SHOGUN  v1.1.0
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines
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
[legend]

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

constructor

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

Parameters:
valuesvalues[0]: coverage of that intron; values[1]: associated quality score
from_posstart position of intron
to_posend 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]
Returns:
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

Parameters:
all_poslist of candidate positions
lennumber 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

Parameters:
start_posarray of start positions
end_posarray of end positions
qualityquality scores for introns in list
lennumber 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:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines

SHOGUN Machine Learning Toolbox - Documentation