RDKit
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SparseBitVect.h
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1 //
2 // Copyright (c) 2003-2008 greg Landrum and Rational Discovery LLC
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #include <RDGeneral/export.h>
11 #ifndef __RD_SPARSEBITVECTS_H__
12 #define __RD_SPARSEBITVECTS_H__
13 
14 #include "BitVect.h"
15 
16 #include <set>
17 using std::set;
18 #include <iterator>
19 #include <algorithm>
20 
21 typedef set<int> IntSet;
22 typedef IntSet::iterator IntSetIter;
23 typedef IntSet::const_iterator IntSetConstIter;
24 
25 //! a class for bit vectors that are sparsely occupied.
26 /*!
27  SparseBitVect objects store only their on bits, in an
28  std::set.
29 
30  They are, as you might expect, quite memory efficient for sparsely populated
31  vectors but become rather a nightmare if they need to be negated.
32 
33  */
35  public:
37  //! initialize with a particular size;
38  explicit SparseBitVect(unsigned int size) : dp_bits(nullptr), d_size(0) {
39  _initForSize(size);
40  }
41 
42  //! copy constructor
43  SparseBitVect(const SparseBitVect &other) : BitVect(other) {
44  d_size = 0;
45  dp_bits = nullptr;
46  _initForSize(other.getNumBits());
47  IntSet *bv = other.dp_bits;
48  std::copy(bv->begin(), bv->end(), std::inserter(*dp_bits, dp_bits->end()));
49  }
50  //! construct from a string pickle
51  SparseBitVect(const std::string &);
52  //! construct from a text pickle
53  SparseBitVect(const char *data, const unsigned int dataLen);
54 
56  ~SparseBitVect() override { delete dp_bits; }
57 
58  bool operator[](const unsigned int which) const override;
63 
64  //! returns a (const) pointer to our raw storage
65  const IntSet *getBitSet() const { return dp_bits; }
66 
67  unsigned int getNumBits() const override { return d_size; }
68  bool setBit(const unsigned int which) override;
69  bool setBit(const IntSetIter which);
70  bool unsetBit(const unsigned int which) override;
71  bool getBit(const unsigned int which) const override;
72  bool getBit(const IntVectIter which) const;
73  bool getBit(const IntSetIter which) const;
74 
75  unsigned int getNumOnBits() const override {
76  return static_cast<unsigned int>(dp_bits->size());
77  }
78  unsigned int getNumOffBits() const override {
79  return d_size - static_cast<unsigned int>(dp_bits->size());
80  }
81 
82  std::string toString() const override;
83 
84  void getOnBits(IntVect &v) const override;
85  void clearBits() override { dp_bits->clear(); }
86  IntSet *dp_bits{
87  nullptr}; //!< our raw data, exposed for the sake of efficiency
88 
89  bool operator==(const SparseBitVect &o) const {
90  return *dp_bits == *o.dp_bits;
91  }
92  bool operator!=(const SparseBitVect &o) const {
93  return *dp_bits != *o.dp_bits;
94  }
95 
96  private:
97  unsigned int d_size{0};
98  void _initForSize(const unsigned int size) override;
99 };
100 
101 #endif
std::vector< int > IntVect
Definition: BitVect.h:17
IntVect::iterator IntVectIter
Definition: BitVect.h:18
IntSet::iterator IntSetIter
Definition: SparseBitVect.h:22
IntSet::const_iterator IntSetConstIter
Definition: SparseBitVect.h:23
set< int > IntSet
Definition: SparseBitVect.h:21
Abstract base class for storing BitVectors.
Definition: BitVect.h:24
a class for bit vectors that are sparsely occupied.
Definition: SparseBitVect.h:34
bool setBit(const unsigned int which) override
sets a particular bit and returns its original value
unsigned int getNumOffBits() const override
returns the number of off bits
Definition: SparseBitVect.h:78
bool getBit(const IntSetIter which) const
unsigned int getNumBits() const override
returns the number of bits (the length of the BitVect)
Definition: SparseBitVect.h:67
SparseBitVect operator|(const SparseBitVect &) const
bool getBit(const unsigned int which) const override
returns the value of a particular bit
void clearBits() override
clears (sets to off) all of our bits
Definition: SparseBitVect.h:85
SparseBitVect operator&(const SparseBitVect &) const
~SparseBitVect() override
Definition: SparseBitVect.h:56
bool unsetBit(const unsigned int which) override
unsets a particular bit and returns its original value
SparseBitVect operator~() const
unsigned int getNumOnBits() const override
returns the number of on bits
Definition: SparseBitVect.h:75
void getOnBits(IntVect &v) const override
replaces the contents of v with indices of our on bits
bool operator!=(const SparseBitVect &o) const
Definition: SparseBitVect.h:92
SparseBitVect(const char *data, const unsigned int dataLen)
construct from a text pickle
bool setBit(const IntSetIter which)
bool operator[](const unsigned int which) const override
bool operator==(const SparseBitVect &o) const
Definition: SparseBitVect.h:89
SparseBitVect operator^(const SparseBitVect &) const
SparseBitVect(unsigned int size)
initialize with a particular size;
Definition: SparseBitVect.h:38
IntSet * dp_bits
our raw data, exposed for the sake of efficiency
Definition: SparseBitVect.h:86
std::string toString() const override
returns a serialized (pickled) version of this BitVect
bool getBit(const IntVectIter which) const
SparseBitVect & operator=(const SparseBitVect &)
SparseBitVect(const SparseBitVect &other)
copy constructor
Definition: SparseBitVect.h:43
SparseBitVect(const std::string &)
construct from a string pickle
const IntSet * getBitSet() const
returns a (const) pointer to our raw storage
Definition: SparseBitVect.h:65
#define RDKIT_DATASTRUCTS_EXPORT
Definition: export.h:81