//
//  hhviterbifourmatrix.c
//  GitHHSuite
//
//  Created by Martin Steinegger on 19.11.12.
//  Copyright (c) 2012 -. All rights reserved.
//

#ifndef HHVITERBIMATRIX_c
#define HHVITERBIMATRIX_c
#include "hhviterbimatrix.h"

ViterbiMatrix::ViterbiMatrix(){
    this->bCO_MI_DG_IM_GD_MM_vec=NULL;
    this->cellOff = false;
    this->max_query_length = 0;
    this->max_template_length = 0;
}


ViterbiMatrix::~ViterbiMatrix(){
    DeleteBacktraceMatrix();
}

/////////////////////////////////////////////////////////////////////////////////////
//// Allocate memory for dynamic programming matrix
/////////////////////////////////////////////////////////////////////////////////////
void ViterbiMatrix::AllocateBacktraceMatrix(int Nq, int Nt)
{
    int tmp_query_length = ICEIL(Nq + 1, VECSIZE_FLOAT);
    int tmp_template_length = ICEIL((Nt + 1) * VECSIZE_FLOAT, VECSIZE_FLOAT);

    if(tmp_query_length > max_query_length || tmp_template_length > max_template_length) {
        DeleteBacktraceMatrix();
    }
    else {
        return;
    }

    max_query_length = tmp_query_length;
    max_template_length = tmp_template_length;

    // Allocate posterior prob matrix (matrix rows are padded to make them aligned to multiples of ALIGN_FLOAT)
    bCO_MI_DG_IM_GD_MM_vec = malloc_matrix<unsigned char>(max_query_length + 2, max_template_length + (2 * VECSIZE_FLOAT));
    if (!bCO_MI_DG_IM_GD_MM_vec)
        MemoryError("m_probabilities", __FILE__, __LINE__, __func__);
}



/////////////////////////////////////////////////////////////////////////////////////
//// Delete memory for dynamic programming matrix
/////////////////////////////////////////////////////////////////////////////////////
void ViterbiMatrix::DeleteBacktraceMatrix() {
    if(max_query_length == 0) {
        return;
    }

    free(bCO_MI_DG_IM_GD_MM_vec);
    bCO_MI_DG_IM_GD_MM_vec = NULL;

    max_query_length = 0;
    max_template_length = 0;
}

#endif