SQ_GroupData Class Reference

#include <SQ_GroupData.h>

Inheritance diagram for SQ_GroupData:

Collaboration diagram for SQ_GroupData:

Public Member Functions
	SQ_GroupData ()
virtual	~SQ_GroupData ()
virtual SQ_GroupData &	operator= (const SQ_GroupData &other)=0
virtual SQ_GroupData *	clone () const =0
void	SQ_set_avg_bases (int bases)
int	SQ_get_avg_bases () const
void	SQ_set_avg_gc (double gc)
double	SQ_get_avg_gc () const
void	SQ_count_sequences ()
int	SQ_get_nr_sequences () const
bool	SQ_is_initialized () const
virtual void	SQ_init_consensus (int size)=0
virtual int	SQ_print_on_screen ()=0
virtual consensus_result	SQ_calc_consensus (const char *sequence) const =0
virtual void	SQ_add_sequence (const char *sequence)=0
virtual void	SQ_add (const SQ_GroupData &other)=0
int	getSize () const

Protected Attributes
int	size
int	avg_bases
int	nr_sequences
double	gc_prop
bool	initialized

Detailed Description

Definition at line 39 of file SQ_GroupData.h.

Constructor & Destructor Documentation

SQ_GroupData::SQ_GroupData

(

)

Definition at line 22 of file SQ_GroupData.cxx.

References initialized.

SQ_GroupData::~SQ_GroupData ( )

virtual

Definition at line 30 of file SQ_GroupData.cxx.

Member Function Documentation

virtual SQ_GroupData& SQ_GroupData::operator= ( const SQ_GroupData &  other )

pure virtual

Implemented in SQ_GroupData_RNA, SQ_GroupData_Impl< I >, and SQ_GroupData_Impl< 6 >.

virtual SQ_GroupData* SQ_GroupData::clone ( ) const

pure virtual

Implemented in SQ_GroupData_RNA.

Referenced by create_multi_level_consensus(), and SQ_pass1_on_tree().

void SQ_GroupData::SQ_set_avg_bases ( int  bases )

inline

Definition at line 53 of file SQ_GroupData.h.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

int SQ_GroupData::SQ_get_avg_bases ( ) const

inline

Definition at line 56 of file SQ_GroupData.h.

References nr_sequences.

Referenced by SQ_pass2(), and SQ_pass2_no_tree().

void SQ_GroupData::SQ_set_avg_gc ( double  gc )

inline

Definition at line 59 of file SQ_GroupData.h.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

double SQ_GroupData::SQ_get_avg_gc ( ) const

inline

Definition at line 62 of file SQ_GroupData.h.

References nr_sequences.

Referenced by SQ_pass2(), and SQ_pass2_no_tree().

void SQ_GroupData::SQ_count_sequences ( )

inline

Definition at line 65 of file SQ_GroupData.h.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

int SQ_GroupData::SQ_get_nr_sequences ( ) const

inline

Definition at line 68 of file SQ_GroupData.h.

References nr_sequences.

Referenced by SQ_pass2_no_tree().

bool SQ_GroupData::SQ_is_initialized ( ) const

inline

Definition at line 71 of file SQ_GroupData.h.

References initialized.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

virtual void SQ_GroupData::SQ_init_consensus ( int  size )

pure virtual

Implemented in SQ_GroupData_Impl< I >, and SQ_GroupData_Impl< 6 >.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

virtual int SQ_GroupData::SQ_print_on_screen ( )

pure virtual

Implemented in SQ_GroupData_Impl< I >, and SQ_GroupData_Impl< 6 >.

virtual consensus_result SQ_GroupData::SQ_calc_consensus ( const char *  sequence ) const

pure virtual

Implemented in SQ_GroupData_RNA.

Referenced by SQ_pass2_no_tree().

virtual void SQ_GroupData::SQ_add_sequence ( const char *  sequence )

pure virtual

Implemented in SQ_GroupData_RNA.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

virtual void SQ_GroupData::SQ_add ( const SQ_GroupData &  other )

pure virtual

Implemented in SQ_GroupData_Impl< I >, and SQ_GroupData_Impl< 6 >.

Referenced by SQ_pass1_on_tree().

int SQ_GroupData::getSize ( ) const

inline

Definition at line 81 of file SQ_GroupData.h.

References size.

Referenced by SQ_pass1(), and SQ_pass1_on_tree().

Member Data Documentation

int SQ_GroupData::size

protected

Definition at line 41 of file SQ_GroupData.h.

Referenced by getSize(), SQ_GroupData_Impl< 6 >::operator=(), SQ_GroupData_Impl< I >::SQ_add(), SQ_GroupData_Impl< I >::SQ_init_consensus(), and SQ_GroupData_Impl< I >::SQ_print_on_screen().

int SQ_GroupData::avg_bases

protected

Definition at line 42 of file SQ_GroupData.h.

Referenced by SQ_GroupData_Impl< 6 >::operator=(), and SQ_GroupData_Impl< I >::SQ_add().

int SQ_GroupData::nr_sequences

protected

Definition at line 43 of file SQ_GroupData.h.

Referenced by SQ_GroupData_Impl< 6 >::operator=(), SQ_GroupData_Impl< I >::SQ_add(), SQ_get_avg_bases(), SQ_get_avg_gc(), and SQ_get_nr_sequences().

double SQ_GroupData::gc_prop

protected

Definition at line 44 of file SQ_GroupData.h.

Referenced by SQ_GroupData_Impl< 6 >::operator=(), and SQ_GroupData_Impl< I >::SQ_add().

bool SQ_GroupData::initialized

protected

Definition at line 45 of file SQ_GroupData.h.

Referenced by SQ_GroupData_Impl< 6 >::operator=(), SQ_GroupData_Impl< I >::SQ_init_consensus(), and SQ_is_initialized().

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

• SEQ_QUALITY/SQ_GroupData.h
• SEQ_QUALITY/SQ_GroupData.cxx