ARB
Public Member Functions | Static Public Member Functions | List of all members
export_sequence_data Class Reference
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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 chargetAlignment () const
 
long getAliLen () const
 
GBDATAget_gb_main () const
 
void set_single_mode (GBDATA *gb_species)
 
bool in_single_mode () const
 
GBDATAfirst_species () const
 
GBDATAnext_species (GBDATA *gb_prev) const
 
const unsigned charget_seq_data (GBDATA *gb_species, size_t &slen, GB_ERROR &error) const
 
size_t count_species ()
 
GB_ERROR detectVerticalGaps ()
 
const charget_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
export_sequence_data::~export_sequence_data ( )
inline

Definition at line 266 of file seq_export.cxx.

References seq.

Member Function Documentation

const char* export_sequence_data::getAlignment ( ) const
inline

Definition at line 273 of file seq_export.cxx.

Referenced by XML_recursive().

long export_sequence_data::getAliLen ( ) const
inline

Definition at line 274 of file seq_export.cxx.

Referenced by SEQIO::export_by_format().

GBDATA* export_sequence_data::get_gb_main ( ) const
inline

Definition at line 275 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 277 of file seq_export.cxx.

Referenced by export_format_multiple().

bool export_sequence_data::in_single_mode ( ) const
inline

Definition at line 278 of file seq_export.cxx.

GBDATA* export_sequence_data::first_species ( ) const
inline

Definition at line 280 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 281 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
static bool export_sequence_data::isGap ( char  c)
inlinestatic

Definition at line 284 of file seq_export.cxx.

References GAP::is_std_gap().

size_t export_sequence_data::count_species ( )
inline
GB_ERROR export_sequence_data::detectVerticalGaps ( )

Definition at line 321 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 405 of file seq_export.cxx.

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

Referenced by exported_sequence().


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