/****************************************************************************************/
/*                                                                                      */
/*  Project     :  1D-BRNN                                                              */
/*  Release     :  3.3                                                                  */
/*                                                                                      */
/*  File        :  Model.h                                                              */
/*  Description :  BRNN model with three neural networks                                */
/*                                                                                      */
/*  Author(s)   :  Christophe Magnan  (2013) - New generic version                      */
/*              :  Jianlin Cheng      (2003) - New custom version for SCRATCH           */
/*              :  Gianluca Pollastri (2001) - Customized version for SCRATCH           */
/*              :  Paolo Frasconi     (1997) - Initial generic version                  */
/*                                                                                      */
/*  Copyright   :  Institute for Genomics and Bioinformatics                            */
/*                 University of California, Irvine                                     */
/*                                                                                      */
/*  Modified    :  2015/07/01                                                           */
/*                                                                                      */
/****************************************************************************************/

#include "Dataset.h"
#include "Network.h"

class Model
{

  public:

  // Model parameters

  int Num_Features;        // Number of data features in input of the BRNN
  int Num_Classes;         // Number of target classes in output of the BRNN
  int Num_Hidden;          // Number of hidden nodes in the main network of the BRNN
  int Num_AdjPos_FWD;      // Number of adjacent positions s.t. outputs of forward network -> inputs of main network
  int Num_AdjPos_BWD;      // Number of adjacent positions s.t. outputs of backward network -> inputs of main network
  int Num_Outputs_FWD;     // Number of output nodes in the forward network of the BRNN
  int Num_Outputs_BWD;     // Number of output nodes in the backward network of the BRNN
  int Num_Hidden_FWD;      // Number of hidden nodes in the forward network of the BRNN
  int Num_Hidden_BWD;      // Number of hidden nodes in the backward network of the BRNN

  // Model data

  Network* MAINnet;        // Main network of the BRNN (with output layer)
  Network* FWDnet;         // Forward network of the BRNN (left context)
  Network* BWDnet;         // Backward network of the BRNN (right context)

  // Propagation data

  float* Inputs_MAIN;      // Next inputs to propagate in the main network of the BRNN
  float* Inputs_FWD;       // Next inputs to propagate in the forward network of the BRNN
  float* Inputs_BWD;       // Next inputs to propagate in the backward network of the BRNN

  // Interface

  Model();
  ~Model();
  void write(char* fileout);
  void load(char* filein);
  void initialize(int feat,int cl,int hid,int cF,int cB,int oF,int oB,int hF,int hB);
  void alloc_backpropagation();
  void propagate(Sequence* seq);
  void expectation(Sequence* seq);
  void maximization(float epsilon);

  private:

  // Methods

  void propagate_FWD(Sequence* seq,int pos);
  void propagate_BWD(Sequence* seq,int pos);
  void propagate_MAIN(Sequence* seq,int pos);
  void back_propagate_FWD(Sequence* seq,int pos);
  void back_propagate_BWD(Sequence* seq,int pos);
  void back_propagate_MAIN(Sequence* seq,int pos);
  void check_viability();

};