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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp_drivers.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp_drivers.h
new file mode 100644 (file)
index 0000000..128dc77
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp_drivers.h
@@ -0,0 +1,43 @@
+/******************************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*******************************/
+Constraint_list *prepare_cl_for_moca ( Constraint_list *CL);
+Alignment ** moca_aln ( Constraint_list *CL);
+Alignment * extract_domain ( Constraint_list *CL);
+Alignment * interactive_domain_extraction ( Constraint_list *CL);
+int print_moca_interactive_choices ();
+
+Alignment * approximate_domain ( int min_start, int max_start, int step_start,int min_len, int max_len, int step_len, int *best_start, int *best_len, int *best_score, Constraint_list *CL);
+ 
+int measure_domain_length ( Constraint_list *CL,Alignment *IN, int start, int min_size, int max_size, int step);
+Alignment *extract_domain_with_coordinates ( Alignment *RESULT,int start, int len, Constraint_list *CL);
+int get_starting_point ( Constraint_list *CL);
+
+Alignment * find_domain_coordinates (Constraint_list *CL, int *start, int *len);
+Alignment * extend_domain ( Constraint_list *CL, int *start, int *len, int dstart, int dlen);
+Alignment * modify_domain ( Constraint_list *CL, Alignment *IN, int *start, int *len, int dstart, int dlen);
+
+int * analyse_sequence ( Constraint_list *CL);