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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_fasta_nw.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_fasta_nw.h
new file mode 100644 (file)
index 0000000..9482b57
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/util_dp_fasta_nw.h
@@ -0,0 +1,69 @@
+/******************************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 hseq* SeqHasch;
+
+typedef struct hseq
+{
+  SeqHasch hl[256];
+  int  n;
+  int  *l;
+} hseq;
+
+int ** ktup_dist_mat ( char **seq, int nseq, int ktup, char *type);
+int ** evaluate_diagonals_for_two_sequences ( char *seq1, char *seq2,int maximise,Constraint_list *CL,int ktup);
+int ** evaluate_diagonals ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+int ** evaluate_segments_with_ktup  ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+int ** evaluate_diagonals_with_ktup ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+
+int ** evaluate_diagonals_with_clist ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+
+int * flag_diagonals (int l1, int l2, int **sorted_diag,float T, int window);                
+int * extract_N_diag (int l1, int l2, int **sorted_diag, int n_chosen_diag, int window);
+
+int hasch_seq(char *seq1, int **hs, int **lu,int ktup, char *alph);
+int fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int cfasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int very_fast_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+
+int make_fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag);
+/*********************************************************************/
+/*                                                                   */
+/*                         KTUP_DP                                   */
+/*                                                                   */
+/*                                                                   */
+/*********************************************************************/
+
+int precomputed_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int ktup_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int ktup_comparison ( char *seq1, char *seq2, int ktup);
+HaschT* hasch_sequence ( char *seq1, int ktup);
+
+SeqHasch * seq2hasch (int i,char *seq, int ktup, SeqHasch *H);
+Constraint_list * hasch2constraint_list (Sequence*S, Constraint_list *CL);
+SeqHasch *cleanhasch       (SeqHasch *H);
+int hasch2sim        (SeqHasch *H, int nseq);