Public Member Functions | Protected Attributes

CIntronList Class Reference

Detailed Description

class IntronList

Definition at line 20 of file IntronList.h.

Inheritance diagram for CIntronList:
Inheritance graph

List of all members.

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

Constructor & Destructor Documentation

CIntronList (  ) 


Definition at line 12 of file IntronList.cpp.

~CIntronList (  )  [virtual]

Definition at line 20 of file IntronList.cpp.

Member Function Documentation

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 (  )  const [virtual]
object name

Implements CSGObject.

Definition at line 57 of file IntronList.h.

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.

Member Data Documentation

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.

The documentation for this class was generated from the following files:
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