SparseBitVect.h
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//
// Copyright (c) 2003-2008 greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_SPARSEBITVECTS_H__
#define __RD_SPARSEBITVECTS_H__
#include "BitVect.h"
#include <set>
using std::set;
#include <iterator>
#include <algorithm>
typedef set<int> IntSet;
typedef IntSet::iterator IntSetIter;
typedef IntSet::const_iterator IntSetConstIter;
//! a class for bit vectors that are sparsely occupied.
/*!
SparseBitVect objects store only their on bits, in an
std::set.
They are, as you might expect, quite memory efficient for sparsely populated
vectors but become rather a nightmare if they need to be negated.
*/
class RDKIT_DATASTRUCTS_EXPORT SparseBitVect : public BitVect {
public:
SparseBitVect() : dp_bits(0), d_size(0){};
//! initialize with a particular size;
explicit SparseBitVect(unsigned int size) : dp_bits(0), d_size(0) {
_initForSize(size);
};
//! copy constructor
SparseBitVect(const SparseBitVect &other) : BitVect(other) {
d_size = 0;
dp_bits = 0;
_initForSize(other.getNumBits());
IntSet *bv = other.dp_bits;
std::copy(bv->begin(), bv->end(), std::inserter(*dp_bits, dp_bits->end()));
}
//! construct from a string pickle
SparseBitVect(const std::string &);
//! construct from a text pickle
SparseBitVect(const char *data, const unsigned int dataLen);
SparseBitVect &operator=(const SparseBitVect &);
~SparseBitVect() { delete dp_bits; };
bool operator[](const unsigned int which) const;
SparseBitVect operator|(const SparseBitVect &) const;
SparseBitVect operator&(const SparseBitVect &)const;
SparseBitVect operator^(const SparseBitVect &) const;
SparseBitVect operator~() const;
//! returns a (const) pointer to our raw storage
const IntSet *getBitSet() const { return dp_bits; }
unsigned int getNumBits() const { return d_size; };
bool setBit(const unsigned int which);
bool setBit(const IntSetIter which);
bool unsetBit(const unsigned int which);
bool getBit(const unsigned int which) const;
bool getBit(const IntVectIter which) const;
bool getBit(const IntSetIter which) const;
unsigned int getNumOnBits() const {
return static_cast<unsigned int>(dp_bits->size());
};
unsigned int getNumOffBits() const {
return d_size - static_cast<unsigned int>(dp_bits->size());
};
std::string toString() const;
void getOnBits(IntVect &v) const;
void clearBits() { dp_bits->clear(); };
IntSet *dp_bits; //!< our raw data, exposed for the sake of efficiency
bool operator==(const SparseBitVect &o) const {
return *dp_bits == *o.dp_bits;
}
bool operator!=(const SparseBitVect &o) const {
return *dp_bits != *o.dp_bits;
}
private:
unsigned int d_size;
void _initForSize(const unsigned int size);
};
#endif
BitVect.h
BitVect::getBit
virtual bool getBit(const unsigned int which) const =0
returns the value of a particular bit
IntVectIter
IntVect::iterator IntVectIter
Definition: BitVect.h:18
BitVect::setBit
virtual bool setBit(const unsigned int which)=0
sets a particular bit and returns its original value
BitVect::operator[]
virtual bool operator[](const unsigned int which) const =0
BitVect::getOnBits
virtual void getOnBits(IntVect &v) const =0
replaces the contents of v with indices of our on bits
SparseBitVect::getNumOffBits
unsigned int getNumOffBits() const
returns the number of off bits
Definition: SparseBitVect.h:78
SparseBitVect::getNumBits
unsigned int getNumBits() const
returns the number of bits (the length of the BitVect)
Definition: SparseBitVect.h:67
SparseBitVect::SparseBitVect
SparseBitVect(unsigned int size)
initialize with a particular size;
Definition: SparseBitVect.h:38
SparseBitVect::getNumOnBits
unsigned int getNumOnBits() const
returns the number of on bits
Definition: SparseBitVect.h:75
IntSetIter
IntSet::iterator IntSetIter
Definition: SparseBitVect.h:22
SparseBitVect::operator!=
bool operator!=(const SparseBitVect &o) const
Definition: SparseBitVect.h:91
BitVect::clearBits
virtual void clearBits()=0
clears (sets to off) all of our bits
RDKIT_DATASTRUCTS_EXPORT
#define RDKIT_DATASTRUCTS_EXPORT
Definition: export.h:112
BitVect::toString
virtual std::string toString() const =0
returns a serialized (pickled) version of this BitVect
IntSetConstIter
IntSet::const_iterator IntSetConstIter
Definition: SparseBitVect.h:23
BitVect
Abstract base class for storing BitVectors.
Definition: BitVect.h:24
SparseBitVect::getBitSet
const IntSet * getBitSet() const
returns a (const) pointer to our raw storage
Definition: SparseBitVect.h:65
IntSet
set< int > IntSet
Definition: SparseBitVect.h:21
SparseBitVect::~SparseBitVect
~SparseBitVect()
Definition: SparseBitVect.h:56
BitVect::unsetBit
virtual bool unsetBit(const unsigned int which)=0
unsets a particular bit and returns its original value
SparseBitVect
a class for bit vectors that are sparsely occupied.
Definition: SparseBitVect.h:34
IntVect
std::vector< int > IntVect
Definition: BitVect.h:17
SparseBitVect::dp_bits
IntSet * dp_bits
our raw data, exposed for the sake of efficiency
Definition: SparseBitVect.h:85
SparseBitVect::SparseBitVect
SparseBitVect()
Definition: SparseBitVect.h:36
SparseBitVect::SparseBitVect
SparseBitVect(const SparseBitVect &other)
copy constructor
Definition: SparseBitVect.h:43
SparseBitVect::operator==
bool operator==(const SparseBitVect &o) const
Definition: SparseBitVect.h:88
export.h