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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_generic_fasta_nw.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_generic_fasta_nw.h
new file mode 100644 (file)
index 0000000..b2ce28e
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_generic_fasta_nw.h
@@ -0,0 +1,90 @@
+/******************************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*******************************/
+struct Dp_Model
+{
+  int *diag;
+
+  int TG_MODE;
+  int F_TG_MODE;
+  int gop;
+  int gep;
+  int f_gop;
+  int f_gep;
+  int nstate;
+  int START;
+  int END;
+  
+  char**model_comments;
+  int **model;
+  int **model_properties;
+  int **bounded_model;
+  int (***model_emission_function)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+
+  int LEN_I;
+  int LEN_J;
+  int DELTA_I;
+  int DELTA_J;
+  int EMISSION;
+  int START_EMISSION;
+  int TERM_EMISSION;
+  
+  int ALN_TYPE;
+  Constraint_list *CL;
+  /*Associated Functions*/
+  
+  /*To Deprecate*/
+  int UM;
+  
+  int TYPE;
+  int F0;
+  int F1;
+  
+  
+  int NON_CODING;
+  int INSERTION;
+  int DELETION;
+  int CODING0;
+  int CODING1;
+  int CODING2;
+  
+
+};
+typedef struct Dp_Model Dp_Model;
+
+struct Dp_Result
+{
+  int *traceback;
+  int len;
+  int score;
+  Dp_Model *Dp_model;
+};
+typedef struct Dp_Result Dp_Result;
+
+Dp_Result * make_fast_generic_dp_pair_wise (Alignment *A, int*ns, int **l_s,Dp_Model *M);
+
+Constraint_list* free_dp_model  (Dp_Model *D);
+Dp_Result * free_dp_result (Dp_Result *D );