SHOGUN
v1.1.0
|
class IntronList
Definition at line 20 of file IntronList.h.
Public Member Functions | |
CIntronList () | |
virtual | ~CIntronList () |
void | init_list (int32_t *all_pos, int32_t len) |
void | read_introns (int32_t *start_pos, int32_t *end_pos, int32_t *quality, int32_t len) |
void | get_intron_support (int32_t *values, int32_t from_pos, int32_t to_pos) |
virtual const char * | get_name () const |
![]() | |
CSGObject () | |
CSGObject (const CSGObject &orig) | |
virtual | ~CSGObject () |
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="") |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
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 () |
SGVector< char * > | get_modelsel_names () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
Protected Attributes | |
int32_t | m_length |
int32_t * | m_all_pos |
int32_t ** | m_intron_list |
int32_t ** | m_quality_list |
Additional Inherited Members | |
![]() | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
![]() | |
virtual void | load_serializable_pre () throw (ShogunException) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
CIntronList | ( | ) |
constructor
Definition at line 12 of file IntronList.cpp.
|
virtual |
Definition at line 20 of file IntronList.cpp.
void get_intron_support | ( | int32_t * | values, |
int32_t | from_pos, | ||
int32_t | to_pos | ||
) |
get coverage and quality score
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
Definition at line 103 of file IntronList.cpp.
|
virtual |
void init_list | ( | int32_t * | all_pos, |
int32_t | len | ||
) |
initialize all arrays with the number of candidate positions
all_pos | list of candidate positions |
len | number of candidate positions |
Definition at line 31 of file IntronList.cpp.
void read_introns | ( | int32_t * | start_pos, |
int32_t * | end_pos, | ||
int32_t * | quality, | ||
int32_t | len | ||
) |
read introns
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 |
Definition at line 52 of file IntronList.cpp.
|
protected |
index of positions in the DNA sequence
Definition at line 63 of file IntronList.h.
|
protected |
data structure storing the introns; for all posible end positions there is a list of start positions stored
Definition at line 69 of file IntronList.h.
|
protected |
number of positions
Definition at line 60 of file IntronList.h.
|
protected |
data structure storing the intron quality scores; the shape is exactly the same as for the introns
Definition at line 74 of file IntronList.h.