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--- a/black_flag.c
+++ b/black_flag.c
@@ -82,7 +82,7 @@
-int handle_crash_init(void (*crash_fun)())
+int handle_crash_init(void (*crash_fun)(int))
{
#define HANDLE_CRASH_MAX 5
int i,signal_type[HANDLE_CRASH_MAX]
--- a/black_flag.h
+++ b/black_flag.h
@@ -230,7 +230,7 @@
((INDEX)<(MINIMUM_BOUND) || (INDEX)>=(MAXIMUM_BOUND))
void handle_crash(int sigcode);
-int handle_crash_init(void (*crash_fun)());
+int handle_crash_init(void (*crash_fun)(int));
int black_flag(int bug_level,
char sourcefile[],
int sourceline,
--- a/default.h
+++ b/default.h
@@ -19,7 +19,6 @@
typedef void *voidptr; /* ~~e: should be moved out to generic typing header
--- */
-typedef int (*funptr)();
#define LOOPB(i,size) for ((i)=(size);(i)-- >0;)
#define LOOP(i,size) for ((i)=(size);(i)-- >0;)
@@ -152,7 +151,7 @@
else if (NULL == ((memptr)=(ATYPE *)calloc((size_t)(N),sizeof(ATYPE)))) { \
fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \
- fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \
+ fprintf(stderr,"requested %d x %zu bytes \n",(N),sizeof(ATYPE)); \
MALLOC_FAILURE_ACTION; \
}
@@ -193,7 +192,7 @@
else { \
fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
fprintf(stderr,"Unable to meet request: %s\n",STRINGIFY(memptr)); \
- fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \
+ fprintf(stderr,"requested %d x %zu bytes \n",(NUM),sizeof(ATYPE)); \
REALLOC_FAILURE_ACTION; \
} \
}
--- a/fasta_format.c
+++ b/fasta_format.c
@@ -2,6 +2,7 @@
#include "default.h"
#include "seq_util.h"
+char *stringptr_cat_pos(stringptr *s1,const char s2[],int *pos);
/** reads FASTA formatted sequence file, and saves the sequences to
--- a/msa_format.c
+++ b/msa_format.c
@@ -16,6 +16,11 @@
#include "msa_format.h"
+void fuse_ring_identities(int len_x,LPOLetter_T seq_x[],
+ int len_y,LPOLetter_T seq_y[],
+ LPOLetterRef_T al_x[],
+ LPOLetterRef_T al_y[]);
+void build_seq_to_po_index(LPOSequence_T *seq);
/** is `ch' an allowed residue? (a-z OR A-Z OR ? OR [ OR ]) */
static int is_residue_char (char ch);
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