LCEphenoexpression.h

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/*
 *  @file LCEphenoexpression.h
 *  Nemo2
 *
 *   Copyright (C) 2023-2024 Max Schmid, Frederic Guillaume
 *
 *   This file is part of Nemo
 *
 *   Nemo is free software; you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation; either version 2 of the License, or
 *   (at your option) any later version.
 *
 *   Nemo 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 General Public License
 *   along with this program; if not, write to the Free Software
 *   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 *  @author Max
 */
 
#ifndef LCEPHENOEXPRESSION_H
#define LCEPHENOEXPRESSION_H
 
#include "lifecycleevent.h"
#include "ttquanti.h"
#include "Uniform.h"
 
//LCE_PhenotypeExpression
class LCE_PhenotypeExpression : public virtual LifeCycleEvent
 
{
 
  unsigned int         _num_trait;
      
  TMatrix              _env_cue;
  
  TMatrix              _e_noise;
  
  TMatrix              _e_rate;
 
  bool                 _e_copy_trait_optimum_value;
 
  TMatrix              _g0_linked_index;
  TMatrix              _g1_linked_index;
  TMatrix              _g2_linked_index;
 
  TMatrix              _g1_values;
  TMatrix              _g2_values;
  TMatrix              _e_values;
  bool                 _g1_evolves;
  bool                 _g2_evolves;
  bool                 _do_change_cue;
  bool                 _is_labile;
  bool                 _has_plasticity;
  bool                 _has_liability;
 
  unsigned int                  _num_liability_trait;
  bool                          _has_evolving_threshold;
  TMatrix                       _liability_linked_index;
  TMatrix                       _liability_threshold_linked_index;
  vector< vector<double> >      _liability_threshold;
  vector< vector<double> >      _liability_values;
 
  bool                          _has_liability_sigmoid;
  TMatrix                       _liability_steepness_linked_index;
  vector<double>                _liability_steepness_fixed;
  bool                          _liability_steepness_allow_negative;
 
  void              (LCE_PhenotypeExpression::* _set_phenotype_func) (unsigned int, TTQuanti*);
  double            (LCE_PhenotypeExpression::* _get_env_cue_func) (unsigned int, unsigned int);
  void              (LCE_PhenotypeExpression::* _set_liability_func) (Patch*, sex_t, age_idx);
 
  TProtoQuanti*    _QuantiProto;
 
 
public:
 
  LCE_PhenotypeExpression ( );
 
  virtual ~LCE_PhenotypeExpression ( ) { }
 
  bool     set_g_value_matrix   (Param* param, TMatrix& mat);
  bool     check_g_index_matrix (Param* param, TMatrix& mat);
  bool     set_env_cue ();
  void     set_phenot_no_evol          (unsigned int patch, TTQuanti* trait);
  void     set_phenot_g1_evol          (unsigned int patch, TTQuanti* trait);
  void     set_phenot_g2_evol          (unsigned int patch, TTQuanti* trait);
  void     set_phenot_g1_g2_evol       (unsigned int patch, TTQuanti* trait);
  double   get_env_cue_no_noise        (unsigned int patch, unsigned int trait);
  double   get_env_cue_noise           (unsigned int patch, unsigned int trait);
 
 
  virtual void execute ();
 
  void   setIndPhenotype                  (Patch* patch, sex_t SEX, age_idx AGE);
  void   setIndPhenotype_labile           (Patch* patch, sex_t SEX, age_idx AGE);
  void   setIndLiability                  (Patch* patch, sex_t SEX, age_idx AGE);
  void   setIndLiability_evolving         (Patch* patch, sex_t SEX, age_idx AGE);
  void   setIndLiability_sigmoid          (Patch* patch, sex_t SEX, age_idx AGE);
  void   setIndLiability_evolving_sigmoid (Patch* patch, sex_t SEX, age_idx AGE);
 
  virtual LifeCycleEvent* clone ( ) {return new LCE_PhenotypeExpression();}
 
  virtual bool setParameters ();
 
//  SimComponent implementation:
 
  virtual void loadFileServices ( FileServices* loader ) {}
 
  virtual void loadStatServices ( StatServices* loader ) {}
 
  virtual bool resetParameterFromSource (std::string param, SimComponent* cmpt) {return false;}
 
  virtual age_t removeAgeClass ( ) {return 0;}
 
  virtual age_t addAgeClass ( ) {return 0;}
 
  virtual age_t requiredAgeClass () {return 0;}
 
};
 
#endif