/* 
 *            Copyright 2009-2018 The VOTCA Development Team
 *                       (http://www.votca.org)
 *
 *      Licensed under the Apache License, Version 2.0 (the "License")
 *
 * You may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *              http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */

#ifndef VOTCA_XTP_QMFRAGMENT_H
#define	VOTCA_XTP_QMFRAGMENT_H
#include <votca/xtp/eigen.h>
#include <limits>
#include <boost/lexical_cast.hpp>

/**
* \brief Container to define fragments of QMmolecules, containing atomindices, no pointers to atoms, it also handles the parsing of strings etc..
* Values should have own destructor
*
* 
* 
*/

namespace votca { namespace xtp {
   
template<class T>
class QMFragment{
    public:
               
    QMFragment(std::string name,int id,std::string atoms):_name(name),_id(id)
                {FillAtomIndices(atoms);}

    void setValue(const T& value){_value=value;}

    const T& getValue()const{return _value;}

    int size()const{return _atomindices.size();}

    const std::vector<int>& getIndices()const{return _atomindices;}


    typename std::vector<int>::const_iterator begin()const{return _atomindices.begin();}
    typename std::vector<int>::const_iterator end()const{return _atomindices.end();}
        
    friend std::ostream &operator<<(std::ostream &out, const QMFragment& fragment){
        out<<"Fragment name:"<<fragment._name<<" id:"<<fragment._name<<std::endl;
        out<<"AtomIndices["<<fragment.size()<<"]:";
        for (int id:fragment._atomindices){
            out<<id<<" ";
        }
        out<<std::endl;
        out<<"Value:"<<fragment._value;
        return out;
    };
            
private:

    void FillAtomIndices(const std::string& atoms){
        tools::Tokenizer tok(atoms," ,\n\t");
        std::vector<std::string> results;
        tok.ToVector(results);
        const std::string delimiter="...";
        for(std::string s:results){ 
            if(s.find(delimiter) != std::string::npos){
                int start = boost::lexical_cast<int>(s.substr(0, s.find(delimiter)));
                int stop = boost::lexical_cast<int>(s.erase(0,s.find(delimiter) + delimiter.length()));
                for(int i=start;i<=stop;i++){
                    _atomindices.push_back(i);
                }
            }
            else{
                _atomindices.push_back(boost::lexical_cast<int>(s));
            }
        }
        
        
    }

    std::vector<int> _atomindices;
    std::string _name;
    int _id;
    T _value;

    

    
        
      };   
    
    
}}

#endif	// VOTCA_XTP_ATOMCONTAINER_H