gnFastTranslator Class Reference

#include <gnFastTranslator.h>

Inheritance diagram for gnFastTranslator:

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Collaboration diagram for gnFastTranslator:

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List of all members.

Public Types

enum  gnTranslatorType { ProteinDNATranslatorType, DNAProteinTranslatorType }

Public Member Functions

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.
gnFastTranslatorClone () const
virtual void Filter (string &seq) const
 Filters the given string.
virtual void Filter (gnSeqC **seq, gnSeqI &len) const
 Filter the given character array.
virtual gnSeqC Filter (const gnSeqC ch) const
 Filter the given character.
gnSeqC GetDefaultChar () const
 gnFastTranslator (const gnFastTranslator &sf)
 gnFastTranslator (gnTranslatorType t_type)
 gnFastTranslator ()
gnFastTranslatoroperator= (const gnFastTranslator &sf)
void RemovePair (const string &ch)
void SetDefaultChar (const gnSeqC ch1)
void SetPair (const string &ch1, const string &ch2)
void UseDefaultChar (const boolean use=true)

Static Public Member Functions

const gnFastTranslatorDNAProteinTranslator ()
const gnFastTranslatorProteinDNATranslator ()

Private Member Functions

void CreateDNAProteinTranslator ()
void CreateProteinDNATranslator ()

Private Attributes

gnSeqC m_defaultChar
map< string, string > m_transCache
const gnTranslatorm_translator
boolean use_default

Member Enumeration Documentation

enum gnFastTranslator::gnTranslatorType
 

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


Constructor & Destructor Documentation

gnFastTranslator::gnFastTranslator  ) 
 

Definition at line 26 of file gnFastTranslator.cpp.

References m_defaultChar, and use_default.

Referenced by 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.


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.

void gnFastTranslator::CreateDNAProteinTranslator  )  [private]
 

void gnFastTranslator::CreateProteinDNATranslator  )  [private]
 

const gnFastTranslator * gnFastTranslator::DNAProteinTranslator  )  [static]
 

Definition at line 20 of file gnFastTranslator.cpp.

References DNAProteinTranslatorType, and gnFastTranslator().

Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator(), and main().

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, uint32, and use_default.

void gnFastTranslator::Filter gnSeqC **  seq,
gnSeqI 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.

References gnSeqC, and gnSeqI.

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.

Referenced by main().

gnSeqC gnFastTranslator::GetDefaultChar  )  const [inline]
 

Definition at line 95 of file gnFastTranslator.h.

References gnSeqC, and m_defaultChar.

gnFastTranslator& gnFastTranslator::operator= const gnFastTranslator sf  ) 
 

const gnFastTranslator * gnFastTranslator::ProteinDNATranslator  )  [static]
 

Definition at line 16 of file gnFastTranslator.cpp.

References gnFastTranslator(), and ProteinDNATranslatorType.

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 gnSeqC, m_defaultChar, and use_default.

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.


Member Data Documentation

gnSeqC gnFastTranslator::m_defaultChar [private]
 

Definition at line 79 of file gnFastTranslator.h.

Referenced by Filter(), GetDefaultChar(), gnFastTranslator(), and SetDefaultChar().

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 Filter(), gnFastTranslator(), SetDefaultChar(), and UseDefaultChar().


The documentation for this class was generated from the following files:
Generated on Mon Feb 14 19:29:50 2005 for libGenome by doxygen 1.3.8