SHOGUN
v1.1.0
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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.
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 |
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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 | |
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SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
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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) |
CBitString | ( | ) |
default constructor
Definition at line 32 of file BitString.h.
CBitString | ( | EAlphabet | alpha, |
int32_t | width = 1 |
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) |
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 | ( | ) |
destructor
Definition at line 67 of file BitString.h.
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 |
Definition at line 329 of file BitString.h.
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virtual |
void load_fasta_file | ( | const char * | fname, |
bool | ignore_invalid = false |
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) |
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 |
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.