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CIntronList Class Reference

Detailed Description

class IntronList

Definition at line 20 of file IntronList.h.

Inheritance diagram for CIntronList:
Inheritance graph
[legend]

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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_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

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:

SHOGUN Machine Learning Toolbox - Documentation