class IntronList
在文件 IntronList.h 第 22 行定义.
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| CIntronList () |
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virtual | ~CIntronList () |
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void | init_list (int32_t *all_pos, int32_t len) |
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void | read_introns (int32_t *start_pos, int32_t *end_pos, int32_t *quality, int32_t len) |
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void | get_intron_support (int32_t *values, int32_t from_pos, int32_t to_pos) |
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virtual const char * | get_name () const |
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virtual CSGObject * | shallow_copy () const |
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virtual CSGObject * | deep_copy () const |
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virtual bool | is_generic (EPrimitiveType *generic) const |
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template<class T > |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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template<> |
void | set_generic () |
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void | unset_generic () |
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virtual void | print_serializable (const char *prefix="") |
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virtual bool | save_serializable (CSerializableFile *file, const char *prefix="") |
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virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
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void | set_global_io (SGIO *io) |
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SGIO * | get_global_io () |
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void | set_global_parallel (Parallel *parallel) |
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Parallel * | get_global_parallel () |
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void | set_global_version (Version *version) |
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Version * | get_global_version () |
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SGStringList< char > | get_modelsel_names () |
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void | print_modsel_params () |
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char * | get_modsel_param_descr (const char *param_name) |
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index_t | get_modsel_param_index (const char *param_name) |
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void | build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict) |
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virtual void | update_parameter_hash () |
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virtual bool | parameter_hash_changed () |
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virtual bool | equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) |
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virtual CSGObject * | clone () |
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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
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dict | dictionary of parameters to be built. |
在文件 SGObject.cpp 第 597 行定义.
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.cpp 第 714 行定义.
A deep copy. All the instance variables will also be copied.
在文件 SGObject.cpp 第 198 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.
- 参数
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other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
- 返回
- true if all parameters were equal, false if not
在文件 SGObject.cpp 第 618 行定义.
void get_intron_support |
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int32_t * |
values, |
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int32_t |
from_pos, |
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int32_t |
to_pos |
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) |
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get coverage and quality score
- 参数
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values | values[0]: coverage of that intron; values[1]: associated quality score |
from_pos | start position of intron |
to_pos | end position of intron |
from_pos and to_pos are indices in the all_pos list not positions in the DNA sequence
在文件 IntronList.cpp 第 102 行定义.
- 返回
- vector of names of all parameters which are registered for model selection
在文件 SGObject.cpp 第 498 行定义.
char * get_modsel_param_descr |
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const char * |
param_name | ) |
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
- 参数
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param_name | name of the parameter |
- 返回
- description of the parameter
在文件 SGObject.cpp 第 522 行定义.
index_t get_modsel_param_index |
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const char * |
param_name | ) |
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inherited |
Returns index of model selection parameter with provided index
- 参数
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param_name | name of model selection parameter |
- 返回
- index of model selection parameter with provided name, -1 if there is no such
在文件 SGObject.cpp 第 535 行定义.
virtual const char* get_name |
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const |
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virtual |
void init_list |
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int32_t * |
all_pos, |
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int32_t |
len |
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) |
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initialize all arrays with the number of candidate positions
- 参数
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all_pos | list of candidate positions |
len | number of candidate positions |
在文件 IntronList.cpp 第 31 行定义.
bool is_generic |
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EPrimitiveType * |
generic | ) |
const |
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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.
- 参数
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generic | set to the type of the generic if returning TRUE |
- 返回
- TRUE if a class template.
在文件 SGObject.cpp 第 296 行定义.
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
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file | where to load from |
prefix | prefix for members |
- 返回
- TRUE if done, otherwise FALSE
在文件 SGObject.cpp 第 369 行定义.
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protectedvirtualinherited |
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protectedvirtualinherited |
bool parameter_hash_changed |
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virtualinherited |
- 返回
- whether parameter combination has changed since last update
在文件 SGObject.cpp 第 262 行定义.
void print_modsel_params |
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inherited |
prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 474 行定义.
void print_serializable |
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const char * |
prefix = "" | ) |
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virtualinherited |
void read_introns |
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int32_t * |
start_pos, |
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int32_t * |
end_pos, |
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int32_t * |
quality, |
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int32_t |
len |
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) |
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read introns
- 参数
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start_pos | array of start positions |
end_pos | array of end positions |
quality | quality scores for introns in list |
len | number of items in all three previous arguments |
在文件 IntronList.cpp 第 51 行定义.
Save this object to file.
- 参数
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file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
- 返回
- TRUE if done, otherwise FALSE
在文件 SGObject.cpp 第 314 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.
- 异常
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被 CKernel 重载.
在文件 SGObject.cpp 第 436 行定义.
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protectedvirtualinherited |
void set_global_io |
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SGIO * |
io | ) |
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inherited |
void set_global_parallel |
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Parallel * |
parallel | ) |
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inherited |
set the parallel object
- 参数
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parallel | parallel object to use |
在文件 SGObject.cpp 第 241 行定义.
void set_global_version |
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Version * |
version | ) |
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inherited |
set the version object
- 参数
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version | version object to use |
在文件 SGObject.cpp 第 283 行定义.
unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 303 行定义.
void update_parameter_hash |
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virtualinherited |
Updates the hash of current parameter combination
在文件 SGObject.cpp 第 248 行定义.
parameters wrt which we can compute gradients
在文件 SGObject.h 第 384 行定义.
data structure storing the introns; for all posible end positions there is a list of start positions stored
在文件 IntronList.h 第 71 行定义.
data structure storing the intron quality scores; the shape is exactly the same as for the introns
在文件 IntronList.h 第 76 行定义.
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