AP_codon_table.hxx File Reference

#include <arb_assert.h>
#include <static_assert.h>
#include <stdint.h>

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Classes
struct	AWT_Codon_Code_Definition
class	TransTables

Macros
#define	pn_assert(cond)   arb_assert(cond)
#define	AWT_CODON_TABLES   25
#define	AWT_MAX_CODONS   64
#define	ALL_TABLES_MASK   ((1<<AWT_CODON_TABLES)-1)

Enumerations
enum	TranslationTableIndexType { TTIT_ARB, TTIT_EMBL }

Functions
void	AP_initialize_codon_tables ()
int	TTIT_embl2arb (int embl_code_nr)
int	TTIT_arb2embl (int arb_code_nr)
bool	AWT_is_codon (char protein, const char *const dna, const TransTables &allowed, TransTables &allowed_left, const char **fail_reason_ptr=NULp)
const char *	AP_get_codons (char protein, int code_nr)
const char *	getAminoAcidAbbr (char aa)
const char *	AWT_get_codon_code_name (int code)

Variables
const int	AWAR_PROTEIN_TYPE_bacterial_code_index = 8

Macro Definition Documentation

#define pn_assert

(

cond

)

arb_assert(cond)

Definition at line 25 of file AP_codon_table.hxx.

Referenced by TransTables::explicit_table(), and TransTables::to_string().

#define AWT_CODON_TABLES   25

Definition at line 39 of file AP_codon_table.hxx.

Referenced by ALI_translate_marked(), TransTables::allowAll(), AP_initialize_codon_tables(), AWT_get_codon_code_name(), AWT_is_codon(), Codon_Group::Codon_Group(), ED4_CreateProteinViewer_window(), TransTables::explicit_table(), get_Codon_Group(), isStartOrStopCodonNr(), NT_create_dna_2_pro_window(), TransTables::to_string(), TTIT_arb2embl(), and TTIT_embl2arb().

#define AWT_MAX_CODONS   64

Definition at line 40 of file AP_codon_table.hxx.

Referenced by addToAmbiguous(), AP_initialize_codon_tables(), AWT_is_codon(), build_codon(), calc_codon_nr(), Codon_Group::Codon_Group(), Codon_Group::expand(), AWT_translator::isStartOrStopCodon(), isStartOrStopCodonNr(), and Codon_Group::operator+=().

#define ALL_TABLES_MASK   ((1<<AWT_CODON_TABLES)-1)

Definition at line 51 of file AP_codon_table.hxx.

Referenced by TransTables::all(), and TransTables::allowAll().

Enumeration Type Documentation

enum TranslationTableIndexType

Enumerator
TTIT_ARB
TTIT_EMBL

Definition at line 53 of file AP_codon_table.hxx.

Function Documentation

void AP_initialize_codon_tables

(

)

Definition at line 285 of file AP_codon_table.cxx.

References AWT_Codon_Code_Definition::aa, addToAmbiguous(), AWT_CODON_TABLE_MAX_NAME_LENGTH, AWT_CODON_TABLES, AWT_MAX_CODONS, codon_tables_initialized, NULp, pn_assert, and AWT_Codon_Code_Definition::startStop.

Referenced by ALI_realign_marked(), and AWT_translator::AWT_translator().

int TTIT_embl2arb

(

int

embl_code_nr

)

Definition at line 220 of file AP_codon_table.cxx.

References AWAR_PROTEIN_TYPE_bacterial_code_index, AWT_CODON_TABLES, EMBL_BACTERIAL_TABLE_INDEX, AWT_Codon_Code_Definition::embl_feature_transl_table, initialized, MAX_EMBL_TRANSL_TABLE_VALUE, pn_assert, and TTIT_arb2embl().

Referenced by translate_gene_sequence(), translate_getInfo(), and TranslateGeneToAminoAcidSequence().

int TTIT_arb2embl

(

int

arb_code_nr

)

Definition at line 259 of file AP_codon_table.cxx.

References AWT_CODON_TABLES, AWT_Codon_Code_Definition::embl_feature_transl_table, and pn_assert.

Referenced by ALI_translate_marked(), AWT_is_codon(), TransTables::to_string(), translate_saveInfo(), and TTIT_embl2arb().

bool AWT_is_codon	(	char	protein,
		const char *const	dna,
		const TransTables &	allowed,
		TransTables &	allowed_left,
		const char **	fail_reason_ptr = NULp
	)

test if 'dna' codes 'protein'

Parameters

protein	amino acid
dna	three nucleotides (gaps allowed, e.g. 'A-C' can be tested vs 'X')
allowed	allowed translation tables
remaining	returns the remaining allowed translation tables (only if this functions returns true)
fail_reason_ptr	if not NULp => store reason for failure here (or set it to NULp on success)

Returns

true if dna translates to protein

Definition at line 583 of file AP_codon_table.cxx.

References TransTables::all(), TransTables::allow(), TransTables::any(), ARB_strBeginsWith(), AWT_CODON_TABLES, AWT_is_codon(), AWT_MAX_CODONS, calc_codon_nr(), codon_tables_initialized, containsProtMatching(), iupac::decode(), TransTables::explicit_table(), TransTables::forbid(), TransTables::forbidAll(), GB_AT_DNA, GBS_global_string(), TransTables::is_allowed(), TransTables::is_subset_of(), isGap(), isStartOrStopCodonNr(), N, neverTranslatesError(), TransTables::none(), NULp, pn_assert, protMatches(), TransTables::to_string(), TTIT_arb2embl(), TTIT_EMBL, and VALID_PROTEIN_NO_X.

Referenced by AWT_is_codon(), AWT_translator::isStartOrStopCodon(), and Distributor::translates_to_Xs().

const char* AP_get_codons	(	char	protein,
		int	code_nr
	)

Definition at line 989 of file AP_codon_table.cxx.

References buffer, Codon_Group::expand(), get_Codon_Group(), MAX_CODON_LIST_LENGTH, offset, and pn_assert.

Referenced by AWT_translator::AWT_translator().

const char* getAminoAcidAbbr

(

char

aa

)

Definition at line 427 of file AP_codon_table.cxx.

References NULp.

Referenced by TranslateGeneToAminoAcidSequence().

const char* AWT_get_codon_code_name

(

int

code

)

Definition at line 392 of file AP_codon_table.cxx.

References AWT_CODON_TABLES, AWT_Codon_Code_Definition::name, and pn_assert.

Referenced by ED4_CreateProteinViewer_window(), and NT_create_dna_2_pro_window().

Variable Documentation

const int AWAR_PROTEIN_TYPE_bacterial_code_index = 8

Definition at line 42 of file AP_codon_table.hxx.

Referenced by ED4_CreateProteinViewer_window(), NT_create_dna_2_pro_window(), PV_CallBackFunction(), and TTIT_embl2arb().