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

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / fastal / fastal_opt_parsing.h

diff --git a/binaries/src/tcoffee/t_coffee_source/fastal/fastal_opt_parsing.h b/binaries/src/tcoffee/t_coffee_source/fastal/fastal_opt_parsing.h
new file mode 100644 (file)
index 0000000..fd8b753
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/fastal/fastal_opt_parsing.h
@@ -0,0 +1,76 @@
+/******************************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*******************************/
+// #include "string.h"
+
+struct Fastal_arguments
+{
+//     char *args[2];
+       //IO
+
+
+       char *sequence_file;
+       char *tree_file;
+       char *output_file;
+       int tree_out;
+
+       char *method;
+       int is_dna;
+       double gop;
+       double gep;
+
+
+
+       char *diag_method;
+//     Tree Computation
+//     int retree;
+       int gap_iterate;
+       int tree_only;
+       char *tree_method;
+       int tree_param1;
+       int tree_param2;
+
+
+       //Scoring
+       char *mat;
+       int agreement_score;
+       int evaluate;
+       int score;
+       int num_ref_aln;
+       int num_seq_in_ref;
+       char *aln_ref;
+       char *aln2test;
+};
+
+
+
+
+void tree_parse(struct Fastal_arguments *arguments, char* param);
+
+
+
+void arg_parse (int argc, char **argv, struct Fastal_arguments *arguments);
+