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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]

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
alphaalphabet to use
lenlen

Definition at line 40 of file Alphabet.cpp.

CAlphabet ( EAlphabet  alpha)

constructor

Parameters
alphaalphabet (type) to use

Definition at line 87 of file Alphabet.cpp.

CAlphabet ( CAlphabet alpha)

constructor

Parameters
alphaalphabet 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
pelement

Definition at line 190 of file Alphabet.h.

void add_string_to_histogram ( T *  p,
int64_t  len 
)

make histogram for whole string

Parameters
pstring
lenlength 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
dictdictionary of parameters to be built.

Definition at line 1204 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_errorif 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_errorif 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
srcalphabet to copy histogram from

Definition at line 639 of file Alphabet.cpp.

virtual CSGObject* deep_copy ( ) const
virtualinherited

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
alphabetalphabet 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_namename 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_namename 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
virtualinherited

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

Parameters
genericset 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
csymbol
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_versionparameter version of the file
current_versionversion from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
filefile to load from
prefixprefix 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_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix 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 
)
virtualinherited

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

Parameters
filewhere to load from
prefixprefix 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)
protectedvirtual

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
ShogunExceptionWill be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 732 of file Alphabet.cpp.

void load_serializable_pre ( ) throw (ShogunException)
protectedvirtualinherited

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
ShogunExceptionWill 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_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset 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 
)
protectedvirtualinherited

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_baseset of TParameter instances to use for migration
targetparameter 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 
)
protectedvirtualinherited

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_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith 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 = "")
virtualinherited

prints registered parameters out

Parameters
prefixprefix 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
celement 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
celement 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 
)
virtualinherited

Save this object to file.

Parameters
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix 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)
protectedvirtualinherited

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
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1043 of file SGObject.cpp.

void save_serializable_pre ( ) throw (ShogunException)
protectedvirtualinherited

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
ShogunExceptionWill 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
alphanew alphabet

Definition at line 107 of file Alphabet.cpp.

void set_generic< floatmax_t > ( )
inherited

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 265 of file SGObject.cpp.

virtual CSGObject* shallow_copy ( ) const
virtualinherited

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
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value

Definition at line 743 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
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value
gapgap

Definition at line 819 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 ( 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 ( 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_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
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value

Definition at line 781 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
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value
gapgap

Definition at line 881 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.

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.

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.

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 ( )
protectedvirtualinherited

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.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 474 of file SGObject.h.

ParameterMap* m_parameter_map
inherited

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.


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

SHOGUN Machine Learning Toolbox - Documentation