Neuropil.h

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/*
 * This file is a part of the Biology project by eons LLC.
 * Biology (aka Develop Biology) is a framework for approaching software
 * development from a natural sciences perspective.
 *
 * Copyright (C) 2023 Séon O'Shannon & eons LLC
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
#pragma once
 
#include "bio/neural/common/Types.h"
#include "bio/neural/common/Class.h"
#include "bio/neural/common/Filters.h"
#include "bio/neural/macro/Macros.h"
#include "bio/cellular/Tissue.h"
#include "bio/common/wrapper/Pointer.h"
 
namespace bio {
namespace neural {
 
class AxonGuide;
 
class Neuropil:
    public neural::Class< Neuropil >,
    public cellular::Tissue
{
public:
 
    BIO_DISAMBIGUATE_ALL_CLASS_METHODS(neural, Neuropil)
 
    BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(
        neural,
        Neuropil,
        filter::Neural()
    )
 
    virtual  ~Neuropil();
 
    virtual Code CacheProteins();
 
    virtual Code CreateDefaultProteins();
 
    virtual Pointer< Synapse > Connect(
        Pointer< Neuron > presynapticNeuron,
        Pointer< Neuron > postsynapticNeuron,
        Pointer< const Synapse > synapse
    );
 
    virtual Pointer< Synapse > Connect(
        const Name& presynapticNeuron,
        const Name& postsynapticNeuron,
        const Name& synapse
    );
    
    virtual Synapses Connect(
        Pointer< Neuropil > presynapticNeuropil,
        Pointer< Neuropil > postsynapticNeuropil,
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > presynapticNeuronAffinity = NULL,
        Pointer< const ::bio::Affinity > postsynapticNeuronAffinity = NULL
    ) const;
 
    virtual Synapses Connect(
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > presynapticNeuronAffinity = NULL,
        Pointer< const ::bio::Affinity > postsynapticNeuronAffinity = NULL
    );
 
    virtual Synapses CreateDendritesFrom(
        Pointer< Neuron > presynapticNeuron,
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > postsynapticNeuronAffinity = NULL
    );
 
    virtual Synapses CreateDendritesFrom(
        Pointer< Neuropil > presynapticNeuropil,
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > presynapticNeuronAffinity = NULL,
        Pointer< const ::bio::Affinity > postsynapticNeuronAffinity = NULL
    );
 
    virtual Synapses CreateAxonsTo(
        Pointer< Neuron > postsynapticNeuron,
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > presynapticNeuronAffinity = NULL
    );
 
    virtual Synapses CreateAxonsTo(
        Pointer< Neuropil > postsynapticNeuropil,
        Pointer< const Synapse > synapse,
        Pointer< AxonGuide > guide,
        Pointer< const ::bio::Affinity > presynapticNeuronAffinity = NULL,
        Pointer< const ::bio::Affinity > postsynapticNeuronAffinity = NULL
    );
 
};
 
} //neural namespace
} //bio namespace