Public Member Functions | Protected Attributes

CSegmentLoss Class Reference


Detailed Description

class IntronList

Definition at line 26 of file SegmentLoss.h.

Inheritance diagram for CSegmentLoss:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CSegmentLoss ()
virtual ~CSegmentLoss ()
float32_t get_segment_loss (int32_t from_pos, int32_t to_pos, int32_t segment_id)
float32_t get_segment_loss_extend (int32_t from_pos, int32_t to_pos, int32_t segment_id)
void set_segment_loss (float64_t *segment_loss, int32_t m, int32_t n)
void set_segment_ids (CArray< int32_t > *segment_ids)
void set_segment_mask (CArray< float64_t > *segment_mask)
void set_num_segment_types (int32_t num_segment_types)
void compute_loss (int32_t *all_pos, int32_t len)
virtual const char * get_name () const

Protected Attributes

CArray2< float32_tm_segment_loss_matrix
CArray3< float64_tm_segment_loss
CArray< int32_t > * m_segment_ids
CArray< float64_t > * m_segment_mask
int32_t m_num_segment_types

Constructor & Destructor Documentation

CSegmentLoss (  ) 

constructor

Definition at line 16 of file SegmentLoss.cpp.

~CSegmentLoss (  )  [virtual]

Definition at line 25 of file SegmentLoss.cpp.


Member Function Documentation

void compute_loss ( int32_t *  all_pos,
int32_t  len 
)

compute loss

Parameters:
all_pos all candidate positions
len number of positions

Definition at line 50 of file SegmentLoss.cpp.

virtual const char* get_name ( void   )  const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 93 of file SegmentLoss.h.

float32_t get_segment_loss ( int32_t  from_pos,
int32_t  to_pos,
int32_t  segment_id 
)

get segment loss for a given range

Parameters:
from_pos start position
to_pos end position
segment_id type of the segment

Definition at line 115 of file SegmentLoss.h.

float32_t get_segment_loss_extend ( int32_t  from_pos,
int32_t  to_pos,
int32_t  segment_id 
)

get segment loss for a given range

Parameters:
from_pos start position
to_pos end position
segment_id type of the segment

Definition at line 153 of file SegmentLoss.h.

void set_num_segment_types ( int32_t  num_segment_types  ) 

set num segment types

Parameters:
num_segment_types num segment types

Definition at line 78 of file SegmentLoss.h.

void set_segment_ids ( CArray< int32_t > *  segment_ids  ) 

set best path segmend ids

Parameters:
segment_ids segment ids

Definition at line 40 of file SegmentLoss.cpp.

void set_segment_loss ( float64_t segment_loss,
int32_t  m,
int32_t  n 
)

set best path segment loss

Parameters:
segment_loss segment loss
m number of segment id1
n number of segment id2

Definition at line 29 of file SegmentLoss.cpp.

void set_segment_mask ( CArray< float64_t > *  segment_mask  ) 

mask parts of the sequence such that there is no loss incured there; this is used if there is uncertainty in the label

Parameters:
segment_mask mask

Definition at line 45 of file SegmentLoss.cpp.


Member Data Documentation

int32_t m_num_segment_types [protected]

number of different segment types (former: max_a_id)

Definition at line 112 of file SegmentLoss.h.

CArray<int32_t>* m_segment_ids [protected]

segment IDs

Definition at line 106 of file SegmentLoss.h.

segment loss two square matrices: one for segment based loss and one for length contribution

Definition at line 103 of file SegmentLoss.h.

segment loss matrix

Definition at line 97 of file SegmentLoss.h.

segment mask

Definition at line 109 of file SegmentLoss.h.


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