#ifndef stock_h
#define stock_h
#include "areatime.h"
#include "agebandmatrix.h"
#include "agebandmatrixratioptrvector.h"
#include "base.h"
#include "conversionindex.h"
#include "stockptrvector.h"
#include "tagptrvector.h"
#include "commentstream.h"
class Stock;
class Keeper;
class NaturalMortality;
class Grower;
class InitialCond;
class Migration;
class Transition;
class PopPredator;
class StockPrey;
class Maturity;
class RenewalData;
class SpawnData;
class StrayData;
/**
* \class Stock
* \brief This is the class used to model a stock within the Gadget model
*
* This class is used to model the population of a stock during a model simulation.
*/
class Stock : public BaseClass {
public:
/**
* \brief This is the Stock constructor
* \param infile is the CommentStream to read the stock parameters from
* \param givenname is the name of the stock
* \param Area is the AreaClass for the current model
* \param TimeInfo is the TimeClass for the current model
* \param keeper is the Keeper for the current model
*/
Stock(CommentStream& infile, const char* givenname, const AreaClass* const Area,
const TimeClass* const TimeInfo, Keeper* const keeper);
/**
* \brief This is the default Stock constructor
* \param givenname is the name of the stock
*/
Stock(const char* givenname);
/**
* \brief This is the default Stock destructor
*/
virtual ~Stock();
/**
* \brief This function will update the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void calcNumbers(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will reduce the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void reducePop(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate the growth of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param Area is the AreaClass for the current model
* \param TimeInfo is the TimeClass for the current model
*/
virtual void Grow(int area, const AreaClass* const Area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate any transition of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updateAgePart1(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate the age increase of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updateAgePart2(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will implement the transiton of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updateAgePart3(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate the spawning of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updatePopulationPart1(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate add the newly matured stock into the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updatePopulationPart2(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate add the new recruits into the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updatePopulationPart3(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate calculate the straying of the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updatePopulationPart4(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate add the strayed stock into the model population for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void updatePopulationPart5(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate the modelled consumption for an area in the model
* \param area is an integer to denote the internal area of interest
* \param Area is the AreaClass for the current model
* \param TimeInfo is the TimeClass for the current model
*/
virtual void calcEat(int area, const AreaClass* const Area, const TimeClass* const TimeInfo);
/**
* \brief This function will check the modelled consumption for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void checkEat(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will adjust the modelled consumption for an area in the model
* \param area is an integer to denote the internal area of interest
* \param TimeInfo is the TimeClass for the current model
*/
virtual void adjustEat(int area, const TimeClass* const TimeInfo);
/**
* \brief This function will reset the model population
* \param TimeInfo is the TimeClass for the current model
*/
virtual void Reset(const TimeClass* const TimeInfo);
/**
* \brief This function will print the model population
* \param outfile is the ofstream that all the model information gets sent to
*/
void Print(ofstream& outfile) const;
/**
* \brief This function will implement the migration of the model population for the model
* \param TimeInfo is the TimeClass for the current model
*/
virtual void Migrate(const TimeClass* const TimeInfo);
/**
* \brief This function will add a AgeBandMatrix to the current stock population
* \param Addition is the AgeBandMatrix that will be added to the population
* \param CI is the ConversionIndex that will convert between the length groups
* \param area is an integer to denote the internal area of interest
* \param ratio is a multiplicative constant applied
*/
void Add(const AgeBandMatrix& Addition, const ConversionIndex* const CI, int area, double ratio);
/**
* \brief This function will add a AgeBandMatrixRatioPtrVector to the current tagged stock population
* \param Addition is the AgeBandMatrixRatioPtrVector that will be added to the tagged population
* \param CI is the ConversionIndex that will convert between the length groups
* \param area is an integer to denote the internal area of interest
* \param ratio is a multiplicative constant applied
*/
void Add(const AgeBandMatrixRatioPtrVector& Addition, const ConversionIndex* const CI, int area, double ratio);
/**
* \brief This will return the prey information for the stock
* \return prey
*/
StockPrey* getPrey() const;
/**
* \brief This will return the migration information for the stock
* \return migration
*/
Migration* getMigration() const;
/**
* \brief This will return the predation information for the stock
* \return predator
*/
PopPredator* getPredator() const;
/**
* \brief This will return the current population of the stock on a given area
* \param area is the area identifier
* \return alkeys, a AgeBandMatrix containing the population of the stock
*/
AgeBandMatrix& getCurrentALK(int area) { return Alkeys[this->areaNum(area)]; };
/**
* \brief This will return the population of the stock on a given area at the start of the current timestep
* \param area is the area identifier
* \return alkeys, a AgeBandMatrix containing the population of the stock
*/
AgeBandMatrix& getConsumptionALK(int area);
/**
* \brief This will return the length group information for the stock
* \return LgrpDiv
*/
const LengthGroupDivision* getLengthGroupDiv() const { return LgrpDiv; };
/**
* \brief This function will initialise the stock and set-up links to any related stocks
* \param stockvec is the StockPtrVector of all the available stocks
*/
void setStock(StockPtrVector& stockvec);
/**
* \brief This function will check to see if the age of the stock should be increased on the current timestep or not
* \param TimeInfo is the TimeClass for the current model
* \return 1 if the age of the stock should be increased, 0 otherwise
*/
int isBirthday(const TimeClass* const TimeInfo) const;
/**
* \brief This function will return the flag used to denote whether the stock is eaten or not
* \return flag
*/
int isEaten() const { return iseaten; };
/**
* \brief This function will return the flag used to denote whether the stock will spawn or not
* \return flag
*/
int doesSpawn() const { return doesspawn; };
/**
* \brief This function will return the flag used to denote whether the stock will stray or not
* \return flag
*/
int doesStray() const { return doesstray; };
/**
* \brief This function will return the flag used to denote whether the stock will move or not
* \return flag
*/
int doesMove() const { return doesmove; };
/**
* \brief This function will return the flag used to denote whether the stock will eat or not
* \return flag
*/
int doesEat() const { return doeseat; };
/**
* \brief This function will return the flag used to denote whether the stock will mature or not
* \return flag
*/
int doesMature() const { return doesmature; };
/**
* \brief This function will return the flag used to denote whether the stock will renew or not
* \return flag
*/
int doesRenew() const { return doesrenew; };
/**
* \brief This function will return the flag used to denote whether the stock will grow or not
* \return flag
*/
int doesGrow() const { return doesgrow; };
/**
* \brief This function will return the flag used to denote whether the stock will migrate or not
* \return flag
*/
int doesMigrate() const { return doesmigrate; };
/**
* \brief This function will return the flag used to denote whether the stock has been tagged or not
* \return flag
*/
int isTagged() const { return istagged; };
/**
* \brief This function will set the flag to denote that the stock has been tagged
*/
void setTaggedStock() { istagged = 1; };
/**
* \brief This function will initialise the tagging experiments for the stock and any related stocks
*/
void setTagged();
/**
* \brief This will return the minimum age of the stock
* \return minimum age
*/
int minAge() const { return Alkeys[0].minAge(); };
/**
* \brief This will return the maximum age of the stock
* \return maximum age
*/
int maxAge() const { return Alkeys[0].maxAge(); };
/**
* \brief This will return the total population size (in numbers) of the stock on a given area
* \param area is the area identifier
* \return population size
*/
double getTotalStockNumber(int area) const;
/**
* \brief This will return the total population size (in numbers) of the stock across all areas
* \return population size
*/
double getTotalStockNumberAllAreas() const;
/**
* \brief This will return the total population biomass of the stock on a given area
* \param area is the area identifier
* \return population biomass
*/
double getTotalStockBiomass(int area) const;
/**
* \brief This will return the total population biomass of the stock across all areas
* \return population biomass
*/
double getTotalStockBiomassAllAreas() const;
/**
* \brief This will return the stocks that this stock will mature in to
* \return maturestocks, a StockPtrVector of the stocks that this stock will mature into
*/
const StockPtrVector& getMatureStocks();
/**
* \brief This will return the stocks that this stock will move in to
* \return transitionstocks, a StockPtrVector of the stocks that this stock will move into
*/
const StockPtrVector& getTransitionStocks();
/**
* \brief This will return the stocks that this stock will stray in to
* \return straystocks, a StockPtrVector of the stocks that this stock will stray into
*/
const StockPtrVector& getStrayStocks();
/**
* \brief This function will add details for a new tagging experiment on the current stock
* \param tagbyagelength is the AgeBandMatrixPtrVector of the new tagged population
* \param newtag is the Tags for the new tagging experiment
* \param tagloss is the proportion of tags that are lost for the new tagging experiment
*/
void addTags(AgeBandMatrixPtrVector* tagbyagelength, Tags* newtag, double tagloss);
/**
* \brief This function will remove a tagging experiment from the current tagged stock population
* \param tagname is the name of the tagging experiment to be removed
*/
void deleteTags(const char* tagname);
protected:
/**
* \brief This is the AgeBandMatrixPtrVector used to store information about the stock population
*/
AgeBandMatrixPtrVector Alkeys;
/**
* \brief This is the AgeBandMatrixRatioPtrVector used to store information about the tagged population from any tagging experiments performed on the stock
*/
AgeBandMatrixRatioPtrVector tagAlkeys;
/**
* \brief This is the TagPtrVector used to store information about the tagging experiments
*/
TagPtrVector allTags;
/**
* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that mature
*/
TagPtrVector matureTags;
/**
* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that move
*/
TagPtrVector transitionTags;
/**
* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that stray
*/
TagPtrVector strayTags;
/**
* \brief This is the StrayData used to calculate information about the straying of the stock
*/
StrayData* stray;
/**
* \brief This is the SpawnData used to calculate information about the spawning of the stock
*/
SpawnData* spawner;
/**
* \brief This is the RenewalData used to calculate information about the renewal of the stock
*/
RenewalData* renewal;
/**
* \brief This is the Maturity used to calculate information about the maturation of the stock
*/
Maturity* maturity;
/**
* \brief This is the Transition used to calculate information about the movement of the stock
*/
Transition* transition;
/**
* \brief This is the Migration used to calculate information about the migration of the stock
*/
Migration* migration;
/**
* \brief This is the Prey used to calculate information about the consumption of the stock
*/
StockPrey* prey;
/**
* \brief This is the PopPredator used to calculate information about the consumption by the stock
*/
PopPredator* predator;
/**
* \brief This is the InitialCond used to calculate information about the initial conditions of the stock
*/
InitialCond* initial;
/**
* \brief This is the LengthGroupDivision used to store length information
*/
LengthGroupDivision* LgrpDiv;
/**
* \brief This is the Grower used to calculate information about the growth of the stock
*/
Grower* grower;
/**
* \brief This is the NaturalMortality used to calculate information about the natural mortality of the stock
*/
NaturalMortality* naturalm;
/**
* \brief This is the flag used to denote whether the stock will eat (ie. is a Predator) or not
*/
int doeseat;
/**
* \brief This is the flag used to denote whether the stock will move or not
*/
int doesmove;
/**
* \brief This is the flag used to denote whether the stock is eaten (ie. is a Prey) or not
*/
int iseaten;
/**
* \brief This is the flag used to denote whether the stock will spawn or not
*/
int doesspawn;
/**
* \brief This is the flag used to denote whether the stock will mature or not
*/
int doesmature;
/**
* \brief This is the flag used to denote whether the stock will renew or not
*/
int doesrenew;
/**
* \brief This is the flag used to denote whether the stock will grow or not
*/
int doesgrow;
/**
* \brief This is the flag used to denote whether the stock will migrate or not
*/
int doesmigrate;
/**
* \brief This is the flag used to denote whether the stock will stray or not
*/
int doesstray;
/**
* \brief This is the timestep that the population will increase in age in the simulation
* \note This is currently set to the last timestep in the year
*/
int birthdate;
/**
* \brief This is the flag used to denote whether the stock has been included in a tagging experiment or not
*/
int istagged;
/**
* \brief This is the PopInfoMatrix used to temporarily store the population during the growth calculation
*/
PopInfoMatrix tmpPopulation;
/**
* \brief This is the PopInfoVector used to temporarily store the population during the migration calculation
*/
PopInfoVector tmpMigrate;
};
#endif
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