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gnFastTranslator Class Reference

#include <gnFastTranslator.h>

Inheritance diagram for gnFastTranslator:

List of all members.

Public Types
enum	gnTranslatorType { ProteinDNATranslatorType, DNAProteinTranslatorType }
Public Member Functions
	gnFastTranslator ()
	gnFastTranslator (gnTranslatorType t_type)
	gnFastTranslator (const gnFastTranslator &sf)
gnFastTranslator &	operator= (const gnFastTranslator &sf)
gnFastTranslator *	Clone () const
virtual void	CacheTranslator (const gnTranslator *tranny, string inputs, const gnSeqI input_width)
	Queries the specified gnTranslator for every possible combination translation of the characters specified in the inputs string.
virtual gnSeqC	Filter (const gnSeqC ch) const
	Filter the given character.
virtual void	Filter (gnSeqC **seq, uint32 &len) const
	Filter the given character array.
virtual void	Filter (string &seq) const
	Filters the given string.
void	SetDefaultChar (const gnSeqC ch1)
gnSeqC	GetDefaultChar () const
void	UseDefaultChar (const boolean use=true)
void	SetPair (const string &ch1, const string &ch2)
void	RemovePair (const string &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 gnFastTranslator *	ProteinDNATranslator ()
const gnFastTranslator *	DNAProteinTranslator ()
Protected Attributes
string	m_name
Private Member Functions
void	CreateProteinDNATranslator ()
void	CreateDNAProteinTranslator ()
Private Attributes
map< string, string >	m_transCache
const gnTranslator *	m_translator
boolean	use_default
gnSeqC	m_defaultChar

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Member Enumeration Documentation

enum gnFastTranslator::gnTranslatorType

Enumeration values: ProteinDNATranslatorType  DNAProteinTranslatorType  Definition at line 32 of file gnFastTranslator.h.

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Constructor & Destructor Documentation

gnFastTranslator::gnFastTranslator (    )

Definition at line 26 of file gnFastTranslator.cpp. References m_defaultChar, and use_default. Referenced by Clone(), DNAProteinTranslator(), and ProteinDNATranslator().

gnFastTranslator::gnFastTranslator (  gnTranslatorType    t_type )

Definition at line 39 of file gnFastTranslator.cpp. References CacheTranslator(), DNAProteinTranslatorType, m_defaultChar, ProteinDNATranslatorType, and use_default.

gnFastTranslator::gnFastTranslator (  const gnFastTranslator &    sf )

Definition at line 32 of file gnFastTranslator.cpp. References m_defaultChar, gnBaseFilter::m_name, m_transCache, and use_default.

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Member Function Documentation

void gnFastTranslator::CacheTranslator (  const gnTranslator *    tranny, string    inputs, const gnSeqI    input_width )  [virtual]

Queries the specified gnTranslator for every possible combination translation of the characters specified in the inputs string. An input_width may be specified so that every possible combination of "input_width" characters in "inputs" will be cached. This is useful for DNA to protein translations, for example. Parameters: tranny  The gnTranslator to cache. inputs  The characters to cache from tranny. input_width  The number of characters in each query to make to tranny. Definition at line 125 of file gnFastTranslator.cpp. References gnTranslator::Filter(), gnSeqI, and m_transCache. Referenced by gnFastTranslator().

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

Implements gnBaseFilter. Definition at line 83 of file gnFastTranslator.h. References gnFastTranslator().

void gnFastTranslator::CreateDNAProteinTranslator (    )  [private]

void gnFastTranslator::CreateProteinDNATranslator (    )  [private]

const gnFastTranslator * gnFastTranslator::DNAProteinTranslator (    )  [static]

Definition at line 20 of file gnFastTranslator.cpp. References gnFastTranslator(). Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator().

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

Filters the given string. Parameters: seq  The string to filter Implements gnBaseFilter. Definition at line 94 of file gnFastTranslator.cpp. References gnSeqC, m_defaultChar, m_transCache, and uint32.

void gnFastTranslator::Filter (  gnSeqC **    seq, uint32 &    len )  const [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 63 of file gnFastTranslator.cpp.

gnSeqC gnFastTranslator::Filter (  const gnSeqC    ch )  const [virtual]

Filter the given character. Parameters: ch  The character to filter Returns: The filtered character Implements gnBaseFilter. Definition at line 54 of file gnFastTranslator.cpp. References gnSeqC, and m_defaultChar.

gnSeqC gnFastTranslator::GetDefaultChar (    )  const [inline]

Definition at line 95 of file gnFastTranslator.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.

gnFastTranslator& gnFastTranslator::operator= (  const gnFastTranslator &    sf )

const gnFastTranslator * gnFastTranslator::ProteinDNATranslator (    )  [static]

Definition at line 16 of file gnFastTranslator.cpp. References gnFastTranslator(). Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator().

void gnFastTranslator::RemovePair (  const string &    ch )

void gnFastTranslator::SetDefaultChar (  const gnSeqC    ch1 )  [inline]

Definition at line 89 of file gnFastTranslator.h. References m_defaultChar, and use_default.

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 gnFilter::CreateAlphabetCharacterFilter(), gnFilter::CreateBasicDNAFilter(), gnFilter::CreateBasicRNAFilter(), gnFilter::CreateDNAComplementFilter(), gnTranslator::CreateDNAProteinTranslator(), gnFilter::CreateDNAtoRNAFilter(), gnFilter::CreateFullDNAFilter(), gnFilter::CreateFullRNAFilter(), gnFilter::CreateNumberCharacterFilter(), gnTranslator::CreateProteinDNATranslator(), gnFilter::CreateProteinFilter(), gnTranslator::CreateProteinRNATranslator(), gnFilter::CreateRNAComplementFilter(), gnTranslator::CreateRNAProteinTranslator(), and gnFilter::CreateRNAtoDNAFilter().

void gnFastTranslator::SetPair (  const string &    ch1, const string &    ch2 )

void gnFastTranslator::UseDefaultChar (  const boolean    use = true )  [inline]

Definition at line 101 of file gnFastTranslator.h. References use_default.

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Member Data Documentation

gnSeqC gnFastTranslator::m_defaultChar [private]

Definition at line 79 of file gnFastTranslator.h. Referenced by Filter(), GetDefaultChar(), gnFastTranslator(), and SetDefaultChar().

string gnBaseFilter::m_name [protected, inherited]

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

map<string, string> gnFastTranslator::m_transCache [private]

Definition at line 75 of file gnFastTranslator.h. Referenced by CacheTranslator(), Filter(), and gnFastTranslator().

const gnTranslator* gnFastTranslator::m_translator [private]

Definition at line 76 of file gnFastTranslator.h.

boolean gnFastTranslator::use_default [private]

Definition at line 78 of file gnFastTranslator.h. Referenced by gnFastTranslator(), SetDefaultChar(), and UseDefaultChar().

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

• gnFastTranslator.h
• gnFastTranslator.cpp

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