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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 Methods
	gnTranslator ()
	gnTranslator (gnTranslatorType t_type)
	gnTranslator (const gnTranslator &sf)
gnTranslator*	Clone () const
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)
	Sets the default character to insert when no valid translation exists. More...
gnSeqC	GetDefaultChar () const
	Gets the default character which is inserted into the destination sequence when no valid translation exists. More...
void	UseDefaultChar (const boolean use=true)
	Set whether the default character is inserted upon translation failure. More...
void	SetDefaultInputWidth (const uint32 defaultInputWidth)
	Set the expected number of characters in each unit of translation. More...
uint32	GetDefaultInputWidth () const
	Get the expected number of characters in each unit of translation. More...
void	SetPair (const string &input, const string &output)
	Set a translation mapping. More...
void	RemovePair (const string &input)
	Removes a translation mapping. More...
void	SetCompare (const gnCompare *comp)
	Set the comparator to use. More...
Static Public Methods
const gnTranslator*	ProteinDNATranslator ()
const gnTranslator*	ProteinRNATranslator ()
const gnTranslator*	DNAProteinTranslator ()
const gnTranslator*	RNAProteinTranslator ()
Private Methods
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 37 of file gnTranslator.h.

Member Enumeration Documentation

enum gnTranslator::gnTranslatorType

Enumeration values:

ProteinDNATranslatorType

ProteinRNATranslatorType

DNAProteinTranslatorType

RNAProteinTranslatorType

Definition at line 46 of file gnTranslator.h.

Constructor & Destructor Documentation

gnTranslator::gnTranslator ( )

Definition at line 35 of file gnTranslator.cpp.
Referenced by Clone(), DNAProteinTranslator(), ProteinDNATranslator(), ProteinRNATranslator(), and RNAProteinTranslator().

gnTranslator::gnTranslator ( gnTranslatorType t_type )

Definition at line 52 of file gnTranslator.cpp.

gnTranslator::gnTranslator ( const gnTranslator & sf )

Definition at line 42 of file gnTranslator.cpp.

Member Function Documentation

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

Reimplemented from gnBaseFilter.
Definition at line 135 of file gnTranslator.h.

void gnTranslator::CreateDNAProteinTranslator ( ) [private]

Definition at line 225 of file gnTranslator.cpp.
Referenced by gnTranslator().

void gnTranslator::CreateProteinDNATranslator ( ) [private]

Definition at line 161 of file gnTranslator.cpp.
Referenced by gnTranslator().

void gnTranslator::CreateProteinRNATranslator ( ) [private]

Definition at line 193 of file gnTranslator.cpp.
Referenced by gnTranslator().

void gnTranslator::CreateRNAProteinTranslator ( ) [private]

Definition at line 288 of file gnTranslator.cpp.
Referenced by gnTranslator().

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

Definition at line 25 of file gnTranslator.cpp.
Referenced by main().

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

Filters the given string.

Parameters:

seq The string to filter

Reimplemented from gnBaseFilter.
Definition at line 113 of file gnTranslator.cpp.

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

Reimplemented from gnBaseFilter.
Definition at line 82 of file gnTranslator.cpp.

gnSeqC gnTranslator::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 73 of file gnTranslator.cpp.
Referenced by gnFastTranslator::CacheTranslator(), and main().

gnSeqC gnTranslator::GetDefaultChar ( ) const [inline]

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

Parameters:

ch1 The default character

Definition at line 147 of file gnTranslator.h.

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 164 of file gnTranslator.h.

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

Definition at line 17 of file gnTranslator.cpp.

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

Definition at line 21 of file gnTranslator.cpp.

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

Definition at line 29 of file gnTranslator.cpp.

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 150 of file gnTranslator.cpp.

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 169 of file gnTranslator.h.
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 141 of file gnTranslator.h.
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:

The expected input width

Definition at line 159 of file gnTranslator.h.

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 141 of file gnTranslator.cpp.
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 153 of file gnTranslator.h.

Member Data Documentation

const gnCompare * gnTranslator::compare [private]

Definition at line 127 of file gnTranslator.h.

gnSeqC gnTranslator::m_defaultChar [private]

Definition at line 130 of file gnTranslator.h.

uint32 gnTranslator::m_defaultInputWidth [private]

Definition at line 131 of file gnTranslator.h.

vector< string > gnTranslator::m_inputTable<string> [private]

Definition at line 125 of file gnTranslator.h.

vector< string > gnTranslator::m_outputTable [private]

Definition at line 125 of file gnTranslator.h.

boolean gnTranslator::use_default [private]

Definition at line 129 of file gnTranslator.h.

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

Generated at Thu Apr 4 01:52:09 2002 for libGenome by

gnTranslator Class Reference

Public Types

Public Methods

Static Public Methods

Private Methods

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation