Browse code

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 10:54:55
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@@ -244,7 +244,7 @@
244 244
 
245 245
 /* The size of `fpos_t', as computed by sizeof. */
246 246
 #ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
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-#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 12
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+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
248 248
 #endif
249 249
 
250 250
 /* The size of `unsigned int', as computed by sizeof. */
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@@ -254,7 +254,7 @@
254 254
 
255 255
 /* The size of `unsigned long', as computed by sizeof. */
256 256
 #ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
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-#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 4
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
258 258
 #endif
259 259
 
260 260
 /* The size of `unsigned long long', as computed by sizeof. */
Browse code

Multiple fixes; final comit before release; version number bumped to 0.99.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102514 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 15/04/2015 13:20:09
Showing1 changed files
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@@ -244,7 +244,7 @@
244 244
 
245 245
 /* The size of `fpos_t', as computed by sizeof. */
246 246
 #ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
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-#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
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+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 12
248 248
 #endif
249 249
 
250 250
 /* The size of `unsigned int', as computed by sizeof. */
... ...
@@ -254,7 +254,7 @@
254 254
 
255 255
 /* The size of `unsigned long', as computed by sizeof. */
256 256
 #ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
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-#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 4
258 258
 #endif
259 259
 
260 260
 /* The size of `unsigned long long', as computed by sizeof. */
Browse code

add package to the repository

msa


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/04/2015 00:12:33
Showing1 changed files
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new file mode 100644
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@@ -0,0 +1,349 @@
1
+#ifndef _SRC_CLUSTAL_OMEGA_CONFIG_H
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+#define _SRC_CLUSTAL_OMEGA_CONFIG_H 1
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+ 
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+/* src/clustal-omega-config.h. Generated automatically at end of configure. */
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+/* src/config.h.  Generated from config.h.in by configure.  */
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+/* src/config.h.in.  Generated from configure.ac by autoheader.  */
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+
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+/* Define if building universal (internal helper macro) */
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+/* #undef AC_APPLE_UNIVERSAL_BUILD */
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+
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+/* Let all files know they are being used inside Clustal Omega */
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+#ifndef CLUSTAL_OMEGA_CLUSTALO
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+#define CLUSTAL_OMEGA_CLUSTALO 1
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+#endif
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+
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+/* This is a CYGWIN system */
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+/* #undef CYGWIN */
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+
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+/* This is a Darwin system */
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+/* #undef DARWIN */
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+
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+/* Define to 1 if you have the <argtable2.h> header file. */
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+/* #undef HAVE_ARGTABLE2_H */
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+
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+/* Define to 1 if you have the <assert.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_ASSERT_H
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+#define CLUSTAL_OMEGA_HAVE_ASSERT_H 1
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+#endif
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+
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+/* Define to 1 if you have the <ctype.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_CTYPE_H
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+#define CLUSTAL_OMEGA_HAVE_CTYPE_H 1
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+#endif
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+
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+/* Define to 1 if you have the <dlfcn.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_DLFCN_H
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+#define CLUSTAL_OMEGA_HAVE_DLFCN_H 1
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+#endif
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+
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+/* Define to 1 if you have the <float.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_FLOAT_H
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+#define CLUSTAL_OMEGA_HAVE_FLOAT_H 1
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+#endif
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+
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+/* Define to 1 if you have the `fseek64' function. */
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+/* #undef HAVE_FSEEK64 */
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+
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+/* Define to 1 if you have the `fseeko' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO
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+#define CLUSTAL_OMEGA_HAVE_FSEEKO 1
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+#endif
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+
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+/* Define to 1 if you have the `fseeko64' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO64
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+#define CLUSTAL_OMEGA_HAVE_FSEEKO64 1
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+#endif
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+
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+/* Define to 1 if you have the `ftell64' function. */
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+/* #undef HAVE_FTELL64 */
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+
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+/* Define to 1 if you have the `ftello' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO
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+#define CLUSTAL_OMEGA_HAVE_FTELLO 1
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+#endif
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+
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+/* Define to 1 if you have the `ftello64' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO64
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+#define CLUSTAL_OMEGA_HAVE_FTELLO64 1
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+#endif
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+
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+/* Define to 1 if you have the <inttypes.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_INTTYPES_H
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+#define CLUSTAL_OMEGA_HAVE_INTTYPES_H 1
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+#endif
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+
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+/* Define to 1 if you have the `argtable2' library (-largtable2). */
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+/* #undef HAVE_LIBARGTABLE2 */
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+
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+/* Define to 1 if you have the `m' library (-lm). */
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+#ifndef CLUSTAL_OMEGA_HAVE_LIBM
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+#define CLUSTAL_OMEGA_HAVE_LIBM 1
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+#endif
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+
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+/* Define to 1 if you have the <limits.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_LIMITS_H
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+#define CLUSTAL_OMEGA_HAVE_LIMITS_H 1
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+#endif
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+
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+/* Has log2() */
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+#ifndef CLUSTAL_OMEGA_HAVE_LOG2
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+#define CLUSTAL_OMEGA_HAVE_LOG2 1
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+#endif
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+
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+/* Define to 1 if you have the <math.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_MATH_H
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+#define CLUSTAL_OMEGA_HAVE_MATH_H 1
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+#endif
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+
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+/* Define to 1 if you have the <memory.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_MEMORY_H
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+#define CLUSTAL_OMEGA_HAVE_MEMORY_H 1
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+#endif
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+
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+/* Define to 1 if you have the `ntohl' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_NTOHL
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+#define CLUSTAL_OMEGA_HAVE_NTOHL 1
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+#endif
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+
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+/* Define to 1 if you have the `ntohs' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_NTOHS
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+#define CLUSTAL_OMEGA_HAVE_NTOHS 1
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+#endif
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+
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+/* Define to 1 if you have the `ntonl' function. */
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+/* #undef HAVE_NTONL */
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+
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+/* Define to 1 if you have the `ntons' function. */
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+/* #undef HAVE_NTONS */
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+
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+/* Defined if OpenMP should and can be used */
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+#ifndef CLUSTAL_OMEGA_HAVE_OPENMP
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+#define CLUSTAL_OMEGA_HAVE_OPENMP 1
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+#endif
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+
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+/* Define to 1 if you have the <stdarg.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STDARG_H
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+#define CLUSTAL_OMEGA_HAVE_STDARG_H 1
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+#endif
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+
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+/* Define to 1 if you have the <stdint.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STDINT_H
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+#define CLUSTAL_OMEGA_HAVE_STDINT_H 1
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+#endif
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+
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+/* Define to 1 if you have the <stdio.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STDIO_H
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+#define CLUSTAL_OMEGA_HAVE_STDIO_H 1
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+#endif
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+
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+/* Define to 1 if you have the <stdlib.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STDLIB_H
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+#define CLUSTAL_OMEGA_HAVE_STDLIB_H 1
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+#endif
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+
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+/* Define to 1 if you have the <strings.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STRINGS_H
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+#define CLUSTAL_OMEGA_HAVE_STRINGS_H 1
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+#endif
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+
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+/* Define to 1 if you have the <string.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STRING_H
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+#define CLUSTAL_OMEGA_HAVE_STRING_H 1
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+#endif
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+
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+/* Define to 1 if you have the `stroul' function. */
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+/* #undef HAVE_STROUL */
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+
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+/* Define to 1 if you have the `strtoull' function. */
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+#ifndef CLUSTAL_OMEGA_HAVE_STRTOULL
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+#define CLUSTAL_OMEGA_HAVE_STRTOULL 1
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+#endif
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+
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+/* Define to 1 if you have the <sys/stat.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_SYS_STAT_H
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+#define CLUSTAL_OMEGA_HAVE_SYS_STAT_H 1
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+#endif
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+
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+/* Define to 1 if you have the <sys/types.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_SYS_TYPES_H
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+#define CLUSTAL_OMEGA_HAVE_SYS_TYPES_H 1
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+#endif
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+
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+/* Define to 1 if you have the <time.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_TIME_H
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+#define CLUSTAL_OMEGA_HAVE_TIME_H 1
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+#endif
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+
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+/* Define to 1 if you have the <unistd.h> header file. */
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+#ifndef CLUSTAL_OMEGA_HAVE_UNISTD_H
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+#define CLUSTAL_OMEGA_HAVE_UNISTD_H 1
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+#endif
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+
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+/* This is a LINUX system */
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+#ifndef CLUSTAL_OMEGA_LINUX
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+#define CLUSTAL_OMEGA_LINUX 1
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+#endif
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+
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+/* Define to the sub-directory in which libtool stores uninstalled libraries.
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+   */
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+#ifndef CLUSTAL_OMEGA_LT_OBJDIR
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+#define CLUSTAL_OMEGA_LT_OBJDIR ".libs/"
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+#endif
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+
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+/* This is a MinGW system */
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+/* #undef MINGW */
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+
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+/* No-debug Mode */
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+#ifndef CLUSTAL_OMEGA_NDEBUG
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+#define CLUSTAL_OMEGA_NDEBUG /**/
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+#endif
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+
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+/* Some strange OS */
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+/* #undef OTHEROS */
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+
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+/* Name of package */
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+#ifndef CLUSTAL_OMEGA_PACKAGE
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+#define CLUSTAL_OMEGA_PACKAGE "clustal-omega"
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+#endif
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+
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+/* Define to the address where bug reports for this package should be sent. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_BUGREPORT
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+#define CLUSTAL_OMEGA_PACKAGE_BUGREPORT "clustalw@ucd.ie"
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+#endif
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+
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+/* The package code name */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_CODENAME
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+#define CLUSTAL_OMEGA_PACKAGE_CODENAME "AndreaGiacomo"
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+#endif
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+
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+/* Define to the full name of this package. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_NAME
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+#define CLUSTAL_OMEGA_PACKAGE_NAME "Clustal Omega"
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+#endif
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+
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+/* Define to the full name and version of this package. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_STRING
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+#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.0"
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+#endif
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+
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+/* Define to the one symbol short name of this package. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_TARNAME
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+#define CLUSTAL_OMEGA_PACKAGE_TARNAME "clustal-omega"
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+#endif
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+
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+/* Define to the home page for this package. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_URL
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+#define CLUSTAL_OMEGA_PACKAGE_URL ""
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+#endif
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+
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+/* Define to the version of this package. */
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+#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
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+#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.0"
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+#endif
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+
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+/* The size of `fpos_t', as computed by sizeof. */
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+#ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
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+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
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+#endif
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+
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+/* The size of `unsigned int', as computed by sizeof. */
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+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT 4
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+#endif
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+
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+/* The size of `unsigned long', as computed by sizeof. */
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+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
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+#endif
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+
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+/* The size of `unsigned long long', as computed by sizeof. */
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+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG 8
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+#endif
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+
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+/* The size of `unsigned short', as computed by sizeof. */
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+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT 2
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+#endif
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+
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+/* This is a Solaris system */
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+/* #undef SOLARIS */
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+
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+/* This is a BSD system */
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+/* #undef SOMEBSD */
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+
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+/* Define to 1 if you have the ANSI C header files. */
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+#ifndef CLUSTAL_OMEGA_STDC_HEADERS
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+#define CLUSTAL_OMEGA_STDC_HEADERS 1
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+#endif
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+
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+/* Enable extensions on AIX 3, Interix.  */
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+#ifndef _ALL_SOURCE
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+# define _ALL_SOURCE 1
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+#endif
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+/* Enable GNU extensions on systems that have them.  */
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+#ifndef _GNU_SOURCE
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+# define _GNU_SOURCE 1
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+#endif
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+/* Enable threading extensions on Solaris.  */
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+#ifndef _POSIX_PTHREAD_SEMANTICS
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+# define _POSIX_PTHREAD_SEMANTICS 1
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+#endif
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+/* Enable extensions on HP NonStop.  */
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+#ifndef _TANDEM_SOURCE
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+# define _TANDEM_SOURCE 1
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+#endif
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+/* Enable general extensions on Solaris.  */
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+#ifndef __EXTENSIONS__
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+# define __EXTENSIONS__ 1
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+#endif
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+
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+
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+/* Version number of package */
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+#ifndef CLUSTAL_OMEGA_VERSION
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+#define CLUSTAL_OMEGA_VERSION "1.2.0"
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+#endif
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+
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+/* Define if using the dmalloc debugging malloc package */
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+/* #undef WITH_DMALLOC */
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+
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+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
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+   significant byte first (like Motorola and SPARC, unlike Intel). */
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+#if defined AC_APPLE_UNIVERSAL_BUILD
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+# if defined __BIG_ENDIAN__
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+#  define WORDS_BIGENDIAN 1
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+# endif
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+#else
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+# ifndef WORDS_BIGENDIAN
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+/* #  undef WORDS_BIGENDIAN */
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+# endif
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+#endif
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+
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+/* Define to 1 if on MINIX. */
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+/* #undef _MINIX */
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+
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+/* Define to 2 if the system does not provide POSIX.1 features except with
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+   this defined. */
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+/* #undef _POSIX_1_SOURCE */
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+
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+/* Define to 1 if you need to in order for `stat' and other things to work. */
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+/* #undef _POSIX_SOURCE */
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+
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+/* Define to empty if `const' does not conform to ANSI C. */
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+/* #undef const */
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+
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+/* Define to `__inline__' or `__inline' if that's what the C compiler
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+   calls it, or to nothing if 'inline' is not supported under any name.  */
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+#ifndef __cplusplus
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+/* #undef inline */
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+#endif
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+
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+/* Define to `long int' if <sys/types.h> does not define. */
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+/* #undef off_t */
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+
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+/* Define to `unsigned int' if <sys/types.h> does not define. */
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+/* #undef size_t */
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+ 
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+/* once: _SRC_CLUSTAL_OMEGA_CONFIG_H */
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+#endif