text: /*
   *                             The MIT License
   *
   * Wavefront Alignments Algorithms
   * Copyright (c) 2017 by Santiago Marco-Sola  <santiagomsola@gmail.com>
   *
   * This file is part of Wavefront Alignments Algorithms.
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy
   * of this software and associated documentation files (the "Software"), to deal
   * in the Software without restriction, including without limitation the rights
   * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the Software is
   * furnished to do so, subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in all
   * copies or substantial portions of the Software.
   *
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   * SOFTWARE.
   *
   * PROJECT: Wavefront Alignments Algorithms
   * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
   * DESCRIPTION: Score matrix for alignment using dynamic programming
   */
  
  #include "wflambda/alignment/score_matrix.h"
  
  #ifdef WFLAMBDA_NAMESPACE
  namespace wflambda {
  #endif
  
  /*
   * Setup
   */
  void score_matrix_allocate(
      score_matrix_t* const score_matrix,
      const int num_rows,
      const int num_columns,
      mm_allocator_t* const mm_allocator) {
    // Allocate DP matrix
    int h;
    score_matrix->num_rows = num_rows;
    score_matrix->num_columns = num_columns;
    score_matrix->columns = mm_allocator_malloc(mm_allocator,num_columns*sizeof(int*),int*); // Columns
    for (h=0;h<num_columns;++h) {
      score_matrix->columns[h] = mm_allocator_calloc(mm_allocator,num_rows,int,false); // Rows
    }
    // MM
    score_matrix->mm_allocator = mm_allocator;
  }
  void score_matrix_free(
      score_matrix_t* const score_matrix) {
    // Parameters
    mm_allocator_t* const mm_allocator = score_matrix->mm_allocator;
    // DP matrix
    const int num_columns = score_matrix->num_columns;
    int h;
    for (h=0;h<num_columns;++h) {
      mm_allocator_free(mm_allocator,score_matrix->columns[h]);
    }
    mm_allocator_free(mm_allocator,score_matrix->columns);
    // Handler
    mm_allocator_free(mm_allocator,score_matrix);
  }
  /*
   * Display
   */
  void score_matrix_print_score(
      FILE* const stream,
      const int score) {
    if (-1 < score && score < 10000) {
      fprintf(stream," %3d ",score);
    } else {
      fprintf(stream,"  *  ");
    }
  }
  void score_matrix_print_char(
      FILE* const stream,
      const char c) {
    fprintf(stream,"  %c  ",c);
  }
  void score_matrix_print(
      FILE* const stream,
      const score_matrix_t* const score_matrix,
      const char* const pattern,
      const char* const text) {
    // Parameters
    int** const matrix = score_matrix->columns;
    const int num_columns = score_matrix->num_columns;
    const int num_rows = score_matrix->num_rows;
    int h;
    // Print Header
    fprintf(stream,"       ");
    for (h=0;h<num_columns-1;++h) {
      score_matrix_print_char(stream,text[h]);
    }
    fprintf(stream,"\n ");
    for (h=0;h<num_columns;++h) {
      score_matrix_print_score(stream,h);
    }
    fprintf(stream,"\n ");
    for (h=0;h<num_columns;++h) {
      score_matrix_print_score(stream,matrix[h][0]);
    }
    fprintf(stream,"\n");
    // Print Rows
    int v;
    for (v=1;v<num_rows;++v) {
      fprintf(stream,"%c",pattern[v-1]);
      for (h=0;h<num_columns;++h) {
        score_matrix_print_score(stream,matrix[h][v]);
      }
      fprintf(stream,"\n");
    }
    fprintf(stream,"\n");
  }
  
  #ifdef WFLAMBDA_NAMESPACE
  }
  #endif
  