removing tcoffee to update

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

diff --git a/binaries/src/tcoffee/t_coffee_source/util_analyse_constraints_list.c b/binaries/src/tcoffee/t_coffee_source/util_analyse_constraints_list.c
deleted file mode 100644 (file)
index f6e1b96..0000000
--- a/binaries/src/tcoffee/t_coffee_source/util_analyse_constraints_list.c
+++ /dev/null
@@ -1,115 +0,0 @@
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-
-
-void print_list(Constraint_list *CL)
-     {
-
-     fprintf ( stderr, "\nPRINT LIST");
-     output_list ( CL, stderr);
-     }
-void save_full_list (Constraint_list *CL, char*fname)
-     {
-     FILE *fp;
-     fp=vfopen ( fname, "w");
-     fp=output_list ( CL, fp);
-     fclose ( fp);
-     }
-FILE * output_list ( Constraint_list *CL, FILE *fp)
-     {
-     int a;
-     
-     fprintf ( fp, "\nPRINT LIST: %d Elements\n", CL->ne);
-     for ( a=0; a<CL->ne; a++)fp=output_pair(CL, a, fp);
-     fprintf (fp, "\n");
-     return fp;
-     }
-FILE * output_pair (Constraint_list *CL,int p, FILE *fp)
-       {       
-       int a;
-       fprintf (fp, "\n");
-       for ( a=0; a<CL->entry_len; a++)
-               {
-               fprintf (fp, "%4d ", vread_clist(CL,p,a));
-               }
-       return fp;
-       }
-void print_pair (Constraint_list *CL,int p)
-       {       
-       int a;
-       fprintf ( stderr, "\n");
-       for ( a=0; a<CL->entry_len; a++)
-               {
-               fprintf ( stderr, "%d ", vread_clist(CL,p,a));
-               }
-       fprintf ( stderr, "\n");
-       }
-
-int** bin_list (Constraint_list *CL,int field, int Threshold)
-        {
-       int  a, c;
-       int max;
-       int **bin_list;
-       CLIST_TYPE x;
-       
-       max=return_max_constraint_list (CL, CONS);
-       
-       bin_list=declare_int (max+1, 5);
-       for (c=0,a=0; a<(CL->ne); a++)
-           if ( vread_clist(CL,a,field)!=UNDEFINED && vread_clist(CL,a,field)>Threshold )
-               {
-               x=vread_clist(CL,a,CONS);
-               bin_list[x][0]=x;
-               bin_list[x][1]++;
-               bin_list[x][2]+=vread_clist(CL, a, field);
-               c++;
-               }
-       
-       for ( a=0; a<= max; a++)
-           {
-           if (bin_list[a][0]>0)
-               {
-               bin_list[a][3]=bin_list[a][2]/bin_list[a][1];
-               bin_list[a][4]=(a==0)?0:(bin_list[a][3]/a);
-               }
-           }
-
-       return bin_list;
-       }
-  
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/