ARB
Macros | Typedefs | Functions
GDE_arbdb_io.cxx File Reference
#include "GDE_proto.h"
#include <aw_msg.hxx>
#include <AW_rename.hxx>
#include <AP_filter.hxx>
#include <aw_awar_defs.hxx>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <algorithm>
Include dependency graph for GDE_arbdb_io.cxx:

Go to the source code of this file.

Macros

#define GET_FIELD_CONTENT(fieldname, buffer, bufsize)
 

Typedefs

typedef unsigned int UINT
 

Functions

int Arbdb_get_curelem (NA_Alignment &dataset)
 
static void set_constant_fields (NA_Sequence *this_elem)
 
static void AppendNA_and_free (NA_Sequence *this_elem, uchar *&sequfilt)
 
static __ATTR__USERESULT int InsertDatainGDE (NA_Alignment &dataset, GBDATA **the_species, unsigned char **the_names, unsigned char **the_sequences, unsigned long numberspecies, unsigned long maxalignlen, const AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo)
 
int ReadArbdb2 (NA_Alignment &dataset, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo)
 
int ReadArbdb (NA_Alignment &dataset, bool marked, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo)
 
int getelem (NA_Sequence *a, int b)
 
void putelem (NA_Sequence *a, int b, NA_Base c)
 

Macro Definition Documentation

#define GET_FIELD_CONTENT (   fieldname,
  buffer,
  bufsize 
)
Value:
do { \
gbd = GB_entry(gb_species, fieldname); \
if (gbd) { \
const char *val = GB_read_char_pntr(gbd); \
strcpy_truncate(buffer, val, bufsize); \
} \
else buffer[0] = 0; \
} while(0)
char buffer[MESSAGE_BUFFERSIZE]
Definition: seq_search.cxx:34
void strcpy_truncate(char *dest, const char *source, size_t dest_size)
Definition: GDE_def.h:137
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")
Definition: AW_awar.cxx:166
GB_CSTR GB_read_char_pntr(GBDATA *gbd)
Definition: arbdb.cxx:898
GBDATA * GB_entry(GBDATA *father, const char *key)
Definition: adquery.cxx:334

Referenced by InsertDatainGDE().

Typedef Documentation

typedef unsigned int UINT

Definition at line 16 of file GDE_arbdb_io.cxx.

Function Documentation

int Arbdb_get_curelem ( NA_Alignment dataset)
static void set_constant_fields ( NA_Sequence this_elem)
static
static void AppendNA_and_free ( NA_Sequence this_elem,
uchar *&  sequfilt 
)
static

Definition at line 40 of file GDE_arbdb_io.cxx.

References AppendNA().

Referenced by InsertDatainGDE().

static __ATTR__USERESULT int InsertDatainGDE ( NA_Alignment dataset,
GBDATA **  the_species,
unsigned char **  the_names,
unsigned char **  the_sequences,
unsigned long  numberspecies,
unsigned long  maxalignlen,
const AP_filter filter,
GapCompression  compress,
bool  cutoff_stop_codon,
TypeInfo  typeinfo 
)
static
int ReadArbdb2 ( NA_Alignment dataset,
AP_filter filter,
GapCompression  compress,
bool  cutoff_stop_codon,
TypeInfo  typeinfo 
)
int ReadArbdb ( NA_Alignment dataset,
bool  marked,
AP_filter filter,
GapCompression  compress,
bool  cutoff_stop_codon,
TypeInfo  typeinfo 
)
int getelem ( NA_Sequence a,
int  b 
)
void putelem ( NA_Sequence a,
int  b,
NA_Base  c 
)