Public Member Functions

CBitString Class Reference

Detailed Description

a string class embedding a string in a compact bit representation

especially useful to compactly represent genomic DNA

(or any other string of small alphabet size)

Definition at line 28 of file BitString.h.

Inheritance diagram for CBitString:
Inheritance graph

List of all members.

Public Member Functions

 CBitString (void)
 CBitString (EAlphabet alpha, int32_t width=1)
 ~CBitString ()
void cleanup ()
void obtain_from_char (char *str, uint64_t len)
void load_fasta_file (const char *fname, bool ignore_invalid=false)
void set_string (uint64_t *str, uint64_t len)
void create (uint64_t len)
uint64_t operator[] (uint64_t index) const
void set_binary_word (uint16_t word, uint64_t index)
uint64_t get_length () const
virtual const char * get_name () const

Constructor & Destructor Documentation

CBitString ( void   ) 

default constructor

Definition at line 32 of file BitString.h.

CBitString ( EAlphabet  alpha,
int32_t  width = 1 

default constructor

creates an empty Bitstring

alpha Alphabet
width return this many bits upon str[idx] access operations

Definition at line 50 of file BitString.h.

~CBitString (  ) 


Definition at line 67 of file BitString.h.

Member Function Documentation

void cleanup (  ) 

free up memory

Definition at line 74 of file BitString.h.

void create ( uint64_t  len  ) 

creates string of all zeros of len bits

len length of string in bits

Definition at line 221 of file BitString.h.

uint64_t get_length (  )  const
length of the string in bits

Definition at line 329 of file BitString.h.

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

Implements CSGObject.

Definition at line 332 of file BitString.h.

void load_fasta_file ( const char *  fname,
bool  ignore_invalid = false 

load fasta file as bit string

fname filename to load from
ignore_invalid if set to true, characters other than A,C,G,T are converted to A
if loading was successful

Definition at line 123 of file BitString.h.

void obtain_from_char ( char *  str,
uint64_t  len 

convert string of length len into bit sequence

str string
len length of string in bits

Definition at line 86 of file BitString.h.

uint64_t operator[] ( uint64_t  index  )  const

access array by [] operator

index index into array

Definition at line 263 of file BitString.h.

void set_binary_word ( uint16_t  word,
uint64_t  index 

set a binary word

word 16 bit word to be set
index word based index

Definition at line 289 of file BitString.h.

void set_string ( uint64_t *  str,
uint64_t  len 

set string of length len embedded in a uint64_t sequence

str string
len length of string in bits

Definition at line 210 of file BitString.h.

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