new version of tcoffee 8.99 not yet compiled for ia32 linux (currently compiled for...

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / util_dp_est.c

diff --git a/binaries/src/tcoffee/t_coffee_source/util_dp_est.c b/binaries/src/tcoffee/t_coffee_source/util_dp_est.c
new file mode 100644 (file)
index 0000000..5a80f1f
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/util_dp_est.c
@@ -0,0 +1,89 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <stdarg.h>
+#include <string.h>
+
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+#include "dp_lib_header.h"
+
+
+
+int evaluate_est_order (Sequence *S, char *concat, Constraint_list *CL, int ktuple)
+    {
+       int a;
+        static char *alphabet;
+       int  *hasched_seq, *hasched_seq1, *hasched_seq2;
+       int  *lu_seq, *lu_seq1, *lu_seq2;
+       int pos_ktup1, pos_ktup2;
+       double score=0;
+       int n_ktup;
+       int n_dots=0;
+       
+       if ( !alphabet)alphabet=get_alphabet ( concat, alphabet);
+       n_ktup=(int)pow ( (double)alphabet[0]+1, (double)ktuple);
+       
+       hasch_seq (concat,&hasched_seq, &lu_seq,ktuple, alphabet);
+       hasched_seq1=hasched_seq2=hasched_seq;
+       lu_seq1=lu_seq2=lu_seq;
+       
+
+
+       for ( a=1; a< n_ktup; a++)
+           {
+               pos_ktup1=lu_seq1[a];
+               
+               while (TRUE)
+                   {
+                   
+                    if (!pos_ktup1)break;
+                    pos_ktup2=lu_seq2[a];
+                    while (pos_ktup2) 
+                           {
+                           score+=abs ((int)(pos_ktup1-pos_ktup2));
+                           pos_ktup2=hasched_seq2[pos_ktup2];
+                           n_dots++;
+                           }
+                 pos_ktup1=hasched_seq1[pos_ktup1];
+                 }
+           }
+       
+       score=(score/(double)(n_dots*strlen(concat)))*100000;
+       vfree ( hasched_seq);
+       vfree(lu_seq);
+
+
+       return score;
+    }
+       
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*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*******************************/