/******************************COPYRIGHT NOTICE*******************************/
/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  30 Nov 2019 - 10:22.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
/*                                                                                          */
/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
/*    it under the terms of the GNU General Public License as published by                  */
/*    the Free Software Foundation; either version 2 of the License, or                     */
/*    (at your option) any later version.                                                   */
/*                                                                                          */
/*    T-COFFEE is distributed in the hope that it will be useful,                           */
/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
/*    GNU General Public License for more details.                                          */
/*                                                                                          */
/*    You should have received a copy of the GNU General Public License                     */
/*    along with Foobar; if not, write to the Free Software                                 */
/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
/*...............................................                                           */
/*  If you need some more information                                                       */
/*  cedric.notredame@gmail.com                                                             */
/*...............................................                                           */
/******************************COPYRIGHT NOTICE*******************************/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <stdarg.h>
#include <string.h>

#include "io_lib_header.h"
#include "util_lib_header.h"
#include "define_header.h"

/*********************************************************************/
/*                                                                   */
/*                         MISCEANELLOUS                             */
/*                                                                   */
/*                                                                   */
/*********************************************************************/	
int ** get_undefined_list (Constraint_list *CL)
         {
	 int **list;
	 int a;
	 CLIST_TYPE x;
	 int *e;
	 list=declare_int ( (CL->S)->nseq+1, (CL->S)->max_len+1);


	 while (e=extract_entry (CL))
	   {
	     x=e[WE];
	     list[e[SEQ1]][e[R1]]=(x==UNDEFINED);
	     list[e[SEQ2]][e[R2]]=(x==UNDEFINED);
	   }
	 return list;
	 }



