSet with which to mask this BitSet
        Since:
        1.2
      • hashCode

        public int hashCode()
        Returns a hash code value for this bit set. The hash code depends only on which bits have been set within this BitSet. The algorithm used to compute it may be described as follows.

        Suppose the bits in the BitSet were to be stored in an array of long integers called, say, words, in such a manner that bit k is set in the BitSet (for nonnegative values of k) if and only if the expression

         ((k >> 6) < words.length) && ((words[k >> 6] & (1L << (bit & 0x3F))) != 0)
         
        is true. Then the following definition of the hashCode method would be a correct implementation of the actual algorithm:
         public int hashCode() {
          long h = 1234;
          for (int i = words.length; --i >= 0;) {
            h ˆ= words[i] * (i + 1);
          }
          return (int) ((h >> 32) ˆ h);
         }
         
        Note that the hash code values change if the set of bits is altered.

        Overrides the hashCode method of Object.

        Overrides:
        hashCode in class java.lang.Object
        Returns:
        a hash code value for this bit set.
      • size

        public int size()
        Returns the number of bits of space actually in use by this BitSet to represent bit values. The maximum element in the set is the size - 1st element.
        Returns:
        the number of bits currently in this bit set
      • equals

        public boolean equals​(java.lang.Object obj)
        Compares this object against the specified object. The result is true if and only if the argument is not null and is a Bitset object that has exactly the same set of bits set to true as this bit set. That is, for every nonnegative int index k,
         ((BitSet) obj).get(k) == this.get(k)
         
        must be true. The current sizes of the two bit sets are not compared.
        Overrides:
        equals in class java.lang.Object
        Parameters:
        obj - the object to compare with
        Returns:
        true if the objects are the same; false otherwise
        See Also:
        size()
      • clone

        public java.lang.Object clone()
        Cloning this BitSet produces a new BitSet that is equal to it. The clone of the bit set is another bit set that has exactly the same bits set to true as this bit set.
        Overrides:
        clone in class java.lang.Object
        Returns:
        a clone of this bit set
        See Also:
        size()
      • setLength

        private void setLength​(int n)
      • toString

        public java.lang.String toString()
        Returns a string representation of this bit set. For every index for which this BitSet contains a bit in the set state, the decimal representation of that index is included in the result. Such indices are listed in order from lowest to highest, separated by ", " (a comma and a space) and surrounded by braces, resulting in the usual mathematical notation for a set of integers.

        Example:

         BitSet drPepper = new BitSet();
         
        Now drPepper.toString() returns empty braces.

         drPepper.set(2);
         
        Now drPepper.toString() returns "{2}".

         drPepper.set(4);
         drPepper.set(10);
         
        Now drPepper.toString() returns "({2, 4, 10})".
        Overrides:
        toString in class java.lang.Object
        Returns:
        a string representation of this bit set
      • cardinalityN

        public int cardinalityN​(int max)
        Parameters:
        max -
        Returns:
        n bits below max
      • toJSON

        public java.lang.String toJSON()
        Specified by:
        toJSON in interface javajs.api.JSONEncodable
      • unescape

        public static BS unescape​(java.lang.String str)
        ({ 1 2 3:5 }) or ({null}) or [{ 1 2 3:5 }]
        Parameters:
        str -
        Returns:
        BS
      • escape

        public static java.lang.String escape​(BS bs,
                                              char chOpen,
                                              char chClose)