Translate.cxx File Reference

#include "Translate.hxx"
#include <AP_pro_a_nucs.hxx>
#include <AP_codon_table.hxx>
#include <arbdbt.h>
#include <arb_global_defs.h>
#include <cctype>

Include dependency graph for Translate.cxx:

Go to the source code of this file.

Macros
#define	tl_assert(cond)   arb_assert(cond)

Functions
GB_ERROR	translate_saveInfo (GBDATA *gb_species, int arb_transl_table, int codon_start)
GB_ERROR	translate_removeInfo (GBDATA *gb_species)
GB_ERROR	translate_getInfo (GBDATA *gb_item, int &arb_transl_table, int &codon_start)
void	memcpy3 (char *dest, const char *source)
int	translate_nuc2aa (int arb_code_nr, char *data, size_t size, size_t pos, bool translate_all, bool create_start_codon, bool append_stop_codon, int *translatedSize)

Macro Definition Documentation

#define tl_assert

(

cond

)

arb_assert(cond)

Definition at line 20 of file Translate.cxx.

Referenced by translate_saveInfo().

Function Documentation

GB_ERROR translate_saveInfo	(	GBDATA *	gb_species,
		int	arb_transl_table,
		int	codon_start
	)

Definition at line 22 of file Translate.cxx.

References error(), GBS_global_string(), GBT_write_string(), tl_assert, and TTIT_arb2embl().

Referenced by ALI_realign_marked(), and ALI_translate_marked().

GB_ERROR translate_removeInfo

(

GBDATA *

gb_species

)

Definition at line 34 of file Translate.cxx.

References error(), GB_delete(), GB_entry(), and NULp.

GB_ERROR translate_getInfo	(	GBDATA *	gb_item,
		int &	arb_transl_table,
		int &	codon_start
	)

Definition at line 48 of file Translate.cxx.

References error(), GB_entry(), GB_read_char_pntr(), GBS_global_string(), GBT_get_name_or_description(), GBT_write_string(), NULp, and TTIT_embl2arb().

Referenced by ALI_realign_marked(), ALI_translate_marked(), and translate_gene_sequence().

void memcpy3 ( char *  dest, const char *  source  )

inline

Definition at line 102 of file Translate.cxx.

Referenced by translate_nuc2aa().

int translate_nuc2aa	(	int	arb_code_nr,
		char *	data,
		size_t	size,
		size_t	pos,
		bool	translate_all,
		bool	create_start_codon,
		bool	append_stop_codon,
		int *	translatedSize
	)

Definition at line 108 of file Translate.cxx.

References arb_assert, AWT_translator::CodeNr(), AWT_translator::codon2aa(), GAP::is_std_gap(), AWT_translator::isStartCodon(), AWT_translator::isStopCodon(), and memcpy3().

Referenced by ALI_translate_marked(), PV_WriteTranslatedSequenceToDB(), translate_gene_sequence(), and TranslateGeneToAminoAcidSequence().