/****************************************************************************************/
/*                                                                                      */
/*  Project     :  1D-BRNN                                                              */
/*  Release     :  3.3                                                                  */
/*                                                                                      */
/*  File        :  Sequence.h                                                           */
/*  Description :  Sequence data and model predictions for the sequence                 */
/*                                                                                      */
/*  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 "Import.h"

class Sequence
{

  public:

  // Sequence data

  int Num_Positions;        // Number of positions in the sequence
  int Num_Classes;          // Number of possible target classes
  int* Classes;             // Target class of each position in the sequence
  float** Targets;          // Target outputs of the BRNN for each position
  float** Features;         // Input data features for each position

  // Propagation data

  int* Predictions;         // Predicted class of each position in the sequence
  float** Outputs_MAIN;     // Outputs of the main network of the BRNN for each position
  float** Outputs_FWD;      // Outputs of the forward network of the BRNN for each position
  float** Outputs_BWD;      // Outputs of the backward network of the BRNN for each position

  // Back-Propagation data

  float** BackProp_FWD;     // Next values to back propagate in the forward network of the BRNN
  float** BackProp_BWD;     // Next values to back propagate in the backward network of the BRNN

  // Interface

  Sequence();
  ~Sequence();
  void load(istream& is,int feat,int cl);
  void alloc_propagation(int out_fwd,int out_bwd);
  void alloc_backpropagation(int out_fwd,int out_bwd);
  void reset_backpropagation(int out_fwd,int out_bwd);
  void write_predictions(ostream& os);
  float prediction_error(int pos);
  void check_viability();

};