stomachcontent.h

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#ifndef stomachcontent_h
#define stomachcontent_h
 
#include "commentstream.h"
#include "lengthgroup.h"
#include "predatorptrvector.h"
#include "preyptrvector.h"
#include "doublematrixptrmatrix.h"
#include "intmatrix.h"
#include "formulamatrix.h"
#include "actionattimes.h"
#include "charptrmatrix.h"
#include "predatoraggregator.h"
#include "multinomial.h"
 
class SC : public HasName {
public:
  SC(CommentStream& infile, const AreaClass* const Area, const TimeClass* const TimeInfo,
    Keeper* const keeper, const char* datafilename, const char* givenname);
  virtual ~SC();
  virtual double calcLikelihood(const TimeClass* const TimeInfo);
  virtual void Reset();
  virtual void Print(ofstream& outfile) const;
  virtual void setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys);
  virtual void printSummary(ofstream& outfile, double weight);
  virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
  virtual void aggregate(int i);
protected:
  virtual double calcLikelihood() = 0;
  DoubleMatrixPtrMatrix obsConsumption;
  DoubleMatrixPtrMatrix modelConsumption;
  DoubleMatrix likelihoodValues;
  CharPtrVector predatornames;
  CharPtrMatrix preynames;
  CharPtrVector areaindex;
  CharPtrVector predindex;
  CharPtrVector preyindex;
  IntVector Years;
  IntVector Steps;
  DoubleVector predatorlengths;
  IntMatrix predatorages;
  DoubleMatrix preylengths;
  IntMatrix areas;
  int usepredages;
  PredatorAggregator** aggregator;
  LengthGroupDivision** preyLgrpDiv;
  LengthGroupDivision* predLgrpDiv;
  int timeindex;
  ActionAtTimes AAT;
  FormulaMatrix digestioncoeff;
  DoubleMatrix digestion;
  double epsilon;
  const DoubleMatrix* dptr;
};
 
class SCNumbers : public SC {
public:
  SCNumbers(CommentStream& infile, const AreaClass* const Area, const TimeClass* const TimeInfo,
    Keeper* const keeper, const char* datafilename, const char* givenname);
  virtual ~SCNumbers() {};
  virtual void aggregate(int i);
protected:
  void readStomachNumberContent(CommentStream& infile, const TimeClass* const TimeInfo);
  virtual double calcLikelihood();
  Multinomial MN;
  DoubleVector mndata;
  DoubleVector mndist;
};
 
class SCAmounts : public SC {
public:
  SCAmounts(CommentStream& infile, const AreaClass* const Area,
    const TimeClass* const TimeInfo, Keeper* const keeper,
    const char* datafilename, const char* numfilename, const char* givenname);
  virtual ~SCAmounts();
  virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
protected:
  void readStomachAmountContent(CommentStream& infile, const TimeClass* const TimeInfo);
  void readStomachSampleContent(CommentStream& infile, const TimeClass* const TimeInfo);
  virtual double calcLikelihood();
  DoubleMatrixPtrMatrix stddev;
  DoubleMatrixPtrVector number;
};
 
class SCRatios : public SCAmounts {
public:
  SCRatios(CommentStream& infile, const AreaClass* const Area,
    const TimeClass* const TimeInfo, Keeper* const keeper,
    const char* datafilename, const char* numfilename, const char* givenname)
    : SCAmounts(infile, Area, TimeInfo, keeper, datafilename, numfilename, givenname) {};
  virtual ~SCRatios() {};
  virtual void setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys);
protected:
  virtual double calcLikelihood();
};
 
class SCSimple : public SC {
public:
  SCSimple(CommentStream& infile, const AreaClass* const Area, const TimeClass* const TimeInfo,
    Keeper* const keeper, const char* datafilename, const char* givenname);
  virtual ~SCSimple() {};
  virtual void setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys);
protected:
  void readStomachSimpleContent(CommentStream& infile, const TimeClass* const TimeInfo);
  virtual double calcLikelihood();
};
 
class StomachContent : public Likelihood {
public:
  StomachContent(CommentStream& infile, const AreaClass* const Area,
    const TimeClass* const TimeInfo, Keeper* const keeper, double weight, const char* name);
  virtual ~StomachContent();
  virtual void addLikelihood(const TimeClass* const TimeInfo);
  virtual void Reset(const Keeper* const keeper);
  virtual void Print(ofstream& outfile) const;
  void setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys)
    { StomCont->setPredatorsAndPreys(Predators, Preys); };
  virtual void printSummary(ofstream& outfile) {
    StomCont->printSummary(outfile, weight); };
  virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
    StomCont->printLikelihood(outfile, TimeInfo); };
private:
  char* functionname;
  SC* StomCont;
};
 
#endif