--- /dev/null
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdarg.h>
+#include <ctype.h>
+
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+
+
+/*
+* Prototypes
+*/
+
+
+void fatal(char *,...);
+void error(char *,...);
+void warning(char *,...);
+char *rtrim(char *);
+char *blank_to_(char *); /* DES change blanks to _ */
+char *upstr(char *);
+char *lowstr(char *);
+void getstr(char *,char *);
+double getreal(char *,double,double,double);
+int getint(char *,int,int,int);
+void do_system(void);
+Boolean linetype(char *,char *);
+Boolean blankline(char *);
+void get_path(char *,char *);
+
+/*
+* ckalloc()
+*
+* Tries to allocate "bytes" bytes of memory. Exits program if failed.
+* Return value:
+* Generic pointer to the newly allocated memory.
+*/
+
+void *ckalloc(size_t bytes)
+{
+ register void *ret;
+ extern void *vcalloc (size_t nelem, size_t elsize);
+
+ if( (ret = vcalloc(bytes, sizeof(char))) == NULL)
+/*
+ if( (ret = vmalloc(bytes)) == NULL)
+*/
+ fatal("Out of memory\n");
+ else
+ return ret;
+ return ret;
+}
+
+/*
+* ckvrealloc()
+*
+* Tries to vreallocate "bytes" bytes of memory. Exits program if failed.
+* Return value:
+* Generic pointer to the re-allocated memory.
+*/
+
+void *ckvrealloc(void *ptr, size_t bytes)
+{
+ register void *ret;
+ extern void *vrealloc (void *ptr, size_t size);
+
+ if( (ret = vrealloc(ptr, bytes)) == NULL)
+ fatal("Out of memory\n");
+ else
+ return ret;
+ return ret;
+}
+
+/*
+* ckfree()
+*
+* Tries to free memory allocated by ckalloc.
+* Return value:
+* None.
+*/
+
+void ckfree(void *ptr)
+{
+ vfree(ptr);
+}
+
+
+/*
+* fatal()
+*
+* Prints error msg to stderr and exits.
+* Variadic parameter list can be passed.
+*
+* Return values:
+* none
+*/
+
+void fatal( char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap,msg);
+ fprintf(stderr,"\n\nFATAL ERROR: ");
+ vfprintf(stderr,msg,ap);
+ fprintf(stderr,"\n\n");
+ va_end(ap);
+ myexit(EXIT_FAILURE);
+}
+
+/*
+* error()
+*
+* Prints error msg to stderr.
+* Variadic parameter list can be passed.
+*
+* Return values:
+* none
+*/
+
+void error( char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap,msg);
+ fprintf(stderr,"\n\nERROR: ");
+ vfprintf(stderr,msg,ap);
+ fprintf(stderr,"\n\n");
+ va_end(ap);
+}
+
+/*
+* warning()
+*
+* Prints warning msg to stderr.
+* Variadic parameter list can be passed.
+*
+* Return values:
+* none
+*/
+
+void warning( char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap,msg);
+ fprintf(stderr,"\n\nWARNING: ");
+ vfprintf(stderr,msg,ap);
+ fprintf(stderr,"\n\n");
+ va_end(ap);
+}
+
+
+/*
+* rtrim()
+*
+* Removes trailing blanks from a string
+*
+* Return values:
+* Pointer to the processed string
+*/
+
+char * rtrim(char *str)
+{
+ register int p;
+
+ p = strlen(str) - 1;
+
+ while ( isspace(str[p]) )
+ p--;
+
+ str[p + 1] = EOS;
+
+ return str;
+}
+
+
+/*
+* blank_to_()
+*
+* Replace blanks in a string with underscores
+*
+* Also replaces , ; : ( or ) with _
+*
+* Return value:
+* Pointer to the processed string
+*/
+
+char * blank_to_(char *str)
+{
+ int i,p;
+
+
+ p = strlen(str) - 1;
+ for(i=0;i<=p;i++)
+ {
+ if( strrchr(";,():",str[i]))str[i]='_';
+ else if (isspace(str[i]));
+ }
+ return str;
+}
+
+
+/*
+* upstr()
+*
+* Converts string str to uppercase.
+* Return values:
+* Pointer to the converted string.
+*/
+
+char * upstr(char *str)
+{
+ register char *s = str;
+
+ while( (*s = toupper(*s)) )
+ s++;
+
+ return str;
+}
+
+/*
+* lowstr()
+*
+* Converts string str to lower case.
+* Return values:
+* Pointer to the converted string.
+*/
+
+char * lowstr(char *str)
+{
+ register char *s = str;
+
+ while( (*s = tolower(*s)) )
+ s++;
+
+ return str;
+}
+
+void getstr(char *instr,char *outstr)
+{
+ fprintf(stdout,"%s: ",instr);
+ fgets(outstr, 100, stdin);
+}
+
+double getreal(char *instr,double minx,double maxx,double def)
+{
+ int status;
+ double ret;
+ char line[MAXLINE];
+
+ while(TRUE) {
+ fprintf(stdout,"%s (%.1lf-%.1lf) [%.1lf]: ",instr,minx,maxx,def);
+ fgets(line, MAXLINE, stdin);
+ status=sscanf(line,"%lf",&ret);
+ if(status == EOF) return def;
+ if(ret>maxx) {
+ fprintf(stderr,"ERROR: Max. value=%.1lf\n\n",maxx);
+ continue;
+ }
+ if(ret<minx) {
+ fprintf(stderr,"ERROR: Min. value=%.1lf\n\n",minx);
+ continue;
+ }
+ break;
+ }
+ return ret;
+}
+
+
+int getint(char *instr,int minx,int maxx, int def)
+{
+ int ret,status;
+ char line[MAXLINE];
+
+ while(TRUE) {
+ fprintf(stdout,"%s (%d..%d) [%d]: ",
+ instr,(pint)minx,(pint)maxx,(pint)def);
+ fgets(line, MAXLINE, stdin);
+ status=sscanf(line,"%d",&ret);
+ if(status == EOF) return def;
+ if(ret>maxx) {
+ fprintf(stderr,"ERROR: Max. value=%d\n\n",(pint)maxx);
+ continue;
+ }
+ if(ret<minx) {
+ fprintf(stderr,"ERROR: Min. value=%d\n\n",(pint)minx);
+ continue;
+ }
+ break;
+ }
+ return ret;
+}
+
+void do_system()
+{
+ char line[MAXLINE];
+
+ getstr("\n\nEnter system command",line);
+ if(*line != EOS)
+ system(line);
+ fprintf(stdout,"\n\n");
+}
+
+
+Boolean linetype(char *line,char *code)
+{
+ return( strncmp(line,code,strlen(code)) == 0 );
+}
+
+Boolean blankline(char *line)
+{
+ int i;
+
+ for(i=0;line[i]!='\n' && line[i]!=EOS;i++) {
+ if( isdigit(line[i]) ||
+ isspace(line[i]) ||
+ (line[i] == '*') ||
+ (line[i] == '.'))
+ ;
+ else
+ return FALSE;
+ }
+ return TRUE;
+}
+
+
+void get_path(char *str,char *path)
+{
+ register int i;
+
+ strcpy(path,str);
+ for(i=strlen(path)-1;i>-1;--i) {
+ if(str[i]==DIRDELIM) {
+ i = -1;
+ break;
+ }
+ if(str[i]=='.') break;
+ }
+ if(i<0)
+ strcat(path,".");
+ else
+ path[i+1]=EOS;
+}
+/******************************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*******************************/
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