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:

Public Member Functions
	CBitString ()
	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
Public Member Functions inherited from CSGObject
	CSGObject ()
	CSGObject (const CSGObject &orig)
virtual	~CSGObject ()
virtual bool	is_generic (EPrimitiveType *generic) const
template<class T >
void	set_generic ()
void	unset_generic ()
virtual void	print_serializable (const char *prefix="")
virtual bool	save_serializable (CSerializableFile *file, const char *prefix="")
virtual bool	load_serializable (CSerializableFile *file, const char *prefix="")
void	set_global_io (SGIO *io)
SGIO *	get_global_io ()
void	set_global_parallel (Parallel *parallel)
Parallel *	get_global_parallel ()
void	set_global_version (Version *version)
Version *	get_global_version ()
SGVector< char * >	get_modelsel_names ()
char *	get_modsel_param_descr (const char *param_name)
index_t	get_modsel_param_index (const char *param_name)

Additional Inherited Members
Public Attributes inherited from CSGObject
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters
Protected Member Functions inherited from CSGObject
virtual void	load_serializable_pre () throw (ShogunException)
virtual void	load_serializable_post () throw (ShogunException)
virtual void	save_serializable_pre () throw (ShogunException)
virtual void	save_serializable_post () throw (ShogunException)

Constructor & Destructor Documentation

CBitString

(

)

default constructor

Definition at line 32 of file BitString.h.

CBitString	(	EAlphabet	alpha,
		int32_t	width = 1
	)

default constructor

creates an empty Bitstring

Parameters

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

Definition at line 50 of file BitString.h.

~CBitString

(

)

destructor

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

Parameters

len	length of string in bits

Definition at line 221 of file BitString.h.

uint64_t get_length

(

)

const

Returns

length of the string in bits

Definition at line 329 of file BitString.h.

virtual const char* get_name ( ) const

virtual

Returns

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

Parameters

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

Returns

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

Parameters

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

Parameters

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

Parameters

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

Parameters

str	string
len	length of string in bits

Definition at line 210 of file BitString.h.

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

• BitString.h