SHOGUN
4.1.0
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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.h 第 91 行定义.
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 CSGObject * | shallow_copy () const |
virtual CSGObject * | deep_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) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_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 void | update_parameter_hash () |
virtual bool | parameter_hash_changed () |
virtual bool | equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) |
virtual CSGObject * | clone () |
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 | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
Parameter * | m_gradient_parameters |
ParameterMap * | m_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 TParameter * | migrate (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)] |
CAlphabet | ( | ) |
default constructor
在文件 Alphabet.cpp 第 35 行定义.
CAlphabet | ( | char * | alpha, |
int32_t | len | ||
) |
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virtual |
在文件 Alphabet.cpp 第 104 行定义.
void add_byte_to_histogram | ( | uint8_t | p | ) |
void add_string_to_histogram | ( | T * | p, |
int64_t | len | ||
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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.
dict | dictionary of parameters to be built. |
在文件 SGObject.cpp 第 1244 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
print_error | if errors shall be printed |
在文件 Alphabet.cpp 第 617 行定义.
bool check_alphabet_size | ( | bool | print_error = true | ) |
check whether symbols in histogram ALL fit in alphabet
print_error | if errors shall be printed |
在文件 Alphabet.cpp 第 639 行定义.
void clear_histogram | ( | ) |
clear histogram
在文件 Alphabet.cpp 第 544 行定义.
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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.
在文件 SGObject.cpp 第 1361 行定义.
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protected |
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virtualinherited |
A deep copy. All the instance variables will also be copied.
在文件 SGObject.cpp 第 200 行定义.
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.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
在文件 SGObject.cpp 第 1265 行定义.
EAlphabet get_alphabet | ( | ) | const |
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static |
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inherited |
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inherited |
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SGVector< int64_t > get_histogram | ( | ) |
int32_t get_max_value_in_histogram | ( | ) |
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inherited |
在文件 SGObject.cpp 第 1136 行定义.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
在文件 SGObject.cpp 第 1160 行定义.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
在文件 SGObject.cpp 第 1173 行定义.
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int32_t get_num_bits | ( | ) | const |
get number of bits necessary to store all symbols in alphabet
在文件 Alphabet.h 第 149 行定义.
int32_t get_num_bits_in_histogram | ( | ) |
return number of bits required to store all symbols in histogram
在文件 Alphabet.cpp 第 577 行定义.
int32_t get_num_symbols | ( | ) | const |
int32_t get_num_symbols_in_histogram | ( | ) |
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protected |
init map table
在文件 Alphabet.cpp 第 179 行定义.
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virtualinherited |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
在文件 SGObject.cpp 第 298 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
c | symbol |
在文件 Alphabet.h 第 221 行定义.
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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)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 705 行定义.
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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
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 |
在文件 SGObject.cpp 第 546 行定义.
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virtualinherited |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
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) |
在文件 SGObject.cpp 第 375 行定义.
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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.
ShogunException | Will be thrown if an error occurres. |
重载 CSGObject .
在文件 Alphabet.cpp 第 749 行定义.
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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.
ShogunException | will be thrown if an error occurs. |
被 CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.
在文件 SGObject.cpp 第 1058 行定义.
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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
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 |
在文件 SGObject.cpp 第 743 行定义.
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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
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
在文件 SGObject.cpp 第 950 行定义.
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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)
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 |
在文件 SGObject.cpp 第 890 行定义.
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virtualinherited |
在文件 SGObject.cpp 第 264 行定义.
void print_histogram | ( | ) |
print histogram
在文件 Alphabet.cpp 第 587 行定义.
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prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 1112 行定义.
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uint8_t remap_to_bin | ( | uint8_t | c | ) |
remap element e.g translate ACGT to 0123
c | element to remap |
在文件 Alphabet.h 第 159 行定义.
uint8_t remap_to_char | ( | uint8_t | c | ) |
remap element e.g translate 0123 to ACGT
c | element to remap |
在文件 Alphabet.h 第 169 行定义.
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Save this object to file.
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) |
在文件 SGObject.cpp 第 316 行定义.
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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.
ShogunException | will be thrown if an error occurs. |
被 CKernel 重载.
在文件 SGObject.cpp 第 1073 行定义.
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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.
ShogunException | will be thrown if an error occurs. |
被 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.cpp 第 1068 行定义.
bool set_alphabet | ( | EAlphabet | alpha | ) |
set alphabet and initialize mapping table (for remap)
alpha | new alphabet |
在文件 Alphabet.cpp 第 108 行定义.
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在文件 SGObject.cpp 第 42 行定义.
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在文件 SGObject.cpp 第 47 行定义.
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在文件 SGObject.cpp 第 52 行定义.
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在文件 SGObject.cpp 第 57 行定义.
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在文件 SGObject.cpp 第 62 行定义.
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在文件 SGObject.cpp 第 67 行定义.
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在文件 SGObject.cpp 第 72 行定义.
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在文件 SGObject.cpp 第 77 行定义.
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在文件 SGObject.cpp 第 82 行定义.
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在文件 SGObject.cpp 第 87 行定义.
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在文件 SGObject.cpp 第 92 行定义.
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在文件 SGObject.cpp 第 97 行定义.
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在文件 SGObject.cpp 第 102 行定义.
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在文件 SGObject.cpp 第 107 行定义.
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在文件 SGObject.cpp 第 112 行定义.
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set generic type to T
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virtualinherited |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
被 CGaussianKernel 重载.
在文件 SGObject.cpp 第 194 行定义.
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translate from single order
obs | observation |
sequence_length | length of sequence |
start | start |
p_order | order |
max_val | maximum value |
在文件 Alphabet.cpp 第 760 行定义.
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static |
translate from single order
obs | observation |
sequence_length | length of sequence |
start | start |
p_order | order |
max_val | maximum value |
gap | gap |
在文件 Alphabet.cpp 第 836 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.cpp 第 955 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.cpp 第 959 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.cpp 第 963 行定义.
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static |
translate from single order reversed
obs | observation |
sequence_length | length of sequence |
start | start |
p_order | order |
max_val | maximum value |
在文件 Alphabet.cpp 第 798 行定义.
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static |
translate from single order reversed
obs | observation |
sequence_length | length of sequence |
start | start |
p_order | order |
max_val | maximum value |
gap | gap |
在文件 Alphabet.cpp 第 898 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.cpp 第 967 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.cpp 第 971 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.cpp 第 975 行定义.
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inherited |
unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 305 行定义.
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virtualinherited |
Updates the hash of current parameter combination
在文件 SGObject.cpp 第 250 行定义.
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alphabet
在文件 Alphabet.h 第 353 行定义.
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alphabet names
在文件 Alphabet.h 第 338 行定义.
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B_0
在文件 Alphabet.h 第 334 行定义.
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B_A
在文件 Alphabet.h 第 326 行定义.
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B_C
在文件 Alphabet.h 第 328 行定义.
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B_G
在文件 Alphabet.h 第 330 行定义.
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B_T
在文件 Alphabet.h 第 332 行定义.
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histogram
在文件 Alphabet.h 第 365 行定义.
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io
在文件 SGObject.h 第 496 行定义.
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parameters wrt which we can compute gradients
在文件 SGObject.h 第 511 行定义.
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Hash of parameter values
在文件 SGObject.h 第 517 行定义.
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model selection parameters
在文件 SGObject.h 第 508 行定义.
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map for different parameter versions
在文件 SGObject.h 第 514 行定义.
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parameters
在文件 SGObject.h 第 505 行定义.
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maptable to bin
在文件 Alphabet.h 第 361 行定义.
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maptable to char
在文件 Alphabet.h 第 363 行定义.
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MAPTABLE UNDEF
在文件 Alphabet.h 第 336 行定义.
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number of bits
在文件 Alphabet.h 第 357 行定义.
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number of symbols
在文件 Alphabet.h 第 355 行定义.
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parallel
在文件 SGObject.h 第 499 行定义.
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valid chars
在文件 Alphabet.h 第 359 行定义.
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version
在文件 SGObject.h 第 502 行定义.