View of /trunk/gadget/stray.h

#ifndef stray_h
#define stray_h

#include "areatime.h"
#include "formulavector.h"
#include "commentstream.h"
#include "agebandmatrix.h"
#include "intmatrix.h"
#include "livesonareas.h"
#include "selectfunc.h"
#include "stock.h"

/**
 * \class StrayData
 * \brief This is the class used to calculate the movement from one stock to other stocks
 *
 * This class moves a proportion of fish from one stock to the corresponding age-length cell in other stocks.  This is an extension to the Transition class, since it can move fish from more than one age group.  The length groups of the new stocks are checked, and any fish that haven't yet reached the minimum length of the new stock remain in the original stock.
 */
class StrayData : public HasName, protected LivesOnAreas {
public:
  /**
   * \brief This is the StrayData constructor
   * \param infile is the CommentStream to read the straying data from
   * \param LgrpDiv is the LengthGroupDivision that the straying stock will be calculated on
   * \param areas is the IntVector of areas that the straying stock will be calculated on
   * \param Area is the AreaClass for the current model
   * \param givenname is the name of the stock for this StrayData class
   * \param TimeInfo is the TimeClass for the current model
   * \param keeper is the Keeper for the current model
   */
  StrayData(CommentStream& infile, const LengthGroupDivision* const LgrpDiv,
    const IntVector& areas, const AreaClass* const Area, const char* givenname,
    const TimeClass* const TimeInfo, Keeper* const keeper);
  /**
   * \brief This is the default StrayData destructor
   */
  ~StrayData();
  /**
   * \brief This function will print the straying information
   * \param outfile is the ofstream that all the model information gets sent to
   */
  void Print(ofstream& outfile) const;
  /**
   * \brief This will select the stocks required for the straying process
   * \param stockvec is the StockPtrVector of all the available stocks
   */
  void setStock(StockPtrVector& stockvec);
  /**
   * \brief This will move the calculated straying stock from the current stock into the new stock age-length cells
   * \param area is the area that the straying process is being calculated on
   * \param TimeInfo is the TimeClass for the current model
   */
  void addStrayStock(int area, const TimeClass* const TimeInfo);
  /**
   * \brief This will store the part of the current stock that will stray into other stocks
   * \param area is the area that the straying is being calculated on
   * \param Alkeys is the AgeBandMatrix of the stock that fish will move from
   * \param TimeInfo is the TimeClass for the current model
   */
  void storeStrayingStock(int area, AgeBandMatrix& Alkeys, const TimeClass* const TimeInfo);
  /**
   * \brief This will store the part of the current stock that will stray into other stocks
   * \param area is the area that the straying is being calculated on
   * \param Alkeys is the AgeBandMatrix of the stock that fish will move from
   * \param TagAlkeys is the AgeBandMatrixRatio of the tagged stock that fish will move from
   * \param TimeInfo is the TimeClass for the current model
   */
  void storeStrayingStock(int area, AgeBandMatrix& Alkeys,
    AgeBandMatrixRatio& TagAlkeys, const TimeClass* const TimeInfo);
  /**
   * \brief This will check if the straying process will take place on the current timestep
   * \param area is the area that the straying is being calculated on
   * \param TimeInfo is the TimeClass for the current model
   * \return 1 if the straying process will take place, 0 otherwise
   */
  int isStrayStepArea(int area, const TimeClass* const TimeInfo);
  /**
   * \brief This will reset the straying information for the current model run
   * \param TimeInfo is the TimeClass for the current model
   */
  void Reset(const TimeClass* const TimeInfo);
  /**
   * \brief This will calculate the stocks the current stock can stray into
   * \return stray stocks
   */
  const StockPtrVector& getStrayStocks();
  /**
   * \brief This function will initialise the tagging experiments for the straying calculations
   */
  void setTagged();
  /**
   * \brief This will add a tagging experiment to the straying calculations
   * \param tagname is the name of the tagging experiment
   */
  void addStrayTag(const char* tagname);
  /**
   * \brief This will remove a tagging experiment from the straying calculations
   * \param tagname is the name of the tagging experiment
   */
  void deleteStrayTag(const char* tagname);
protected:
  /**
   * \brief This is the StockPtrVector of the stocks that the straying fish will move to
   */
  StockPtrVector strayStocks;
  /**
   * \brief This is the CharPtrVector of the names of the straying stocks
   */
  CharPtrVector strayStockNames;
  /**
   * \brief This is the FormulaVector of the ratio of the stock that will stray
   */
  FormulaVector strayRatio;
  /**
   * \brief This is used to scale the ratios to ensure that they will always sum to 1
   */
  double ratioscale;
  /**
   * \brief This is the IntVector used as an index for the ratio vector
   */
  IntVector ratioindex;
  /**
   * \brief This is the IntVector of timesteps that the straying will take place on
   */
  IntVector strayStep;
  /**
   * \brief This is the IntVector of areas that the straying will take place on
   */
  IntVector strayArea;
  /**
   * \brief This is the LengthGroupDivision of the stock
   */
  LengthGroupDivision* LgrpDiv;
  /**
   * \brief This is the DoubleVector of the proportion of each length group of the stock that will stray
   */
  DoubleVector strayProportion;
  /**
   * \brief This is the SelectFunc used to calculate of the proportion of each length group of the stock that will stray
   */
  SelectFunc* fnProportion;
  /**
   * \brief This is the AgeBandMatrixPtrVector used to store the calculated straying stocks
   */
  AgeBandMatrixPtrVector Storage;
  /**
   * \brief This is the AgeBandMatrixRatioPtrVector used to store the calculated straying tagged stocks
   */
  AgeBandMatrixRatioPtrVector tagStorage;
  /**
   * \brief This is the ConversionIndexPtrVector used to convert from the current stock lengths to the straying stock lengths
   */
  ConversionIndexPtrVector CI;
  /**
   * \brief This is the minimum length group division of the straying stock
   */
  int minStrayLength;
  /**
   * \brief This is the flag used to denote whether the stock has been included in a tagging experiment or not
   */
  int istagged;
};

#endif