Public Member Functions | Static Public Member Functions | Public Attributes | 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 88 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
SGVector< int64_t > get_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
template<>
void translate_from_single_order (float32_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<>
void translate_from_single_order (float64_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<>
void translate_from_single_order (floatmax_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<>
void translate_from_single_order_reversed (float32_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<>
void translate_from_single_order_reversed (float64_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
template<>
void translate_from_single_order_reversed (floatmax_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap)
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_copy () const
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="", int32_t param_version=VERSION_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
void set_global_io (SGIO *io)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_global_version ()
SGStringList< char > get_modelsel_names ()
void print_modsel_params ()
char * get_modsel_param_descr (const char *param_name)
index_t get_modsel_param_index (const char *param_name)
void build_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

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)

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
ParameterMapm_parameter_map
uint32_t m_hash

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 () throw (ShogunException)
virtual TParametermigrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
virtual void load_serializable_pre () throw (ShogunException)
virtual void save_serializable_pre () throw (ShogunException)
virtual void save_serializable_post () throw (ShogunException)
virtual bool update_parameter_hash ()

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 190 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 180 of file Alphabet.h.

void build_parameter_dictionary ( CMap< TParameter *, CSGObject * > &  dict  )  [inherited]

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

Parameters:
dict dictionary of parameters to be built.

Definition at line 1201 of file SGObject.cpp.

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 600 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 622 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 639 of file Alphabet.cpp.

virtual CSGObject* deep_copy (  )  const [virtual, inherited]

A deep copy. All the instance variables will also be copied.

Definition at line 131 of file SGObject.h.

EAlphabet get_alphabet (  )  const

get alphabet

Returns:
alphabet

Definition at line 127 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 652 of file Alphabet.cpp.

SGIO * get_global_io (  )  [inherited]

get the io object

Returns:
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel (  )  [inherited]

get the parallel object

Returns:
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version (  )  [inherited]

get the version object

Returns:
version object

Definition at line 272 of file SGObject.cpp.

SGVector< int64_t > get_histogram (  ) 

get histogram

Returns:
histogram

Definition at line 595 of file Alphabet.cpp.

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.

SGStringList< char > get_modelsel_names (  )  [inherited]
Returns:
vector of names of all parameters which are registered for model selection

Definition at line 1108 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name  )  [inherited]

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters:
param_name name of the parameter
Returns:
description of the parameter

Definition at line 1132 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name  )  [inherited]

Returns index of model selection parameter with provided index

Parameters:
param_name name of model selection parameter
Returns:
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1145 of file SGObject.cpp.

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

Implements CSGObject.

Definition at line 258 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 146 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 136 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_generic ( EPrimitiveType *  generic  )  const [virtual, inherited]

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters:
generic set to the type of the generic if returning TRUE
Returns:
TRUE if a class template.

Definition at line 278 of file SGObject.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 218 of file Alphabet.h.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

Parameters:
file_version parameter version of the file
current_version version from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
file file to load from
prefix prefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 679 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

Parameters:
param_info information of parameter
file_version parameter version of the file, must be <= provided parameter version
file file to load from
prefix prefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters:
file where to load from
prefix prefix for members
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 354 of file SGObject.cpp.

void load_serializable_post (  )  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 732 of file Alphabet.cpp.

void load_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

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

Exceptions:
ShogunException Will be thrown if an error occurres.

Definition at line 1028 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
) [inherited]

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

Parameters:
param_base set of TParameter instances that are mapped to the provided target parameter infos
base_version version of the parameter base
target_param_infos set of SGParamInfo instances that specify the target parameter base

Definition at line 717 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
) [protected, virtual, inherited]

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
Returns:
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 923 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
replacement (used as output) here the TParameter instance which is returned by migration is created into
to_migrate the only source that is used for migration
old_name with this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void print_histogram (  ) 

print histogram

Definition at line 586 of file Alphabet.cpp.

void print_modsel_params (  )  [inherited]

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

void print_serializable ( const char *  prefix = ""  )  [virtual, inherited]

prints registered parameters out

Parameters:
prefix prefix for members

Definition at line 290 of file SGObject.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 156 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 166 of file Alphabet.h.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

Save this object to file.

Parameters:
file where to save the object; will be closed during returning if PREFIX is an empty string.
prefix prefix for members
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 296 of file SGObject.cpp.

void save_serializable_post (  )  throw (ShogunException) [protected, virtual, inherited]

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::SAVE_SERIALIZABLE_POST is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1043 of file SGObject.cpp.

void save_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

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

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

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.

void set_generic< floatmax_t > (  )  [inherited]

set generic type to T

void set_global_io ( SGIO io  )  [inherited]

set the io object

Parameters:
io io object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel  )  [inherited]

set the parallel object

Parameters:
parallel parallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version  )  [inherited]

set the version object

Parameters:
version version object to use

Definition at line 265 of file SGObject.cpp.

virtual CSGObject* shallow_copy (  )  const [virtual, inherited]

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 122 of file SGObject.h.

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 743 of file Alphabet.cpp.

void translate_from_single_order ( float32_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 938 of file Alphabet.cpp.

void translate_from_single_order ( floatmax_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 946 of file Alphabet.cpp.

void translate_from_single_order ( float64_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 942 of file Alphabet.cpp.

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 819 of file Alphabet.cpp.

template void translate_from_single_order_reversed< float32_t > ( float32_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 950 of file Alphabet.cpp.

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 881 of file Alphabet.cpp.

template void translate_from_single_order_reversed< floatmax_t > ( floatmax_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 958 of file Alphabet.cpp.

template void translate_from_single_order_reversed< float64_t > ( float64_t obs,
int32_t  sequence_length,
int32_t  start,
int32_t  p_order,
int32_t  max_val,
int32_t  gap 
)

Definition at line 954 of file Alphabet.cpp.

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 781 of file Alphabet.cpp.

void unset_generic (  )  [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 285 of file SGObject.cpp.

bool update_parameter_hash (  )  [protected, virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 237 of file SGObject.cpp.


Member Data Documentation

EAlphabet alphabet [protected]

alphabet

Definition at line 350 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 335 of file Alphabet.h.

const uint8_t B_0 = 4 [static]

B_0

Definition at line 331 of file Alphabet.h.

const uint8_t B_A = 0 [static]

B_A

Definition at line 323 of file Alphabet.h.

const uint8_t B_C = 1 [static]

B_C

Definition at line 325 of file Alphabet.h.

const uint8_t B_G = 2 [static]

B_G

Definition at line 327 of file Alphabet.h.

const uint8_t B_T = 3 [static]

B_T

Definition at line 329 of file Alphabet.h.

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

histogram

Definition at line 362 of file Alphabet.h.

SGIO* io [inherited]

io

Definition at line 462 of file SGObject.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 480 of file SGObject.h.

model selection parameters

Definition at line 474 of file SGObject.h.

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 471 of file SGObject.h.

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

maptable to bin

Definition at line 358 of file Alphabet.h.

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

maptable to char

Definition at line 360 of file Alphabet.h.

const uint8_t MAPTABLE_UNDEF = 0xff [static]

MAPTABLE UNDEF

Definition at line 333 of file Alphabet.h.

int32_t num_bits [protected]

number of bits

Definition at line 354 of file Alphabet.h.

int32_t num_symbols [protected]

number of symbols

Definition at line 352 of file Alphabet.h.

Parallel* parallel [inherited]

parallel

Definition at line 465 of file SGObject.h.

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

valid chars

Definition at line 356 of file Alphabet.h.

Version* version [inherited]

version

Definition at line 468 of file SGObject.h.


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