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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/fastal/diagonal.h b/binaries/src/tcoffee/t_coffee_source/fastal/diagonal.h
new file mode 100644 (file)
index 0000000..ddf3a6c
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/fastal/diagonal.h
@@ -0,0 +1,51 @@
+/******************************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*******************************/
+
+
+
+
+
+
+
+typedef struct
+{
+       ///field saving the positions [x1,y1,l1,x2,y2,l2,...]
+       int *segments;
+       /// points to the current used segment
+       int *current_pos;
+       /// saves the previous diagonal position.
+       int prev_position;
+       /// diagonal number
+//     int diagonal_num;
+}
+Segment;
+
+
+Segment* extend_diagonals(Diagonal *diagonals, int *num_diagonals, int l1, int l2);
+int seq_pair2blast_diagonal2(char *seq_file_name1, char *seq_file_name2, Diagonal **diagonals, int *dig_length, int l1, int l2, int is_dna);
+
+int ** segments2int(Segment *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);