CAlphabet Class Reference

Inheritance diagram for CAlphabet:

Inheritance graph
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List of all members.


Detailed Description

class Alphabet

Definition at line 19 of file Alphabet.h.


Public Member Functions

 CAlphabet (CHAR *alpha, INT len)
 CAlphabet (E_ALPHABET alpha)
 CAlphabet (CAlphabet *alpha)
 ~CAlphabet ()
bool set_alphabet (E_ALPHABET alpha)
E_ALPHABET get_alphabet ()
INT get_num_symbols ()
INT get_num_bits ()
BYTE remap_to_bin (BYTE c)
BYTE remap_to_char (BYTE c)
void clear_histogram ()
 clear histogram
void add_string_to_histogram (CHAR *p, LONG len)
void add_string_to_histogram (BYTE *p, LONG len)
void add_string_to_histogram (SHORT *p, LONG len)
void add_string_to_histogram (WORD *p, LONG len)
void add_string_to_histogram (INT *p, LONG len)
void add_string_to_histogram (UINT *p, LONG len)
void add_string_to_histogram (LONG *p, LONG len)
void add_string_to_histogram (ULONG *p, LONG len)
void add_byte_to_histogram (BYTE p)
void print_histogram ()
 print histogram
void get_hist (LONG **h, INT *len)
const LONGget_histogram ()
 get pointer to histogram
bool check_alphabet (bool print_error=true)
bool check_alphabet_size (bool print_error=true)
INT get_num_symbols_in_histogram ()
INT get_max_value_in_histogram ()
INT get_num_bits_in_histogram ()

Static Public Member Functions

static const CHARget_alphabet_name (E_ALPHABET alphabet)

Static Public Attributes

static const BYTE B_A = 0
static const BYTE B_C = 1
static const BYTE B_G = 2
static const BYTE B_T = 3
static const BYTE MAPTABLE_UNDEF = 0xff
static const CHARalphabet_names [11] = {"DNA", "RAWDNA", "RNA", "PROTEIN", "ALPHANUM", "CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID", "NONE", "UNKNOWN"}
static CParallel parallel
static CIO io
static CVersion version

Protected Member Functions

void init_map_table ()
void copy_histogram (CAlphabet *src)

Protected Attributes

E_ALPHABET alphabet
INT num_symbols
INT num_bits
BYTE valid_chars [1<< (sizeof(BYTE)*8)]
BYTE maptable_to_bin [1<< (sizeof(BYTE)*8)]
BYTE maptable_to_char [1<< (sizeof(BYTE)*8)]
LONG histogram [1<< (sizeof(BYTE)*8)]

Constructor & Destructor Documentation

CAlphabet::CAlphabet ( CHAR alpha,
INT  len 
)

constructor

Parameters:
alpha alphabet to use
len len

Definition at line 25 of file Alphabet.cpp.

CAlphabet::CAlphabet ( E_ALPHABET  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 ( E_ALPHABET  alpha  ) 

set alphabet and initialize mapping table (for remap)

Parameters:
alpha new alphabet

Definition at line 74 of file Alphabet.cpp.

E_ALPHABET CAlphabet::get_alphabet (  ) 

get alphabet

Returns:
alphabet

Definition at line 52 of file Alphabet.h.

INT CAlphabet::get_num_symbols (  ) 

get number of symbols in alphabet

Returns:
number of symbols

Definition at line 61 of file Alphabet.h.

INT CAlphabet::get_num_bits (  ) 

get number of bits necessary to store all symbols in alphabet

Returns:
number of necessary storage bits

Definition at line 71 of file Alphabet.h.

BYTE CAlphabet::remap_to_bin ( BYTE  c  ) 

remap element e.g translate ACGT to 0123

Parameters:
c element to remap
Returns:
remapped element

Definition at line 81 of file Alphabet.h.

BYTE CAlphabet::remap_to_char ( BYTE  c  ) 

remap element e.g translate 0123 to ACGT

Parameters:
c element to remap
Returns:
remapped element

Definition at line 91 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,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 391 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( BYTE p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 385 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( SHORT p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 405 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( WORD p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 397 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( INT p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 413 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( UINT p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 421 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( LONG p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 429 of file Alphabet.cpp.

void CAlphabet::add_string_to_histogram ( ULONG p,
LONG  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 437 of file Alphabet.cpp.

void CAlphabet::add_byte_to_histogram ( BYTE  p  ) 

add element to histogram

Parameters:
p element

Definition at line 159 of file Alphabet.h.

void CAlphabet::print_histogram (  ) 

print histogram

Definition at line 481 of file Alphabet.cpp.

void CAlphabet::get_hist ( LONG **  h,
INT len 
)

get histogram

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

Definition at line 172 of file Alphabet.h.

const LONG* CAlphabet::get_histogram (  ) 

get pointer to histogram

Definition at line 184 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 490 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 512 of file Alphabet.cpp.

INT CAlphabet::get_num_symbols_in_histogram (  ) 

return number of symbols in histogram

Returns:
number of symbols in histogram

Definition at line 460 of file Alphabet.cpp.

INT CAlphabet::get_max_value_in_histogram (  ) 

return maximum value in histogram

Returns:
maximum value in histogram

Definition at line 445 of file Alphabet.cpp.

INT 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 472 of file Alphabet.cpp.

const CHAR * CAlphabet::get_alphabet_name ( E_ALPHABET  alphabet  )  [static]

return alphabet name

Parameters:
alphabet alphabet type to get name from

Definition at line 534 of file Alphabet.cpp.

void CAlphabet::init_map_table (  )  [protected]

init map table

Definition at line 124 of file Alphabet.cpp.

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

copy histogram

Parameters:
src alphabet to copy histogram from

Definition at line 529 of file Alphabet.cpp.


Member Data Documentation

const BYTE CAlphabet::B_A = 0 [static]

B_A

Definition at line 242 of file Alphabet.h.

const BYTE CAlphabet::B_C = 1 [static]

B_C

Definition at line 244 of file Alphabet.h.

const BYTE CAlphabet::B_G = 2 [static]

B_G

Definition at line 246 of file Alphabet.h.

const BYTE CAlphabet::B_T = 3 [static]

B_T

Definition at line 248 of file Alphabet.h.

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

MAPTABLE UNDEF

Definition at line 250 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 252 of file Alphabet.h.

alphabet

Definition at line 256 of file Alphabet.h.

number of symbols

Definition at line 258 of file Alphabet.h.

INT CAlphabet::num_bits [protected]

number of bits

Definition at line 260 of file Alphabet.h.

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

valid chars

Definition at line 262 of file Alphabet.h.

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

maptable to bin

Definition at line 264 of file Alphabet.h.

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

maptable to char

Definition at line 266 of file Alphabet.h.

LONG CAlphabet::histogram[1<< (sizeof(BYTE)*8)] [protected]

histogram

Definition at line 268 of file Alphabet.h.

CParallel CSGObject::parallel [static, inherited]

Definition at line 105 of file SGObject.h.

CIO CSGObject::io [static, inherited]

Definition at line 106 of file SGObject.h.

CVersion CSGObject::version [static, inherited]

Definition at line 107 of file SGObject.h.


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

SHOGUN Machine Learning Toolbox - Documentation