binaries/src/tcoffee/t_coffee_source/util_dp_est.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <math.h>
   4 #include <stdarg.h>
   5 #include <string.h>
   6
   7 #include "io_lib_header.h"
   8 #include "util_lib_header.h"
   9 #include "define_header.h"
  10 #include "dp_lib_header.h"
  11
  12
  13
  14 int evaluate_est_order (Sequence *S, char *concat, Constraint_list *CL, int ktuple)
  15     {
  16         int a;
  17         static char *alphabet;
  18         int  *hasched_seq, *hasched_seq1, *hasched_seq2;
  19         int  *lu_seq, *lu_seq1, *lu_seq2;
  20         int pos_ktup1, pos_ktup2;
  21         double score=0;
  22         int n_ktup;
  23         int n_dots=0;
  24
  25         if ( !alphabet)alphabet=get_alphabet ( concat, alphabet);
  26         n_ktup=(int)pow ( (double)alphabet[0]+1, (double)ktuple);
  27
  28         hasch_seq (concat,&hasched_seq, &lu_seq,ktuple, alphabet);
  29         hasched_seq1=hasched_seq2=hasched_seq;
  30         lu_seq1=lu_seq2=lu_seq;
  31
  32
  33
  34         for ( a=1; a< n_ktup; a++)
  35             {
  36                 pos_ktup1=lu_seq1[a];
  37
  38                 while (TRUE)
  39                     {
  40
  41                      if (!pos_ktup1)break;
  42                      pos_ktup2=lu_seq2[a];
  43                      while (pos_ktup2)
  44                             {
  45                             score+=abs ((int)(pos_ktup1-pos_ktup2));
  46                             pos_ktup2=hasched_seq2[pos_ktup2];
  47                             n_dots++;
  48                             }
  49                   pos_ktup1=hasched_seq1[pos_ktup1];
  50                   }
  51             }
  52
  53         score=(score/(double)(n_dots*strlen(concat)))*100000;
  54         vfree ( hasched_seq);
  55         vfree(lu_seq);
  56
  57
  58         return score;
  59     }
  60
  61 /*********************************COPYRIGHT NOTICE**********************************/
  62 /*© Centro de Regulacio Genomica */
  63 /*and */
  64 /*Cedric Notredame */
  65 /*Tue Oct 27 10:12:26 WEST 2009. */
  66 /*All rights reserved.*/
  67 /*This file is part of T-COFFEE.*/
  68 /**/
  69 /*    T-COFFEE is free software; you can redistribute it and/or modify*/
  70 /*    it under the terms of the GNU General Public License as published by*/
  71 /*    the Free Software Foundation; either version 2 of the License, or*/
  72 /*    (at your option) any later version.*/
  73 /**/
  74 /*    T-COFFEE is distributed in the hope that it will be useful,*/
  75 /*    but WITHOUT ANY WARRANTY; without even the implied warranty of*/
  76 /*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the*/
  77 /*    GNU General Public License for more details.*/
  78 /**/
  79 /*    You should have received a copy of the GNU General Public License*/
  80 /*    along with Foobar; if not, write to the Free Software*/
  81 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA*/
  82 /*...............................................                                                                                      |*/
  83 /*  If you need some more information*/
  84 /*  cedric.notredame@europe.com*/
  85 /*...............................................                                                                                                                                     |*/
  86 /**/
  87 /**/
  88 /*      */
  89 /*********************************COPYRIGHT NOTICE**********************************/