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

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / util_lib / aln_compare.h

diff --git a/binaries/src/tcoffee/t_coffee_source/util_lib/aln_compare.h b/binaries/src/tcoffee/t_coffee_source/util_lib/aln_compare.h
new file mode 100644 (file)
index 0000000..369b75c
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/util_lib/aln_compare.h
@@ -0,0 +1,115 @@
+/******************************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
+{   Alignment *A;
+    Alignment *B;
+    Alignment *sim_A;
+    Sequence  *S;
+    Structure *ST;
+/*PARAMETERS*/
+    char ***grep_list;
+    int n_greps;
+
+    char *sim_aln;
+    char *alignment1_file;
+    char *alignment2_file;
+    
+    char *io_format;
+
+    int n_structure;
+    char **struct_file;
+    char **struct_format;
+    int *n_symbol;
+    char ***symbol_list;
+
+/*LIST VARIABLES*/
+    int **code_A;
+    int **code_B;
+    int n_elementsA;
+    int n_elementsB;
+    
+    int **end_index;
+    int **start_index;
+/*RESULTS_VARIABLES*/
+    int **tot_count;
+    int **pos_count;
+    int ***pw_tot_count;
+    int ***pw_pos_count;
+    int *glob;
+    int **pw_glob;
+/*IO VARIABLES*/
+    int n_categories;
+    char ***category;
+    char *category_list;
+    int *n_sub_categories;
+    char sep_l;
+    char sep_r;
+/*Sims VARIABLES*/
+    float **sim;
+    float **sim_param;
+    char *sim_matrix;
+    
+    int sim_n_categories;
+    char ***sim_category;
+    char *sim_category_list;
+    int *sim_n_sub_categories;
+}Result;
+
+
+#define MAX_N_CATEGORIES 100
+#define MAX_N_STRUC      100
+    
+
+    
+
+int aln_compare (int argc, char *argv[]);
+int **analyse_distance ( Alignment *A, int **dis);
+
+Structure * read_structure (char *fname, char *format, Alignment *A,Alignment *B, Structure *ST, int n_symbols, char **symbol_table);
+
+
+int is_in_struct_category ( int s1, int s2, int r1, int r2, Structure *ST, char **cat, int n_sub_cat);
+char * get_structure_residue (int s, int r, Structure *S);
+int parse_category_list ( char *category_list, char ***category, int *sub_n_categories);
+int struc_matches_pattern ( char *struc, char *pattern);
+float **get_aln_compare_sim ( Alignment *A, Structure *S, char **cat, int n_cat, char *matrix);
+float **analyse_sim ( Alignment *A, float **dis);
+
+/*Output*/
+FILE *output_format (char *iof, FILE *fp, Result *R);
+FILE *output_pair_wise_sequence_results (FILE *fp,  Result *R);
+FILE *output_sequence_results (FILE *fp,  Result *R);
+FILE *output_total_results (FILE *fp,  Result *R);
+FILE *output_header (FILE *fp, Result *R);
+FILE *output_large_header ( FILE *fp, Result *R);
+
+/*Parameter Checking*/
+int is_a_struc_format (char *format);
+void get_separating_char ( char s, char *l, char *r);
+void output_informations ();
+
+int check_configuration4program();