ARB: AWT_translator Class Reference

ARB

#include <AP_pro_a_nucs.hxx>

Inheritance diagram for AWT_translator:

Inheritance graph

Collaboration diagram for AWT_translator:

Collaboration graph

Public Member Functions
	AWT_translator (int arb_protein_code_nr)

	~AWT_translator ()

const AWT_distance_meter *	getDistanceMeter () const

AWT_distance_meter *	getDistanceMeter ()

int	CodeNr () const

const arb_r2a_pro_2_nuc *	S2str (int index) const

const arb_r2a_pro_2_nuc const	S2strArray () const

long	index2bitset (int index) const

unsigned char	index2spro (int index) const

int	RealmaxAA () const

int	MaxAA () const

char	codon2aa (const char *codon) const

char	isStartOrStopCodon (const char *codon) const

char	isStartCodon (const char *codon) const

char	isStopCodon (const char *codon) const

Detailed Description

Definition at line 82 of file AP_pro_a_nucs.hxx.

Constructor & Destructor Documentation

AWT_translator::AWT_translator ( int arb_protein_code_nr )

Definition at line 158 of file AP_pro_a_nucs.cxx.

References AP_create_dna_to_ap_bases(), AP_get_codons(), AP_initialize_codon_tables(), codon_defined_in(), GB_IGNORE_CASE, GBS_create_hash(), GBS_hash_elements(), pn_assert, and T2I_ENTRIES_MAX.

AWT_translator::~AWT_translator ( )

Definition at line 241 of file AP_pro_a_nucs.cxx.

References GBS_free_hash().

Member Function Documentation

const AWT_distance_meter * AWT_translator::getDistanceMeter ( ) const

Definition at line 254 of file AP_pro_a_nucs.cxx.

Referenced by getDistanceMeter().

AWT_distance_meter* AWT_translator::getDistanceMeter ( )

inline

Definition at line 107 of file AP_pro_a_nucs.hxx.

References getDistanceMeter().

int AWT_translator::CodeNr ( ) const

inline

Definition at line 111 of file AP_pro_a_nucs.hxx.

Referenced by isStartOrStopCodon(), and translate_nuc2aa().

const arb_r2a_pro_2_nuc* AWT_translator::S2str ( int index ) const

inline

Definition at line 112 of file AP_pro_a_nucs.hxx.

Referenced by AWT_distance_meter::AWT_distance_meter(), and nuc_dist().

const arb_r2a_pro_2_nuc* const* AWT_translator::S2strArray ( ) const

inline

Definition at line 113 of file AP_pro_a_nucs.hxx.

long AWT_translator::index2bitset ( int index ) const

inline

Definition at line 115 of file AP_pro_a_nucs.hxx.

Referenced by AP_pos_var::retrieve().

unsigned char AWT_translator::index2spro ( int index ) const

inline

Definition at line 116 of file AP_pro_a_nucs.hxx.

Referenced by AWT_distance_meter::AWT_distance_meter(), and AP_pos_var::retrieve().

int AWT_translator::RealmaxAA ( ) const

inline

Definition at line 118 of file AP_pro_a_nucs.hxx.

Referenced by AWT_distance_meter::AWT_distance_meter().

int AWT_translator::MaxAA ( ) const

inline

Definition at line 119 of file AP_pro_a_nucs.hxx.

Referenced by AWT_distance_meter::AWT_distance_meter(), and AP_pos_var::retrieve().

char AWT_translator::codon2aa ( const char * codon ) const

inline

Definition at line 121 of file AP_pro_a_nucs.hxx.

References GBS_read_hash().

Referenced by translate_nuc2aa().

char AWT_translator::isStartOrStopCodon ( const char * codon ) const

test whether 'codon' is a start- or stop-codon.

Parameters

codon three bases definining the codon

Returns: '*' for stop-codons, 'M' for start-codons, 0 otherwise

Definition at line 521 of file AP_codon_table.cxx.

References AWT_is_codon(), AWT_MAX_CODONS, calc_codon_nr(), CodeNr(), TransTables::forbidAllBut(), isStartOrStopCodonNr(), NULp, pn_assert, and result.

Referenced by isStartCodon(), and isStopCodon().

char AWT_translator::isStartCodon ( const char * codon ) const

inline

Definition at line 127 of file AP_pro_a_nucs.hxx.

References isStartOrStopCodon(), and start.

Referenced by translate_nuc2aa().

char AWT_translator::isStopCodon ( const char * codon ) const

inline

Definition at line 131 of file AP_pro_a_nucs.hxx.

References isStartOrStopCodon().

Referenced by translate_nuc2aa().

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