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// $Id: BitVect.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// 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 "BitVect.h"
#include <sstream>
#include <limits>
#include <RDGeneral/StreamOps.h>
#include "base64.h"
#ifdef WIN32
#include <ios>
#endif
#include <boost/cstdint.hpp>
BitVect::~BitVect() {}; // must always implement virtual destructors
void BitVect::initFromText(const char *data,const unsigned int dataLen,
bool isBase64,bool allowOldFormat){
std::stringstream ss(std::ios_base::binary|std::ios_base::in|std::ios_base::out);
if(isBase64){
unsigned int actualLen;
char *decoded;
decoded = Base64Decode((const char *)data,&actualLen);
ss.write(decoded,actualLen);
delete [] decoded;
} else {
ss.write(data,dataLen);
}
boost::int32_t format=0;
boost::uint32_t nOn=0;
boost::int32_t size;
boost::int32_t version=0;
// earlier versions of the code did not have the version number encoded, so
// we'll use that to distinguish version 0
RDKit::streamRead(ss,size);
if(size<0){
version = -1*size;
if (version == 16) {
format=1;
}
else if (version == 32) {
format=2;
}
else {
throw ValueErrorException("bad version in BitVect pickle");
}
RDKit::streamRead(ss,size);
} else if( !allowOldFormat ) {
throw ValueErrorException("invalid BitVect pickle");
}
RDKit::streamRead(ss,nOn);
_initForSize(static_cast<int>(size));
// if the either have older version or or version 16 with ints for on bits
if( (format==0) ||
( (format == 1) && (size >= std::numeric_limits<unsigned short>::max()) ) ) {
boost::uint32_t tmp;
for(unsigned int i=0; i<nOn; i++){
RDKit::streamRead(ss,tmp);
setBit(tmp);
}
} else if (format == 1) { // version 16 and on bits stored as short ints
boost::uint16_t tmp;
for(unsigned int i=0; i<nOn; i++){
RDKit::streamRead(ss,tmp);
setBit(tmp);
}
} else if (format == 2) { // run length encoded format
boost::uint32_t curr=0;
for (unsigned int i=0; i<nOn; i++) {
curr += RDKit::readPackedIntFromStream(ss);
setBit(curr);
curr++;
}
}
}
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