Package org.snpeff.collections
Class OpenBitSet
java.lang.Object
org.snpeff.collections.OpenBitSet
- All Implemented Interfaces:
Serializable
,Cloneable
An "open" BitSet implementation that allows direct access to the array of words
storing the bits.
Unlike java.util.bitset, the fact that bits are packed into an array of longs
is part of the interface. This allows efficient implementation of other algorithms
by someone other than the author. It also allows one to efficiently implement
alternate serialization or interchange formats.
BitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.
Test system: AMD Opteron, 64 bit linux, Sun Java 1.5_06 -server -Xbatch -Xmx64M
BitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.
OpenBitSet
is faster than java.util.BitSet
in most operations
and *much* faster at calculating cardinality of sets and results of set operations.
It can also handle sets of larger cardinality (up to 64 * 2**32-1)
The goals of OpenBitSet
are the fastest implementation possible, and
maximum code reuse. Extra safety and encapsulation
may always be built on top, but if that's built in, the cost can never be removed (and
hence people re-implement their own version in order to get better performance).
If you want a "safe", totally encapsulated (and slower and limited) BitSet
class, use java.util.BitSet
.
Performance Results
Test system: Pentium 4, Sun Java 1.5_06 -server -Xbatch -Xmx64MBitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.
cardinality | intersect_count | union | nextSetBit | get | iterator | |
---|---|---|---|---|---|---|
50% full | 3.36 | 3.96 | 1.44 | 1.46 | 1.99 | 1.58 |
1% full | 3.31 | 3.90 | 1.04 | 0.99 |
Test system: AMD Opteron, 64 bit linux, Sun Java 1.5_06 -server -Xbatch -Xmx64M
BitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.
cardinality | intersect_count | union | nextSetBit | get | iterator | |
---|---|---|---|---|---|---|
50% full | 2.50 | 3.50 | 1.00 | 1.03 | 1.12 | 1.25 |
1% full | 2.51 | 3.49 | 1.00 | 1.02 |
- Version:
- $Id: OpenBitSet.java,v 1.1 2011/03/10 12:18:16 pcingola Exp $
- See Also:
-
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionOpenBitSet
(long numBits) Constructs an OpenBitSet large enough to hold numBits.OpenBitSet
(long[] bits, int numWords) Constructs an OpenBitSet from an existing long[]. -
Method Summary
Modifier and TypeMethodDescriptionvoid
and
(OpenBitSet other) void
andNot
(OpenBitSet other) static long
andNotCount
(OpenBitSet a, OpenBitSet b) Returns the popcount or cardinality of "a and not b" or "intersection(a, not(b))".static int
bits2words
(long numBits) returns the number of 64 bit words it would take to hold numBitslong
capacity()
Returns the current capacity in bits (1 greater than the index of the last bit)long
void
clear
(int startIndex, int endIndex) Clears a range of bits.void
clear
(long index) clears a bit, allowing access beyond the current set size without changing the size.void
clear
(long startIndex, long endIndex) Clears a range of bits.clone()
void
ensureCapacity
(long numBits) Ensure that the long[] is big enough to hold numBits, expanding it if necessary.void
ensureCapacityWords
(int numWords) Expand the long[] with the size given as a number of words (64 bit longs).boolean
returns true if both sets have the same bits setprotected int
expandingWordNum
(long index) void
fastClear
(int index) clears a bit.void
fastClear
(long index) clears a bit.void
fastFlip
(int index) flips a bit.void
fastFlip
(long index) flips a bit.boolean
fastGet
(int index) Returns true or false for the specified bit index.boolean
fastGet
(long index) Returns true or false for the specified bit index.void
fastSet
(int index) Sets the bit at the specified index.void
fastSet
(long index) Sets the bit at the specified index.void
flip
(long index) flips a bit, expanding the set size if necessaryvoid
flip
(long startIndex, long endIndex) Flips a range of bits, expanding the set size if necessaryboolean
flipAndGet
(int index) flips a bit and returns the resulting bit value.boolean
flipAndGet
(long index) flips a bit and returns the resulting bit value.boolean
get
(int index) Returns true or false for the specified bit index.boolean
get
(long index) Returns true or false for the specified bit indexboolean
getAndSet
(int index) Sets a bit and returns the previous value.boolean
getAndSet
(long index) Sets a bit and returns the previous value.int
getBit
(int index) returns 1 if the bit is set, 0 if not.long[]
getBits()
Expert: returns the long[] storing the bitsint
Expert: gets the number of longs in the array that are in useint
hashCode()
void
intersect
(OpenBitSet other) this = this AND otherstatic long
Returns the popcount or cardinality of the intersection of the two sets.boolean
intersects
(OpenBitSet other) returns true if the sets have any elements in commonboolean
isEmpty()
Returns true if there are no set bitsint
nextSetBit
(int index) Returns the index of the first set bit starting at the index specified.long
nextSetBit
(long index) Returns the index of the first set bit starting at the index specified.void
or
(OpenBitSet other) void
remove
(OpenBitSet other) Remove all elements set in other.void
set
(long index) sets a bit, expanding the set size if necessaryvoid
set
(long startIndex, long endIndex) Sets a range of bits, expanding the set size if necessaryvoid
setBits
(long[] bits) Expert: sets a new long[] to use as the bit storagevoid
setNumWords
(int nWords) Expert: sets the number of longs in the array that are in uselong
size()
Returns the current capacity of this set.void
Lowers numWords, the number of words in use, by checking for trailing zero words.void
union
(OpenBitSet other) this = this OR otherstatic long
unionCount
(OpenBitSet a, OpenBitSet b) Returns the popcount or cardinality of the union of the two sets.void
xor
(OpenBitSet other) this = this XOR otherstatic long
xorCount
(OpenBitSet a, OpenBitSet b) Returns the popcount or cardinality of the exclusive-or of the two sets.
-
Field Details
-
bits
protected long[] bits -
wlen
protected int wlen
-
-
Constructor Details
-
OpenBitSet
public OpenBitSet() -
OpenBitSet
public OpenBitSet(long numBits) Constructs an OpenBitSet large enough to hold numBits.- Parameters:
numBits
-
-
OpenBitSet
public OpenBitSet(long[] bits, int numWords) Constructs an OpenBitSet from an existing long[].
The first 64 bits are in long[0], with bit index 0 at the least significant bit, and bit index 63 at the most significant. Given a bit index, the word containing it is long[index/64], and it is at bit number index%64 within that word.numWords are the number of elements in the array that contain set bits (non-zero longs). numWords should be invalid input: '<'= bits.length, and any existing words in the array at position invalid input: '>'= numWords should be zero.
-
-
Method Details
-
andNotCount
Returns the popcount or cardinality of "a and not b" or "intersection(a, not(b))". Neither set is modified. -
bits2words
public static int bits2words(long numBits) returns the number of 64 bit words it would take to hold numBits -
intersectionCount
Returns the popcount or cardinality of the intersection of the two sets. Neither set is modified. -
unionCount
Returns the popcount or cardinality of the union of the two sets. Neither set is modified. -
xorCount
Returns the popcount or cardinality of the exclusive-or of the two sets. Neither set is modified. -
and
-
andNot
-
capacity
public long capacity()Returns the current capacity in bits (1 greater than the index of the last bit) -
cardinality
public long cardinality()- Returns:
- the number of set bits
-
clear
public void clear(int startIndex, int endIndex) Clears a range of bits. Clearing past the end does not change the size of the set.- Parameters:
startIndex
- lower indexendIndex
- one-past the last bit to clear
-
clear
public void clear(long index) clears a bit, allowing access beyond the current set size without changing the size. -
clear
public void clear(long startIndex, long endIndex) Clears a range of bits. Clearing past the end does not change the size of the set.- Parameters:
startIndex
- lower indexendIndex
- one-past the last bit to clear
-
clone
-
ensureCapacity
public void ensureCapacity(long numBits) Ensure that the long[] is big enough to hold numBits, expanding it if necessary. getNumWords() is unchanged by this call. -
ensureCapacityWords
public void ensureCapacityWords(int numWords) Expand the long[] with the size given as a number of words (64 bit longs). getNumWords() is unchanged by this call. -
equals
returns true if both sets have the same bits set -
expandingWordNum
protected int expandingWordNum(long index) -
fastClear
public void fastClear(int index) clears a bit. The index should be less than the OpenBitSet size. -
fastClear
public void fastClear(long index) clears a bit. The index should be less than the OpenBitSet size. -
fastFlip
public void fastFlip(int index) flips a bit. The index should be less than the OpenBitSet size. -
fastFlip
public void fastFlip(long index) flips a bit. The index should be less than the OpenBitSet size. -
fastGet
public boolean fastGet(int index) Returns true or false for the specified bit index. The index should be less than the OpenBitSet size -
fastGet
public boolean fastGet(long index) Returns true or false for the specified bit index. The index should be less than the OpenBitSet size. -
fastSet
public void fastSet(int index) Sets the bit at the specified index. The index should be less than the OpenBitSet size. -
fastSet
public void fastSet(long index) Sets the bit at the specified index. The index should be less than the OpenBitSet size. -
flip
public void flip(long index) flips a bit, expanding the set size if necessary -
flip
public void flip(long startIndex, long endIndex) Flips a range of bits, expanding the set size if necessary- Parameters:
startIndex
- lower indexendIndex
- one-past the last bit to flip
-
flipAndGet
public boolean flipAndGet(int index) flips a bit and returns the resulting bit value. The index should be less than the OpenBitSet size. -
flipAndGet
public boolean flipAndGet(long index) flips a bit and returns the resulting bit value. The index should be less than the OpenBitSet size. -
get
public boolean get(int index) Returns true or false for the specified bit index. -
get
public boolean get(long index) Returns true or false for the specified bit index -
getAndSet
public boolean getAndSet(int index) Sets a bit and returns the previous value. The index should be less than the OpenBitSet size. -
getAndSet
public boolean getAndSet(long index) Sets a bit and returns the previous value. The index should be less than the OpenBitSet size. -
getBit
public int getBit(int index) returns 1 if the bit is set, 0 if not. The index should be less than the OpenBitSet size -
getBits
public long[] getBits()Expert: returns the long[] storing the bits -
getNumWords
public int getNumWords()Expert: gets the number of longs in the array that are in use -
hashCode
public int hashCode() -
intersect
this = this AND other -
intersects
returns true if the sets have any elements in common -
isEmpty
public boolean isEmpty()Returns true if there are no set bits -
nextSetBit
public int nextSetBit(int index) Returns the index of the first set bit starting at the index specified. -1 is returned if there are no more set bits. -
nextSetBit
public long nextSetBit(long index) Returns the index of the first set bit starting at the index specified. -1 is returned if there are no more set bits. -
or
-
remove
Remove all elements set in other. this = this AND_NOT other -
set
public void set(long index) sets a bit, expanding the set size if necessary -
set
public void set(long startIndex, long endIndex) Sets a range of bits, expanding the set size if necessary- Parameters:
startIndex
- lower indexendIndex
- one-past the last bit to set
-
setBits
public void setBits(long[] bits) Expert: sets a new long[] to use as the bit storage -
setNumWords
public void setNumWords(int nWords) Expert: sets the number of longs in the array that are in use -
size
public long size()Returns the current capacity of this set. Included for compatibility. This is *not* equal tocardinality()
-
trimTrailingZeros
public void trimTrailingZeros()Lowers numWords, the number of words in use, by checking for trailing zero words. -
union
this = this OR other -
xor
this = this XOR other
-