---

gnFastTranslator Class Reference

#include <gnFastTranslator.h>

Inheritance diagram for gnFastTranslator::

List of all members.

Public Types
enum	gnTranslatorType { ProteinDNATranslatorType, DNAProteinTranslatorType }
Public Methods
	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. More...
virtual gnSeqC	Filter (const gnSeqC ch) const
	Filter the given character. More...
virtual void	Filter (gnSeqC **seq, uint32 &len) const
	Filter the given character array. More...
virtual void	Filter (string &seq) const
	Filters the given string. More...
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)
Static Public Methods
const gnFastTranslator*	ProteinDNATranslator ()
const gnFastTranslator*	DNAProteinTranslator ()
Private Methods
void	CreateProteinDNATranslator ()
void	CreateDNAProteinTranslator ()
Private Attributes
map<string, string>	m_transCache
const gnTranslator*	m_translator
boolean	use_default
gnSeqC	m_defaultChar

---

Member Enumeration Documentation

enum gnFastTranslator::gnTranslatorType

Enumeration values: ProteinDNATranslatorType   DNAProteinTranslatorType   Definition at line 33 of file gnFastTranslator.h.

---

Constructor & Destructor Documentation

gnFastTranslator::gnFastTranslator ( )

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

gnFastTranslator::gnFastTranslator ( gnTranslatorType t_type )

Definition at line 39 of file gnFastTranslator.cpp.

gnFastTranslator::gnFastTranslator ( const gnFastTranslator & sf )

Definition at line 32 of file gnFastTranslator.cpp.

---

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. Referenced by gnFastTranslator().

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

Reimplemented from gnBaseFilter. Definition at line 84 of file gnFastTranslator.h.

void gnFastTranslator::CreateDNAProteinTranslator ( ) [private]

void gnFastTranslator::CreateProteinDNATranslator ( ) [private]

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

Definition at line 20 of file gnFastTranslator.cpp. Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator(), and main().

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

Filters the given string. Parameters: seq   The string to filter Reimplemented from gnBaseFilter. Definition at line 94 of file gnFastTranslator.cpp.

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 Reimplemented from 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 Reimplemented from gnBaseFilter. Definition at line 54 of file gnFastTranslator.cpp. Referenced by main().

gnSeqC gnFastTranslator::GetDefaultChar ( ) const [inline]

Definition at line 96 of file gnFastTranslator.h.

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

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

void gnFastTranslator::RemovePair ( const string & ch )

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

Definition at line 90 of file gnFastTranslator.h.

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

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

Definition at line 102 of file gnFastTranslator.h.

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

---

Member Data Documentation

gnSeqC gnFastTranslator::m_defaultChar [private]

Definition at line 80 of file gnFastTranslator.h.

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

Definition at line 76 of file gnFastTranslator.h.

const gnTranslator * gnFastTranslator::m_translator [private]

Definition at line 77 of file gnFastTranslator.h.

boolean gnFastTranslator::use_default [private]

Definition at line 79 of file gnFastTranslator.h.

---

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

• gnFastTranslator.h
• gnFastTranslator.cpp

---