/*****************************************************************************/
/*                                                                           */
/* UNIT: NTL1_Consensus_Sequence  (Level 1 library routine)                  */
/*                                                                           */
/* Author: Nikola Stojanovic                                                 */
/*                                                                           */
/* Revision:    25 JUL 97   Version 1.0                                      */
/*                                                                           */
/* Function:                                                                 */
/*                                                                           */
/*   Procedure decides the consensus sequence for the entire received        */
/* alignment, based on the majority occurence of characters in any of its    */
/* columns and guidelines about the treatment of gaps; returns the pointer   */
/* to the consensus sequence                                                 */
/*                                                                           */
/*****************************************************************************/


#include <stdio.h>
#include <stdlib.h>
#include "ntl1.h"


/*****************************************************************************/

char *NTL1_Consensus_Sequence (restricted_ptr alignment, int gaps_treatment)
{
 char *consensus, *column; long int position, index; int row;

 consensus = (char *) NTL0_ckalloc (((alignment -> size) + 1) * sizeof (char));
 consensus [alignment -> size] = '\0';

 column = (char *)
          NTL0_ckalloc (((alignment -> dimension) + 1) * sizeof (char));
 column [alignment -> dimension] = '\0';

 for (position = 0; position < alignment -> size; position++) {
  index = 0;
  for (row = 0; row < alignment -> dimension; row++) {
   if (((alignment -> starts) [row] <= position) &&
       ((alignment -> stops) [row] >= position)) {
    column [index++] = (alignment -> texts) [row] [position];
   }
  }
  column [index] = '\0';

  consensus [position] = NTL1_Consensus_Column (column, index, gaps_treatment);
 }
 free (column); return consensus;
}