ARB
Public Member Functions | Protected Attributes | List of all members
SQ_GroupData Class Referenceabstract

#include <SQ_GroupData.h>

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Collaboration diagram for SQ_GroupData:
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Public Member Functions

 SQ_GroupData ()
 
virtual ~SQ_GroupData ()
 
virtual SQ_GroupDataoperator= (const SQ_GroupData &other)=0
 
virtual SQ_GroupDataclone () 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
virtual SQ_GroupData* SQ_GroupData::clone ( ) const
pure virtual
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
virtual int SQ_GroupData::SQ_print_on_screen ( )
pure virtual
virtual consensus_result SQ_GroupData::SQ_calc_consensus ( const char sequence) const
pure virtual

Implemented in SQ_GroupData_PRO, and 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_PRO, and SQ_GroupData_RNA.

Referenced by SQ_pass1(), and SQ_pass1_no_tree().

virtual void SQ_GroupData::SQ_add ( const SQ_GroupData other)
pure virtual
int SQ_GroupData::getSize ( ) const
inline

Definition at line 81 of file SQ_GroupData.h.

References size.

Referenced by SQ_calc_and_apply_group_data().

Member Data Documentation

int SQ_GroupData::size
protected
int SQ_GroupData::avg_bases
protected
int SQ_GroupData::nr_sequences
protected
double SQ_GroupData::gc_prop
protected
bool SQ_GroupData::initialized
protected

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