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/*! \libinternal \file
 * \brief
 * Utility classes for manipulating \c t_atoms structures.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \inlibraryapi
 */
#ifndef GMX_TOPOLOGY_ATOMSBUILDER_H
#define GMX_TOPOLOGY_ATOMSBUILDER_H

#include <memory>
#include <vector>

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"

struct t_atoms;
struct t_resinfo;
struct t_symtab;

namespace gmx
{

class AtomsBuilder
{
public:
    AtomsBuilder(t_atoms* atoms, t_symtab* symtab);
    ~AtomsBuilder();

    void reserve(int atomCount, int residueCount);
    void clearAtoms();

    int currentAtomCount() const;

    void setNextResidueNumber(int number);
    void addAtom(const t_atoms& atoms, int i);
    void startResidue(const t_resinfo& resinfo);
    void finishResidue(const t_resinfo& resinfo);
    void discardCurrentResidue();

    void mergeAtoms(const t_atoms& atoms);

private:
    char** symtabString(char** source);

    t_atoms*  atoms_;
    t_symtab* symtab_;
    int       nrAlloc_;
    int       nresAlloc_;
    int       currentResidueIndex_;
    int       nextResidueNumber_;

    GMX_DISALLOW_COPY_AND_ASSIGN(AtomsBuilder);
};

class AtomsRemover
{
public:
    explicit AtomsRemover(const t_atoms& atoms);
    ~AtomsRemover();

    void refreshAtomCount(const t_atoms& atoms);

    void markAll();
    void markResidue(const t_atoms& atoms, int atomIndex, bool bStatus);
    bool isMarked(int atomIndex) const { return removed_[atomIndex] != 0; }

    void removeMarkedElements(std::vector<RVec>* container) const;
    void removeMarkedElements(std::vector<real>* container) const;
    void removeMarkedAtoms(t_atoms* atoms) const;

private:
    std::vector<char> removed_;

    GMX_DISALLOW_COPY_AND_ASSIGN(AtomsRemover);
};

} // namespace gmx

#endif
