CAlphabet Class Reference


Detailed Description

The class Alphabet implements an alphabet and alphabet utility functions.

These utility functions can be used 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 67 of file Alphabet.h.

Inheritance diagram for CAlphabet:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CAlphabet (char *alpha, int32_t len)
 CAlphabet (EAlphabet alpha)
 CAlphabet (CAlphabet *alpha)
virtual ~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
template<class T >
void add_string_to_histogram (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 is_valid (uint8_t c)
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 ()
virtual const char * get_name () const

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
bool 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 (  )  [virtual]

Definition at line 70 of file Alphabet.cpp.


Member Function Documentation

void CAlphabet::add_byte_to_histogram ( uint8_t  p  ) 

add element to histogram

Parameters:
p element

Definition at line 163 of file Alphabet.h.

template<class T >
void CAlphabet::add_string_to_histogram ( T *  p,
int64_t  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 153 of file Alphabet.h.

bool CAlphabet::check_alphabet ( bool  print_error = true  ) 

check whether symbols in histogram are valid in alphabet e.g. for DNA if only letters ACGT appear

Parameters:
print_error if errors shall be printed
Returns:
if symbols in histogram are valid in alphabet

Definition at line 430 of file Alphabet.cpp.

bool CAlphabet::check_alphabet_size ( bool  print_error = true  ) 

check whether symbols in histogram ALL fit in alphabet

Parameters:
print_error if errors shall be printed
Returns:
if symbols in histogram ALL fit in alphabet

Definition at line 452 of file Alphabet.cpp.

void CAlphabet::clear_histogram (  ) 

clear histogram

Definition at line 379 of file Alphabet.cpp.

void CAlphabet::copy_histogram ( CAlphabet src  )  [protected]

copy histogram

Parameters:
src alphabet to copy histogram from

Definition at line 469 of file Alphabet.cpp.

EAlphabet CAlphabet::get_alphabet (  ) 

get alphabet

Returns:
alphabet

Definition at line 100 of file Alphabet.h.

const char * CAlphabet::get_alphabet_name ( EAlphabet  alphabet  )  [static]

return alphabet name

Parameters:
alphabet alphabet type to get name from

Definition at line 474 of file Alphabet.cpp.

void CAlphabet::get_hist ( int64_t **  h,
int32_t *  len 
)

get histogram

Parameters:
h where the histogram will be stored
len length of histogram

Definition at line 176 of file Alphabet.h.

const int64_t* CAlphabet::get_histogram (  ) 

get pointer to histogram

Definition at line 188 of file Alphabet.h.

int32_t CAlphabet::get_max_value_in_histogram (  ) 

return maximum value in histogram

Returns:
maximum value in histogram

Definition at line 385 of file Alphabet.cpp.

virtual const char* CAlphabet::get_name (  )  const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 247 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 119 of file Alphabet.h.

int32_t CAlphabet::get_num_bits_in_histogram (  ) 

return number of bits required to store all symbols in histogram

Returns:
number of bits required to store all symbols in histogram

Definition at line 412 of file Alphabet.cpp.

int32_t CAlphabet::get_num_symbols (  ) 

get number of symbols in alphabet

Returns:
number of symbols

Definition at line 109 of file Alphabet.h.

int32_t CAlphabet::get_num_symbols_in_histogram (  ) 

return number of symbols in histogram

Returns:
number of symbols in histogram

Definition at line 400 of file Alphabet.cpp.

void CAlphabet::init_map_table (  )  [protected]

init map table

Definition at line 124 of file Alphabet.cpp.

bool CAlphabet::is_valid ( uint8_t  c  ) 

check whether symbols are valid in alphabet e.g. for DNA if symbol is one of the A,C,G or T

Parameters:
c symbol
Returns:
if symbol is a valid character in alphabet

Definition at line 207 of file Alphabet.h.

void CAlphabet::print_histogram (  ) 

print histogram

Definition at line 421 of file Alphabet.cpp.

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 129 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 139 of file Alphabet.h.

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.


Member Data Documentation

alphabet

Definition at line 276 of file Alphabet.h.

const char * CAlphabet::alphabet_names = {"DNA", "RAWDNA", "RNA", "PROTEIN", "ALPHANUM", "CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID", "NONE", "UNKNOWN"} [static]

alphabet names

Definition at line 272 of file Alphabet.h.

const uint8_t CAlphabet::B_A = 0 [static]

B_A

Definition at line 262 of file Alphabet.h.

const uint8_t CAlphabet::B_C = 1 [static]

B_C

Definition at line 264 of file Alphabet.h.

const uint8_t CAlphabet::B_G = 2 [static]

B_G

Definition at line 266 of file Alphabet.h.

const uint8_t CAlphabet::B_T = 3 [static]

B_T

Definition at line 268 of file Alphabet.h.

int64_t CAlphabet::histogram[1<< (sizeof(uint8_t)*8)] [protected]

histogram

Definition at line 288 of file Alphabet.h.

uint8_t CAlphabet::maptable_to_bin[1<< (sizeof(uint8_t)*8)] [protected]

maptable to bin

Definition at line 284 of file Alphabet.h.

uint8_t CAlphabet::maptable_to_char[1<< (sizeof(uint8_t)*8)] [protected]

maptable to char

Definition at line 286 of file Alphabet.h.

const uint8_t CAlphabet::MAPTABLE_UNDEF = 0xff [static]

MAPTABLE UNDEF

Definition at line 270 of file Alphabet.h.

int32_t CAlphabet::num_bits [protected]

number of bits

Definition at line 280 of file Alphabet.h.

int32_t CAlphabet::num_symbols [protected]

number of symbols

Definition at line 278 of file Alphabet.h.

bool CAlphabet::valid_chars[1<< (sizeof(uint8_t)*8)] [protected]

valid chars

Definition at line 282 of file Alphabet.h.


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

SHOGUN Machine Learning Toolbox - Documentation