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

  
      
  
 

int cfasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
int fasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
Dp_Model* initialize_dna_dp_model (Constraint_list *CL);
Dp_Result * make_fast_dp_pair_wise (Alignment *A,int*ns, int **l_s, Constraint_list *CL,Dp_Model *M);
int make_fasta_cdna_pair_wise (Alignment *B,Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag);



int ** evaluate_diagonals_cdna ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list, int ktup);
int cfasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
