mitochondria.h

#pragma once
 
#include <map>
#include <memory>
 
#include <morphio/mito_section.h>
#include <morphio/properties.h>
#include <morphio/types.h>
 
#include <morphio/mut/mito_section.h>
 
namespace morphio {
namespace mut {
 
using mito_upstream_iterator = morphio::upstream_iterator_t<std::shared_ptr<MitoSection>>;
using mito_breadth_iterator =
    morphio::breadth_iterator_t<std::shared_ptr<MitoSection>, Mitochondria>;
using mito_depth_iterator = morphio::depth_iterator_t<std::shared_ptr<MitoSection>, Mitochondria>;
 
class Mitochondria
{
    using MitoSectionP = std::shared_ptr<MitoSection>;
 
  public:
    Mitochondria() = default;
 
    const std::vector<MitoSectionP>& children(const MitoSectionP&) const;
    const MitoSectionP& section(uint32_t id) const;
    const std::map<uint32_t, MitoSectionP>& sections() const noexcept;
 
    mito_depth_iterator depth_begin() const;
    mito_depth_iterator depth_begin(const MitoSectionP& section) const;
    mito_depth_iterator depth_end() const;
 
    mito_breadth_iterator breadth_begin() const;
    mito_breadth_iterator breadth_begin(const MitoSectionP& section) const;
    mito_breadth_iterator breadth_end() const;
 
    mito_upstream_iterator upstream_begin() const;
    mito_upstream_iterator upstream_begin(const MitoSectionP& section) const;
    mito_upstream_iterator upstream_end() const;
 
    const MitoSectionP& parent(const MitoSectionP& parent) const;
 
    bool isRoot(const MitoSectionP& section) const;
 
    const std::vector<MitoSectionP>& rootSections() const noexcept;
 
    MitoSectionP appendRootSection(const Property::MitochondriaPointLevel& points);
 
    MitoSectionP appendRootSection(const morphio::MitoSection&, bool recursive = false);
    MitoSectionP appendRootSection(const MitoSectionP&, bool recursive = false);
 
    const MitoSectionP& mitoSection(uint32_t id) const;
 
    void _buildMitochondria(Property::Properties& properties) const;
 
  private:
    friend class MitoSection;
 
    uint32_t _register(const MitoSectionP& section);
 
    uint32_t _counter = 0;
    std::map<uint32_t, std::vector<MitoSectionP>> children_;
    std::map<uint32_t, uint32_t> parent_;
    std::vector<MitoSectionP> root_sections_;
    std::map<uint32_t, MitoSectionP> sections_;
};
 
inline const std::map<uint32_t, Mitochondria::MitoSectionP>& Mitochondria::sections() const
    noexcept {
    return sections_;
}
 
inline const std::vector<Mitochondria::MitoSectionP>& Mitochondria::rootSections() const noexcept {
    return root_sections_;
}
 
}  // namespace mut
}  // namespace morphio