SEQIO Namespace Reference

Classes
struct	ExportFormatInfo

Enumerations
enum	ExportWhich { EBF_ALL, EBF_MARKED, EBF_ONE }

Functions
GB_ERROR	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	get_exportFormat_information (const char *eft_formname, ExportFormatInfo &info)
char *	get_exportFormat_evalForm (const char *eft_formname, GB_ERROR &error)
char *	fgets_smartLF (char *s, int size, FILE *stream)
bool	read_string_pair (FILE *in, char *&s1, char *&s2, size_t &lineNr)
void	appendTo (char *&content, char sep, char *&toAppend)

Enumeration Type Documentation

enum SEQIO::ExportWhich

Enumerator
EBF_ALL
EBF_MARKED
EBF_ONE

Definition at line 28 of file seqio.hxx.

Function Documentation

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
	)

Definition at line 763 of file seq_export.cxx.

References ARB_ERROR::deliver(), export_sequence_data::detectVerticalGaps(), error(), esd, export_format_multiple(), exported_sequence(), GB_have_error(), GB_set_export_sequence_hook(), GBS_static_string(), export_sequence_data::getAliLen(), ErrorOr< TYPE >::getError(), ErrorOr< TYPE >::getValue(), ErrorOr< TYPE >::hasError(), AP_filter::is_invalid(), NULp, and sio_assert.

Referenced by export_go_cb(), FINAL_TYPE< SEQTYPE >::finish(), and update_exportTest_result_cb().

GB_ERROR SEQIO::get_exportFormat_information	(	const char *	eft_formname,
		ExportFormatInfo &	info
	)

Definition at line 812 of file seq_export.cxx.

References SEQIO::ExportFormatInfo::description, export_format::description, error(), NULp, read_export_format(), SEQIO::ExportFormatInfo::suffix, and export_format::suffix.

Referenced by update_format_description_and_suffix().

char * SEQIO::get_exportFormat_evalForm	(	const char *	eft_formname,
		GB_ERROR &	error
	)

Definition at line 830 of file seq_export.cxx.

References ARB_strdup(), export_format::export_mode, EXPORT_USING_FORM, EXPORT_XML, export_format::form, GB_split_full_path(), GBS_global_string(), NULp, export_format::pre_format, read_export_format(), and sio_assert.

Referenced by ExportFieldScanner::scanFields().

char * SEQIO::fgets_smartLF	(	char *	s,
		int	size,
		FILE *	stream
	)

Definition at line 19 of file seqio.cxx.

References NULp, and s.

Referenced by ArbImporter::read_line(), and read_string_pair().

bool SEQIO::read_string_pair	(	FILE *	in,
		char *&	s1,
		char *&	s2,
		size_t &	lineNr
	)

Definition at line 37 of file seqio.cxx.

References buffer, BUFSIZE, fgets_smartLF(), NULp, and sio_assert.

Referenced by read_export_format(), and read_import_format().

void SEQIO::appendTo ( char *&  content, char  sep, char *&  toAppend  )

inline

Definition at line 34 of file seqio.hxx.

References GBS_global_string_copy().

Referenced by read_export_format(), and read_import_format().