JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / km_coffee / km_util.c

diff --git a/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.c b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.c
new file mode 100644 (file)
index 0000000..2c39b8d
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.c
@@ -0,0 +1,110 @@
+/******************************COPYRIGHT NOTICE*******************************/
+/*  (c) Centro de Regulacio Genomica                                                        */
+/*  and                                                                                     */
+/*  Cedric Notredame                                                                        */
+/*  12 Aug 2014 - 22:07.                                                                    */
+/*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*******************************/
+// #include "km_util.h"
+#include "km_coffee_header.h"
+FILE *
+my_fopen(char *name_f, char *mode)
+{
+       FILE *name_F = fopen(name_f, mode);
+       if (name_F == NULL)
+       {
+               fprintf(stderr, "ERROR: Cannot open file %s!\n", name_f);
+               exit(1);
+       }
+       else
+               return name_F;
+}
+
+
+void *
+my_malloc(size_t size)
+{
+       void *p = malloc(size);
+       if (p == NULL)
+       {
+               fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size);
+               exit(1);
+       }
+       return p;
+}
+
+void *
+my_calloc ( size_t num, size_t size )
+{
+       void *p = calloc(num, size);
+       if (p == NULL)
+       {
+               fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num);
+               exit(1);
+       }
+       return p;
+}
+
+
+void *
+my_realloc(void *p, size_t size)
+{
+       p = realloc(p, size);
+       if (p == NULL)
+       {
+               fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size);
+               exit(1);
+       }
+       return p;
+}
+
+
+
+
+char *
+my_make_temp_dir(char *templatee, char *function)
+{
+
+       char *temp_dir_name = (char*)malloc(20 * sizeof(char*));
+       sprintf(temp_dir_name, "%s", templatee);
+//     char hostname[50];
+//     gethostname(hostname, 50);
+//     printf("%s %s\n",hostname, temp_dir_name);
+       if ((temp_dir_name = mkdtemp(temp_dir_name))==NULL)
+       {
+               int errsv = errno;
+               fprintf(stderr, "ERROR! A temporary directory could not be created: %s\n",strerror(errsv));
+               fprintf(stderr, "This error was caused by '%s' in '%s'\n", function);
+
+               exit(-1);
+       }
+       return temp_dir_name;
+}
+
+
+
+
+
+
+
+
+