#include <gnTranslator.h>
Inheritance diagram for gnTranslator:
Public Types | |
enum | gnTranslatorType { ProteinDNATranslatorType, ProteinRNATranslatorType, DNAProteinTranslatorType, RNAProteinTranslatorType } |
Public Member Functions | |
gnTranslator * | Clone () 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 |
Gets the default character which is inserted into the destination sequence when no valid translation exists. | |
uint32 | GetDefaultInputWidth () const |
Get the expected number of characters in each unit of translation. | |
gnTranslator (const gnTranslator &sf) | |
gnTranslator (gnTranslatorType t_type) | |
gnTranslator () | |
void | RemovePair (const string &input) |
Removes a translation mapping. | |
void | SetCompare (const gnCompare *comp) |
Set the comparator to use. | |
void | SetDefaultChar (const gnSeqC ch1) |
Sets the default character to insert when no valid translation exists. | |
void | SetDefaultInputWidth (const uint32 defaultInputWidth) |
Set the expected number of characters in each unit of translation. | |
void | SetPair (const string &input, const string &output) |
Set a translation mapping. | |
void | UseDefaultChar (const boolean use=true) |
Set whether the default character is inserted upon translation failure. | |
Static Public Member Functions | |
const gnTranslator * | DNAProteinTranslator () |
const gnTranslator * | ProteinDNATranslator () |
const gnTranslator * | ProteinRNATranslator () |
const gnTranslator * | RNAProteinTranslator () |
Private Member Functions | |
void | CreateDNAProteinTranslator () |
void | CreateProteinDNATranslator () |
void | CreateProteinRNATranslator () |
void | CreateRNAProteinTranslator () |
Private Attributes | |
const gnCompare * | compare |
gnSeqC | m_defaultChar |
uint32 | m_defaultInputWidth |
vector< string > | m_inputTable |
vector< string > | m_outputTable |
boolean | use_default |
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.
Definition at line 36 of file gnTranslator.h.
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Definition at line 34 of file gnTranslator.cpp. References m_defaultChar, m_defaultInputWidth, and use_default. Referenced by DNAProteinTranslator(), ProteinDNATranslator(), ProteinRNATranslator(), and RNAProteinTranslator(). |
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Definition at line 51 of file gnTranslator.cpp. References CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), CreateRNAProteinTranslator(), DNAProteinTranslatorType, m_defaultChar, ProteinDNATranslatorType, ProteinRNATranslatorType, RNAProteinTranslatorType, and use_default. |
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Definition at line 41 of file gnTranslator.cpp. References compare, m_defaultChar, m_defaultInputWidth, m_inputTable, gnBaseFilter::m_name, m_outputTable, and use_default. |
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Implements gnBaseFilter. Definition at line 134 of file gnTranslator.h. |
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Definition at line 224 of file gnTranslator.cpp. References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and use_default. Referenced by gnTranslator(). |
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Definition at line 160 of file gnTranslator.cpp. References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), and SetPair(). Referenced by gnTranslator(). |
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Definition at line 192 of file gnTranslator.cpp. References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), and SetPair(). Referenced by gnTranslator(). |
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Definition at line 287 of file gnTranslator.cpp. References m_defaultInputWidth, SetCompare(), SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and use_default. Referenced by gnTranslator(). |
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Definition at line 24 of file gnTranslator.cpp. References DNAProteinTranslatorType, and gnTranslator(). Referenced by main(). |
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Filters the given string.
Implements gnBaseFilter. Definition at line 112 of file gnTranslator.cpp. References compare, gnCompare::Contains(), m_defaultChar, m_defaultInputWidth, m_inputTable, m_outputTable, uint32, and use_default. |
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Filter the given character array.
Implements gnBaseFilter. Definition at line 81 of file gnTranslator.cpp. References compare, gnCompare::Contains(), gnSeqC, gnSeqI, m_defaultChar, m_defaultInputWidth, m_inputTable, m_outputTable, uint32, and use_default. |
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Filter the given 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(), and main(). |
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Gets the default character which is inserted into the destination sequence when no valid translation exists.
References gnSeqC, and m_defaultChar. |
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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.
References m_defaultInputWidth, and uint32. |
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Definition at line 16 of file gnTranslator.cpp. References gnTranslator(), and ProteinDNATranslatorType. |
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Definition at line 20 of file gnTranslator.cpp. References gnTranslator(), and ProteinRNATranslatorType. |
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Removes a translation mapping. RemovePair removes the translation mapping corresponding to the given input string.
References m_inputTable, m_outputTable, and uint32. |
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Definition at line 28 of file gnTranslator.cpp. References gnTranslator(), and RNAProteinTranslatorType. |
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Set the comparator to use. Ambiguous base matching is facilitated using a gnCompare object. This must be set to allow sequences to be compared.
References compare. Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator(). |
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Sets the default character to insert when no valid translation exists.
References gnSeqC, m_defaultChar, and use_default. Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator(). |
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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.
References m_defaultInputWidth, and uint32. |
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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.
References m_inputTable, and m_outputTable. Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), and CreateRNAProteinTranslator(). |
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Set whether the default character is inserted upon translation failure.
References use_default. |
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Definition at line 126 of file gnTranslator.h. Referenced by Filter(), gnTranslator(), and SetCompare(). |
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Definition at line 129 of file gnTranslator.h. Referenced by Filter(), GetDefaultChar(), gnTranslator(), and SetDefaultChar(). |
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Definition at line 130 of file gnTranslator.h. Referenced by CreateDNAProteinTranslator(), CreateProteinDNATranslator(), CreateProteinRNATranslator(), CreateRNAProteinTranslator(), Filter(), GetDefaultInputWidth(), gnTranslator(), and SetDefaultInputWidth(). |
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Definition at line 124 of file gnTranslator.h. Referenced by Filter(), gnTranslator(), RemovePair(), and SetPair(). |
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Definition at line 124 of file gnTranslator.h. Referenced by Filter(), gnTranslator(), RemovePair(), and SetPair(). |
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Definition at line 128 of file gnTranslator.h. Referenced by CreateDNAProteinTranslator(), CreateRNAProteinTranslator(), Filter(), gnTranslator(), SetDefaultChar(), and UseDefaultChar(). |