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Classes | Namespaces | Macros | Enumerations | Functions | Variables
seq_export.cxx File Reference
#include "seqio.hxx"
#include <AP_filter.hxx>
#include <xferset.h>
#include <arbdbt.h>
#include <gb_aci.h>
#include <arb_strarray.h>
#include <arb_file.h>
#include <arb_diff.h>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <xml.hxx>
#include <unistd.h>
Include dependency graph for seq_export.cxx:

Go to the source code of this file.

Classes

struct  export_format
 
class  SpeciesSelector
 
class  export_sequence_data
 

Namespaces

 SEQIO
 

Macros

#define sio_assert(cond)   arb_assert(cond)
 

Enumerations

enum  EXPORT_CMD { EXPORT_XML, EXPORT_INVALID, EXPORT_USING_FORM }
 

Functions

static EXPORT_CMD check_internal (const char *command)
 
static GB_ERROR read_export_format (export_format *efo, const char *file, bool load_complete_form)
 
static const charexported_sequence (GBDATA *gb_species, size_t *seq_len, GB_ERROR *error)
 
static GB_ERROR XML_recursive (GBDATA *gbd, int depth)
 
static GB_ERROR export_species_using_form (FILE *out, const char *form, const GBL_call_env &callEnv)
 
static GB_ERROR export_write_species (GBDATA *gb_species, FILE *out, const GBL_env &env, const export_format &efo)
 
static GB_ERROR export_format_single (const char *db_name, const char *formname, const char *outname, char **resulting_outname, RuleSetPtr ruleset)
 
static GB_ERROR export_format_multiple (const char *dbname, const char *formname, const char *outname, bool multiple, char **resulting_outname, RuleSetPtr ruleset)
 
GB_ERROR SEQIO::export_by_format (GBDATA *gb_main, ExportWhich which, const char *one_species, AP_filter *filter, int cut_stop_codon, int compress, const char *dbname, const char *formname, const char *field_transfer_set, const char *outname, int multiple, char **real_outname)
 
GB_ERROR SEQIO::get_exportFormat_information (const char *eft_formname, ExportFormatInfo &info)
 
charSEQIO::get_exportFormat_evalForm (const char *eft_formname, GB_ERROR &error)
 

Variables

static const charinternal_export_commands []
 
static export_sequence_dataesd = NULp
 

Macro Definition Documentation

#define sio_assert (   cond)    arb_assert(cond)

Enumeration Type Documentation

enum EXPORT_CMD
Enumerator
EXPORT_XML 
EXPORT_INVALID 
EXPORT_USING_FORM 

Definition at line 38 of file seq_export.cxx.

Function Documentation

static EXPORT_CMD check_internal ( const char command)
static

Definition at line 51 of file seq_export.cxx.

References EXPORT_INVALID.

Referenced by read_export_format().

static GB_ERROR read_export_format ( export_format efo,
const char file,
bool  load_complete_form 
)
static
static const char* exported_sequence ( GBDATA gb_species,
size_t *  seq_len,
GB_ERROR error 
)
static
static GB_ERROR XML_recursive ( GBDATA gbd,
int  depth 
)
static
static GB_ERROR export_species_using_form ( FILE *  out,
const char form,
const GBL_call_env callEnv 
)
static
static GB_ERROR export_write_species ( GBDATA gb_species,
FILE *  out,
const GBL_env env,
const export_format efo 
)
static
static GB_ERROR export_format_single ( const char db_name,
const char formname,
const char outname,
char **  resulting_outname,
RuleSetPtr  ruleset 
)
static
static GB_ERROR export_format_multiple ( const char dbname,
const char formname,
const char outname,
bool  multiple,
char **  resulting_outname,
RuleSetPtr  ruleset 
)
static

Variable Documentation

const char* internal_export_commands[]
static
Initial value:
= {
"xml_write",
}
#define NULp
Definition: cxxforward.h:97

Definition at line 46 of file seq_export.cxx.

export_sequence_data* esd = NULp
static

Definition at line 471 of file seq_export.cxx.

Referenced by SEQIO::export_by_format().