#include <gnFilter.h>
Inheritance diagram for gnFilter:
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Definition at line 75 of file gnFilter.cpp. References gnSeqC, GNSEQC_MAX, m_defaultChar, m_pairArray, m_rDefaultChar, and NO_REVCOMP_CHAR. Referenced by alphabetCharacterFilter(), basicDNASeqFilter(), basicRNASeqFilter(), DNAComplementFilter(), DNAtoRNAFilter(), fullDNASeqFilter(), fullRNASeqFilter(), numberCharacterFilter(), proteinSeqFilter(), RNAComplementFilter(), and RNAtoDNAFilter(). |
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Creates a gnFilter for a predefined filter type. Used by the static sequence constructors to avoid the "static initialization order fiasco"
References alphabetCharacterFilterType, basicDNASeqFilterType, basicRNASeqFilterType, CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), CreateRNAtoDNAFilter(), DNAComplementFilterType, DNAtoRNAFilterType, fullDNASeqFilterType, fullRNASeqFilterType, gnSeqC, GNSEQC_MAX, m_pairArray, NO_REVCOMP_CHAR, numberCharacterFilterType, proteinSeqFilterType, RNAComplementFilterType, and RNAtoDNAFilterType. |
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Definition at line 82 of file gnFilter.cpp. References gnSeqC, GNSEQC_MAX, m_defaultChar, m_pairArray, m_rDefaultChar, and NO_REVCOMP_CHAR. |
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Definition at line 90 of file gnFilter.cpp. References gnSeqC, GNSEQC_MAX, m_defaultChar, gnBaseFilter::m_name, m_pairArray, and m_rDefaultChar. |
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Definition at line 140 of file gnFilter.cpp. |
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Definition at line 17 of file gnFilter.cpp. References alphabetCharacterFilterType, and gnFilter(). |
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Definition at line 33 of file gnFilter.cpp. References basicDNASeqFilterType, and gnFilter(). |
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Definition at line 43 of file gnFilter.cpp. References basicRNASeqFilterType, and gnFilter(). |
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Implements gnBaseFilter. Definition at line 128 of file gnFilter.h. |
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Definition at line 222 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetPair(). Referenced by gnFilter(). |
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Definition at line 317 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 373 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 499 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 427 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 335 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 389 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 254 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 270 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 537 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 463 of file gnFilter.cpp. References SetDefaultChar(), gnBaseFilter::SetName(), SetPair(), and SetSingle(). Referenced by gnFilter(). |
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Definition at line 63 of file gnFilter.cpp. References DNAComplementFilterType, and gnFilter(). Referenced by gnContigSpec::SeqRead(). |
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Definition at line 53 of file gnFilter.cpp. References DNAtoRNAFilterType, and gnFilter(). |
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Filters the given string.
Implements gnBaseFilter. Definition at line 186 of file gnFilter.cpp. References gnSeqI, IsValid(), m_pairArray, and uint32. |
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Filter the given character array.
Implements gnBaseFilter. Definition at line 145 of file gnFilter.cpp. References gnSeqC, gnSeqI, IsValid(), m_pairArray, and uint32. |
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Filter the given character.
Implements gnBaseFilter. Definition at line 145 of file gnFilter.h. References gnSeqC, m_defaultChar, m_pairArray, NO_REVCOMP_CHAR, and uint. |
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Definition at line 38 of file gnFilter.cpp. References fullDNASeqFilterType, and gnFilter(). Referenced by gnABISource::gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), and gnSEQSource::gnSEQSource(). |
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Definition at line 48 of file gnFilter.cpp. References fullRNASeqFilterType, and gnFilter(). |
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Definition at line 190 of file gnFilter.h. References gnSeqC, and m_defaultChar. |
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Definition at line 195 of file gnFilter.h. References gnSeqC, and m_rDefaultChar. |
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Definition at line 172 of file gnFilter.h. |
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IsValid() scans the supplied character array for invalid characters.
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Definition at line 135 of file gnFilter.h. References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint. Referenced by Filter(), IsValid(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), and gnFASSource::SeqStartPos(). |
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Definition at line 177 of file gnFilter.h. References gnSeqC, and MakeValid(). |
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Definition at line 162 of file gnFilter.h. References gnSeqC, MakeValid(), and uint32. |
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Definition at line 140 of file gnFilter.h. References gnSeqC, m_defaultChar, m_pairArray, NO_REVCOMP_CHAR, and uint. Referenced by MakeValid(). |
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Definition at line 22 of file gnFilter.cpp. References gnFilter(), and numberCharacterFilterType. |
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Definition at line 28 of file gnFilter.cpp. References gnFilter(), and proteinSeqFilterType. Referenced by gnGBKSource::gnGBKSource(). |
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Definition at line 212 of file gnFilter.h. References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint. |
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Definition at line 219 of file gnFilter.h. References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint. |
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Definition at line 194 of file gnFilter.cpp. References gnSeqC, m_pairArray, NO_REVCOMP_CHAR, and uint32. |
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Definition at line 157 of file gnFilter.cpp. References gnSeqC, gnSeqI, m_pairArray, NO_REVCOMP_CHAR, and uint32. Referenced by gnContigSpec::SeqRead(). |
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Definition at line 68 of file gnFilter.cpp. References gnFilter(), and RNAComplementFilterType. |
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Definition at line 58 of file gnFilter.cpp. References gnFilter(), and RNAtoDNAFilterType. |
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Definition at line 184 of file gnFilter.h. References gnSeqC, m_defaultChar, and m_rDefaultChar. Referenced by CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). |
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Definition at line 206 of file gnFilter.h. References gnSeqC, m_pairArray, and uint. Referenced by CreateAlphabetCharacterFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). |
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Definition at line 201 of file gnFilter.h. References gnSeqC, m_pairArray, and uint. Referenced by CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). |
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Definition at line 122 of file gnFilter.h. Referenced by Filter(), GetDefaultChar(), gnFilter(), MakeValid(), and SetDefaultChar(). |
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Definition at line 121 of file gnFilter.h. Referenced by Filter(), gnFilter(), IsValid(), MakeValid(), RemovePair(), RemoveSingle(), ReverseFilter(), SetPair(), and SetSingle(). |
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Definition at line 123 of file gnFilter.h. Referenced by GetRDefaultChar(), gnFilter(), and SetDefaultChar(). |