Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes

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, BINARY, ALPHANUM, CUBE, RAW, IUPAC_NUCLEIC_ACID and IUPAC_AMINO_ACID.

Definition at line 89 of file Alphabet.h.

Inheritance diagram for CAlphabet:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CAlphabet ()
 CAlphabet (char *alpha, int32_t len)
 CAlphabet (EAlphabet alpha)
 CAlphabet (CAlphabet *alpha)
virtual ~CAlphabet ()
bool set_alphabet (EAlphabet alpha)
EAlphabet get_alphabet () const
int32_t get_num_symbols () const
int32_t get_num_bits () const
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)
template<class ST >
static void translate_from_single_order (ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val)
template<class ST >
static void translate_from_single_order_reversed (ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val)
template<class ST >
static void translate_from_single_order (ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<class ST >
static void translate_from_single_order_reversed (ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)

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 B_0 = 4
static const uint8_t MAPTABLE_UNDEF = 0xff
static const char * alphabet_names [18]

Protected Member Functions

void init_map_table ()
void copy_histogram (CAlphabet *src)
virtual void load_serializable_post (void) throw (ShogunException)

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 (  ) 

default constructor

Definition at line 34 of file Alphabet.cpp.

CAlphabet ( char *  alpha,
int32_t  len 
)

constructor

Parameters:
alpha alphabet to use
len len

Definition at line 40 of file Alphabet.cpp.

CAlphabet ( EAlphabet  alpha  ) 

constructor

Parameters:
alpha alphabet (type) to use

Definition at line 87 of file Alphabet.cpp.

CAlphabet ( CAlphabet alpha  ) 

constructor

Parameters:
alpha alphabet to use

Definition at line 94 of file Alphabet.cpp.

~CAlphabet (  )  [virtual]

Definition at line 103 of file Alphabet.cpp.


Member Function Documentation

void add_byte_to_histogram ( uint8_t  p  ) 

add element to histogram

Parameters:
p element

Definition at line 191 of file Alphabet.h.

void add_string_to_histogram ( T *  p,
int64_t  len 
)

make histogram for whole string

Parameters:
p string
len length of string

Definition at line 181 of file Alphabet.h.

bool 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 594 of file Alphabet.cpp.

bool 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 616 of file Alphabet.cpp.

void clear_histogram (  ) 

clear histogram

Definition at line 543 of file Alphabet.cpp.

void copy_histogram ( CAlphabet src  )  [protected]

copy histogram

Parameters:
src alphabet to copy histogram from

Definition at line 633 of file Alphabet.cpp.

EAlphabet get_alphabet (  )  const

get alphabet

Returns:
alphabet

Definition at line 128 of file Alphabet.h.

const char * get_alphabet_name ( EAlphabet  alphabet  )  [static]

return alphabet name

Parameters:
alphabet alphabet type to get name from

Definition at line 638 of file Alphabet.cpp.

void 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 204 of file Alphabet.h.

const int64_t* get_histogram (  ) 

get pointer to histogram

Definition at line 215 of file Alphabet.h.

int32_t get_max_value_in_histogram (  ) 

return maximum value in histogram

Returns:
maximum value in histogram

Definition at line 549 of file Alphabet.cpp.

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

Implements CSGObject.

Definition at line 274 of file Alphabet.h.

int32_t get_num_bits (  )  const

get number of bits necessary to store all symbols in alphabet

Returns:
number of necessary storage bits

Definition at line 147 of file Alphabet.h.

int32_t 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 576 of file Alphabet.cpp.

int32_t get_num_symbols (  )  const

get number of symbols in alphabet

Returns:
number of symbols

Definition at line 137 of file Alphabet.h.

int32_t get_num_symbols_in_histogram (  ) 

return number of symbols in histogram

Returns:
number of symbols in histogram

Definition at line 564 of file Alphabet.cpp.

void init_map_table (  )  [protected]

init map table

Definition at line 178 of file Alphabet.cpp.

bool 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 234 of file Alphabet.h.

void load_serializable_post ( void   )  throw (ShogunException) [protected, virtual]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 718 of file Alphabet.cpp.

void print_histogram (  ) 

print histogram

Definition at line 585 of file Alphabet.cpp.

uint8_t 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 157 of file Alphabet.h.

uint8_t 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 167 of file Alphabet.h.

bool set_alphabet ( EAlphabet  alpha  ) 

set alphabet and initialize mapping table (for remap)

Parameters:
alpha new alphabet

Definition at line 107 of file Alphabet.cpp.

static void translate_from_single_order ( ST *  obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val 
) [static]

translate from single order

Parameters:
obs observation
sequence_length length of sequence
start start
p_order order
max_val maximum value

Definition at line 285 of file Alphabet.h.

static void translate_from_single_order ( ST *  obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
) [static]

translate from single order

Parameters:
obs observation
sequence_length length of sequence
start start
p_order order
max_val maximum value
gap gap

Definition at line 378 of file Alphabet.h.

static void translate_from_single_order_reversed ( ST *  obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val 
) [static]

translate from single order reversed

Parameters:
obs observation
sequence_length length of sequence
start start
p_order order
max_val maximum value

Definition at line 331 of file Alphabet.h.

static void translate_from_single_order_reversed ( ST *  obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
) [static]

translate from single order reversed

Parameters:
obs observation
sequence_length length of sequence
start start
p_order order
max_val maximum value
gap gap

Definition at line 449 of file Alphabet.h.


Member Data Documentation

EAlphabet alphabet [protected]

alphabet

Definition at line 550 of file Alphabet.h.

const char * alphabet_names [static]
Initial value:
{
    "DNA","RAWDNA", "RNA", "PROTEIN", "BINARY", "ALPHANUM",
    "CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID",
    "NONE", "DIGIT", "DIGIT2", "RAWDIGIT", "RAWDIGIT2", "UNKNOWN",
    "SNP", "RAWSNP"}

alphabet names

Definition at line 535 of file Alphabet.h.

const uint8_t B_0 = 4 [static]

B_0

Definition at line 531 of file Alphabet.h.

const uint8_t B_A = 0 [static]

B_A

Definition at line 523 of file Alphabet.h.

const uint8_t B_C = 1 [static]

B_C

Definition at line 525 of file Alphabet.h.

const uint8_t B_G = 2 [static]

B_G

Definition at line 527 of file Alphabet.h.

const uint8_t B_T = 3 [static]

B_T

Definition at line 529 of file Alphabet.h.

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

histogram

Definition at line 562 of file Alphabet.h.

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

maptable to bin

Definition at line 558 of file Alphabet.h.

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

maptable to char

Definition at line 560 of file Alphabet.h.

const uint8_t MAPTABLE_UNDEF = 0xff [static]

MAPTABLE UNDEF

Definition at line 533 of file Alphabet.h.

int32_t num_bits [protected]

number of bits

Definition at line 554 of file Alphabet.h.

int32_t num_symbols [protected]

number of symbols

Definition at line 552 of file Alphabet.h.

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

valid chars

Definition at line 556 of file Alphabet.h.


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