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gnFilter Class Reference #include <gnFilter.h> Inheritance diagram for gnFilter:: List of all members. Public Types enum   gnFilterType {   alphabetCharacterFilterType, numberCharacterFilterType, proteinSeqFilterType, basicDNASeqFilterType,   fullDNASeqFilterType, basicRNASeqFilterType, fullRNASeqFilterType, DNAtoRNAFilterType,   RNAtoDNAFilterType, DNAComplementFilterType, RNAComplementFilterType } Public Methods   gnFilter ()   gnFilter (const gnFilterType f_type)   Creates a gnFilter for a predefined filter type. More...   gnFilter (const gnSeqC defaultChar, const gnSeqC rdefaultChar)   gnFilter (const gnFilter &sf)   ~gnFilter () gnFilter*  Clone () const boolean  IsValid (const gnSeqC ch) const gnSeqC  MakeValid (const gnSeqC ch) const gnSeqC  Filter (const gnSeqC ch) const   Filter the given character. More... uint32  IsValid (const gnSeqC *seq, const uint32 len) const   IsValid() scans the supplied character array for invalid characters. More... void  MakeValid (gnSeqC *seq, const uint32 len) const void  Filter (gnSeqC **seq, uint32 &len) const   Filter the given character array. More... void  ReverseFilter (gnSeqC **seq, uint32 &len) const uint32  IsValid (const string &seq) const void  MakeValid (string &seq) const void  Filter (string &seq) const   Filters the given string. More... void  ReverseFilter (string &seq) const void  SetDefaultChar (const gnSeqC ch1, const gnSeqC ch2) gnSeqC  GetDefaultChar () const gnSeqC  GetRDefaultChar () const void  SetSingle (const gnSeqC ch) void  SetPair (const gnSeqC ch1, const gnSeqC ch2) boolean  RemovePair (const gnSeqC ch) boolean  RemoveSingle (const gnSeqC ch) Static Public Methods const gnFilter*  alphabetCharacterFilter () const gnFilter*  numberCharacterFilter () const gnFilter*  proteinSeqFilter () const gnFilter*  basicDNASeqFilter () const gnFilter*  fullDNASeqFilter () const gnFilter*  basicRNASeqFilter () const gnFilter*  fullRNASeqFilter () const gnFilter*  DNAtoRNAFilter () const gnFilter*  RNAtoDNAFilter () const gnFilter*  DNAComplementFilter () const gnFilter*  RNAComplementFilter () Private Methods void  CreateAlphabetCharacterFilter () void  CreateNumberCharacterFilter () void  CreateProteinFilter () void  CreateBasicDNAFilter () void  CreateFullDNAFilter () void  CreateBasicRNAFilter () void  CreateFullRNAFilter () void  CreateDNAtoRNAFilter () void  CreateRNAtoDNAFilter () void  CreateDNAComplementFilter () void  CreateRNAComplementFilter () Private Attributes string  m_name gnSeqC  m_pairArray [GNSEQC_MAX] gnSeqC  m_defaultChar gnSeqC  m_rDefaultChar Member Enumeration Documentation enum gnFilter::gnFilterType   Enumeration values: alphabetCharacterFilterType   numberCharacterFilterType   proteinSeqFilterType   basicDNASeqFilterType   fullDNASeqFilterType   basicRNASeqFilterType   fullRNASeqFilterType   DNAtoRNAFilterType   RNAtoDNAFilterType   DNAComplementFilterType   RNAComplementFilterType   Definition at line 42 of file gnFilter.h. Constructor & Destructor Documentation gnFilter::gnFilter ( )   Definition at line 76 of file gnFilter.cpp. Referenced by Clone(), DNAComplementFilter(), DNAtoRNAFilter(), RNAComplementFilter(), RNAtoDNAFilter(), alphabetCharacterFilter(), basicDNASeqFilter(), basicRNASeqFilter(), fullDNASeqFilter(), fullRNASeqFilter(), numberCharacterFilter(), and proteinSeqFilter(). gnFilter::gnFilter ( const gnFilterType f_type )   Creates a gnFilter for a predefined filter type. Used by the static sequence constructors to avoid the "static initialization order fiasco" Parameters: f_type   The type of filter to create. See also: gnFilterType Definition at line 100 of file gnFilter.cpp. gnFilter::gnFilter ( const gnSeqC defaultChar, const gnSeqC rdefaultChar )   Definition at line 83 of file gnFilter.cpp. gnFilter::gnFilter ( const gnFilter & sf )   Definition at line 91 of file gnFilter.cpp. gnFilter::~gnFilter ( )   Definition at line 141 of file gnFilter.cpp. Member Function Documentation gnFilter * gnFilter::Clone ( ) const [inline, virtual]   Reimplemented from gnBaseFilter. Definition at line 131 of file gnFilter.h. void gnFilter::CreateAlphabetCharacterFilter ( ) [private]   Definition at line 223 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateBasicDNAFilter ( ) [private]   Definition at line 318 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateBasicRNAFilter ( ) [private]   Definition at line 374 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateDNAComplementFilter ( ) [private]   Definition at line 500 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateDNAtoRNAFilter ( ) [private]   Definition at line 428 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateFullDNAFilter ( ) [private]   Definition at line 336 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateFullRNAFilter ( ) [private]   Definition at line 390 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateNumberCharacterFilter ( ) [private]   Definition at line 255 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateProteinFilter ( ) [private]   Definition at line 271 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateRNAComplementFilter ( ) [private]   Definition at line 538 of file gnFilter.cpp. Referenced by gnFilter(). void gnFilter::CreateRNAtoDNAFilter ( ) [private]   Definition at line 464 of file gnFilter.cpp. Referenced by gnFilter(). const gnFilter * gnFilter::DNAComplementFilter ( ) [static]   Definition at line 64 of file gnFilter.cpp. Referenced by gnContigSpec::SeqRead(). const gnFilter * gnFilter::DNAtoRNAFilter ( ) [static]   Definition at line 54 of file gnFilter.cpp. void gnFilter::Filter ( string & seq ) const [virtual]   Filters the given string. Parameters: seq   The string to filter Reimplemented from gnBaseFilter. Definition at line 187 of file gnFilter.cpp. void gnFilter::Filter ( gnSeqC ** seq, uint32 & len ) const [inline, 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 146 of file gnFilter.cpp. gnSeqC gnFilter::Filter ( const gnSeqC ch ) const [inline, virtual]   Filter the given character. Parameters: ch   The character to filter Returns: The filtered character Reimplemented from gnBaseFilter. Definition at line 148 of file gnFilter.h. gnSeqC gnFilter::GetDefaultChar ( ) const [inline]   Definition at line 193 of file gnFilter.h. gnSeqC gnFilter::GetRDefaultChar ( ) const [inline]   Definition at line 198 of file gnFilter.h. uint32 gnFilter::IsValid ( const string & seq ) const [inline]   Definition at line 175 of file gnFilter.h. uint32 gnFilter::IsValid ( const gnSeqC * seq, const uint32 len ) const [inline]   IsValid() scans the supplied character array for invalid characters. Parameters: seq   The sequence to scan. This is a generic character array. len   The length of the sequence to scan. Returns: The index of the first invalid character, or len if none exists Definition at line 155 of file gnFilter.h. boolean gnFilter::IsValid ( const gnSeqC ch ) const [inline]   Definition at line 138 of file gnFilter.h. Referenced by Filter(), and IsValid(). void gnFilter::MakeValid ( string & seq ) const [inline]   Definition at line 180 of file gnFilter.h. void gnFilter::MakeValid ( gnSeqC * seq, const uint32 len ) const [inline]   Definition at line 165 of file gnFilter.h. gnSeqC gnFilter::MakeValid ( const gnSeqC ch ) const [inline]   Definition at line 143 of file gnFilter.h. Referenced by MakeValid(). const gnFilter * gnFilter::RNAComplementFilter ( ) [static]   Definition at line 69 of file gnFilter.cpp. const gnFilter * gnFilter::RNAtoDNAFilter ( ) [static]   Definition at line 59 of file gnFilter.cpp. boolean gnFilter::RemovePair ( const gnSeqC ch ) [inline]   Definition at line 215 of file gnFilter.h. boolean gnFilter::RemoveSingle ( const gnSeqC ch ) [inline]   Definition at line 222 of file gnFilter.h. void gnFilter::ReverseFilter ( string & seq ) const   Definition at line 195 of file gnFilter.cpp. void gnFilter::ReverseFilter ( gnSeqC ** seq, uint32 & len ) const   Definition at line 158 of file gnFilter.cpp. Referenced by gnContigSpec::SeqRead(). void gnFilter::SetDefaultChar ( const gnSeqC ch1, const gnSeqC ch2 ) [inline]   Definition at line 187 of file gnFilter.h. Referenced by CreateAlphabetCharacterFilter(), CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). void gnFilter::SetPair ( const gnSeqC ch1, const gnSeqC ch2 ) [inline]   Definition at line 209 of file gnFilter.h. Referenced by CreateAlphabetCharacterFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). void gnFilter::SetSingle ( const gnSeqC ch ) [inline]   Definition at line 204 of file gnFilter.h. Referenced by CreateBasicDNAFilter(), CreateBasicRNAFilter(), CreateDNAComplementFilter(), CreateDNAtoRNAFilter(), CreateFullDNAFilter(), CreateFullRNAFilter(), CreateNumberCharacterFilter(), CreateProteinFilter(), CreateRNAComplementFilter(), and CreateRNAtoDNAFilter(). const gnFilter * gnFilter::alphabetCharacterFilter ( ) [static]   Definition at line 18 of file gnFilter.cpp. const gnFilter * gnFilter::basicDNASeqFilter ( ) [static]   Definition at line 34 of file gnFilter.cpp. const gnFilter * gnFilter::basicRNASeqFilter ( ) [static]   Definition at line 44 of file gnFilter.cpp. const gnFilter * gnFilter::fullDNASeqFilter ( ) [static]   Definition at line 39 of file gnFilter.cpp. Referenced by gnABISource::gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), gnGBKSource::gnGBKSource(), and gnSEQSource::gnSEQSource(). const gnFilter * gnFilter::fullRNASeqFilter ( ) [static]   Definition at line 49 of file gnFilter.cpp. const gnFilter * gnFilter::numberCharacterFilter ( ) [static]   Definition at line 23 of file gnFilter.cpp. const gnFilter * gnFilter::proteinSeqFilter ( ) [static]   Definition at line 29 of file gnFilter.cpp. Member Data Documentation gnSeqC gnFilter::m_defaultChar [private]   Definition at line 125 of file gnFilter.h. string gnFilter::m_name [private]   Reimplemented from gnBaseFilter. Definition at line 122 of file gnFilter.h. gnSeqC gnFilter::m_pairArray [private]   Definition at line 124 of file gnFilter.h. gnSeqC gnFilter::m_rDefaultChar [private]   Definition at line 126 of file gnFilter.h. The documentation for this class was generated from the following files: gnFilter.h gnFilter.cpp