ALMaSS/Vole/vole__all_8h_source.html

/*

*******************************************************************************************************

Copyright (c) 2011, Christopher John Topping, University of Aarhus

All rights reserved.


Redistribution and use in source and binary forms, with or without modification, are permitted provided

that the following conditions are met:


Redistributions of source code must retain the above copyright notice, this list of conditions and the

following disclaimer.

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 HOLDER OR CONTRIBUTORS

BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,

BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR

BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT

LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

********************************************************************************************************

*/

//---------------------------------------------------------------------------

#ifndef Vole_allH

#define Vole_allH


#include "GeneticMaterial.h"


class MovementMap16;


//---------------------------------------------------------------------------

//---------------------------------------------------------------------------


typedef enum

{

      tovs_InitialState=0,

  //Males

      tovs_JuvenileExploration,

      tovs_MMaturation,

      tovs_MEvaluateExplore,

      tovs_Infanticide,

      tovs_MDying,

  //Females

      tovs_FEvaluateExplore,

      tovs_ReproBehaviour,

      tovs_Lactating,

      tovs_GiveBirth,

      tovs_FMaturation,

      tovs_Mating,

      tovs_UpdateGestation,

      tovs_SpecialExplore,

      tovs_FDying,

} TTypeOfVoleState;


typedef enum {

    vdisp_CarryOn = 0,

    vdisp_Die,

    vdisp_Mature,

    vdisp_Infanticide

} VoleDispersalReturns;

//------------------------------------------------------------------------------


// Forward Declarations


class Vole_Population_Manager;

class Landscape;

class AlleleFreq1616;

class GeneticMaterial1616;

class GeneticMaterial256_16;

class AlleleFreq;

class GeneticMaterial;


//------------------------------------------------------------------------------


typedef enum

{

    vob_JuvenileMale = 0,

    vob_JuvenileFemale,

    vob_Male,

    vob_Female,

    vob_foobar

} VoleObject;


class InTrapPosition: public AnimalPosition

{

public:

    bool m_inAtrap;

};


class struct_Vole_Adult

{

 public:

  int x;

  int y;

  int age;

  double weight;

  int xborn;

  int yborn;

  int PolyRefBorn;

  int ElemBorn;

  int VegBorn;

  int BirthYear;

  int FatherId;

  int MotherId;

  int FatherStateAtBirth;

  Landscape* L;

  Vole_Population_Manager * VPM;

  //GeneticMaterial256_16 Genes256_16;

  GeneticMaterial Genes;

  bool m_flag;

  bool m_gflag;

  bool m_dflag;

  double misc_use; // used to pass a parameter e.g. for pesticide use

};

//------------------------------------------------------------------------------

class Vole_Base : public TAnimal

{

// Attributes

protected:

    int m_BirthYear;

    bool m_BornLastYear;

    unsigned int m_MinTerrRange;

    unsigned m_MotherId;

    unsigned m_FatherId;

    int m_Death;

    int m_TerrRange;

    bool m_Sex;

    bool m_Mature;

    int m_Age;

    int m_XBorn; //*TD*

    int m_YBorn; //*TD*

    int m_PolyRefBorn;

    int m_ElemBorn; //*TD*

    int m_VegBorn; //*TD*

    int m_LifeSpan;

    double m_Weight;

    bool m_fertile;

#ifdef __VoleStarvationDays


    int m_StarvationDays;

#endif

    // No of young produced;

    int m_NoOfYoungTotal;

    int m_DispVector;

    bool m_Have_Territory;

    int m_Reserves;

    unsigned IDNo;

    int SimH, SimW;

    //GeneticMaterial256_16 MyGenes;

    GeneticMaterial m_MyGenes;

    InTrapPosition m_intrappos;

    static unsigned int m_MaxMaleTerritorySize;

    static unsigned int m_MaxFemaleTerritorySize;

    static unsigned int m_MinMaleTerritorySize;

    static unsigned int m_MinFemaleTerritorySize;

    static double m_MinFVoleHabQual;

    static double m_MinJMVoleHabQual;

    static double m_MinMVoleHabQual;

    static double m_MaleTerritoryRangeSlope;

    static double m_FemaleTerritoryRangeSlope;

    // The values below were fitted by trial and error but await a detailed sensitivity analysis when spatial data is available

    static double m_FHabQualThreshold3;

    static double m_FHabQualThreshold2;

    static double m_FHabQualThreshold1;

    static double m_MHabQualThreshold3;

    static double m_MHabQualThreshold2;

    static double m_MHabQualThreshold1;

    static bool m_BreedingSeason;

#ifdef __VoleStarvationDays


    static int m_MaxStarvationDays;

#endif


#ifdef __VOLEPESTICIDEON

public:

    double SupplyPesticideLoad() { return m_pesticideload; }

    double SupplyBioDegradeRate() { return m_pesticideBioDegradeRate; }

    void SetPesticideInfluenced1(bool a_bool) { m_pesticideInfluenced1 = a_bool; }

    void SetPesticideInfluenced2(bool a_bool) { m_pesticideInfluenced2 = a_bool; }

    bool GetPesticideInfluenced1() { return m_pesticideInfluenced1; }

    bool GetPesticideInfluenced2() { return m_pesticideInfluenced2; }

protected:

    bool m_pesticideInfluenced1;

    bool m_pesticideInfluenced2;

    double m_pesticideInfluenced3;

    double m_pesticideload;

    double m_pesticideBioDegradeRate;

    void AddToPesticidLoad(double a_pestamount) { m_pesticideload+=a_pestamount; }

    void BioDegradePesticide() { m_pesticideload *= m_pesticideBioDegradeRate; }

    void ClearPesticidLoad() { m_pesticideload = 0.0; }

    void SetBioDegradeRate(double a_rate) { m_pesticideBioDegradeRate = a_rate; }

    virtual void PesticideIngestion( void );

    virtual void ActOnPesticideDose( void );

    virtual void ModelinkPesticide() { ; }

    virtual void ModelinkPesticide21TWA(double /* a_dose */ ) { ; }

    virtual void Vinclozolin(double /* a_dose */ ) { ; }

    virtual void GeneralOrganophosphate(double /* a_dose */) { ; }

    virtual void GeneralEndocrineDisruptor(double /* a_dose */) { ; }

    virtual void GeneticDemoPesticide(double /* a_dose */){ ; }

#endif

#ifdef __VOLERODENTICIDEON

    virtual void RodenticideIngestion(void);

#endif

public:

// Functions

    Vole_Base(struct_Vole_Adult * p_aVoleStruct);

    virtual ~Vole_Base();

    virtual void Init(struct_Vole_Adult * p_aVoleStruct);

    virtual void ReInit(struct_Vole_Adult * p_aVoleStruct);

    virtual void BeginStep() {};

    virtual void Step() {};

    virtual void EndStep();

    void st_Dying();


    void SetBreedingSeason( bool a_flag ) { m_BreedingSeason = a_flag; }

    void SetWeight(double W) {m_Weight=W;}

    void Setm_Mature() { m_Mature = true; }

    void Set_BirthYear(int BirthYear) {m_BirthYear = BirthYear;}


    void Set_MotherId(unsigned MotherIdNo) {m_MotherId = MotherIdNo;}; // ***TD***

    void Set_FatherId(unsigned FatherIdNo) {m_FatherId = FatherIdNo;}; // ***TD***

    void Set_NoYoungTot (int a_NoOfYoung) {m_NoOfYoungTotal+=a_NoOfYoung;}; // ***TD***

    void Set_XBorn (int a_Location_x) {m_XBorn = a_Location_x;}; // ***TD***

    void Set_YBorn (int a_Location_y) {m_YBorn = a_Location_y;}; // ***TD***

    void Set_ElemBorn (int a_Location_x, int a_Location_y) // ***TD***

    {

            TTypesOfLandscapeElement m_EBorn = m_OurLandscape->SupplyElementType(a_Location_x, a_Location_y);

            m_ElemBorn = m_OurLandscape->BackTranslateEleTypes(m_EBorn);

    }

    void Set_VegBorn (int a_Location_x, int a_Location_y) // ***TD***

    {

            TTypesOfVegetation m_VBorn = (m_OurLandscape->SupplyVegType(a_Location_x, a_Location_y));

            m_VegBorn = (m_OurLandscape->BackTranslateVegTypes(m_VBorn));

    }

    void Set_PolyRefBorn (int a_Location_x, int a_Location_y) {m_PolyRefBorn = (m_OurLandscape->SupplyPolyRef(a_Location_x, a_Location_y));}; // ***TD***

    void Set_Age(int Age) {m_Age=Age;}


    virtual int WhatState() {return CurrentVState;}

    bool SupplyBornLastYear() { return m_BornLastYear; }

    bool SupplyTerritorial() {return m_Have_Territory;} // ***TD***

    int SupplyFatherId() {return m_FatherId;}; // ***TD***

    int SupplyMotherId() {return m_MotherId;};  // ***TD***

    bool SupplySex() {return m_Sex;};

    int SupplyBirthYear() {return m_BirthYear;}; // ***TD***

    int SupplyTotNoYoung() {return m_NoOfYoungTotal;}; // ***TD***

    int SupplyXBorn() {return m_XBorn;}; // ***TD***

    int SupplyYBorn() {return m_YBorn;}; // ***TD***

    int SupplyPolyRefBorn() {return m_PolyRefBorn;}; // ***TD***

    int SupplyElemBorn() {return m_ElemBorn;}; // ***TD***

    TTypesOfLandscapeElement SupplyElemType() { return m_OurLandscape->SupplyElementType(m_Location_x, m_Location_y ); };

    int SupplyVegBorn() {return m_VegBorn;}; // ***TD***

    int SupplyTerrRange() {return m_TerrRange;}; // ***TD***

    double SupplyWeight() {return m_Weight;};

    int SupplyIDNo() {return IDNo;}; // ***TD***

    bool SupplyMature() {return m_Mature;};

    int SupplyDeathCause() {return m_Death;}; // ***TD***

    unsigned SupplyAge() {return m_Age;};

    unsigned SupplyX() {return m_Location_x;};

    unsigned SupplyY() {return m_Location_y;};

    bool SupplyInTrap() { return m_intrappos.m_inAtrap; }

    InTrapPosition SupplyTrapPosition() { return m_intrappos; }

    void SetFree() { m_intrappos.m_inAtrap = false; }

    int SupplyHomoZyg() {return m_MyGenes.HomozygosityCount();}

    int SupplyHeteroZyg() {return m_MyGenes.HeterozygosityCount();}

    int SupplyAllele(int locus, int allele) { return m_MyGenes.GetAllele(locus,allele); }

    uint32 SupplyMyAllele(int i, int j)

                                        {return m_MyGenes.GetAllele(i, j);} //*TD

    int GetGeneticFlag() { return m_MyGenes.GetGeneticFlag(); }

    int GetDirectFlag() { return m_MyGenes.GetDirectFlag(); }

    void SetGeneticFlag() { m_MyGenes.SetGeneticFlag(); }

    void SetDirectFlag() { m_MyGenes.SetDirectFlag(); }

    void UnsetGeneticFlag() { m_MyGenes.UnsetGeneticFlag(); }

    void UnsetDirectFlag() { m_MyGenes.UnsetDirectFlag(); }

    GeneticMaterial SupplyGenes() {return m_MyGenes;}


    virtual void OnKilled() {};

    virtual bool MortalityTest();

    TTypeOfVoleState CurrentVState;

    Vole_Population_Manager * m_OurPopulation;

    void CopyMyself( VoleObject a_vole );

    void SetFertile(bool f) {

        m_fertile=f;

    }

    bool GetFertile() {

        return m_fertile;

    }

protected:

    double CalculateCarryingCapacity( int x, int y, int a_ddep );

    //double CalculateCarryingCapacity(int x,int y,int &p_stand_x,int &p_stand_y);

    int MoveQuality(int p_x, int p_y);

    void MoveTo(int p_Vector,int p_Distance, int iterations);

    void DoWalking(int p_Distance,int &p_Vector, int &vx, int &vy);

    void DoWalkingCorrect(int p_Distance,int &p_Vector, int &vx, int &vy);

    void Escape(int p_Vector,int p_Distance);

    void CheckTraps();

    virtual void SetLocation() {};

    virtual void FreeLocation() {};

    virtual bool GetLocation(int , int ) {return false;};

};

//------------------------------------------------------------------------------


class Vole_JuvenileMale : public Vole_Base

{

public:

    Vole_JuvenileMale(struct_Vole_Adult * p_aVoleStruct);

    virtual ~Vole_JuvenileMale();

    virtual void ReInit(struct_Vole_Adult * p_aVoleStruct);

    virtual bool OnFarmEvent(FarmToDo event);

    virtual void BeginStep();

    virtual void Step();

    virtual void EndStep();

    virtual void OnKilled();

protected:

    virtual void SetLocation();

    virtual void FreeLocation();

    virtual bool GetLocation(int px, int py);

    TTypeOfVoleState Dispersal(double p_OldQual, int p_Distance);

    void DetermineTerritorySize();

    inline bool CanFeed();

    void st_JuvenileExplore(void);

    void st_BecomeSubAdult(void);

    TTypeOfVoleState st_Eval_n_Explore(void);

#ifdef __VOLEPESTICIDEON

    virtual void ModelinkPesticide();

    virtual void ModelinkPesticide21TWA(double a_dose);

    virtual void Vinclozolin(double a_dose);

    virtual void GeneralOrganophosphate(double a_dose);

    virtual void GeneralEndocrineDisruptor(double /* a_dose */);

    virtual void GeneticDemoPesticide(double /* a_dose */);


#endif

};

//------------------------------------------------------------------------------


class Vole_Male : public Vole_JuvenileMale

{

public:

    Vole_Male(struct_Vole_Adult * p_aVoleStruct);

    virtual void ReInit(struct_Vole_Adult * p_aVoleStruct);

    virtual ~Vole_Male();

    //virtual bool OnFarmEvent(FarmToDo event);

    //virtual void BeginStep();

    virtual void Step();

    virtual void EndStep();

protected:

    VoleDispersalReturns Dispersal(double p_OldQual, int p_Distance);

    void DetermineTerritorySize();

    inline bool CanFeed();

    int st_Maturation(void);

    void st_Infanticide(void);

    virtual bool MortalityTest();

    TTypeOfVoleState st_Eval_n_Explore(void);

#ifdef __VOLEPESTICIDEON

    virtual void ModelinkPesticide();

    virtual void ModelinkPesticide21TWA(double a_dose);

    virtual void Vinclozolin(double a_dose);

    virtual void GeneralOrganophosphate(double a_dose);

    virtual void GeneralEndocrineDisruptor(double /* a_dose */);

    virtual void GeneticDemoPesticide(double /* a_dose */);

#endif

};

//------------------------------------------------------------------------------


class Vole_JuvenileFemale : public Vole_Base

{

public:

   Vole_JuvenileFemale(struct_Vole_Adult * p_aVoleStruct);

   virtual void ReInit(struct_Vole_Adult * p_aVoleStruct);

   virtual ~Vole_JuvenileFemale();

   virtual bool OnFarmEvent(FarmToDo event);

   virtual void BeginStep();

   virtual void Step();

   virtual void EndStep();

   virtual void OnKilled();

protected:

    // Methods

    int Dispersal(double p_OldQual, int p_Distance);

    int st_Evaluate_n_Explore();

    void st_BecomeSubAdult(void);

    //unsigned HowManyOldFemales(int p_x, int p_y);

    virtual void SetLocation();

    virtual void FreeLocation();

    virtual bool GetLocation(int px, int py);

#ifdef __VOLEPESTICIDEON

    double m_maturitydelay;

    virtual void ModelinkPesticide();

    virtual void ModelinkPesticide21TWA(double a_dose);

    virtual void Vinclozolin(double a_dose);

    virtual void GeneralOrganophosphate(double a_dose);

    virtual void GeneralEndocrineDisruptor(double /* a_dose */);

    virtual void GeneticDemoPesticide(double /* a_dose */);

public:

    void SetMaturityDelay(double a_delay) { m_maturitydelay = a_delay; }

#endif

};

//---------------------------------------------------------------------------


class Vole_Female : public Vole_JuvenileFemale

{

public:

   Vole_Female(struct_Vole_Adult * p_aVoleStruct);

   void ReInit(struct_Vole_Adult * p_aVoleStruct);

   virtual ~Vole_Female();

   virtual void Step();

   int SupplyNoOfYoung() {return m_NoOfYoung;};


   int SupplyMateId() {return m_MatesIdNo;};

   int SupplyMateSB() {return m_MateLive;};


   unsigned SupplyYoungAge() {return m_YoungAge;};

   bool SupplyPregnant() {return m_Pregnant;};


   void Set_MateState(int MateState) {m_MateLive = MateState;};

   void OnInfanticideAttempt();

protected:

//Attributes


    int m_MateLive;

    int m_MatesIdNo;

    int m_NoOfYoung;

    bool m_Pregnant;

    int m_DaysUntilBirth;

    unsigned m_YoungAge;

    GeneticMaterial m_MatesGenes;


    // Methods

    TTypeOfVoleState st_ReproBehaviour();

    TTypeOfVoleState st_UpdateGestation();

    TTypeOfVoleState st_BecomeReproductive();

    TTypeOfVoleState st_GiveBirth();

    TTypeOfVoleState st_Lactating();

    int st_Evaluate_n_Explore();

    int st_Special_Explore();

    TTypeOfVoleState st_Mating();

#ifdef __VOLEPESTICIDEON

    unsigned int m_pesticideloadindex;

    double m_pesticideloadarray[21];

    virtual void ModelinkPesticide();

    virtual void ModelinkPesticide21TWA(double a_dose);

    virtual void Vinclozolin(double a_dose);

    virtual void GeneralOrganophosphate(double a_dose);

    virtual void GeneralEndocrineDisruptor(double /* a_dose */);

    static int m_EndoCrineDisruptionGestationLength;

    virtual void GeneticDemoPesticide(double /* a_dose */);

#endif

};

//---------------------------------------------------------------------------

#endif