export_sequence_data Class Reference

Inheritance diagram for export_sequence_data:

Collaboration diagram for export_sequence_data:

Public Member Functions
	export_sequence_data (GBDATA *Gb_Main, ExportWhich which, const char *one_species, AP_filter *Filter, bool CutStopCodon, int Compress)
	~export_sequence_data ()
const char *	getAlignment () const
long	getAliLen () const
GBDATA *	get_gb_main () const
void	set_single_mode (GBDATA *gb_species)
bool	in_single_mode () const
GBDATA *	first_species () const
GBDATA *	next_species (GBDATA *gb_prev) const
const unsigned char *	get_seq_data (GBDATA *gb_species, size_t &slen, GB_ERROR &error) const
size_t	count_species ()
GB_ERROR	detectVerticalGaps ()
const char *	get_export_sequence (GBDATA *gb_species, size_t &seq_len, GB_ERROR &error)

Static Public Member Functions
static bool	isGap (char c)

Detailed Description

Definition at line 208 of file seq_export.cxx.

Constructor & Destructor Documentation

export_sequence_data::export_sequence_data ( GBDATA *  Gb_Main, ExportWhich  which, const char *  one_species, AP_filter *  Filter, bool  CutStopCodon, int  Compress  )

inline

Definition at line 232 of file seq_export.cxx.

References GB_AT_AA, GB_AT_UNKNOWN, GB_warning(), GB_warningf(), GBT_get_alignment_len(), GBT_get_alignment_type(), GBT_get_default_alignment(), AP_filter::get_length(), AP_filter::is_invalid(), and sio_assert.

export_sequence_data::~export_sequence_data ( )

inline

Definition at line 272 of file seq_export.cxx.

References seq.

Member Function Documentation

const char* export_sequence_data::getAlignment ( ) const

inline

Definition at line 279 of file seq_export.cxx.

Referenced by XML_recursive().

long export_sequence_data::getAliLen ( ) const

inline

Definition at line 280 of file seq_export.cxx.

Referenced by SEQIO::export_by_format().

GBDATA* export_sequence_data::get_gb_main ( ) const

inline

Definition at line 281 of file seq_export.cxx.

References gb_main, and sio_assert.

Referenced by export_format_single().

void export_sequence_data::set_single_mode ( GBDATA *  gb_species )

inline

Definition at line 283 of file seq_export.cxx.

Referenced by export_format_multiple().

bool export_sequence_data::in_single_mode ( ) const

inline

Definition at line 284 of file seq_export.cxx.

GBDATA* export_sequence_data::first_species ( ) const

inline

Definition at line 286 of file seq_export.cxx.

References SpeciesSelector::select_first().

Referenced by export_format_multiple(), and export_format_single().

GBDATA* export_sequence_data::next_species ( GBDATA *  gb_prev ) const

inline

Definition at line 287 of file seq_export.cxx.

References NULp, and SpeciesSelector::select_next().

Referenced by export_format_multiple(), and export_format_single().

const unsigned char * export_sequence_data::get_seq_data	(	GBDATA *	gb_species,
		size_t &	slen,
		GB_ERROR &	error
	)		const

Definition at line 310 of file seq_export.cxx.

References GB_read_char_pntr(), GB_read_count(), GBS_global_string_copy(), GBT_find_sequence(), GBT_get_name_or_description(), and NULp.

static bool export_sequence_data::isGap ( char  c )

inlinestatic

Definition at line 290 of file seq_export.cxx.

References GAP::is_std_gap().

size_t export_sequence_data::count_species ( )

inline

Definition at line 292 of file seq_export.cxx.

References SpeciesSelector::select_first(), SpeciesSelector::select_next(), and sio_assert.

Referenced by export_format_multiple().

GB_ERROR export_sequence_data::detectVerticalGaps

(

)

Definition at line 327 of file seq_export.cxx.

References arb_progress::inc_and_check_user_abort(), isGap(), NULp, seq, and sio_assert.

Referenced by SEQIO::export_by_format().

const char * export_sequence_data::get_export_sequence	(	GBDATA *	gb_species,
		size_t &	seq_len,
		GB_ERROR &	error
	)

Definition at line 411 of file seq_export.cxx.

References error(), isGap(), NULp, and seq.

Referenced by exported_sequence().

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The documentation for this class was generated from the following file:

• SL/SEQIO/seq_export.cxx