reader.h

//
// Created by Jon on 21/08/2015.
//

#ifndef XYZ_CIFREADER_H
#define XYZ_CIFREADER_H

// for file input
#include <string>
#include <fstream>
#include <streambuf>
#include <regex>
#include <sstream>
#include <vector>

#include <Eigen/Dense>

#include "utilities.h"
#include "atomsite.h"
#include "symmetryoperation.h"
#include "unitcell.h"
#include "cellgeometry.h"

namespace CIF {
    class Reader {
    public:
        Reader() = default;

        // constructor that takes filename
        explicit Reader(std::string filePath, bool attempt_fixes = false);

        // method to return a class instance that will contain the unit cell information
        UnitCell getUnitCell() { return UnitCell(cell, atomsites); }

        std::string getFilePath(){return file_path;}

    private:
        // class instance to hold unit cell information
        std::vector<Symmetry> symmetrylist;

        std::vector<AtomSite> atomsites;

        CellGeometry cell;

        std::string file_path;

        bool fix;

        // methods to read
        // 1. atom positions
        // 2. symmetry
        // 3. basis geometry
        void readAtoms(const std::string &input);

        void readSymmetryOperations(const std::string &input);

        void readCellGeometry(const std::string &input);

        void readAtomPositions(const std::vector<std::string> &headers, const std::vector<std::string> &entries);

        void readThermalParameters(const std::vector<std::string> &headers, const std::vector<std::string> &entries);
    };
}

#endif //XYZ_CIFREADER_H