org.snpeff.collections.OpenBitSet Maven / Gradle / Ivy
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/**
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.snpeff.collections;
import java.io.Serializable;
import java.util.Arrays;
/**
* This class is originally from Apache Lucene-3.0.3 project.
* Only a few minor changes.
*/
/** 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.
*
* 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 -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 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 $
*/
@SuppressWarnings("serial")
public class OpenBitSet implements Cloneable, Serializable {
protected long[] bits;
protected int wlen; // number of words (elements) used in the array
/** Returns the popcount or cardinality of "a and not b"
* or "intersection(a, not(b))".
* Neither set is modified.
*/
public static long andNotCount(OpenBitSet a, OpenBitSet b) {
long tot = BitUtil.pop_andnot(a.bits, b.bits, 0, Math.min(a.wlen, b.wlen));
if( a.wlen > b.wlen ) {
tot += BitUtil.pop_array(a.bits, b.wlen, a.wlen - b.wlen);
}
return tot;
}
/** returns the number of 64 bit words it would take to hold numBits */
public static int bits2words(long numBits) {
return (int) (((numBits - 1) >>> 6) + 1);
}
/** Returns the popcount or cardinality of the intersection of the two sets.
* Neither set is modified.
*/
public static long intersectionCount(OpenBitSet a, OpenBitSet b) {
return BitUtil.pop_intersect(a.bits, b.bits, 0, Math.min(a.wlen, b.wlen));
}
/** Returns the popcount or cardinality of the union of the two sets.
* Neither set is modified.
*/
public static long unionCount(OpenBitSet a, OpenBitSet b) {
long tot = BitUtil.pop_union(a.bits, b.bits, 0, Math.min(a.wlen, b.wlen));
if( a.wlen < b.wlen ) {
tot += BitUtil.pop_array(b.bits, a.wlen, b.wlen - a.wlen);
} else if( a.wlen > b.wlen ) {
tot += BitUtil.pop_array(a.bits, b.wlen, a.wlen - b.wlen);
}
return tot;
}
/** Returns the popcount or cardinality of the exclusive-or of the two sets.
* Neither set is modified.
*/
public static long xorCount(OpenBitSet a, OpenBitSet b) {
long tot = BitUtil.pop_xor(a.bits, b.bits, 0, Math.min(a.wlen, b.wlen));
if( a.wlen < b.wlen ) {
tot += BitUtil.pop_array(b.bits, a.wlen, b.wlen - a.wlen);
} else if( a.wlen > b.wlen ) {
tot += BitUtil.pop_array(a.bits, b.wlen, a.wlen - b.wlen);
}
return tot;
}
public OpenBitSet() {
this(64);
}
/** Constructs an OpenBitSet large enough to hold numBits.
*
* @param numBits
*/
public OpenBitSet(long numBits) {
bits = new long[bits2words(numBits)];
wlen = bits.length;
}
/** 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 <= bits.length, and
* any existing words in the array at position >= numWords should be zero.
*
*/
public OpenBitSet(long[] bits, int numWords) {
this.bits = bits;
wlen = numWords;
}
//** see {@link intersect} */
public void and(OpenBitSet other) {
intersect(other);
}
//** see {@link andNot} */
public void andNot(OpenBitSet other) {
remove(other);
}
/** Returns the current capacity in bits (1 greater than the index of the last bit) */
public long capacity() {
return bits.length << 6;
}
/** @return the number of set bits */
public long cardinality() {
return BitUtil.pop_array(bits, 0, wlen);
}
/** Clears a range of bits. Clearing past the end does not change the size of the set.
*
* @param startIndex lower index
* @param endIndex one-past the last bit to clear
*/
public void clear(int startIndex, int endIndex) {
if( endIndex <= startIndex ) return;
int startWord = (startIndex >> 6);
if( startWord >= wlen ) return;
// since endIndex is one past the end, this is index of the last
// word to be changed.
int endWord = ((endIndex - 1) >> 6);
long startmask = -1L << startIndex;
long endmask = -1L >>> -endIndex; // 64-(endIndex&0x3f) is the same as -endIndex due to wrap
// invert masks since we are clearing
startmask = ~startmask;
endmask = ~endmask;
if( startWord == endWord ) {
bits[startWord] &= (startmask | endmask);
return;
}
bits[startWord] &= startmask;
int middle = Math.min(wlen, endWord);
Arrays.fill(bits, startWord + 1, middle, 0L);
if( endWord < wlen ) {
bits[endWord] &= endmask;
}
}
/** clears a bit, allowing access beyond the current set size without changing the size.*/
public void clear(long index) {
int wordNum = (int) (index >> 6); // div 64
if( wordNum >= wlen ) return;
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] &= ~bitmask;
}
/*
// alternate implementation of get()
public boolean get1(int index) {
int i = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
return ((bits[i]>>>bit) & 0x01) != 0;
// this does a long shift and a bittest (on x86) vs
// a long shift, and a long AND, (the test for zero is prob a no-op)
// testing on a P4 indicates this is slower than (bits[i] & bitmask) != 0;
}
*/
/** Clears a range of bits. Clearing past the end does not change the size of the set.
*
* @param startIndex lower index
* @param endIndex one-past the last bit to clear
*/
public void clear(long startIndex, long endIndex) {
if( endIndex <= startIndex ) return;
int startWord = (int) (startIndex >> 6);
if( startWord >= wlen ) return;
// since endIndex is one past the end, this is index of the last
// word to be changed.
int endWord = (int) ((endIndex - 1) >> 6);
long startmask = -1L << startIndex;
long endmask = -1L >>> -endIndex; // 64-(endIndex&0x3f) is the same as -endIndex due to wrap
// invert masks since we are clearing
startmask = ~startmask;
endmask = ~endmask;
if( startWord == endWord ) {
bits[startWord] &= (startmask | endmask);
return;
}
bits[startWord] &= startmask;
int middle = Math.min(wlen, endWord);
Arrays.fill(bits, startWord + 1, middle, 0L);
if( endWord < wlen ) {
bits[endWord] &= endmask;
}
}
/*
public boolean get2(int index) {
int word = index >> 6; // div 64
int bit = index & 0x0000003f; // mod 64
return (bits[word] << bit) < 0; // hmmm, this would work if bit order were reversed
// we could right shift and check for parity bit, if it was available to us.
}
*/
@Override
public Object clone() {
try {
OpenBitSet obs = (OpenBitSet) super.clone();
obs.bits = obs.bits.clone(); // hopefully an array clone is as fast(er) than arraycopy
return obs;
} catch(CloneNotSupportedException e) {
throw new RuntimeException(e);
}
}
/** Ensure that the long[] is big enough to hold numBits, expanding it if necessary.
* getNumWords() is unchanged by this call.
*/
public void ensureCapacity(long numBits) {
ensureCapacityWords(bits2words(numBits));
}
/** Expand the long[] with the size given as a number of words (64 bit longs).
* getNumWords() is unchanged by this call.
*/
public void ensureCapacityWords(int numWords) {
if( bits.length < numWords ) {
bits = ArrayUtil.grow(bits, numWords);
}
}
/** returns true if both sets have the same bits set */
@Override
public boolean equals(Object o) {
if( this == o ) return true;
if( !(o instanceof OpenBitSet) ) return false;
OpenBitSet a;
OpenBitSet b = (OpenBitSet) o;
// make a the larger set.
if( b.wlen > wlen ) {
a = b;
b = this;
} else {
a = this;
}
// check for any set bits out of the range of b
for( int i = a.wlen - 1; i >= b.wlen; i-- ) {
if( a.bits[i] != 0 ) return false;
}
for( int i = b.wlen - 1; i >= 0; i-- ) {
if( a.bits[i] != b.bits[i] ) return false;
}
return true;
}
protected int expandingWordNum(long index) {
int wordNum = (int) (index >> 6);
if( wordNum >= wlen ) {
ensureCapacity(index + 1);
wlen = wordNum + 1;
}
return wordNum;
}
/** clears a bit.
* The index should be less than the OpenBitSet size.
*/
public void fastClear(int index) {
int wordNum = index >> 6;
int bit = index & 0x03f;
long bitmask = 1L << bit;
bits[wordNum] &= ~bitmask;
// hmmm, it takes one more instruction to clear than it does to set... any
// way to work around this? If there were only 63 bits per word, we could
// use a right shift of 10111111...111 in binary to position the 0 in the
// correct place (using sign extension).
// Could also use Long.rotateRight() or rotateLeft() *if* they were converted
// by the JVM into a native instruction.
// bits[word] &= Long.rotateLeft(0xfffffffe,bit);
}
/** clears a bit.
* The index should be less than the OpenBitSet size.
*/
public void fastClear(long index) {
int wordNum = (int) (index >> 6); // div 64
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] &= ~bitmask;
}
/** flips a bit.
* The index should be less than the OpenBitSet size.
*/
public void fastFlip(int index) {
int wordNum = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] ^= bitmask;
}
/** flips a bit.
* The index should be less than the OpenBitSet size.
*/
public void fastFlip(long index) {
int wordNum = (int) (index >> 6); // div 64
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] ^= bitmask;
}
/** Returns true or false for the specified bit index.
* The index should be less than the OpenBitSet size
*/
public boolean fastGet(int index) {
int i = index >> 6; // div 64
// signed shift will keep a negative index and force an
// array-index-out-of-bounds-exception, removing the need for an explicit check.
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
return (bits[i] & bitmask) != 0;
}
/** Returns true or false for the specified bit index.
* The index should be less than the OpenBitSet size.
*/
public boolean fastGet(long index) {
int i = (int) (index >> 6); // div 64
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
return (bits[i] & bitmask) != 0;
}
/** Sets the bit at the specified index.
* The index should be less than the OpenBitSet size.
*/
public void fastSet(int index) {
int wordNum = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] |= bitmask;
}
/** Sets the bit at the specified index.
* The index should be less than the OpenBitSet size.
*/
public void fastSet(long index) {
int wordNum = (int) (index >> 6);
int bit = (int) index & 0x3f;
long bitmask = 1L << bit;
bits[wordNum] |= bitmask;
}
/** flips a bit, expanding the set size if necessary */
public void flip(long index) {
int wordNum = expandingWordNum(index);
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] ^= bitmask;
}
/** Flips a range of bits, expanding the set size if necessary
*
* @param startIndex lower index
* @param endIndex one-past the last bit to flip
*/
public void flip(long startIndex, long endIndex) {
if( endIndex <= startIndex ) return;
int startWord = (int) (startIndex >> 6);
// since endIndex is one past the end, this is index of the last
// word to be changed.
int endWord = expandingWordNum(endIndex - 1);
/*** Grrr, java shifting wraps around so -1L>>>64 == -1
* for that reason, make sure not to use endmask if the bits to flip will
* be zero in the last word (redefine endWord to be the last changed...)
long startmask = -1L << (startIndex & 0x3f); // example: 11111...111000
long endmask = -1L >>> (64-(endIndex & 0x3f)); // example: 00111...111111
***/
long startmask = -1L << startIndex;
long endmask = -1L >>> -endIndex; // 64-(endIndex&0x3f) is the same as -endIndex due to wrap
if( startWord == endWord ) {
bits[startWord] ^= (startmask & endmask);
return;
}
bits[startWord] ^= startmask;
for( int i = startWord + 1; i < endWord; i++ ) {
bits[i] = ~bits[i];
}
bits[endWord] ^= endmask;
}
/** flips a bit and returns the resulting bit value.
* The index should be less than the OpenBitSet size.
*/
public boolean flipAndGet(int index) {
int wordNum = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] ^= bitmask;
return (bits[wordNum] & bitmask) != 0;
}
/** flips a bit and returns the resulting bit value.
* The index should be less than the OpenBitSet size.
*/
public boolean flipAndGet(long index) {
int wordNum = (int) (index >> 6); // div 64
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
bits[wordNum] ^= bitmask;
return (bits[wordNum] & bitmask) != 0;
}
/** Returns true or false for the specified bit index. */
public boolean get(int index) {
int i = index >> 6; // div 64
// signed shift will keep a negative index and force an
// array-index-out-of-bounds-exception, removing the need for an explicit check.
if( i >= bits.length ) return false;
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
return (bits[i] & bitmask) != 0;
}
/*
public static int pop(long v0, long v1, long v2, long v3) {
// derived from pop_array by setting last four elems to 0.
// exchanges one pop() call for 10 elementary operations
// saving about 7 instructions... is there a better way?
long twosA=v0 & v1;
long ones=v0^v1;
long u2=ones^v2;
long twosB =(ones&v2)|(u2&v3);
ones=u2^v3;
long fours=(twosA&twosB);
long twos=twosA^twosB;
return (pop(fours)<<2)
+ (pop(twos)<<1)
+ pop(ones);
}
*/
/** Returns true or false for the specified bit index
*/
public boolean get(long index) {
int i = (int) (index >> 6); // div 64
if( i >= bits.length ) return false;
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
return (bits[i] & bitmask) != 0;
}
/** Sets a bit and returns the previous value.
* The index should be less than the OpenBitSet size.
*/
public boolean getAndSet(int index) {
int wordNum = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
long bitmask = 1L << bit;
boolean val = (bits[wordNum] & bitmask) != 0;
bits[wordNum] |= bitmask;
return val;
}
/** Sets a bit and returns the previous value.
* The index should be less than the OpenBitSet size.
*/
public boolean getAndSet(long index) {
int wordNum = (int) (index >> 6); // div 64
int bit = (int) index & 0x3f; // mod 64
long bitmask = 1L << bit;
boolean val = (bits[wordNum] & bitmask) != 0;
bits[wordNum] |= bitmask;
return val;
}
/** returns 1 if the bit is set, 0 if not.
* The index should be less than the OpenBitSet size
*/
public int getBit(int index) {
int i = index >> 6; // div 64
int bit = index & 0x3f; // mod 64
return ((int) (bits[i] >>> bit)) & 0x01;
}
/** Expert: returns the long[] storing the bits */
public long[] getBits() {
return bits;
}
/** Expert: gets the number of longs in the array that are in use */
public int getNumWords() {
return wlen;
}
@Override
public int hashCode() {
// Start with a zero hash and use a mix that results in zero if the input is zero.
// This effectively truncates trailing zeros without an explicit check.
long h = 0;
for( int i = bits.length; --i >= 0; ) {
h ^= bits[i];
h = (h << 1) | (h >>> 63); // rotate left
}
// fold leftmost bits into right and add a constant to prevent
// empty sets from returning 0, which is too common.
return (int) ((h >> 32) ^ h) + 0x98761234;
}
/** this = this AND other */
public void intersect(OpenBitSet other) {
int newLen = Math.min(wlen, other.wlen);
long[] thisArr = bits;
long[] otherArr = other.bits;
// testing against zero can be more efficient
int pos = newLen;
while(--pos >= 0) {
thisArr[pos] &= otherArr[pos];
}
if( wlen > newLen ) {
// fill zeros from the new shorter length to the old length
Arrays.fill(bits, newLen, wlen, 0);
}
wlen = newLen;
}
/** returns true if the sets have any elements in common */
public boolean intersects(OpenBitSet other) {
int pos = Math.min(wlen, other.wlen);
long[] thisArr = bits;
long[] otherArr = other.bits;
while(--pos >= 0) {
if( (thisArr[pos] & otherArr[pos]) != 0 ) return true;
}
return false;
}
/** Returns true if there are no set bits */
public boolean isEmpty() {
return cardinality() == 0;
}
/** Returns the index of the first set bit starting at the index specified.
* -1 is returned if there are no more set bits.
*/
public int nextSetBit(int index) {
int i = index >> 6;
if( i >= wlen ) return -1;
int subIndex = index & 0x3f; // index within the word
long word = bits[i] >> subIndex; // skip all the bits to the right of index
if( word != 0 ) { return (i << 6) + subIndex + BitUtil.ntz(word); }
while(++i < wlen) {
word = bits[i];
if( word != 0 ) return (i << 6) + BitUtil.ntz(word);
}
return -1;
}
/** Returns the index of the first set bit starting at the index specified.
* -1 is returned if there are no more set bits.
*/
public long nextSetBit(long index) {
int i = (int) (index >>> 6);
if( i >= wlen ) return -1;
int subIndex = (int) index & 0x3f; // index within the word
long word = bits[i] >>> subIndex; // skip all the bits to the right of index
if( word != 0 ) { return (((long) i) << 6) + (subIndex + BitUtil.ntz(word)); }
while(++i < wlen) {
word = bits[i];
if( word != 0 ) return (((long) i) << 6) + BitUtil.ntz(word);
}
return -1;
}
// some BitSet compatability methods
//** see {@link union} */
public void or(OpenBitSet other) {
union(other);
}
/** Remove all elements set in other. this = this AND_NOT other */
public void remove(OpenBitSet other) {
int idx = Math.min(wlen, other.wlen);
long[] thisArr = bits;
long[] otherArr = other.bits;
while(--idx >= 0) {
thisArr[idx] &= ~otherArr[idx];
}
}
/** sets a bit, expanding the set size if necessary */
public void set(long index) {
int wordNum = expandingWordNum(index);
int bit = (int) index & 0x3f;
long bitmask = 1L << bit;
bits[wordNum] |= bitmask;
}
/** Sets a range of bits, expanding the set size if necessary
*
* @param startIndex lower index
* @param endIndex one-past the last bit to set
*/
public void set(long startIndex, long endIndex) {
if( endIndex <= startIndex ) return;
int startWord = (int) (startIndex >> 6);
// since endIndex is one past the end, this is index of the last
// word to be changed.
int endWord = expandingWordNum(endIndex - 1);
long startmask = -1L << startIndex;
long endmask = -1L >>> -endIndex; // 64-(endIndex&0x3f) is the same as -endIndex due to wrap
if( startWord == endWord ) {
bits[startWord] |= (startmask & endmask);
return;
}
bits[startWord] |= startmask;
Arrays.fill(bits, startWord + 1, endWord, -1L);
bits[endWord] |= endmask;
}
/** Expert: sets a new long[] to use as the bit storage */
public void setBits(long[] bits) {
this.bits = bits;
}
/** Expert: sets the number of longs in the array that are in use */
public void setNumWords(int nWords) {
wlen = nWords;
}
/**
* Returns the current capacity of this set. Included for
* compatibility. This is *not* equal to {@link #cardinality}
*/
public long size() {
return capacity();
}
/** Lowers numWords, the number of words in use,
* by checking for trailing zero words.
*/
public void trimTrailingZeros() {
int idx = wlen - 1;
while(idx >= 0 && bits[idx] == 0)
idx--;
wlen = idx + 1;
}
/** this = this OR other */
public void union(OpenBitSet other) {
int newLen = Math.max(wlen, other.wlen);
ensureCapacityWords(newLen);
long[] thisArr = bits;
long[] otherArr = other.bits;
int pos = Math.min(wlen, other.wlen);
while(--pos >= 0) {
thisArr[pos] |= otherArr[pos];
}
if( wlen < newLen ) {
System.arraycopy(otherArr, wlen, thisArr, wlen, newLen - wlen);
}
wlen = newLen;
}
/** this = this XOR other */
public void xor(OpenBitSet other) {
int newLen = Math.max(wlen, other.wlen);
ensureCapacityWords(newLen);
long[] thisArr = bits;
long[] otherArr = other.bits;
int pos = Math.min(wlen, other.wlen);
while(--pos >= 0) {
thisArr[pos] ^= otherArr[pos];
}
if( wlen < newLen ) {
System.arraycopy(otherArr, wlen, thisArr, wlen, newLen - wlen);
}
wlen = newLen;
}
}