tfStateVector.h

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/*******************************************************************************
 * This file is part of Tissue Forge.
 * Copyright (c) 2022-2024 T.J. Sego
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * 
 ******************************************************************************/
 
#ifndef _SOURCE_STATE_TFSTATEVECTOR_H_
#define _SOURCE_STATE_TFSTATEVECTOR_H_
 
#include <tf_port.h>
#include <io/tf_io.h>
#include <stdio.h>
#include <string>
 
#include "tfSpeciesList.h"
 
 
namespace TissueForge {
 
 
    namespace state {
 
 
        enum StateVectorFlags {
            STATEVECTOR_NONE            = 0,
            STATEVECTOR_OWNMEMORY       = 1 << 0,
        };
 
        struct CAPI_EXPORT StateVector {
            uint32_t flags;
            uint32_t size;
 
            struct TissueForge::state::SpeciesList *species;
            
            void *owner;
            
            void* data;
            
            // vector of values
            FloatP_t *fvec;
            
            // vector of fluxes
            FloatP_t *q;
            
            // vector of species flags
            uint32_t *species_flags;
            
            // reset the species values based on the values specified in the species.
            void reset();
            const std::string str() const;
 
            FloatP_t *item(const int &i);
            void setItem(const int &i, const FloatP_t &val);
 
            StateVector();
            StateVector(TissueForge::state::SpeciesList *species, 
                        void *owner=NULL, 
                        StateVector *existingStateVector=NULL,
                        uint32_t flags=STATEVECTOR_NONE, 
                        void *data=NULL);
            StateVector(const StateVector &other);
            ~StateVector();
 
            std::string toString();
 
            static StateVector *fromString(const std::string &str);
        };
 
    }
 
    namespace io { 
 
        template <>
        HRESULT toFile(const TissueForge::state::StateVector &dataElement, const MetaData &metaData, IOElement &fileElement);
 
        template <>
        HRESULT fromFile(const IOElement &fileElement, const MetaData &metaData, TissueForge::state::StateVector **dataElement);
 
    }
 
};
 
#endif // _SOURCE_STATE_TFSTATEVECTOR_H_