ALMaSS/Vole/_vole_population_manager_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 VolePopulationManagerH

#define VolePopulationManagerH


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


class struct_Vole_Adult;

class TAnimal;

class Vole_Male;

class Vole_Female;

class AlleleFreq1616;

class AlleleFreq;

class APoint;


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


typedef vector < Vole_Male* > Vole_MaleList;

typedef vector < Vole_Female* > Vole_FemaleList;


typedef enum  {

    tovm_Infanticide=0

} TTypeOfVoleMessage;


typedef enum  {

    tovmort_MStarve=0,

    tovmort_FStarve,

    tovmort_MBck,

    tovmort_FBck,

    tovmort_MFarm,

    tovmort_FFarm,

    tovmort_MDisp,

    tovmort_FDisp,

    tovmort_MPred,

    tovmort_FPred,

    tovmort_MLife,

    tovmort_FLife,

    tovmort_MPest,

    tovmort_FPest

} TTypeOfVoleMortality;


class TrapLineMap: public BinaryMapBase

{

public:

    TrapLineMap( unsigned int a_width, unsigned int a_height, unsigned int a_resolution, const char* a_file );

    ~TrapLineMap();

    bool IsTrap(unsigned a_x, unsigned a_y) {

        if (GetValue( a_x, a_y ) == 1) return true;

        return false;

    };

    void Output(InTrapPosition a_tp, int a_day, int a_sex, bool a_terr, int a_age, int a_bx, int a_by, int a_ID );

protected:

    void Init( const char* a_inifile );

    unsigned m_noTraps;

    vector < APoint > m_TrapCoords;

    FILE* m_ofile;

};


class VoleSummaryOutput

{

public:

    VoleSummaryOutput(const char* a_filename, Landscape* a_land, int a_numdataINT, int a_numdataDOUBLE);

    virtual~VoleSummaryOutput();

    virtual void OPrint();

    virtual void OPrint(int a_value);

    virtual void OPrint(double a_value);

    virtual void OPrint(const char* a_value);

    virtual void OPrintEndl();

    void ResetData();

    void ChangeData(int a_data, int a_value);

    void ChangeData(int a_data, double a_value);

protected:

    ofstream* m_File;

    Landscape* m_landscape;

    int m_ndInt;

    int m_ndDouble;

    int m_dataI[100]; // This is way more than we should ever need

    double m_dataD[100]; // This is way more than we should ever need

    void OpenOutput( const char* a_filename );

    void CloseOutput();


};


class Vole_Population_Manager: public Population_Manager

{

 protected:


    int thisYear, YearsTotal;

    void DoFirst();

    virtual void Catastrophe();

    int m_GrowthStartDate;

    int m_male1;

    int m_female1;

    int m_total1;


    int m_male2;

    int m_female2;

    int m_total2;


    int m_male3;

    int m_female3;

    int m_total3;

    //double m_BaseVoleDensity;

    TrapLineMap* m_Traplines;

    vector<double> VoleHabitatBaseQualities;

    bool OpenSexRatiosProbe();

    void CloseSexRatiosProbe();

    bool SuitableStartingLocation(int a_x,  int a_y);

    double AssessHabitat(int p_Polyref);


#ifdef __VOLEPESTICIDEON

public:

    void AddToImpacted() {m_impacted++;}

    void AddToNotImpacted() {m_notimpacted++;}

    void AddToGeneticImpacted() {m_geneticimpacted++;}

    void incLittersLost() { m_LittersLost++; }

    void incLittersProduced() { m_LittersProduced++; }

protected:

    int m_impacted; // counter for voles hit and affected by pesticide

    int m_notimpacted; // counter for voles not hit and affected by pesticide

    int m_geneticimpacted; // counter for voles not hit and affected by pesticide

    double m_geneticsterilitychance;

    double m_f1sterilitychance;

    int m_LittersLost;

    int m_LittersProduced;

#endif

    ofstream* m_VoleAgeSexLocationFile;

    ofstream* m_VoleResistanceOutputFile;

 public:

    VoleSummaryOutput* m_VoleRecordMort;

    FILE * SexRatiosPrb;

    uint32 GetVoleAllele(int a_list, int a_vole, int a_locus, int a_chromosome)

    {

        Vole_Base*  new_VB;

        new_VB = dynamic_cast<Vole_Base *>(TheArray[a_list][a_vole]);

        return new_VB->SupplyMyAllele(a_locus, a_chromosome);

    }

    virtual void ImpactedProbe(  );

     bool IsTrap(int p_x, int p_y) { m_TheLandscape->CorrectCoords(p_x,p_y); return m_Traplines->IsTrap(p_x, p_y); };

    //virtual void Catastrophe(int a_mort);

    void TheAgeSexLocationProbe();

    virtual void TheAOROutputProbe();

    virtual void TheRipleysOutputProbe(FILE* a_prb);

    virtual void TheReallyBigOutputProbe();

    virtual void TheSexRatiosProbe();

    virtual void LandscapeQuadrantOutputProbe(int a_day);

    void AddToFrag1Male() {m_male1++;} // ***TD***

    void AddToFrag1Female() {m_female1++;}

    void AddToFrag2Male() {m_male2++;}

    void AddToFrag2Female() {m_female2++;}

    void AddToFrag3Male() {m_male3++;}

    void AddToFrag3Female() {m_female3++;}

    int ReproTable [4][12]; // Filled in by init function

    unsigned IDNumber;

    Vole_FemaleList FList;

    Vole_MaleList MList;

    Vole_Population_Manager(Landscape* p_L);

    virtual ~Vole_Population_Manager();

   void CreateObjects(VoleObject ob_type, TAnimal *pvo, struct_Vole_Adult* as,int number);

   void CreateObjects_Init(VoleObject ob_type, TAnimal *pvo, struct_Vole_Adult* as,int number);

   virtual void Init (void);

   bool RecordGeneticsToday(int p_today, int p_year, int p_start_year, int p_interval);

   double GetHabitatQuality(int a_index) { return VoleHabitatBaseQualities[a_index]; }

   bool SupplyOlderFemales(unsigned p_x, unsigned p_y, unsigned p_Age,

                                             unsigned p_range);

   int SupplyHowManyVoles(unsigned p_x, unsigned p_y, unsigned p_size);

   int SupplyGrowthStartDate() { return m_GrowthStartDate; }

   int SupplyInOlderTerr(unsigned p_x, unsigned p_y,

                                             unsigned p_Age, unsigned p_Range);

   int SupplyCountFemales(unsigned p_x, unsigned p_y, unsigned p_TerrRange);

   void SendMessage(TTypeOfVoleMessage p_message,unsigned p_x, unsigned p_y,

                                 unsigned p_range, bool p_sex, double p_Weight /*, unsigned p_IDNo*/ );

   vector<Vole_Base*>* SupplyVoleList(unsigned x, unsigned y, unsigned range);

   bool InSquare(int p_x, int p_y,int p_sqx,int p_sqy, int p_range);

   int ListClosestFemales(int p_x, int p_y, int p_steps);

   int ListClosestMales(int p_x, int p_y, int p_steps);

   Vole_Female* FindClosestFemale(int p_x, int p_y, int p_steps);

   Vole_Male* FindClosestMale(int p_x, int p_y, int p_steps);

   Vole_Male* FindRandomMale();

   void AddToYoung(int young) {YoungProducedToday+=young;}

   Vole_Male* FindWithinRadiusMale(int p_x, int p_y);

   Vole_Male* FindOutsideRadiusMale(int p_x, int p_y); // ***TD***

   bool BarrierSearch(int F_x, int F_y, int M_x, int M_y);   // ***TD***

   void AddToYoungYr(int young) {YoungProducedToday+=young;}

   void AddToJuvs(int juvs) {JuvsProducedToday+=juvs;}

   void AddToNoYoungInfanticideCount (int m_NoOfYoung, int m_YoungAge) { // ***TD***

       NoYoungKilledToday+=m_NoOfYoung;

       if (m_YoungAge<5) {

           NoYoungKilledToday4+=m_NoOfYoung;

       }

       else if (m_YoungAge<9){

           NoYoungKilledToday8+=m_NoOfYoung;

       }

       else {NoYoungKilledToday9+=m_NoOfYoung; }

   }

   void ReproductionProbe();

   /* THIS FUNCTION IS OUTDATED; BUT MAYBE A REPLACEMENT IS NEEDED!!

   void TheGeneticProbe(unsigned listindex,int ProbeNo,unsigned &SubSize);

   */

   void GeneticsOutputFile(unsigned listindex);

   virtual void GeneticsResultsOutput(FILE* ofile,unsigned listindex);

   void OpenResistanceOutput();

   void CloseResistanceOutput();

   void ResistanceOutput();


// Attributes

   AlleleFreq* AFreq;

   int YoungProducedToday, JuvsProducedToday;

   int NoYoungKilledToday, NoYoungKilledToday4, NoYoungKilledToday8, NoYoungKilledToday9;

   FILE* YoungsFile;

   IDMap<TAnimal*> *m_VoleMap;

   int m_geneticproductfertilityeffect;


};


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

#endif