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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.h
new file mode 100644 (file)
index 0000000..d8c6100
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.h
@@ -0,0 +1,34 @@
+/******************************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*******************************/
+Sequence *pavie_seq2random_seq (Sequence *S, char *subst); 
+double **pavie_seq2pavie_aln(Sequence *S,char *mat, char *mode);
+Alignment *pavie_seq2pavie_sort ( Sequence *S, char *mat, char *mode);
+Alignment* pavie_seq2pavie_msa  ( Sequence *S, char *mat, char *mode);
+NT_node pavie_seq2pavie_tree ( Sequence *S, char *mat, char *mode);
+int **pavie_seq2trained_pavie_mat(Sequence *S, char *param);
+int pavie_pair_wise (Alignment *A,int *ns, int **l_s,Constraint_list *CL );
+Sequence *pavie_seq2noisy_seq (Sequence *S, int val,char *subst);