CAlphabet Class Reference

Inheritance diagram for CAlphabet:

Detailed Description

The class Alphabet implements an alphabet and utility functions, to remap characters to more (bit-)efficient representations, check if a string is valid, compute histograms etc.

Currently supported alphabets are DNA, RAWDNA, RNA, PROTEIN, ALPHANUM, CUBE, RAW, IUPAC_NUCLEIC_ACID and IUPAC_AMINO_ACID.

Definition at line 65 of file Alphabet.h.


Public Member Functions
	CAlphabet (char *alpha, int32_t len)
	CAlphabet (EAlphabet alpha)
	CAlphabet (CAlphabet *alpha)
	~CAlphabet ()
bool	set_alphabet (EAlphabet alpha)
EAlphabet	get_alphabet ()
int32_t	get_num_symbols ()
int32_t	get_num_bits ()
uint8_t	remap_to_bin (uint8_t c)
uint8_t	remap_to_char (uint8_t c)
void	clear_histogram ()
	clear histogram
void	add_string_to_histogram (char *p, int64_t len)
void	add_string_to_histogram (uint8_t *p, int64_t len)
void	add_string_to_histogram (int16_t *p, int64_t len)
void	add_string_to_histogram (uint16_t *p, int64_t len)
void	add_string_to_histogram (int32_t *p, int64_t len)
void	add_string_to_histogram (uint32_t *p, int64_t len)
void	add_string_to_histogram (int64_t *p, int64_t len)
void	add_string_to_histogram (uint64_t *p, int64_t len)
void	add_byte_to_histogram (uint8_t p)
void	print_histogram ()
	print histogram
void	get_hist (int64_t *h, int32_t len)
const int64_t *	get_histogram ()
	get pointer to histogram
bool	check_alphabet (bool print_error=true)
bool	check_alphabet_size (bool print_error=true)
int32_t	get_num_symbols_in_histogram ()
int32_t	get_max_value_in_histogram ()
int32_t	get_num_bits_in_histogram ()
Static Public Member Functions
static const char *	get_alphabet_name (EAlphabet alphabet)
Static Public Attributes
static const uint8_t	B_A = 0
static const uint8_t	B_C = 1
static const uint8_t	B_G = 2
static const uint8_t	B_T = 3
static const uint8_t	MAPTABLE_UNDEF = 0xff
static const char *	alphabet_names [11] = {"DNA", "RAWDNA", "RNA", "PROTEIN", "ALPHANUM", "CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID", "NONE", "UNKNOWN"}
Protected Member Functions
void	init_map_table ()
void	copy_histogram (CAlphabet *src)
Protected Attributes
EAlphabet	alphabet
int32_t	num_symbols
int32_t	num_bits
uint8_t	valid_chars [1<< (sizeof(uint8_t)*8)]
uint8_t	maptable_to_bin [1<< (sizeof(uint8_t)*8)]
uint8_t	maptable_to_char [1<< (sizeof(uint8_t)*8)]
int64_t	histogram [1<< (sizeof(uint8_t)*8)]

Constructor & Destructor Documentation

CAlphabet::CAlphabet	(	char *	alpha,
		int32_t	len
	)

constructor

Parameters:

	alpha	alphabet to use
	len	len

Definition at line 25 of file Alphabet.cpp.

CAlphabet::CAlphabet ( EAlphabet alpha )

constructor

Parameters:

alpha

alphabet (type) to use

Definition at line 56 of file Alphabet.cpp.

CAlphabet::CAlphabet ( CAlphabet * alpha )

constructor

Parameters:

alpha

alphabet to use

Definition at line 62 of file Alphabet.cpp.

CAlphabet::~CAlphabet ( )

Definition at line 70 of file Alphabet.cpp.

Member Function Documentation

bool CAlphabet::set_alphabet ( EAlphabet alpha )

set alphabet and initialize mapping table (for remap)

Parameters:

alpha

new alphabet

Definition at line 74 of file Alphabet.cpp.

EAlphabet CAlphabet::get_alphabet ( )

get alphabet

Returns:: alphabet

Definition at line 98 of file Alphabet.h.

int32_t CAlphabet::get_num_symbols ( )

get number of symbols in alphabet

Returns:: number of symbols

Definition at line 107 of file Alphabet.h.

int32_t CAlphabet::get_num_bits ( )

get number of bits necessary to store all symbols in alphabet

Returns:: number of necessary storage bits

Definition at line 117 of file Alphabet.h.

uint8_t CAlphabet::remap_to_bin ( uint8_t c )

remap element e.g translate ACGT to 0123

Parameters:

c

element to remap

Returns:: remapped element

Definition at line 127 of file Alphabet.h.

uint8_t CAlphabet::remap_to_char ( uint8_t c )

remap element e.g translate 0123 to ACGT

Parameters:

c

element to remap

Returns:: remapped element

Definition at line 137 of file Alphabet.h.

void CAlphabet::clear_histogram ( )

clear histogram

Definition at line 379 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram	(	char *	p,
		int64_t	len
	)