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gnFilter Class Reference

#include <gnFilter.h>

Inheritance diagram for gnFilter:


Public Types
enum	gnFilterType { alphabetCharacterFilterType, numberCharacterFilterType, proteinSeqFilterType, basicDNASeqFilterType, fullDNASeqFilterType, basicRNASeqFilterType, fullRNASeqFilterType, DNAtoRNAFilterType, RNAtoDNAFilterType, DNAComplementFilterType, RNAComplementFilterType }
Public Member Functions
	gnFilter ()
	gnFilter (const gnFilterType f_type)
	Creates a gnFilter for a predefined filter type.
	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.
uint32	IsValid (const gnSeqC *seq, const uint32 len) const
	IsValid() scans the supplied character array for invalid characters.
void	MakeValid (gnSeqC *seq, const uint32 len) const
void	Filter (gnSeqC **seq, gnSeqI &len) const
	Filter the given character array.
void	ReverseFilter (gnSeqC **seq, gnSeqI &len) const
uint32	IsValid (const string &seq) const
void	MakeValid (string &seq) const
void	Filter (string &seq) const
	Filters the given string.
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)
virtual string	GetName () const
	Gets the name of this filter.
virtual void	SetName (string name)
	Sets the name of this filter.
Static Public Member Functions
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 ()
Protected Attributes
string	m_name
Private Member Functions
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

Member Enumeration Documentation

enum gnFilter::gnFilterType

Enumeration values:

alphabetCharacterFilterType

numberCharacterFilterType

proteinSeqFilterType

basicDNASeqFilterType

fullDNASeqFilterType

basicRNASeqFilterType

fullRNASeqFilterType

DNAtoRNAFilterType

RNAtoDNAFilterType

DNAComplementFilterType

RNAComplementFilterType

Definition at line 41 of file gnFilter.h.

Constructor & Destructor Documentation

gnFilter::gnFilter ( )

Definition at line 75 of file gnFilter.cpp.
References gnSeqC, GNSEQC_MAX, m_defaultChar, m_pairArray, m_rDefaultChar, and NO_REVCOMP_CHAR.
Referenced by alphabetCharacterFilter(), basicDNASeqFilter(), basicRNASeqFilter(), Clone(), DNAComplementFilter(), DNAtoRNAFilter(), fullDNASeqFilter(), fullRNASeqFilter(), numberCharacterFilter(), proteinSeqFilter(), RNAComplementFilter(), and RNAtoDNAFilter().

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 99 of file gnFilter.cpp.
References alphabetCharacterFilterType, basicDNASeqFilterType, basicRNASeqFilterType, CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), CreateRNAtoDNAFilter(), DNAComplementFilterType, DNAtoRNAFilterType, fullDNASeqFilterType, fullRNASeqFilterType, gnSeqC, GNSEQC_MAX, m_pairArray, NO_REVCOMP_CHAR, numberCharacterFilterType, proteinSeqFilterType, RNAComplementFilterType, and RNAtoDNAFilterType.

gnFilter::gnFilter ( const gnSeqC defaultChar,

const gnSeqC rdefaultChar

)

Definition at line 82 of file gnFilter.cpp.
References gnSeqC, GNSEQC_MAX, m_defaultChar, m_pairArray, m_rDefaultChar, and NO_REVCOMP_CHAR.

gnFilter::gnFilter ( const gnFilter & sf )

Definition at line 90 of file gnFilter.cpp.
References gnSeqC, GNSEQC_MAX, m_defaultChar, gnBaseFilter::m_name, m_pairArray, and m_rDefaultChar.

gnFilter::~gnFilter ( )

Definition at line 140 of file gnFilter.cpp.

Member Function Documentation

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

Definition at line 17 of file gnFilter.cpp.
References gnFilter().

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

Definition at line 33 of file gnFilter.cpp.
References gnFilter().

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

Definition at line 43 of file gnFilter.cpp.
References gnFilter().

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

Implements gnBaseFilter.
Definition at line 128 of file gnFilter.h.
References gnFilter().

void gnFilter::CreateAlphabetCharacterFilter ( ) [private]

Definition at line 222 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetPair().
Referenced by gnFilter().

void gnFilter::CreateBasicDNAFilter ( ) [private]

Definition at line 317 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateBasicRNAFilter ( ) [private]

Definition at line 373 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateDNAComplementFilter ( ) [private]

Definition at line 499 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateDNAtoRNAFilter ( ) [private]

Definition at line 427 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateFullDNAFilter ( ) [private]

Definition at line 335 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateFullRNAFilter ( ) [private]

Definition at line 389 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateNumberCharacterFilter ( ) [private]

Definition at line 254 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateProteinFilter ( ) [private]

Definition at line 270 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateRNAComplementFilter ( ) [private]

Definition at line 537 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle().
Referenced by gnFilter().

void gnFilter::CreateRNAtoDNAFilter ( ) [private]

Definition at line 463 of file gnFilter.cpp.
References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle().
Referenced by gnFilter().

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

Definition at line 63 of file gnFilter.cpp.
References gnFilter().
Referenced by gnContigSpec::SeqRead().

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

Definition at line 53 of file gnFilter.cpp.
References gnFilter().

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

Filters the given string.

Parameters:

seq The string to filter

Implements gnBaseFilter.
Definition at line 186 of file gnFilter.cpp.
References gnSeqI, IsValid(), m_pairArray, and uint32.

void gnFilter::Filter ( gnSeqC ** seq,

gnSeqI & 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

Implements gnBaseFilter.
Definition at line 145 of file gnFilter.cpp.
References Array< T >::data, gnSeqC, gnSeqI, IsValid(), m_pairArray, and uint32.

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

Filter the given character.

Parameters:

ch The character to filter

Returns:
The filtered character

Implements gnBaseFilter.
Definition at line 145 of file gnFilter.h.
References gnSeqC, m_defaultChar, m_pairArray, and NO_REVCOMP_CHAR.

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

Definition at line 38 of file gnFilter.cpp.
References gnFilter().
Referenced by gnABISource::gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), gnGBKSource::gnGBKSource(), and gnSEQSource::gnSEQSource().

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

Definition at line 48 of file gnFilter.cpp.
References gnFilter().

gnSeqC gnFilter::GetDefaultChar ( ) const [inline]

Definition at line 190 of file gnFilter.h.
References gnSeqC, and m_defaultChar.

string gnBaseFilter::GetName ( ) const [inline, virtual, inherited]

Gets the name of this filter.

Returns:
the filter name

Definition at line 65 of file gnBaseFilter.h.
References gnBaseFilter::m_name.

gnSeqC gnFilter::GetRDefaultChar ( ) const [inline]

Definition at line 195 of file gnFilter.h.
References gnSeqC, and m_rDefaultChar.

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

Definition at line 172 of file gnFilter.h.
References IsValid(), and uint32.

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 152 of file gnFilter.h.
References IsValid(), and uint32.

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

Definition at line 135 of file gnFilter.h.
References m_pairArray, and NO_REVCOMP_CHAR.
Referenced by Filter(), IsValid(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), and gnFASSource::SeqStartPos().

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

Definition at line 177 of file gnFilter.h.
References MakeValid().

void gnFilter::MakeValid ( gnSeqC * seq,

const uint32 len

) const [inline]

Definition at line 162 of file gnFilter.h.
References MakeValid(), and uint32.

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

Definition at line 140 of file gnFilter.h.
References gnSeqC, m_defaultChar, m_pairArray, and NO_REVCOMP_CHAR.
Referenced by MakeValid().

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

Definition at line 22 of file gnFilter.cpp.
References gnFilter().

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

Definition at line 28 of file gnFilter.cpp.
References gnFilter().

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

Definition at line 212 of file gnFilter.h.
References m_pairArray, and NO_REVCOMP_CHAR.

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

Definition at line 219 of file gnFilter.h.
References m_pairArray, and NO_REVCOMP_CHAR.

void gnFilter::ReverseFilter ( string & seq ) const

Definition at line 194 of file gnFilter.cpp.
References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint32.

void gnFilter::ReverseFilter ( gnSeqC ** seq,

gnSeqI & len

) const

Definition at line 157 of file gnFilter.cpp.
References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint32.
Referenced by gnContigSpec::SeqRead().

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

Definition at line 68 of file gnFilter.cpp.
References gnFilter().

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

Definition at line 58 of file gnFilter.cpp.
References gnFilter().

void gnFilter::SetDefaultChar ( const gnSeqC ch1,

const gnSeqC ch2

) [inline]

Definition at line 184 of file gnFilter.h.
References m_defaultChar, and m_rDefaultChar.
Referenced by CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

void gnBaseFilter::SetName ( string name ) [inline, virtual, inherited]

Sets the name of this filter.

Parameters:

name the new filter name

Definition at line 70 of file gnBaseFilter.h.
References gnBaseFilter::m_name.
Referenced by CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), gnTranslator::CreateDNAProteinTranslator(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), gnTranslator::CreateProteinDNATranslator(), CreateProteinFilter(), gnTranslator::CreateProteinRNATranslator(), CreateRNAComplementFilter(), gnTranslator::CreateRNAProteinTranslator(), and CreateRNAtoDNAFilter().

void gnFilter::SetPair ( const gnSeqC ch1,

const gnSeqC ch2

) [inline]

Definition at line 206 of file gnFilter.h.
References m_pairArray.
Referenced by CreateAlphabetCharacterFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

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

Definition at line 201 of file gnFilter.h.
References m_pairArray.
Referenced by CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter().

Member Data Documentation

gnSeqC gnFilter::m_defaultChar [private]

Definition at line 122 of file gnFilter.h.
Referenced by Filter(), GetDefaultChar(), gnFilter(), MakeValid(), and SetDefaultChar().

string gnBaseFilter::m_name [protected, inherited]

Definition at line 60 of file gnBaseFilter.h.
Referenced by gnBaseFilter::GetName(), gnFastTranslator::gnFastTranslator(), gnFilter(), gnPosSpecificTranslator::gnPosSpecificTranslator(), gnTranslator::gnTranslator(), and gnBaseFilter::SetName().

gnSeqC gnFilter::m_pairArray[GNSEQC_MAX] [private]

Definition at line 121 of file gnFilter.h.
Referenced by Filter(), gnFilter(), IsValid(), MakeValid(), RemovePair(), RemoveSingle(), ReverseFilter(), SetPair(), and SetSingle().

gnSeqC gnFilter::m_rDefaultChar [private]

Definition at line 123 of file gnFilter.h.
Referenced by GetRDefaultChar(), gnFilter(), and SetDefaultChar().

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

Generated on Fri May 9 12:57:58 2003 for libGenome by

1.3-rc3

gnFilter Class Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation