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first pass, using google style

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This commit is contained in:
Greg Landrum
2015-11-14 14:58:11 +01:00
parent 80bb809b31
commit e08e0d16d8
619 changed files with 138877 additions and 133381 deletions
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344
Code/DataStructs/ExplicitBitVect.cpp
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@@ -21,207 +21,209 @@
#endif
#include <boost/cstdint.hpp>
ExplicitBitVect::ExplicitBitVect(unsigned int size, bool bitsSet)
{
d_size=0;dp_bits = 0;d_numOnBits=0;
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
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 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 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(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);
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);
}
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]);
};
}
d_numOnBits = dp_bits->count();
return *this;
};
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(*this);
return ans += other;
};
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);
};
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;
};
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;
};
// 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);
}
};
ExplicitBitVect& ExplicitBitVect::operator&= (const ExplicitBitVect &other) {
*(dp_bits) &= *(other.dp_bits);
d_numOnBits=dp_bits->count();
return *this;
};
void ExplicitBitVect::_initForSize(unsigned int size) {
d_size = size;
delete dp_bits;
dp_bits = new boost::dynamic_bitset<>(size);
d_numOnBits = 0;
};
ExplicitBitVect& ExplicitBitVect::operator|= (const ExplicitBitVect &other) {
*(dp_bits) |= *(other.dp_bits);
d_numOnBits=dp_bits->count();
return *this;
};
ExplicitBitVect::~ExplicitBitVect() {
delete dp_bits;
dp_bits = NULL;
};
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
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
// 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.
// 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
// 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);
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);
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;
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;
zeroes = d_size - prev - 1;
RDKit::appendPackedIntToStream(ss, zeroes);
std::string res(ss.str());
return res;
}