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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.h b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.h
new file mode 100644 (file)
index 0000000..9d1c3e9
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_util.h
@@ -0,0 +1,87 @@
+/******************************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*******************************/
+#ifndef KM_UTIL_H_
+#define KM_UTIL_H_
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <signal.h>
+
+
+/**
+ * \brief Wrapper for fopen.
+ *
+ * \param name_f The name of the file to open.
+ * \param mode The mode in which to open the file
+ * \return The opend File. On failure an error message is printed and the program exits.
+ */
+FILE *
+my_fopen(char *name_f, char *mode);
+
+/**
+ * \brief Wrapper for the malloc function.
+ * \param size The size of the memory block to allocate
+ * \return Pointer to the newly allocated block of memory. On failure an error message is printed and the program exits.
+ */
+void *
+my_malloc(size_t size);
+
+/**
+* \brief Wrapper for the realloc function.
+* \param size The size of the memory block to allocate
+* \return Pointer to the newly allocated block of memory. On failure an error message is printed and the program exits.
+*/
+void *
+my_realloc(void *p, size_t size);
+
+/**
+* \brief Wrapper for the calloc function.
+* \param size The size of the memory block to allocate
+* \return Pointer to the newly allocated block of memory. On failure an error message is printed and the program exits.
+*/
+void *
+my_calloc ( size_t num, size_t size );
+
+/**
+ * \brief Makes a temporary file.
+ *
+ * In case of failure, the program exits.
+ * \param templatee The template to used for making the temporary file.
+ * \param function The function from where this was called (For error message)
+ */
+char *
+my_make_temp_dir(char *templatee, char *function);
+
+
+
+
+
+#endif
+