added ifdefs for extern c

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 0d2da75284049cd377d9cf209de5d0eb44b4034c..025987fd04bc676cadc7a59f14b19eb9862b5620 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -8,8 +8,13 @@
  */
 
 #include "clearcutcommand.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
 #include "clearcut.h"
-
+#ifdef __cplusplus
+}
+#endif
 //**********************************************************************************************************************
 vector<string> ClearcutCommand::getValidParameters(){  
        try {

diff --git a/distclearcut.h b/distclearcut.h
index 25a654197cc6ee4f99d83a15d9c8a3eb32c44eac..e4abef23eb06fbd75e47e2dc8f20b49c83e79c84 100644 (file)
--- a/distclearcut.h
+++ b/distclearcut.h
@@ -51,6 +51,11 @@
 #ifndef _INC_DIST_H_
 #define _INC_DIST_H_ 1
 
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "fasta.h"
 #include "clearcut.h"
 
@@ -112,6 +117,9 @@ NJ_DNA_count_tt(NJ_alignment *alignment,
                long int *transversions,
                long int *residues);
 
+#ifdef __cplusplus
+}
+#endif
 
 #endif /* _INC_DIST_H_ */
 

diff --git a/dmat.h b/dmat.h
index 1c2be5501f8951f3d61ca38a3319a343204d26d1..04305abfdc5495e30c635ec575320354123ac525 100644 (file)
--- a/dmat.h
+++ b/dmat.h
@@ -50,6 +50,10 @@
 #ifndef _INC_DMAT_H_
 #define _INC_DMAT_H_ 1
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "clearcut.h"
 
 
@@ -86,6 +90,9 @@ void
 NJ_output_matrix(NJ_ARGS *nj_args,
                 DMAT *dmat);
 
+#ifdef __cplusplus
+}
+#endif
 
 #endif /* _INC_DMAT_H_ */
 

diff --git a/fasta.h b/fasta.h
index 29ea288e26d27fdd819c6d7f306cadc676d31387..8b9e3d664b16320ce89e0a92682d250b1e47e70a 100644 (file)
--- a/fasta.h
+++ b/fasta.h
@@ -47,6 +47,10 @@
 #ifndef _INC_NJ_FASTA_H_
 #define _INC_NJ_FASTA_H_ 1
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "clearcut.h"
 
 #define NJ_INITIAL_BUFFER_SIZE   512
@@ -82,6 +86,10 @@ NJ_free_alignment(NJ_alignment *alignment);
 int
 NJ_taxaname_unique(NJ_alignment *alignment);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* _INC_NJ_FASTA_H_ */
 
 

diff --git a/getopt_long.h b/getopt_long.h
index a1a9add17677e750850209e1bf293d258021a610..dbf799276993640fb08d21d7401da3c7406c43e8 100644 (file)
--- a/getopt_long.h
+++ b/getopt_long.h
@@ -28,6 +28,10 @@
 
 #ifndef _GETOPT_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 struct option {
     const char *name;
     int has_arg;
@@ -49,4 +53,8 @@ int getopt_long(int argc, char **argv,
                 struct option *longopts,
                 int *indexptr);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* _GETOPT_H */

diff --git a/mothur b/mothur
index ac8ea8a4afaf78fef42c97af9d14fb87ea7891b6..484ba58b9f04e78a155e4f2a450adebabf45f45c 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/prng.h b/prng.h
index 64f8ef3f54a6c6b5a157a7d41aa183d5e4dedf89..9eb15102f1c71b2497659d085e3a12f4445412c8 100644 (file)
--- a/prng.h
+++ b/prng.h
@@ -51,6 +51,10 @@
 #ifndef _INC_PRNG_H_
 #define _INC_PRNG_H_ 1
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #define NJ_RAND_MAX 0x7fffffffUL
 
 
@@ -83,6 +87,10 @@ genrand_res53(void);
 long int
 NJ_genrand_int31_top(long int top);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* _INC_PRNG_H_ */