//
//  Copyright (C) 2004-2006 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 <RDGeneral/export.h>
#ifndef __CHEMICALFEATUREFACTORY_H_02122004_1545__
#define __CHEMICALFEATUREFACTORY_H_02122004_1545__

#include "MolChemicalFeatureDef.h"
#include <iostream>
#include <boost/shared_ptr.hpp>

namespace RDKit {
class MolChemicalFeature;
typedef boost::shared_ptr<MolChemicalFeature> FeatSPtr;
typedef std::list<FeatSPtr> FeatSPtrList;
typedef FeatSPtrList::iterator FeatSPtrList_I;

//! The class for finding chemical features in molecules
class RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory {
 public:
  //! returns the number of feature definitions
  int getNumFeatureDefs() const { return d_featDefs.size(); };

  //! returns an iterator referring to the first feature definition
  MolChemicalFeatureDef::CollectionType::iterator beginFeatureDefs() {
    return d_featDefs.begin();
  };
  //! returns an iterator referring to the end of the feature definitions
  MolChemicalFeatureDef::CollectionType::iterator endFeatureDefs() {
    return d_featDefs.end();
  };

  //! returns a const_iterator referring to the first feature definition
  MolChemicalFeatureDef::CollectionType::const_iterator beginFeatureDefs()
      const {
    return d_featDefs.begin();
  };
  //! returns a const_iterator referring to the end of the feature definitions
  MolChemicalFeatureDef::CollectionType::const_iterator endFeatureDefs() const {
    return d_featDefs.end();
  };

  //! appends a feature definition to the collection of features defs.
  void addFeatureDef(
      MolChemicalFeatureDef::CollectionType::value_type featDef) {
    d_featDefs.push_back(featDef);
  }

  //! returns a list of features on the molecule
  /*!
    \param mol          The molecule of interest
    \param includeOnly  (optional) if this is non-null, only features in this
                        family will be returned
    \param confId       (optional) the conformer id to use
  */
  FeatSPtrList getFeaturesForMol(const ROMol &mol, const char *includeOnly = "",
                                 int confId = -1) const;

 private:
  MolChemicalFeatureDef::CollectionType d_featDefs;
};

//! constructs a MolChemicalFeatureFactory from the data in a stream
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory *buildFeatureFactory(
    std::istream &inStream);
//! constructs a MolChemicalFeatureFactory from the data in a string
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory *buildFeatureFactory(
    const std::string &featureData);

}  // end of namespace RDKit

#endif
