View of /trunk/gadget/initialcond.h

#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