/*
  This file is part of the FRED system.

  Copyright (c) 2010-2015, University of Pittsburgh, John Grefenstette,
  Shawn Brown, Roni Rosenfield, Alona Fyshe, David Galloway, Nathan
  Stone, Jay DePasse, Anuroop Sriram, and Donald Burke.

  Licensed under the BSD 3-Clause license.  See the file "LICENSE" for
  more information.
*/

//
//
// File: ODEIntraHost.h
//

#ifndef _FRED_ODEIntraHost_H
#define _FRED_ODEIntraHost_H

#include <map>
#include <vector>

#include "IntraHost.h"

class Infection;
class Trajectory;

using namespace std;

class ODEIntraHost : public IntraHost {
  // TODO set params from params file
  // TODO set all initial values

public:
  Trajectory* get_trajectory();
  void setup(Disease *disease);
  int get_days_symp() {
    return 1;  // TODO
  }

private:
  double get_inoculum_particles (double infector_particles);
  vector<double> getInfectivities(double *viralTiter, int duration);
  vector<double> get_symptomaticity(double *interferon, int duration);

  static const int MAX_LENGTH = 10;

  double viral_titer_scaling;
  double viral_titer_latent_threshold;
  double interferon_scaling;
  double interferon_threshold;
};


#endif