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CAlphabet类 参考

详细描述

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.

在文件 Alphabet.h88 行定义.

类 CAlphabet 继承关系图:
Inheritance graph
[图例]

Public 成员函数

 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 更多...
 
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 更多...
 
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 ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
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::get_version_parameter())
 
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_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_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict)
 
virtual bool update_parameter_hash ()
 
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
 
virtual CSGObjectclone ()
 

静态 Public 成员函数

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 属性

SGIOio
 
Parallelparallel
 
Versionversion
 
Parameterm_parameters
 
Parameterm_model_selection_parameters
 
Parameterm_gradient_parameters
 
ParameterMapm_parameter_map
 
uint32_t m_hash
 

静态 Public 属性

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 成员函数

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)
 

Protected 属性

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)]
 

构造及析构函数说明

CAlphabet ( )

default constructor

在文件 Alphabet.cpp35 行定义.

CAlphabet ( char *  alpha,
int32_t  len 
)

constructor

参数
alphaalphabet to use
lenlen

在文件 Alphabet.cpp41 行定义.

CAlphabet ( EAlphabet  alpha)

constructor

参数
alphaalphabet (type) to use

在文件 Alphabet.cpp88 行定义.

CAlphabet ( CAlphabet alpha)

constructor

参数
alphaalphabet to use

在文件 Alphabet.cpp95 行定义.

~CAlphabet ( )
virtual

在文件 Alphabet.cpp104 行定义.

成员函数说明

void add_byte_to_histogram ( uint8_t  p)

add element to histogram

参数
pelement

在文件 Alphabet.h190 行定义.

void add_string_to_histogram ( T *  p,
int64_t  len 
)

make histogram for whole string

参数
pstring
lenlength of string

在文件 Alphabet.h180 行定义.

void build_gradient_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.

参数
dictdictionary of parameters to be built.

在文件 SGObject.cpp1156 行定义.

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

参数
print_errorif errors shall be printed
返回
if symbols in histogram are valid in alphabet

在文件 Alphabet.cpp617 行定义.

bool check_alphabet_size ( bool  print_error = true)

check whether symbols in histogram ALL fit in alphabet

参数
print_errorif errors shall be printed
返回
if symbols in histogram ALL fit in alphabet

在文件 Alphabet.cpp639 行定义.

void clear_histogram ( )

clear histogram

在文件 Alphabet.cpp544 行定义.

CSGObject * clone ( )
virtualinherited

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

返回
an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

在文件 SGObject.cpp1273 行定义.

void copy_histogram ( CAlphabet src)
protected

copy histogram

参数
srcalphabet to copy histogram from

在文件 Alphabet.cpp656 行定义.

virtual CSGObject* deep_copy ( ) const
virtualinherited

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

在文件 SGObject.h126 行定义.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0 
)
virtualinherited

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

参数
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
返回
true if all parameters were equal, false if not

在文件 SGObject.cpp1177 行定义.

EAlphabet get_alphabet ( ) const

get alphabet

返回
alphabet

在文件 Alphabet.h127 行定义.

const char * get_alphabet_name ( EAlphabet  alphabet)
static

return alphabet name

参数
alphabetalphabet type to get name from

在文件 Alphabet.cpp669 行定义.

SGIO * get_global_io ( )
inherited

get the io object

返回
io object

在文件 SGObject.cpp174 行定义.

Parallel * get_global_parallel ( )
inherited

get the parallel object

返回
parallel object

在文件 SGObject.cpp209 行定义.

Version * get_global_version ( )
inherited

get the version object

返回
version object

在文件 SGObject.cpp222 行定义.

SGVector< int64_t > get_histogram ( )

get histogram

返回
histogram

在文件 Alphabet.cpp612 行定义.

int32_t get_max_value_in_histogram ( )

return maximum value in histogram

返回
maximum value in histogram

在文件 Alphabet.cpp550 行定义.

SGStringList< char > get_modelsel_names ( )
inherited
返回
vector of names of all parameters which are registered for model selection

在文件 SGObject.cpp1060 行定义.

char * get_modsel_param_descr ( const char *  param_name)
inherited

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

参数
param_namename of the parameter
返回
description of the parameter

在文件 SGObject.cpp1084 行定义.

index_t get_modsel_param_index ( const char *  param_name)
inherited

Returns index of model selection parameter with provided index

参数
param_namename of model selection parameter
返回
index of model selection parameter with provided name, -1 if there is no such

在文件 SGObject.cpp1097 行定义.

virtual const char* get_name ( ) const
virtual
返回
object name

实现了 CSGObject.

在文件 Alphabet.h258 行定义.

int32_t get_num_bits ( ) const

get number of bits necessary to store all symbols in alphabet

返回
number of necessary storage bits

在文件 Alphabet.h146 行定义.

int32_t get_num_bits_in_histogram ( )

return number of bits required to store all symbols in histogram

返回
number of bits required to store all symbols in histogram

在文件 Alphabet.cpp577 行定义.

int32_t get_num_symbols ( ) const

get number of symbols in alphabet

返回
number of symbols

在文件 Alphabet.h136 行定义.

int32_t get_num_symbols_in_histogram ( )

return number of symbols in histogram

返回
number of symbols in histogram

在文件 Alphabet.cpp565 行定义.

void init_map_table ( )
protected

init map table

在文件 Alphabet.cpp179 行定义.

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.

参数
genericset to the type of the generic if returning TRUE
返回
TRUE if a class template.

在文件 SGObject.cpp228 行定义.

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

参数
csymbol
返回
if symbol is a valid character in alphabet

在文件 Alphabet.h218 行定义.

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)

参数
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use Version::get_version_parameter() for this in most cases)
filefile to load from
prefixprefix for members
返回
(sorted) array of created TParameter instances with file data

在文件 SGObject.cpp633 行定义.

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

参数
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
返回
new array with TParameter instances with the attached data

在文件 SGObject.cpp474 行定义.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_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!

参数
filewhere to load from
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
返回
TRUE if done, otherwise FALSE

在文件 SGObject.cpp305 行定义.

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.

异常
ShogunExceptionWill be thrown if an error occurres.

重载 CSGObject .

在文件 Alphabet.cpp749 行定义.

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.

异常
ShogunExceptionWill be thrown if an error occurres.

CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.

在文件 SGObject.cpp984 行定义.

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

参数
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

在文件 SGObject.cpp671 行定义.

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

参数
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
返回
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

在文件 SGObject.cpp878 行定义.

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)

参数
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

在文件 SGObject.cpp818 行定义.

void print_histogram ( )

print histogram

在文件 Alphabet.cpp587 行定义.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

在文件 SGObject.cpp1036 行定义.

void print_serializable ( const char *  prefix = "")
virtualinherited

prints registered parameters out

参数
prefixprefix for members

在文件 SGObject.cpp240 行定义.

uint8_t remap_to_bin ( uint8_t  c)

remap element e.g translate ACGT to 0123

参数
celement to remap
返回
remapped element

在文件 Alphabet.h156 行定义.

uint8_t remap_to_char ( uint8_t  c)

remap element e.g translate 0123 to ACGT

参数
celement to remap
返回
remapped element

在文件 Alphabet.h166 行定义.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
)
virtualinherited

Save this object to file.

参数
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)
返回
TRUE if done, otherwise FALSE

在文件 SGObject.cpp246 行定义.

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.

异常
ShogunExceptionWill be thrown if an error occurres.

CKernel 重载.

在文件 SGObject.cpp999 行定义.

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.

异常
ShogunExceptionWill be thrown if an error occurres.

CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.

在文件 SGObject.cpp994 行定义.

bool set_alphabet ( EAlphabet  alpha)

set alphabet and initialize mapping table (for remap)

参数
alphanew alphabet

在文件 Alphabet.cpp108 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp41 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp46 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp51 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp56 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp61 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp66 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp71 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp76 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp81 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp86 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp91 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp96 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp101 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp106 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp111 行定义.

void set_generic ( )
inherited

set generic type to T

void set_global_io ( SGIO io)
inherited

set the io object

参数
ioio object to use

在文件 SGObject.cpp167 行定义.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

参数
parallelparallel object to use

在文件 SGObject.cpp180 行定义.

void set_global_version ( Version version)
inherited

set the version object

参数
versionversion object to use

在文件 SGObject.cpp215 行定义.

virtual CSGObject* shallow_copy ( ) const
virtualinherited

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

CGaussianKernel 重载.

在文件 SGObject.h117 行定义.

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

参数
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value

在文件 Alphabet.cpp760 行定义.

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

参数
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value
gapgap

在文件 Alphabet.cpp836 行定义.

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 
)

在文件 Alphabet.cpp955 行定义.

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 
)

在文件 Alphabet.cpp959 行定义.

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 
)

在文件 Alphabet.cpp963 行定义.

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

参数
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value

在文件 Alphabet.cpp798 行定义.

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

参数
obsobservation
sequence_lengthlength of sequence
startstart
p_orderorder
max_valmaximum value
gapgap

在文件 Alphabet.cpp898 行定义.

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 
)

在文件 Alphabet.cpp967 行定义.

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 
)

在文件 Alphabet.cpp971 行定义.

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 
)

在文件 Alphabet.cpp975 行定义.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

在文件 SGObject.cpp235 行定义.

bool update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination.

返回
bool if parameter combination has changed since last update.

在文件 SGObject.cpp187 行定义.

类成员变量说明

EAlphabet alphabet
protected

alphabet

在文件 Alphabet.h350 行定义.

const char * alphabet_names
static
初始值:
={
"DNA","RAWDNA", "RNA", "PROTEIN", "BINARY", "ALPHANUM",
"CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID",
"NONE", "DIGIT", "DIGIT2", "RAWDIGIT", "RAWDIGIT2", "UNKNOWN",
"SNP", "RAWSNP"}

alphabet names

在文件 Alphabet.h335 行定义.

const uint8_t B_0 =4
static

B_0

在文件 Alphabet.h331 行定义.

const uint8_t B_A =0
static

B_A

在文件 Alphabet.h323 行定义.

const uint8_t B_C =1
static

B_C

在文件 Alphabet.h325 行定义.

const uint8_t B_G =2
static

B_G

在文件 Alphabet.h327 行定义.

const uint8_t B_T =3
static

B_T

在文件 Alphabet.h329 行定义.

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

histogram

在文件 Alphabet.h362 行定义.

SGIO* io
inherited

io

在文件 SGObject.h473 行定义.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

在文件 SGObject.h488 行定义.

uint32_t m_hash
inherited

Hash of parameter values

在文件 SGObject.h494 行定义.

Parameter* m_model_selection_parameters
inherited

model selection parameters

在文件 SGObject.h485 行定义.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

在文件 SGObject.h491 行定义.

Parameter* m_parameters
inherited

parameters

在文件 SGObject.h482 行定义.

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

maptable to bin

在文件 Alphabet.h358 行定义.

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

maptable to char

在文件 Alphabet.h360 行定义.

const uint8_t MAPTABLE_UNDEF =0xff
static

MAPTABLE UNDEF

在文件 Alphabet.h333 行定义.

int32_t num_bits
protected

number of bits

在文件 Alphabet.h354 行定义.

int32_t num_symbols
protected

number of symbols

在文件 Alphabet.h352 行定义.

Parallel* parallel
inherited

parallel

在文件 SGObject.h476 行定义.

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

valid chars

在文件 Alphabet.h356 行定义.

Version* version
inherited

version

在文件 SGObject.h479 行定义.


该类的文档由以下文件生成:

SHOGUN Machine Learning Toolbox - Documentation