CSegmentLoss Class Reference

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Detailed Description

class IntronList

Definition at line 26 of file SegmentLoss.h.

Inheritance diagram for CSegmentLoss:

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_t >	m_segment_loss_matrix
CArray3< float64_t >	m_segment_loss
CArray< int32_t > *	m_segment_ids
CArray< float64_t > *	m_segment_mask
int32_t	m_num_segment_types

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Constructor & Destructor Documentation

CSegmentLoss

(

)

constructor

Definition at line 16 of file SegmentLoss.cpp.

~CSegmentLoss

(

)

[virtual]

Definition at line 25 of file SegmentLoss.cpp.

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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.

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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.

CArray3<float64_t> m_segment_loss [protected]

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

Definition at line 103 of file SegmentLoss.h.

CArray2<float32_t> m_segment_loss_matrix [protected]

segment loss matrix

Definition at line 97 of file SegmentLoss.h.

CArray<float64_t>* m_segment_mask [protected]

segment mask

Definition at line 109 of file SegmentLoss.h.

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

• SegmentLoss.h
• SegmentLoss.cpp