#include "AP_codon_table.hxx"
#include "AP_pro_a_nucs.hxx"
#include "iupac.h"
#include <arb_global_defs.h>
#include <arb_str.h>
#include <cctype>

Include dependency graph for AP_codon_table.cxx:

Go to the source code of this file.

Classes
class	Codon_Group

Macros
#define	pn_assert(cond) arb_assert(cond)

#define	EMBL_BACTERIAL_TABLE_INDEX 11

#define	AWT_CODON_TABLE_MAX_NAME_LENGTH 57

#define	VALID_PROTEIN "ABCDEFGHIJKLMNPQRSTVWXYZ*"

#define	VALID_PROTEIN_NO_X "ABCDEFGHIJKLMNPQRSTVWYZ*"

#define	MAX_EMBL_TRANSL_TABLE_VALUE 31

#define	MAX_CODON_LIST_LENGTH (70*3)

Functions
int	TTIT_embl2arb (int embl_code_nr)

int	TTIT_arb2embl (int arb_code_nr)

static void	addToAmbiguous (int codon_nr, char possible_translation)

void	AP_initialize_codon_tables ()

int	dna2idx (char c)

char	idx2dna (int idx)

int	calc_codon_nr (const char *dna)

void	build_codon (int codon_nr, char *to_buffer)

const char *	AWT_get_codon_code_name (int code)

const char *	getAminoAcidAbbr (char aa)

char	isStartOrStopCodonNr (int codon_nr, int code_nr)

bool	protMatches (char p1, char p2)

bool	containsProtMatching (const char *pstr, char p)

bool	isGap (char c)

GB_ERROR	neverTranslatesError (const char *dna, char protein)

bool	AWT_is_codon (char protein, const char const dna, const TransTables &allowed, TransTables &remaining, const char *fail_reason_ptr)

int	legal_dna_no (int i)

const char *	buildMixedCodon (const char const con1, const char const con2)

static int	expandMore (const char bufferStart, int no_of_condons, char &to_buffer)

static Codon_Group *	get_Codon_Group (char protein, int code_nr)

const char *	AP_get_codons (char protein, int code_nr)

Variables
static AWT_Codon_Code_Definition	AWT_codon_def [AWT_CODON_TABLES+1]

static bool	codon_tables_initialized = false

static char	definite_translation [AWT_MAX_CODONS]

static char *	ambiguous_codons [AWT_MAX_CODONS]

static const char *	aa_3letter_name [26+1]

Macro Definition Documentation

#define pn_assert ( cond ) arb_assert(cond)

Definition at line 21 of file AP_codon_table.cxx.

Referenced by AP_get_codons(), AP_initialize_codon_tables(), AWT_get_codon_code_name(), AWT_is_codon(), build_codon(), buildMixedCodon(), calc_codon_nr(), Codon_Group::Codon_Group(), containsProtMatching(), Codon_Group::expand(), get_Codon_Group(), idx2dna(), AWT_translator::isStartOrStopCodon(), isStartOrStopCodonNr(), protMatches(), TTIT_arb2embl(), and TTIT_embl2arb().

#define EMBL_BACTERIAL_TABLE_INDEX 11

Definition at line 23 of file AP_codon_table.cxx.

Referenced by TTIT_embl2arb().

#define AWT_CODON_TABLE_MAX_NAME_LENGTH 57

Definition at line 24 of file AP_codon_table.cxx.

Referenced by AP_initialize_codon_tables().

#define VALID_PROTEIN "ABCDEFGHIJKLMNPQRSTVWXYZ*"

Definition at line 26 of file AP_codon_table.cxx.

Referenced by neverTranslatesError().

#define VALID_PROTEIN_NO_X "ABCDEFGHIJKLMNPQRSTVWYZ*"

Definition at line 27 of file AP_codon_table.cxx.

Referenced by AWT_is_codon().

#define MAX_EMBL_TRANSL_TABLE_VALUE 31

Definition at line 216 of file AP_codon_table.cxx.

Referenced by TTIT_embl2arb().

#define MAX_CODON_LIST_LENGTH (70*3)

Definition at line 987 of file AP_codon_table.cxx.

Referenced by AP_get_codons().

Function Documentation

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().

static void addToAmbiguous	(	int	codon_nr,
		char	possible_translation
	)

static

Definition at line 269 of file AP_codon_table.cxx.

References AWT_MAX_CODONS, and length.

Referenced by AP_initialize_codon_tables().

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 dna2idx ( char c )

inline

Definition at line 358 of file AP_codon_table.cxx.

Referenced by calc_codon_nr().

char idx2dna ( int idx )

inline

Definition at line 369 of file AP_codon_table.cxx.

References pn_assert.

Referenced by build_codon().

int calc_codon_nr ( const char * dna )

inline

Definition at line 374 of file AP_codon_table.cxx.

References AWT_MAX_CODONS, dna2idx(), and pn_assert.

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

void build_codon	(	int	codon_nr,
		char *	to_buffer
	)

inline

Definition at line 384 of file AP_codon_table.cxx.

References AWT_MAX_CODONS, idx2dna(), and pn_assert.

Referenced by Codon_Group::expand().

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().

const char* getAminoAcidAbbr ( char aa )

Definition at line 427 of file AP_codon_table.cxx.

References NULp.

Referenced by TranslateGeneToAminoAcidSequence().

char isStartOrStopCodonNr	(	int	codon_nr,
		int	code_nr
	)

inline

Definition at line 503 of file AP_codon_table.cxx.

References arb_assert, AWT_CODON_TABLES, AWT_MAX_CODONS, implicated, pn_assert, and AWT_Codon_Code_Definition::startStop.

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

bool protMatches	(	char	p1,
		char	p2
	)

inline

return true if p1 matches p2

Parameters

p1	"normal" protein (neither B, Z nor J)
p2	any protein (B, Z and J ok) B is a shortcut for Asp(=D) or Asn(=N) J is a shortcut for Ile(=I) or Leu(=L) Z is a shortcut for Glu(=E) or Gln(=Q)

Definition at line 546 of file AP_codon_table.cxx.

References pn_assert.

Referenced by AWT_is_codon().

bool containsProtMatching	(	const char *	pstr,
		char	p
	)

inline

return true, if 'pstr' contains any protein that matches 'p'. uses same logic as protMatches()

Definition at line 564 of file AP_codon_table.cxx.

References pn_assert.

Referenced by AWT_is_codon().

bool isGap ( char c )

inline

Definition at line 574 of file AP_codon_table.cxx.

References GAP::is_std_gap().

Referenced by AWT_is_codon().

GB_ERROR neverTranslatesError	(	const char *	dna,
		char	protein
	)

inline

Definition at line 576 of file AP_codon_table.cxx.

References GBS_global_string(), and VALID_PROTEIN.

Referenced by AWT_is_codon().

bool AWT_is_codon	(	char	protein,
		const char *const	dna,
		const TransTables &	allowed,
		TransTables &	remaining,
		const char **	fail_reason_ptr
	)

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().

int legal_dna_no ( int i )

inline

Definition at line 851 of file AP_codon_table.cxx.

const char* buildMixedCodon	(	const char *const	con1,
		const char *const	con2
	)

inline

Definition at line 853 of file AP_codon_table.cxx.

References iupac::combine(), GB_AT_DNA, NULp, and pn_assert.

Referenced by expandMore().

static int expandMore	(	const char *	bufferStart,
		int	no_of_condons,
		char *&	to_buffer
	)

static

Definition at line 891 of file AP_codon_table.cxx.

References buildMixedCodon(), and result.

Referenced by Codon_Group::expand().

static Codon_Group* get_Codon_Group	(	char	protein,
		int	code_nr
	)

static

Definition at line 960 of file AP_codon_table.cxx.

References AWT_CODON_TABLES, codon_tables_initialized, N, NULp, and pn_assert.

Referenced by AP_get_codons().

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().

Variable Documentation

AWT_Codon_Code_Definition AWT_codon_def[AWT_CODON_TABLES+1]

static

Definition at line 42 of file AP_codon_table.cxx.

bool codon_tables_initialized = false

static

Definition at line 265 of file AP_codon_table.cxx.

Referenced by AP_initialize_codon_tables(), AWT_is_codon(), and get_Codon_Group().

char definite_translation[AWT_MAX_CODONS]

static

Definition at line 266 of file AP_codon_table.cxx.

char* ambiguous_codons[AWT_MAX_CODONS]

static

Definition at line 267 of file AP_codon_table.cxx.

const char* aa_3letter_name[26+1]

static

Initial value:

= {
    "Ala", 
    "Asx", 
    "Cys", 
    "Asp", 
    "Glu", 
    "Phe", 
    "Gly", 
    "His", 
    "Ile", 
    "Xle", 
    "Lys", 
    "Leu", 
    "Met", 
    "Asn", 
    NULp,  
    "Pro", 
    "Gln", 
    "Arg", 
    "Ser", 
    "Thr", 
    NULp,  
    "Val", 
    "Trp", 
    "Xaa", 
    "Tyr", 
    "Glx", 
    NULp
}

Definition at line 397 of file AP_codon_table.cxx.

Classes

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation