JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / dp_lib / util_dp_gotoh_sw.h

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_gotoh_sw.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_gotoh_sw.h
new file mode 100644 (file)
index 0000000..a84a85c
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_gotoh_sw.h
@@ -0,0 +1,49 @@
+/******************************COPYRIGHT NOTICE*******************************/
+/*  (c) Centro de Regulacio Genomica                                                        */
+/*  and                                                                                     */
+/*  Cedric Notredame                                                                        */
+/*  12 Aug 2014 - 22:07.                                                                    */
+/*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@europe.com                                                             */
+/*...............................................                                           */
+/******************************COPYRIGHT NOTICE*******************************/
+
+int gotoh_pair_wise_lalign ( Alignment *A, int*ns, int **l_s,Constraint_list *CL);
+Constraint_list * undefine_sw_aln ( Alignment *A, Constraint_list *CL);
+Constraint_list * undefine_sw_pair ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int sw_pair_is_defined ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+
+int gotoh_pair_wise_sw (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+
+Alignment * get_best_local_aln ( Alignment *IN,Constraint_list *CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int greedy);
+Alignment * get_best_nol_local_aln ( Alignment *IN, Constraint_list *CL, int gop, int gep,int sw_t,int sw_l, int sw_z, int mode);
+double compute_penalty   (Constraint_list *CL, char *mode, int len);
+double compute_scale ( Constraint_list *CL,char *mode, int len);
+int evaluate_penalty (Alignment *A, Constraint_list *CL, int *scale,char *scale_mode, int *penalty, char *penalty_mode, int len_seq);
+Alignment ** t_coffee_lalign   (Constraint_list *CL, int scale, int penalty,int maximise,Sequence *S, int sw_t, int sw_l, int sw_z,int *sw_n, int sw_io);
+Alignment * add_seq2aln   (Constraint_list *CL, Alignment *IN,Sequence  *S);
+
+
+
+
+
+
+