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 |
Protected Attributes | |
int32_t | m_length |
int32_t * | m_all_pos |
int32_t ** | m_intron_list |
int32_t ** | m_quality_list |
CIntronList | ( | ) |
constructor
Definition at line 12 of file IntronList.cpp.
~CIntronList | ( | ) | [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 const char* get_name | ( | void | ) | const [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.
int32_t* m_all_pos [protected] |
index of positions in the DNA sequence
Definition at line 63 of file IntronList.h.
int32_t** m_intron_list [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.
int32_t m_length [protected] |
number of positions
Definition at line 60 of file IntronList.h.
int32_t** m_quality_list [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.