CIntronList Class Reference

Detailed Description

class IntronList

Definition at line 20 of file IntronList.h.

Inheritance diagram for CIntronList:

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
Public Member Functions inherited from CSGObject
	CSGObject ()
	CSGObject (const CSGObject &orig)
virtual	~CSGObject ()
virtual bool	is_generic (EPrimitiveType *generic) const
template<class T >
void	set_generic ()
void	unset_generic ()
virtual void	print_serializable (const char *prefix="")
virtual bool	save_serializable (CSerializableFile *file, const char *prefix="")
virtual bool	load_serializable (CSerializableFile *file, const char *prefix="")
void	set_global_io (SGIO *io)
SGIO *	get_global_io ()
void	set_global_parallel (Parallel *parallel)
Parallel *	get_global_parallel ()
void	set_global_version (Version *version)
Version *	get_global_version ()
SGVector< char * >	get_modelsel_names ()
char *	get_modsel_param_descr (const char *param_name)
index_t	get_modsel_param_index (const char *param_name)

Protected Attributes
int32_t	m_length
int32_t *	m_all_pos
int32_t **	m_intron_list
int32_t **	m_quality_list

Additional Inherited Members
Public Attributes inherited from CSGObject
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters
Protected Member Functions inherited from CSGObject
virtual void	load_serializable_pre () throw (ShogunException)
virtual void	load_serializable_post () throw (ShogunException)
virtual void	save_serializable_pre () throw (ShogunException)
virtual void	save_serializable_post () throw (ShogunException)

Constructor & Destructor Documentation

CIntronList

(

)

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

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

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_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

Parameters

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.

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

• IntronList.h
• IntronList.cpp