#ifndef initialcond_h
#define initialcond_h
#include "formulamatrixptrvector.h"
#include "areatime.h"
#include "conversionindex.h"
#include "commentstream.h"
#include "agebandmatrixptrvector.h"
#include "livesonareas.h"
#include "keeper.h"
/**
* \class InitialCond
* \brief This is the class used to calculate the initial population of a stock
*
* This class calculates the initial population for a model run. There are 2 ways to do this - either by specifying a normal distribution or by specifying the actual population to be used.
*
* For the normal distribution, Gadget will calculate a length distribution for a population of 10,000 fish for each age group, which will then be multiplied by age and area factors to give the initial population.
*
* For the numbers, Gadget will read a list of the population in each age-length cell for each area.
*
* The initial weight for each age-length cell will be set to the reference weight, multiplied by a conditioning factor.
*/
class InitialCond : public HasName, protected LivesOnAreas {
public:
/**
* \brief This is the InitialCond constructor
* \param infile is the CommentStream to read the initial conditions data from
* \param areas is the IntVector of areas that the initial population will be calculated on
* \param keeper is the Keeper for the current model
* \param refWeightFile is the name of the reference weight file
* \param givenname is the name of the stock for this InitialCond class
* \param Area is the AreaClass for the current model
* \param DL is the step length of the length groups of the stock
*/
InitialCond(CommentStream& infile, const IntVector& areas, Keeper* const keeper,
const char* refWeightFile, const char* givenname, const AreaClass* const Area, double DL);
/**
* \brief This is the default InitialCond destructor
*/
~InitialCond();
/**
* \brief This function will set the initial population of the stock to that specified in the initial conditions file
* \param Alkeys is the AgeBandMatrixPtrVector that will contain the initial population of the stock
*/
void Initialise(AgeBandMatrixPtrVector& Alkeys);
/**
* \brief This will set the ConversionIndex required for to calculate the initial conditions
* \param GivenLDiv is the LengthGroupDivision for the stock
*/
void setCI(const LengthGroupDivision* const GivenLDiv);
/**
* \brief This function will print the initial population
* \param outfile is the ofstream that all the model information gets sent to
*/
void Print(ofstream& outfile) const;
protected:
/**
* \brief This is the function used to read the normal distribution and condition factor for the initial condtion data
* \param infile is the CommentStream to read the initial conditions data from
* \param keeper is the Keeper for the current model
* \param numage is the number of age groups for the initial population
* \param minage is the minimum age for the initial population
* \param Area is the AreaClass for the current model
*/
void readNormalConditionData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area);
/**
* \brief This is the function used to read the normal distribution for the initial condtion data
* \param infile is the CommentStream to read the initial conditions data from
* \param keeper is the Keeper for the current model
* \param numage is the number of age groups for the initial population
* \param minage is the minimum age for the initial population
* \param Area is the AreaClass for the current model
*/
void readNormalParameterData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area);
/**
* \brief This is the function used to read the numbers of the initial population
* \param infile is the CommentStream to read the initial conditions data from
* \param keeper is the Keeper for the current model
* \param numage is the number of age groups for the initial population
* \param minage is the minimum age for the initial population
* \param Area is the AreaClass for the current model
*/
void readNumberData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area);
/**
* \brief This is the LengthGroupDivision of the initial population of the stock
*/
LengthGroupDivision* LgrpDiv;
/**
* \brief This is the ConversionIndex used to convert from the initial population LengthGroupDivision to the stock LengthGroupDivision
*/
ConversionIndex* CI;
/**
* \brief This is the AgeBandMatrixPtrVector used to store the initial population
*/
AgeBandMatrixPtrVector initialPop;
/**
* \brief This is the FormulaMatrixPtrVector that contains the number (from the input file) of the initial population
*/
FormulaMatrixPtrVector initialNumber;
/**
* \brief This is the FormulaMatrix of the area factor used to calculate the initial population
*/
FormulaMatrix areaFactor;
/**
* \brief This is the FormulaMatrix of the age factor used to calculate the initial population
*/
FormulaMatrix ageFactor;
/**
* \brief This is the FormulaMatrix of the condition factor used to calculate the weight of the initial population
*/
FormulaMatrix relCond;
/**
* \brief This is the FormulaMatrix of the mean length at age used to calculate the initial population
*/
FormulaMatrix meanLength;
/**
* \brief This is the FormulaMatrix of the standard deviation of the length at age used to calculate the initial population
*/
FormulaMatrix sdevLength;
/**
* \brief This is the FormulaMatrix of the alpha parameter used when calculating the length weight relationship
*/
FormulaMatrix alpha;
/**
* \brief This is the FormulaMatrix of the beta parameter used when calculating the length weight relationship
*/
FormulaMatrix beta;
/**
* \brief This is the optional factor used when calculating the standard deviation of the length
*/
Formula sdevMult;
/**
* \brief This is the DoubleVector of the reference weight values
*/
DoubleVector refWeight;
/**
* \brief This is the identifier of the function to be used to read the initial population data from file
*/
int readoption;
};
#endif