Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / clustal / util.h

diff --git a/binaries/src/clustalo/src/clustal/util.h b/binaries/src/clustalo/src/clustal/util.h
new file mode 100644 (file)
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+++ b/binaries/src/clustalo/src/clustal/util.h
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+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega 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.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ *  RCS $Id: util.h 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#include <limits.h>
+#include <string.h>
+#include <strings.h>
+#include <stdarg.h>
+#include <stdbool.h>
+
+#ifndef CLUSTALO_UTIL_H
+#define CLUSTALO_UTIL_H
+
+
+#define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__)
+#define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__)
+#define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__)
+#define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__))
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+#ifndef MIN
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+/* STR_EQ: strings are equal, case sensitive */
+#define STR_EQ(a,b)         (strcmp((a),(b)) == 0)
+/*  STR_NC_EQ: strings are equal, ignoring case */
+#define STR_NC_EQ(a,b)      (strcasecmp((a),(b)) == 0)
+
+
+/* type boolean and false and true defined in stdbool.h */
+#ifndef TRUE
+#define TRUE true
+#endif
+#ifndef FALSE
+#define FALSE false
+#endif
+
+/* clashes with hhalign
+#define FAIL -1
+#define OK 0
+*/
+
+
+
+/* don't use the following directly; use macros provided above instead
+ */
+void *CkMalloc(size_t size, const char *function, const int line);
+void *CkCalloc(size_t count, size_t size, const char *function, const int line);
+void *CkRealloc(void *ptr, size_t bytes, const char *function, const int line);
+void *CkFree(void *ptr, const char *function, const int line);
+char *CkStrdup(const char *s);
+void PermutationArray(int **array, const int len);
+void RandomUniqueIntArray(int *array, const int array_len, const int max_value);
+int IntCmp(const void *a, const void *b);
+bool FileIsWritable(char *pcFileName);
+void QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort,
+                        const int uArrayLen, const char cOrder, const bool bOverwriteArrayToSort);
+
+#endif