/*-
 * SPDX-License-Identifier: BSD-2-Clause
 *
 * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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#pragma once


#include <cif++/cif++.hpp>
#include <cif++/symmetry.hpp>
#include <clipper/clipper.h>
#include <clipper/core/coords.h>

namespace pdb_redo
{

class BlobFinder
{
  public:
	// /// \brief Find all blobs in the map
	// BlobFinder(clipper::Xmap<float> &xmm, float growingPercentile = 0.95f);

	/// \brief Find only blobs near the molecule(s) in @a structure
	BlobFinder(clipper::Xmap<float> &xmm, cif::mm::structure &structure,
		float growingPercentile = 0.95f);

	std::vector<cif::point> next(float minimalVolume = 17);

  private:
	using GridPoint = clipper::Xmap<float>::Map_reference_coord;

	std::vector<GridPoint> pop();

	[[nodiscard]] bool blobIsInProximityOfAtoms(const std::vector<GridPoint> &blob) const;

	const clipper::Xmap<float> &mXmap;
	std::vector<GridPoint> mPotentialGridPoints;
	std::vector<cif::mm::atom> mProteinAtoms;
	std::vector<std::tuple<cif::point,float>> mResidueSpheres;
    cif::point mProteinCenter;
    cif::crystal mCrystal;
    float mProteinRadius;
	float mGrowingThreshold;
};

} // namespace pdb_redo