File: BitVect.cpp

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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++;
    }
  }

}