#include <gnFastTranslator.h>
Inheritance diagram for gnFastTranslator:
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. | |
gnFastTranslator * | 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 |
gnFastTranslator (const gnFastTranslator &sf) | |
gnFastTranslator (gnTranslatorType t_type) | |
gnFastTranslator () | |
gnFastTranslator & | operator= (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 gnFastTranslator * | DNAProteinTranslator () |
const gnFastTranslator * | ProteinDNATranslator () |
Private Member Functions | |
void | CreateDNAProteinTranslator () |
void | CreateProteinDNATranslator () |
Private Attributes | |
gnSeqC | m_defaultChar |
map< string, string > | m_transCache |
const gnTranslator * | m_translator |
boolean | use_default |
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Definition at line 32 of file gnFastTranslator.h. |
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Definition at line 26 of file gnFastTranslator.cpp. References m_defaultChar, and use_default. Referenced by DNAProteinTranslator(), and ProteinDNATranslator(). |
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Definition at line 39 of file gnFastTranslator.cpp. References CacheTranslator(), DNAProteinTranslatorType, m_defaultChar, ProteinDNATranslatorType, and use_default. |
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Definition at line 32 of file gnFastTranslator.cpp. References m_defaultChar, gnBaseFilter::m_name, m_transCache, and use_default. |
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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.
References gnTranslator::Filter(), gnSeqI, and m_transCache. Referenced by gnFastTranslator(). |
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Implements gnBaseFilter. Definition at line 83 of file gnFastTranslator.h. |
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Definition at line 20 of file gnFastTranslator.cpp. References DNAProteinTranslatorType, and gnFastTranslator(). Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator(), and main(). |
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Filters the given string.
Implements gnBaseFilter. Definition at line 94 of file gnFastTranslator.cpp. References gnSeqC, m_defaultChar, m_transCache, uint32, and use_default. |
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Filter the given character array.
Implements gnBaseFilter. Definition at line 63 of file gnFastTranslator.cpp. |
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Filter the given character.
Implements gnBaseFilter. Definition at line 54 of file gnFastTranslator.cpp. References gnSeqC, and m_defaultChar. Referenced by main(). |
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Definition at line 95 of file gnFastTranslator.h. References gnSeqC, and m_defaultChar. |
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Definition at line 16 of file gnFastTranslator.cpp. References gnFastTranslator(), and ProteinDNATranslatorType. Referenced by gnPosSpecificTranslator::gnPosSpecificTranslator(). |
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Definition at line 89 of file gnFastTranslator.h. References gnSeqC, m_defaultChar, and use_default. |
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Definition at line 101 of file gnFastTranslator.h. References use_default. |
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Definition at line 79 of file gnFastTranslator.h. Referenced by Filter(), GetDefaultChar(), gnFastTranslator(), and SetDefaultChar(). |
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Definition at line 75 of file gnFastTranslator.h. Referenced by CacheTranslator(), Filter(), and gnFastTranslator(). |
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Definition at line 76 of file gnFastTranslator.h. |
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Definition at line 78 of file gnFastTranslator.h. Referenced by Filter(), gnFastTranslator(), SetDefaultChar(), and UseDefaultChar(). |