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gnFilter Class Reference

#include <gnFilter.h>

Inheritance diagram for gnFilter::

List of all members.

Public Types
enum	gnFilterType {   alphabetCharacterFilterType, numberCharacterFilterType, proteinSeqFilterType, basicDNASeqFilterType,   fullDNASeqFilterType, basicRNASeqFilterType, fullRNASeqFilterType, DNAtoRNAFilterType,   RNAtoDNAFilterType, DNAComplementFilterType, RNAComplementFilterType }
Public Methods
	gnFilter ()
	gnFilter (const gnFilterType f_type)
	Creates a gnFilter for a predefined filter type. More...
	gnFilter (const gnSeqC defaultChar, const gnSeqC rdefaultChar)
	gnFilter (const gnFilter &sf)
	~gnFilter ()
gnFilter*	Clone () const
boolean	IsValid (const gnSeqC ch) const
gnSeqC	MakeValid (const gnSeqC ch) const
gnSeqC	Filter (const gnSeqC ch) const
	Filter the given character. More...
uint32	IsValid (const gnSeqC *seq, const uint32 len) const
	IsValid() scans the supplied character array for invalid characters. More...
void	MakeValid (gnSeqC *seq, const uint32 len) const
void	Filter (gnSeqC **seq, uint32 &len) const
	Filter the given character array. More...
void	ReverseFilter (gnSeqC **seq, uint32 &len) const
uint32	IsValid (const string &seq) const
void	MakeValid (string &seq) const
void	Filter (string &seq) const
	Filters the given string. More...
void	ReverseFilter (string &seq) const
void	SetDefaultChar (const gnSeqC ch1, const gnSeqC ch2)
gnSeqC	GetDefaultChar () const
gnSeqC	GetRDefaultChar () const
void	SetSingle (const gnSeqC ch)
void	SetPair (const gnSeqC ch1, const gnSeqC ch2)
boolean	RemovePair (const gnSeqC ch)
boolean	RemoveSingle (const gnSeqC ch)
Static Public Methods
const gnFilter*	alphabetCharacterFilter ()
const gnFilter*	numberCharacterFilter ()
const gnFilter*	proteinSeqFilter ()
const gnFilter*	basicDNASeqFilter ()
const gnFilter*	fullDNASeqFilter ()
const gnFilter*	basicRNASeqFilter ()
const gnFilter*	fullRNASeqFilter ()
const gnFilter*	DNAtoRNAFilter ()
const gnFilter*	RNAtoDNAFilter ()
const gnFilter*	DNAComplementFilter ()
const gnFilter*	RNAComplementFilter ()
Private Methods
void	CreateAlphabetCharacterFilter ()
void	CreateNumberCharacterFilter ()
void	CreateProteinFilter ()
void	CreateBasicDNAFilter ()
void	CreateFullDNAFilter ()
void	CreateBasicRNAFilter ()
void	CreateFullRNAFilter ()
void	CreateDNAtoRNAFilter ()
void	CreateRNAtoDNAFilter ()
void	CreateDNAComplementFilter ()
void	CreateRNAComplementFilter ()
Private Attributes
gnSeqC	m_pairArray [GNSEQC_MAX]
gnSeqC	m_defaultChar
gnSeqC	m_rDefaultChar

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Member Enumeration Documentation

enum gnFilter::gnFilterType

Enumeration values: alphabetCharacterFilterType   numberCharacterFilterType   proteinSeqFilterType   basicDNASeqFilterType   fullDNASeqFilterType   basicRNASeqFilterType   fullRNASeqFilterType   DNAtoRNAFilterType   RNAtoDNAFilterType   DNAComplementFilterType   RNAComplementFilterType   Definition at line 42 of file gnFilter.h.

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Constructor & Destructor Documentation

gnFilter::gnFilter ( )

Definition at line 76 of file gnFilter.cpp. Referenced by Clone(), DNAComplementFilter(), DNAtoRNAFilter(), RNAComplementFilter(), RNAtoDNAFilter(), alphabetCharacterFilter(), basicDNASeqFilter(), basicRNASeqFilter(), fullDNASeqFilter(), fullRNASeqFilter(), numberCharacterFilter(), and proteinSeqFilter().

gnFilter::gnFilter ( const gnFilterType f_type )

Creates a gnFilter for a predefined filter type. Used by the static sequence constructors to avoid the "static initialization order fiasco" Parameters: f_type   The type of filter to create. See also: gnFilterType Definition at line 100 of file gnFilter.cpp.

gnFilter::gnFilter ( const gnSeqC defaultChar, const gnSeqC rdefaultChar )

Definition at line 83 of file gnFilter.cpp.

gnFilter::gnFilter ( const gnFilter & sf )

Definition at line 91 of file gnFilter.cpp.

gnFilter::~gnFilter ( )

Definition at line 141 of file gnFilter.cpp.

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Member Function Documentation

gnFilter * gnFilter::Clone ( ) const [inline, virtual]

Reimplemented from gnBaseFilter. Definition at line 129 of file gnFilter.h.

void gnFilter::CreateAlphabetCharacterFilter ( ) [private]

Definition at line 223 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateBasicDNAFilter ( ) [private]

Definition at line 318 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateBasicRNAFilter ( ) [private]

Definition at line 374 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateDNAComplementFilter ( ) [private]

Definition at line 500 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateDNAtoRNAFilter ( ) [private]

Definition at line 428 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateFullDNAFilter ( ) [private]

Definition at line 336 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateFullRNAFilter ( ) [private]

Definition at line 390 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateNumberCharacterFilter ( ) [private]

Definition at line 255 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateProteinFilter ( ) [private]

Definition at line 271 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateRNAComplementFilter ( ) [private]

Definition at line 538 of file gnFilter.cpp. Referenced by gnFilter().

void gnFilter::CreateRNAtoDNAFilter ( ) [private]

Definition at line 464 of file gnFilter.cpp. Referenced by gnFilter().

const gnFilter * gnFilter::DNAComplementFilter ( ) [static]

Definition at line 64 of file gnFilter.cpp. Referenced by gnContigSpec::SeqRead().

const gnFilter * gnFilter::DNAtoRNAFilter ( ) [static]

Definition at line 54 of file gnFilter.cpp.

void gnFilter::Filter ( string & seq ) const [virtual]

Filters the given string. Parameters: seq   The string to filter Reimplemented from gnBaseFilter. Definition at line 187 of file gnFilter.cpp.

void gnFilter::Filter ( gnSeqC ** seq, uint32 & len ) const [inline, virtual]

Filter the given character array. Parameters: seq   A pointer to the character array len   the length of the character array to filter Returns: The filtered character Reimplemented from gnBaseFilter. Definition at line 146 of file gnFilter.cpp.

gnSeqC gnFilter::Filter ( const gnSeqC ch ) const [inline, virtual]

Filter the given character. Parameters: ch   The character to filter Returns: The filtered character Reimplemented from gnBaseFilter. Definition at line 146 of file gnFilter.h.

gnSeqC gnFilter::GetDefaultChar ( ) const [inline]

Definition at line 191 of file gnFilter.h.

gnSeqC gnFilter::GetRDefaultChar ( ) const [inline]

Definition at line 196 of file gnFilter.h.

uint32 gnFilter::IsValid ( const string & seq ) const [inline]

Definition at line 173 of file gnFilter.h.

uint32 gnFilter::IsValid ( const gnSeqC * seq, const uint32 len ) const [inline]

IsValid() scans the supplied character array for invalid characters. Parameters: seq   The sequence to scan. This is a generic character array. len   The length of the sequence to scan. Returns: The index of the first invalid character, or len if none exists Definition at line 153 of file gnFilter.h.

boolean gnFilter::IsValid ( const gnSeqC ch ) const [inline]

Definition at line 136 of file gnFilter.h. Referenced by Filter(), and IsValid().

void gnFilter::MakeValid ( string & seq ) const [inline]

Definition at line 178 of file gnFilter.h.

void gnFilter::MakeValid ( gnSeqC * seq, const uint32 len ) const [inline]

Definition at line 163 of file gnFilter.h.

gnSeqC gnFilter::MakeValid ( const gnSeqC ch ) const [inline]

Definition at line 141 of file gnFilter.h. Referenced by MakeValid().

const gnFilter * gnFilter::RNAComplementFilter ( ) [static]

Definition at line 69 of file gnFilter.cpp.

const gnFilter * gnFilter::RNAtoDNAFilter ( ) [static]

Definition at line 59 of file gnFilter.cpp.

boolean gnFilter::RemovePair ( const gnSeqC ch ) [inline]

Definition at line 213 of file gnFilter.h.

boolean gnFilter::RemoveSingle ( const gnSeqC ch ) [inline]

Definition at line 220 of file gnFilter.h.

void gnFilter::ReverseFilter ( string & seq ) const

Definition at line 195 of file gnFilter.cpp.

void gnFilter::ReverseFilter ( gnSeqC ** seq, uint32 & len ) const

Definition at line 158 of file gnFilter.cpp. Referenced by gnContigSpec::SeqRead().

void gnFilter::SetDefaultChar ( const gnSeqC ch1, const gnSeqC ch2 ) [inline]

Definition at line 185 of file gnFilter.h. Referenced by CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

void gnFilter::SetPair ( const gnSeqC ch1, const gnSeqC ch2 ) [inline]

Definition at line 207 of file gnFilter.h. Referenced by CreateAlphabetCharacterFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

void gnFilter::SetSingle ( const gnSeqC ch ) [inline]

Definition at line 202 of file gnFilter.h. Referenced by CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

const gnFilter * gnFilter::alphabetCharacterFilter ( ) [static]

Definition at line 18 of file gnFilter.cpp.

const gnFilter * gnFilter::basicDNASeqFilter ( ) [static]

Definition at line 34 of file gnFilter.cpp.

const gnFilter * gnFilter::basicRNASeqFilter ( ) [static]

Definition at line 44 of file gnFilter.cpp.

const gnFilter * gnFilter::fullDNASeqFilter ( ) [static]

Definition at line 39 of file gnFilter.cpp. Referenced by gnABISource::gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), gnGBKSource::gnGBKSource(), and gnSEQSource::gnSEQSource().

const gnFilter * gnFilter::fullRNASeqFilter ( ) [static]

Definition at line 49 of file gnFilter.cpp.

const gnFilter * gnFilter::numberCharacterFilter ( ) [static]

Definition at line 23 of file gnFilter.cpp.

const gnFilter * gnFilter::proteinSeqFilter ( ) [static]

Definition at line 29 of file gnFilter.cpp.

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Member Data Documentation

gnSeqC gnFilter::m_defaultChar [private]

Definition at line 123 of file gnFilter.h.

gnSeqC gnFilter::m_pairArray [private]

Definition at line 122 of file gnFilter.h.

gnSeqC gnFilter::m_rDefaultChar [private]

Definition at line 124 of file gnFilter.h.

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

• gnFilter.h
• gnFilter.cpp

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