+++ /dev/null
-#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*******************************/