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#ifdef __cplusplus
extern "C" {
#endif
#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"
#include <fcntl.h>
#include <string.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <io_lib/scf.h>
#include <io_lib/mFILE.h>

#define SV_SETUV(A) { ret_val = newSViv(1); sv_setuv(ret_val, (A)); } 

#ifdef __cplusplus
}
#endif

MODULE = Bio::SCF	PACKAGE = Bio::SCF

SV *
get_scf_pointer(file_name)
char *file_name
	CODE:
	Scf *scf_data = NULL;   /* internal representation of data from scf file */	
	struct stat *file_stat;
	SV *ret_val;				/* SV which content scf data */
	int i;
	
	/* checking for existance of file and its permissions */
	if( file_name == NULL ) croak("readScf(...) : file_name is NULL");
	file_stat = malloc(sizeof(struct stat));
	i = stat(file_name, file_stat);
	if( i == -1 ){
		switch(errno){
			case ENOENT : 
				croak("get_scf_pointer(...) : file %s doesn't exist\n", file_name);
				break;
			case EACCES : 
				croak("get_scf_pointer(...) : permission denied on file %s\n", file_name);
				break;
			case ENAMETOOLONG :  
				croak("get_scf_pointer(...) : file name %s too long\n", file_name);
				break;
			default     : 
				croak("get_scf_pointer(...) : unable to get stat on file %s, errno %d\n", file_name, errno);
				break;
		}
	}
	free(file_stat);

	/* Reading SCF file, into internal structure */
	if ( (scf_data = read_scf(file_name)) == NULL )
		croak("get_scf_pointer(...) : failed on read_scf(%s)\n", file_name);
	ret_val = newSViv((int)scf_data);
	RETVAL = ret_val;
	OUTPUT:
	RETVAL

SV *
get_scf_fpointer(file_handle)
FILE *file_handle
	CODE:
	Scf *scf_data = NULL;   /* internal representation of data read from scf file */	
	SV *ret_val;				/* SV which content scf data */
        mFILE *mf;
	
	/* we don't need to check existance of file and its permissions becouse we operate 
	here with already opened file handle */
	if( file_handle == NULL ) croak("get_scf_fpointer(...) : file_handle is NULL");

	/* Reading SCF file, into internal structure */
        mf = mfreopen(NULL,"r",file_handle);
        if (mf == NULL)
	        croak("get_scf_fpointer(...) : failed on mfreopen(...)\n");
	if ( (scf_data = mfread_scf(mf)) == NULL )
		croak("get_scf_fpointer(...) : failed on fread_scf(...)\n");
	ret_val = newSViv((int)scf_data);
	RETVAL = ret_val;
	OUTPUT:
	RETVAL

void
scf_free(scf_pointer)
int scf_pointer
CODE:
	scf_deallocate((Scf *)scf_pointer);

SV *
get_comments(scf_pointer)
int scf_pointer
	CODE:
	Scf *scf_data = (Scf *)scf_pointer;