// $Id$
//
//  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 "FragCatParams.h"
#include "FragCatalogUtils.h"
#include <GraphMol/RDKitBase.h>
#include <sstream>
#include <boost/cstdint.hpp>

namespace RDKit{
  using boost::int32_t;
  using boost::uint32_t;

  FragCatParams::FragCatParams(unsigned int lLen, unsigned int uLen,
			       std::string fgroupFile, double tol) {
    d_funcGroups.clear();
    d_typeStr = "Fragment Catalog Parameters";
    CHECK_INVARIANT(lLen<=uLen,"The upper length for fragments must be >= lower length");
    d_lowerFragLen = lLen;
    d_upperFragLen = uLen;
    d_tolerance = tol;
    d_funcGroups = readFuncGroups(fgroupFile);
  }

  FragCatParams::FragCatParams(const FragCatParams &other) {
    d_funcGroups.clear();
    // copy consttructor
    d_typeStr = other.getTypeStr();
    d_lowerFragLen = other.getLowerFragLength();
    d_upperFragLen = other.getUpperFragLength();
    d_tolerance = other.getTolerance();
    
    // std::cout << "In param copier\n";
    const MOL_SPTR_VECT &ofgrps = other.getFuncGroups();
    //const MOL_PTR_VECT &ofgrps = other.getFuncGroups();
    MOL_SPTR_VECT::const_iterator fgi;
    //MOL_PTR_VECT_CI fgi;
    for (fgi = ofgrps.begin(); fgi != ofgrps.end(); fgi++) {
      ROMol *nmol = new ROMol(*(fgi->get()));
      //ROMol *nmol = new ROMol(*(*fgi));
      d_funcGroups.push_back(ROMOL_SPTR(nmol));
      //d_funcGroups.push_back(nmol);
    }
  }

  FragCatParams::FragCatParams(const std::string &pickle) {
    d_typeStr = "Fragment Catalog Parameters";
    this->initFromString(pickle);
  }

  FragCatParams::~FragCatParams() {
  }

  const MOL_SPTR_VECT &FragCatParams::getFuncGroups() const {
    return d_funcGroups;
  }

  const ROMol *FragCatParams::getFuncGroup(unsigned int fid) const {
    RANGE_CHECK(0, fid, d_funcGroups.size());
    //return d_funcGroups[fid];
    return d_funcGroups[fid].get(); 
  }

  void FragCatParams::toStream(std::ostream &ss) const {
    ss << d_lowerFragLen << " " << d_upperFragLen << " " << d_tolerance << "\n";
    ss << d_funcGroups.size() << "\n";
    for(MOL_SPTR_VECT::const_iterator funcGroup=d_funcGroups.begin();
	funcGroup != d_funcGroups.end();
	funcGroup++){
      std::string text;
      (*funcGroup)->getProp("_Name",text);
      ss << text;
      ss << "\t";
      (*funcGroup)->getProp("_fragSMARTS",text);
      ss << text;
      ss << "\n";
    }
  }
  std::string FragCatParams::Serialize() const {
    std::stringstream ss;
    toStream(ss);
    return ss.str();
  }

  void FragCatParams::initFromString(const std::string &text){
    std::stringstream ss(text);
    initFromStream(ss);
  }
  
  void FragCatParams::initFromStream(std::istream &ss){
    ss >> d_lowerFragLen;
    ss >> d_upperFragLen;
    ss >> d_tolerance;
    int nGroups;
    ss >> nGroups;
    //std::cout << "Reading " << nGroups << " Groups" << std::endl;

    d_funcGroups = readFuncGroups(ss,nGroups);
  }
}