Class BS
- java.lang.Object
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- org.jmol.java.BS
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- 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.JSONEncodablea 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
booleanvalue. The bits of aBitSetare indexed by nonnegative integers. Individual be used to modify the contents of anotherBitSetthrough 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
BitSetwill result in aNullPointerException.A
BitSetis not safe for multithreaded use without external synchronization., Arthur van Hoff, Michael McCloskey, Martin Buchholz
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Field Summary
Fields Modifier and Type Field Description private static intADDRESS_BITS_PER_WORDprivate static intBITS_PER_WORDprivate static long[]emptyBitmapprivate booleansizeIsStickyWhether the size of "words" is user-specified.private static longWORD_MASKprivate long[]wordsThe internal field corresponding to the serialField "bits".private intwordsInUseThe number of words in the logical size of this BitSet.
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Constructor Summary
Constructors Constructor Description BS()Creates a new bit set.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description voidand(BS set)Performs a logical AND of this target bit set with the argument bit set.voidandNot(BS set)Clears all of the bits in thisBitSetwhose corresponding bit is set in the specifiedBitSet.intcardinality()Returns the number of bits set totruein thisBitSet.intcardinalityN(int max)voidclear(int bitIndex)Sets the bit specified by the index tofalse.voidclearAll()Sets all of the bits in this BitSet tofalse.voidclearBits(int fromIndex, int toIndex)Sets the bits from the specifiedfromIndex(inclusive) to the specifiedtoIndex(exclusive) tofalse.java.lang.Objectclone()Cloning thisBitSetproduces a newBitSetthat is equal to it.private voidensureCapacity(int wordsRequired)Ensures that the BitSet can hold enough words.booleanequals(java.lang.Object obj)Compares this object against the specified object.static java.lang.Stringescape(BS bs, char chOpen, char chClose)private voidexpandTo(int wordIndex)Ensures that the BitSet can accommodate a given wordIndex, temporarily violating the invariants.booleanget(int bitIndex)Returns the value of the bit with the specified index.inthashCode()Returns a hash code value for this bit set.private voidinit(int nbits)private voidinitWords(int nbits)booleanintersects(BS set)Returns true if the specifiedBitSethas any bits set totruethat are also set totruein thisBitSet.booleanisEmpty()Returns true if thisBitSetcontains no bits that are set totrue.intlength()Returns the "logical size" of thisBitSet: the index of the highest set bit in theBitSetplus one.static BSnewN(int nbits)Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range0throughnbits-1.intnextClearBit(int fromIndex)Returns the index of the first bit that is set tofalsethat occurs on or after the specified starting index.intnextSetBit(int fromIndex)Returns the index of the first bit that is set totruethat occurs on or after the specified starting index.voidor(BS set)Performs a logical OR of this bit set with the bit set argument.private voidrecalculateWordsInUse()Sets the field wordsInUse to the logical size in words of the bit set.voidset(int bitIndex)Sets the bit at the specified index totrue.voidsetBits(int fromIndex, int toIndex)Sets the bits from the specifiedfromIndex(inclusive) to the specifiedtoIndex(exclusive) totrue.voidsetBitTo(int bitIndex, boolean value)Sets the bit at the specified index to the specified value.private voidsetLength(int n)intsize()Returns the number of bits of space actually in use by thisBitSetto represent bit values.java.lang.StringtoJSON()java.lang.StringtoString()Returns a string representation of this bit set.static BSunescape(java.lang.String str)({ 1 2 3:5 }) or ({null}) or [{ 1 2 3:5 }]private static intwordIndex(int bitIndex)Given a bit index, return word index containing it.voidxor(BS set)Performs a logical XOR of this bit set with the bit set argument.
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Field Detail
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ADDRESS_BITS_PER_WORD
private static final int ADDRESS_BITS_PER_WORD
- See Also:
- Constant Field Values
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BITS_PER_WORD
private static final int BITS_PER_WORD
- See Also:
- Constant Field Values
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WORD_MASK
private static final long WORD_MASK
- See Also:
- Constant Field Values
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words
private long[] words
The internal field corresponding to the serialField "bits".
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wordsInUse
private transient int wordsInUse
The number of words in the logical size of this BitSet.
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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.
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emptyBitmap
private static final long[] emptyBitmap
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Method Detail
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wordIndex
private static int wordIndex(int bitIndex)
Given a bit index, return word index containing it.- Parameters:
bitIndex-- Returns:
- index
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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 range0throughnbits-1. All bits are initiallyfalse.- Parameters:
nbits- the initial size of the bit set- Returns:
- bs
- Throws:
java.lang.NegativeArraySizeException- if the specified initial size is negative
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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!
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init
private void init(int nbits)
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initWords
private void initWords(int nbits)
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ensureCapacity
private void ensureCapacity(int wordsRequired)
Ensures that the BitSet can hold enough words.- Parameters:
wordsRequired- the minimum acceptable number of words.
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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.
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set
public void set(int bitIndex)
Sets the bit at the specified index totrue.- Parameters:
bitIndex- a bit index- Throws:
java.lang.IndexOutOfBoundsException- if the specified index is negative- Since:
- JDK1.0
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setBitTo
public void setBitTo(int bitIndex, boolean value)Sets the bit at the specified index to the specified value.- Parameters:
bitIndex- a bit indexvalue- a boolean value to set- Throws:
java.lang.IndexOutOfBoundsException- if the specified index is negative- Since:
- 1.4
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setBits
public void setBits(int fromIndex, int toIndex)Sets the bits from the specifiedfromIndex(inclusive) to the specifiedtoIndex(exclusive) totrue.- Parameters:
fromIndex- index of the first bit to be settoIndex- index after the last bit to be set- Throws:
java.lang.IndexOutOfBoundsException- iffromIndexis negative, ortoIndexis negative, orfromIndexis larger thantoIndex- Since:
- 1.4
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clear
public void clear(int bitIndex)
Sets the bit specified by the index tofalse.- Parameters:
bitIndex- the index of the bit to be cleared- Throws:
java.lang.IndexOutOfBoundsException- if the specified index is negative- Since:
- JDK1.0
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clearBits
public void clearBits(int fromIndex, int toIndex)Sets the bits from the specifiedfromIndex(inclusive) to the specifiedtoIndex(exclusive) tofalse.- Parameters:
fromIndex- index of the first bit to be clearedtoIndex- index after the last bit to be cleared- Throws:
java.lang.IndexOutOfBoundsException- iffromIndexis negative, ortoIndexis negative, orfromIndexis larger thantoIndex- Since:
- 1.4
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clearAll
public void clearAll()
Sets all of the bits in this BitSet tofalse.- Since:
- 1.4
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get
public boolean get(int bitIndex)
Returns the value of the bit with the specified index. The value istrueif the bit with the indexbitIndexis currently set in thisBitSet; otherwise, the result isfalse.- 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
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nextSetBit
public int nextSetBit(int fromIndex)
Returns the index of the first bit that is set totruethat occurs on or after the specified starting index. If no such bit exists then-1is returned.To iterate over the
truebits in aBitSet, use the following loop:
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nextClearBit
public int nextClearBit(int fromIndex)
Returns the index of the first bit that is set tofalsethat 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
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length
public int length()
Returns the "logical size" of thisBitSet: the index of the highest set bit in theBitSetplus one. Returns zero if theBitSetcontains no set bits.- Returns:
- the logical size of this
BitSet - Since:
- 1.2
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isEmpty
public boolean isEmpty()
Returns true if thisBitSetcontains no bits that are set totrue.- Returns:
- boolean indicating whether this
BitSetis empty - Since:
- 1.4
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intersects
public boolean intersects(BS set)
Returns true if the specifiedBitSethas any bits set totruethat are also set totruein thisBitSet.- Parameters:
set-BitSetto intersect with- Returns:
- boolean indicating whether this
BitSetintersects the specifiedBitSet - Since:
- 1.4
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cardinality
public int cardinality()
Returns the number of bits set totruein thisBitSet.- Returns:
- the number of bits set to
truein thisBitSet - Since:
- 1.4
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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 valuetrueif and only if it both initially had the valuetrueand the corresponding bit in the bit set argument also had the valuetrue.- Parameters:
set- a bit set
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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 valuetrueif and only if it either already had the valuetrueor the corresponding bit in the bit set argument has the valuetrue.- Parameters:
set- a bit set
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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 valuetrueif 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 valuefalse. - The bit initially has the value
false, and the corresponding bit in the argument has the valuetrue.
- Parameters:
set- a bit set
- The bit initially has the value
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andNot
public void andNot(BS set)
Clears all of the bits in thisBitSetwhose corresponding bit is set in the specifiedBitSet.- Parameters:
set- theBitSetwith which to mask thisBitSet- Since:
- 1.2
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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 thisBitSet. The algorithm used to compute it may be described as follows.Suppose the bits in the
BitSetwere to be stored in an array oflongintegers called, say,words, in such a manner that bitkis set in theBitSet(for nonnegative values ofk) if and only if the expression((k >> 6) < words.length) && ((words[k >> 6] & (1L << (bit & 0x3F))) != 0)
is true. Then the following definition of thehashCodemethod 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
hashCodemethod ofObject.- Overrides:
hashCodein classjava.lang.Object- Returns:
- a hash code value for this bit set.
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size
public int size()
Returns the number of bits of space actually in use by thisBitSetto represent bit values. The maximum element in the set is the size - 1st element.- Returns:
- the number of bits currently in this bit set
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equals
public boolean equals(java.lang.Object obj)
Compares this object against the specified object. The result istrueif and only if the argument is notnulland is aBitsetobject that has exactly the same set of bits set totrueas this bit set. That is, for every nonnegativeintindexk,((BitSet) obj).get(k) == this.get(k)
must be true. The current sizes of the two bit sets are not compared.- Overrides:
equalsin classjava.lang.Object- Parameters:
obj- the object to compare with- Returns:
trueif the objects are the same;falseotherwise- See Also:
size()
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clone
public java.lang.Object clone()
Cloning thisBitSetproduces a newBitSetthat is equal to it. The clone of the bit set is another bit set that has exactly the same bits set totrueas this bit set.- Overrides:
clonein classjava.lang.Object- Returns:
- a clone of this bit set
- See Also:
size()
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setLength
private void setLength(int n)
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toString
public java.lang.String toString()
Returns a string representation of this bit set. For every index for which thisBitSetcontains 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();
NowdrPepper.toString()returns empty braces.drPepper.set(2);
NowdrPepper.toString()returns "{2}".drPepper.set(4); drPepper.set(10);
NowdrPepper.toString()returns "({2, 4, 10})".- Overrides:
toStringin classjava.lang.Object- Returns:
- a string representation of this bit set
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cardinalityN
public int cardinalityN(int max)
- Parameters:
max-- Returns:
- n bits below max
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toJSON
public java.lang.String toJSON()
- Specified by:
toJSONin interfacejavajs.api.JSONEncodable
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unescape
public static BS unescape(java.lang.String str)
({ 1 2 3:5 }) or ({null}) or [{ 1 2 3:5 }]- Parameters:
str-- Returns:
- BS
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escape
public static java.lang.String escape(BS bs, char chOpen, char chClose)
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