rdkit/Code/DataStructs/ExplicitBitVect.cpp

// $Id$
//
// Copyright (c) 2001-2008 greg Landrum and Rational Discovery LLC
//  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
//
//  @@ 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 <iostream>
#include <RDGeneral/Exceptions.h>
#include "ExplicitBitVect.h"
#include <RDGeneral/StreamOps.h>
#include "base64.h"
#include <sstream>
#include <limits>
#ifdef WIN32
#include <ios>
#endif
#include <boost/cstdint.hpp>

ExplicitBitVect::ExplicitBitVect(unsigned int size, bool bitsSet) {
  d_size = 0;
  dp_bits = 0;
  d_numOnBits = 0;
  _initForSize(size);
  if (bitsSet) {
    dp_bits->set();  // set all bits to 1
    d_numOnBits = size;
  }
}
ExplicitBitVect::ExplicitBitVect(const std::string &s) {
  d_size = 0;
  dp_bits = 0;
  d_numOnBits = 0;
  initFromText(s.c_str(), s.length());
}
ExplicitBitVect::ExplicitBitVect(const char *data, const unsigned int dataLen) {
  d_size = 0;
  dp_bits = 0;
  d_numOnBits = 0;
  initFromText(data, dataLen);
}

ExplicitBitVect::ExplicitBitVect(const ExplicitBitVect &other)
    : BitVect(other) {
  d_size = other.d_size;
  dp_bits = new boost::dynamic_bitset<>(*(other.dp_bits));
  d_numOnBits = other.d_numOnBits;
};

ExplicitBitVect &ExplicitBitVect::operator=(const ExplicitBitVect &other) {
  d_size = other.d_size;
  delete dp_bits;
  dp_bits = new boost::dynamic_bitset<>(*(other.dp_bits));
  d_numOnBits = other.d_numOnBits;
  return *this;
};
bool ExplicitBitVect::operator[](const unsigned int which) const {
  if (which >= d_size) {
    throw IndexErrorException(which);
  }
  return (bool)(*dp_bits)[which];
};
bool ExplicitBitVect::setBit(const unsigned int which) {
  if (which >= d_size) {
    throw IndexErrorException(which);
  }
  if ((bool)(*dp_bits)[which]) {
    return true;
  } else {
    (*dp_bits)[which] = 1;
    ++d_numOnBits;
    return false;
  }
};
bool ExplicitBitVect::unsetBit(const unsigned int which) {
  if (which >= d_size) {
    throw IndexErrorException(which);
  }
  if ((bool)(*dp_bits)[which]) {
    (*dp_bits)[which] = 0;
    --d_numOnBits;
    return true;
  } else {
    return false;
  }
};
bool ExplicitBitVect::getBit(const unsigned int which) const {
  if (which >= d_size) {
    throw IndexErrorException(which);
  }
  return ((bool)(*dp_bits)[which]);
};

ExplicitBitVect ExplicitBitVect::operator^(const ExplicitBitVect &other) const {
  ExplicitBitVect ans(d_size);
  *(ans.dp_bits) = (*dp_bits) ^ *(other.dp_bits);
  ans.d_numOnBits = ans.dp_bits->count();
  return (ans);
};

ExplicitBitVect ExplicitBitVect::operator&(const ExplicitBitVect &other) const {
  ExplicitBitVect ans(d_size);
  *(ans.dp_bits) = (*dp_bits) & *(other.dp_bits);
  ans.d_numOnBits = ans.dp_bits->count();
  return (ans);
};

ExplicitBitVect ExplicitBitVect::operator|(const ExplicitBitVect &other) const {
  ExplicitBitVect ans(d_size);
  *(ans.dp_bits) = (*dp_bits) | *(other.dp_bits);
  ans.d_numOnBits = ans.dp_bits->count();
  return (ans);
};

ExplicitBitVect &ExplicitBitVect::operator^=(const ExplicitBitVect &other) {
  *(dp_bits) ^= *(other.dp_bits);
  d_numOnBits = dp_bits->count();
  return *this;
};

ExplicitBitVect &ExplicitBitVect::operator&=(const ExplicitBitVect &other) {
  *(dp_bits) &= *(other.dp_bits);
  d_numOnBits = dp_bits->count();
  return *this;
};

ExplicitBitVect &ExplicitBitVect::operator|=(const ExplicitBitVect &other) {
  *(dp_bits) |= *(other.dp_bits);
  d_numOnBits = dp_bits->count();
  return *this;
};

ExplicitBitVect ExplicitBitVect::operator~() const {
  ExplicitBitVect ans(d_size);
  *(ans.dp_bits) = ~(*dp_bits);
  ans.d_numOnBits = ans.dp_bits->count();
  return (ans);
};

ExplicitBitVect &ExplicitBitVect::operator+=(const ExplicitBitVect &other) {
  dp_bits->resize(d_size + other.d_size);
  unsigned int original_size = d_size;
  d_size = dp_bits->size();
  for (unsigned i = 0; i < other.d_size; i++) {
    if (other[i]) {
      setBit(i + original_size);
    }
  }
  d_numOnBits = dp_bits->count();
  return *this;
};

ExplicitBitVect ExplicitBitVect::operator+(const ExplicitBitVect &other) const {
  ExplicitBitVect ans(*this);
  return ans += other;
};

unsigned int ExplicitBitVect::getNumBits() const { return d_size; };
unsigned int ExplicitBitVect::getNumOnBits() const { return d_numOnBits; };
unsigned int ExplicitBitVect::getNumOffBits() const {
  return d_size - d_numOnBits;
};

// the contents of v are blown out
void ExplicitBitVect::getOnBits(IntVect &v) const {
  unsigned int nOn = getNumOnBits();
  if (!v.empty()) IntVect().swap(v);
  v.reserve(nOn);
  for (unsigned int i = 0; i < d_size; i++) {
    if ((bool)(*dp_bits)[i]) v.push_back(i);
  }
};

void ExplicitBitVect::_initForSize(unsigned int size) {
  d_size = size;
  delete dp_bits;
  dp_bits = new boost::dynamic_bitset<>(size);
  d_numOnBits = 0;
};

ExplicitBitVect::~ExplicitBitVect() {
  delete dp_bits;
  dp_bits = NULL;
};

std::string ExplicitBitVect::toString() const {
  // This Function replaces the older version (version 16) of writing the onbits
  // to
  // a string
  // the old version does not perform any run length encoding, it only checks to
  // see if
  // the length of the bitvect can be short ints and writes the on bits as
  // shorts
  // other wise the onbits are all written as ints

  // here we do run length encoding and the version number has been bumped to 32
  // as well.
  // only the reader needs to take care of readinf all legacy versions
  // also in this scheme each bit number written to the string is checked to see
  // how many
  // bytes it needs
  std::stringstream ss(std::ios_base::binary | std::ios_base::out |
                       std::ios_base::in);

  boost::int32_t tInt = ci_BITVECT_VERSION * -1;
  RDKit::streamWrite(ss, tInt);
  tInt = d_size;
  RDKit::streamWrite(ss, tInt);
  tInt = getNumOnBits();
  RDKit::streamWrite(ss, tInt);

  int prev = -1;
  unsigned int zeroes;
  for (unsigned int i = 0; i < d_size; i++) {
    if ((bool)(*dp_bits)[i]) {
      zeroes = i - prev - 1;
      RDKit::appendPackedIntToStream(ss, zeroes);
      prev = i;
    }
  }
  zeroes = d_size - prev - 1;
  RDKit::appendPackedIntToStream(ss, zeroes);
  std::string res(ss.str());
  return res;
}