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// $Id: ExplicitBitVect.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// Copyright (c) 2001-2008 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 <iostream>
#include <RDBoost/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(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){
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;
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 ans(d_size);
*(ans.dp_bits) = ~(*dp_bits);
ans.d_numOnBits=ans.dp_bits->count();
return(ans);
};
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;
if(dp_bits) delete dp_bits;
dp_bits = new boost::dynamic_bitset<>(size);
d_numOnBits=0;
};
ExplicitBitVect::~ExplicitBitVect() {
if(dp_bits) delete dp_bits;
};
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;
}
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