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gnTranslator Class Reference

The gnTranslator class facilitates the translation of ambiguous DNA and RNA sequences to protein sequence. More...

#include <gnTranslator.h>

Inheritance diagram for gnTranslator:


Public Types
enum	gnTranslatorType { ProteinDNATranslatorType, ProteinRNATranslatorType, DNAProteinTranslatorType, RNAProteinTranslatorType }
Public Member Functions
	gnTranslator ()
	gnTranslator (gnTranslatorType t_type)
	gnTranslator (const gnTranslator &sf)
gnTranslator *	Clone () const
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)
	Sets the default character to insert when no valid translation exists.
gnSeqC	GetDefaultChar () const
	Gets the default character which is inserted into the destination sequence when no valid translation exists.
void	UseDefaultChar (const boolean use=true)
	Set whether the default character is inserted upon translation failure.
void	SetDefaultInputWidth (const uint32 defaultInputWidth)
	Set the expected number of characters in each unit of translation.
uint32	GetDefaultInputWidth () const
	Get the expected number of characters in each unit of translation.
void	SetPair (const string &input, const string &output)
	Set a translation mapping.
void	RemovePair (const string &input)
	Removes a translation mapping.
void	SetCompare (const gnCompare *comp)
	Set the comparator to use.
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 gnTranslator *	ProteinDNATranslator ()
const gnTranslator *	ProteinRNATranslator ()
const gnTranslator *	DNAProteinTranslator ()
const gnTranslator *	RNAProteinTranslator ()
Protected Attributes
string	m_name
Private Member Functions
void	CreateProteinDNATranslator ()
void	CreateProteinRNATranslator ()
void	CreateDNAProteinTranslator ()
void	CreateRNAProteinTranslator ()
Private Attributes
vector< string >	m_inputTable
vector< string >	m_outputTable
const gnCompare *	compare
boolean	use_default
gnSeqC	m_defaultChar
uint32	m_defaultInputWidth

Detailed Description

The gnTranslator class facilitates the translation of ambiguous DNA and RNA sequences to protein sequence.

It can also perform reverse translation from Protein to RNA or DNA though the utility of this functionality is somewhat questionable since it does not assign nucleotides probabilistically. Do not attempt to instantiate this class unless you are defining a new translation type. Instead use the static member access functions ProteinDNATranslator(), ProteinRNATranslator(), DNAProteinTranslator(), and RNAProteinTranslator() In general, the gnFastTranslator class should be used instead of this one.

See also:: gnFastTranslator

Definition at line 36 of file gnTranslator.h.

Member Enumeration Documentation

enum gnTranslator::gnTranslatorType

Enumeration values:

ProteinDNATranslatorType

ProteinRNATranslatorType

DNAProteinTranslatorType

RNAProteinTranslatorType

Definition at line 45 of file gnTranslator.h.

Constructor & Destructor Documentation

gnTranslator::gnTranslator ( )

Definition at line 34 of file gnTranslator.cpp.
References m_defaultChar, m_defaultInputWidth, and use_default.
Referenced by Clone(), DNAProteinTranslator(), ProteinDNATranslator(), ProteinRNATranslator(), and RNAProteinTranslator().

gnTranslator::gnTranslator ( gnTranslatorType t_type )

Definition at line 51 of file gnTranslator.cpp.
References CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), CreateRNAProteinTranslator(), DNAProteinTranslatorType, m_defaultChar, ProteinDNATranslatorType, ProteinRNATranslatorType, RNAProteinTranslatorType, and use_default.

gnTranslator::gnTranslator ( const gnTranslator & sf )

Definition at line 41 of file gnTranslator.cpp.
References compare, m_defaultChar, m_defaultInputWidth, m_inputTable, gnBaseFilter::m_name, m_outputTable, and use_default.

Member Function Documentation

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

Implements gnBaseFilter.
Definition at line 134 of file gnTranslator.h.
References gnTranslator().

void gnTranslator::CreateDNAProteinTranslator ( ) [private]

Definition at line 224 of file gnTranslator.cpp.
References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and use_default.
Referenced by gnTranslator().

void gnTranslator::CreateProteinDNATranslator ( ) [private]

Definition at line 160 of file gnTranslator.cpp.
References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), and SetPair().
Referenced by gnTranslator().

void gnTranslator::CreateProteinRNATranslator ( ) [private]

Definition at line 192 of file gnTranslator.cpp.
References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), and SetPair().
Referenced by gnTranslator().

void gnTranslator::CreateRNAProteinTranslator ( ) [private]

Definition at line 287 of file gnTranslator.cpp.
References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and use_default.
Referenced by gnTranslator().

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

Definition at line 24 of file gnTranslator.cpp.
References gnTranslator().

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

Filters the given string.

Parameters:

seq The string to filter

Implements gnBaseFilter.
Definition at line 112 of file gnTranslator.cpp.
References compare, gnCompare::Contains(), m_defaultChar, m_defaultInputWidth, m_inputTable, m_outputTable, and uint32.

void gnTranslator::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 81 of file gnTranslator.cpp.
References compare, gnCompare::Contains(), gnSeqC, m_defaultChar, m_defaultInputWidth, m_inputTable, m_outputTable, and uint32.

gnSeqC gnTranslator::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 72 of file gnTranslator.cpp.
References compare, gnCompare::Contains(), gnSeqC, m_defaultChar, m_inputTable, m_outputTable, and uint32.
Referenced by gnFastTranslator::CacheTranslator().

gnSeqC gnTranslator::GetDefaultChar ( ) const [inline]

Gets the default character which is inserted into the destination sequence when no valid translation exists.

Returns:
The default character

Definition at line 146 of file gnTranslator.h.
References gnSeqC, and m_defaultChar.

uint32 gnTranslator::GetDefaultInputWidth ( ) const [inline]

Get the expected number of characters in each unit of translation.
For DNA to Protein, for instance, this is 3 because each codon is 3 characters of input.
Returns:
The expected input width

Definition at line 163 of file gnTranslator.h.
References m_defaultInputWidth, and uint32.

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.

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

Definition at line 16 of file gnTranslator.cpp.
References gnTranslator().

const gnTranslator * gnTranslator::ProteinRNATranslator ( ) [static]

Definition at line 20 of file gnTranslator.cpp.
References gnTranslator().

void gnTranslator::RemovePair ( const string & input )

Removes a translation mapping.
RemovePair removes the translation mapping corresponding to the given input string.
Parameters:

input The input string to delete

Definition at line 149 of file gnTranslator.cpp.
References m_inputTable, m_outputTable, and uint32.

const gnTranslator * gnTranslator::RNAProteinTranslator ( ) [static]

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

void gnTranslator::SetCompare ( const gnCompare * comp ) [inline]

Set the comparator to use.
Ambiguous base matching is facilitated using a gnCompare object. This must be set to allow sequences to be compared.
Parameters:

comp A pointer to the gnCompare object to use.

Definition at line 168 of file gnTranslator.h.
References compare.
Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator().

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

Sets the default character to insert when no valid translation exists.

Parameters:

ch1 The default character

Definition at line 140 of file gnTranslator.h.
References m_defaultChar, and use_default.
Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator().

void gnTranslator::SetDefaultInputWidth ( const uint32 defaultInputWidth ) [inline]

Set the expected number of characters in each unit of translation.
For DNA to Protein, for instance, this is 3 because each codon is 3 characters of input.
Parameters:

defaultInputWidth The expected input width

Definition at line 158 of file gnTranslator.h.
References m_defaultInputWidth.

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(), CreateDNAProteinTranslator(), gnFilter::CreateDNAtoRNAFilter(), gnFilter::CreateFullDNAFilter(), gnFilter::CreateFullRNAFilter(), gnFilter::CreateNumberCharacterFilter(), CreateProteinDNATranslator(), gnFilter::CreateProteinFilter(), CreateProteinRNATranslator(), gnFilter::CreateRNAComplementFilter(), CreateRNAProteinTranslator(), and gnFilter::CreateRNAtoDNAFilter().

void gnTranslator::SetPair ( const string & input,

const string & output

)

Set a translation mapping.
The first value is the input, the second value is the output. During translation, any occurrences of the first string will be transformed to the second string. A gnCompare object is used to facilitate ambiguity matching.
Parameters:

input The input string

output The string to output every time the input string is encountered

Definition at line 140 of file gnTranslator.cpp.
References m_inputTable, and m_outputTable.
Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator().

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

Set whether the default character is inserted upon translation failure.

Parameters:

use True if the default character should be used.

Definition at line 152 of file gnTranslator.h.
References use_default.

Member Data Documentation

const gnCompare* gnTranslator::compare [private]

Definition at line 126 of file gnTranslator.h.
Referenced by Filter(), gnTranslator(), and SetCompare().

gnSeqC gnTranslator::m_defaultChar [private]

Definition at line 129 of file gnTranslator.h.
Referenced by Filter(), GetDefaultChar(), gnTranslator(), and SetDefaultChar().

uint32 gnTranslator::m_defaultInputWidth [private]

Definition at line 130 of file gnTranslator.h.
Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), CreateRNAProteinTranslator(), Filter(), GetDefaultInputWidth(), gnTranslator(), and SetDefaultInputWidth().

vector<string> gnTranslator::m_inputTable [private]

Definition at line 124 of file gnTranslator.h.
Referenced by Filter(), gnTranslator(), RemovePair(), and SetPair().

string gnBaseFilter::m_name [protected, inherited]

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

vector<string> gnTranslator::m_outputTable [private]

Definition at line 124 of file gnTranslator.h.
Referenced by Filter(), gnTranslator(), RemovePair(), and SetPair().

boolean gnTranslator::use_default [private]

Definition at line 128 of file gnTranslator.h.
Referenced by CreateDNAProteinTranslator(), CreateRNAProteinTranslator(), gnTranslator(), SetDefaultChar(), and UseDefaultChar().

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

Generated on Mon Feb 3 02:34:55 2003 for libGenome by

1.3-rc3

gnTranslator Class Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation