CAlnReader Member List

This is the complete list of members for CAlnReader, including all inherited members.

CAlnReader(CNcbiIstream &is, FValidateIds fIdValidate=nullptr)	CAlnReader
CAlnReader(CNcbiIstream &is, FIdValidate fSingleIdValidate)	CAlnReader
CAlnReader(const CAlnReader &value)	CAlnReader	private
eAlpha_Default enum value	CAlnReader
eAlpha_Dna enum value	CAlnReader
eAlpha_Dna_no_ambiguity enum value	CAlnReader
eAlpha_Nucleotide enum value	CAlnReader
eAlpha_Protein enum value	CAlnReader
eAlpha_Rna enum value	CAlnReader
eAlpha_Rna_no_ambiguity enum value	CAlnReader
EAlphabet enum name	CAlnReader
EReadFlags enum name	CAlnReader
fGenerateLocalIDs enum value	CAlnReader
FIdValidate typedef	CAlnReader
fReadDefaults enum value	CAlnReader
FValidateIds typedef	CAlnReader
GenerateID(const string &fasta_defline, const TSeqPos &line_number, TFastaFlags fasta_flags)	CAlnReader	protectedvirtual
GetAlphabet(void) const	CAlnReader	inline
GetAlphabetLetters(EAlphabet)	CAlnReader	static
GetBeginningGap(void) const	CAlnReader	inline
GetDeflineInfo(void) const	CAlnReader	inline
GetDeflines(void) const	CAlnReader	inline
GetDim(void) const	CAlnReader	inline
GetEndGap(void) const	CAlnReader	inline
GetErrorList(void) const	CAlnReader	inline
GetIds(void) const	CAlnReader	inline
GetLastAlignmentFileFormat(void) const	CAlnReader	inline
GetMatch(void) const	CAlnReader	inline
GetMiddleGap(void) const	CAlnReader	inline
GetMissing(void) const	CAlnReader	inline
GetOrganisms(void) const	CAlnReader	inline
GetSeqAlign(TFastaFlags fasta_flags=0, objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader
GetSeqEntry(TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader
GetSeqs(void) const	CAlnReader	inline
GetSequenceMolType(const string &alphabet, const string &seqData, objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader
GetUseNexusInfo() const	CAlnReader	inline
IsAlphabet(EAlphabet alpha) const	CAlnReader	inline
m_AlignFormat	CAlnReader	private
m_Aln	CAlnReader	private
m_DeflineInfo	CAlnReader	private
m_Deflines	CAlnReader	private
m_Dim	CAlnReader	private
m_Entry	CAlnReader	private
m_Errors	CAlnReader	private
m_FastaIdHandler	CAlnReader	protected
m_fValidateIds	CAlnReader	private
m_Ids	CAlnReader	private
m_IdStrings	CAlnReader	private
m_IS	CAlnReader	private
m_MiddleSections	CAlnReader	private
m_Organisms	CAlnReader	private
m_ReadDone	CAlnReader	private
m_ReadSucceeded	CAlnReader	private
m_SeqLen	CAlnReader	private
m_Seqs	CAlnReader	private
m_SeqVec	CAlnReader	private
m_UseNexusInfo	CAlnReader	private
mSequenceInfo	CAlnReader	private
operator=(const CAlnReader &value)	CAlnReader	private
ParseDefline(const string &defline, const SDeflineParseInfo &info, const TIgnoredProblems &ignoredErrors, list< CRef< objects::CSeq_id >> &ids, bool &hasRange, TSeqPos &rangeStart, TSeqPos &rangeEnd, TSeqTitles &seqTitles, objects::ILineErrorListener *pMessageListener)	CAlnReader	protected
Read(bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader
Read(TReadFlags=fReadDefaults, objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader
SDeflineParseInfo typedef	CAlnReader	protected
SetAllGap(const string &value)	CAlnReader	inline
SetAlphabet(const string &value)	CAlnReader	inline
SetAlphabet(EAlphabet alpha)	CAlnReader	inline
SetBeginningGap(const string &value)	CAlnReader	inline
SetClustal(EAlphabet alpha)	CAlnReader
SetEndGap(const string &value)	CAlnReader	inline
SetFastaGap(EAlphabet alpha)	CAlnReader
SetMatch(const string &value)	CAlnReader	inline
SetMiddleGap(const string &value)	CAlnReader	inline
SetMissing(const string &value)	CAlnReader	inline
SetPaup(EAlphabet alpha)	CAlnReader
SetPhylip(EAlphabet alpha)	CAlnReader
SetUseNexusInfo(bool useNexusInfo)	CAlnReader	inline
SLineTextAndLoc typedef	CAlnReader	protected
TAlignMiddleInterval typedef	CAlnReader	private
TAlignMiddles typedef	CAlnReader	private
TErrorList typedef	CAlnReader
TFastaFlags typedef	CAlnReader
TIdList typedef	CAlnReader	private
TIgnoredProblems typedef	CAlnReader	protected
TLineInfo typedef	CAlnReader
TNumrow typedef	CAlnReader	private
TReadFlags typedef	CAlnReader
TSeqTitles typedef	CAlnReader	protected
x_AddMods(const TLineInfo &defline_info, objects::CBioseq &bioseq, objects::ILineErrorListener *pErrorListener)	CAlnReader	private
x_AddTitle(const string &defline, objects::CBioseq &bioseq)	CAlnReader	private
x_AssignDensegIds(TFastaFlags fasta_flags, objects::CDense_seg &denseg)	CAlnReader	private
x_CalculateMiddleSections()	CAlnReader	private
x_GetGCD(const int a, const int b) const	CAlnReader	private
x_GetSeqInst(objects::CSeq_inst::EMol mol, const string &seqData) const	CAlnReader	private
x_GetSequenceMolType(const string &alphabet, const string &seqData, const string &seqId="", objects::ILineErrorListener *pErrorListener=nullptr)	CAlnReader	private
x_IsGap(TNumrow row, TSeqPos pos, const string &residue)	CAlnReader	private
x_IsReplicatedSequence(const char *sequence_data, int sequence_length, int repeat_interval) const	CAlnReader	private
x_ParseAndValidateSeqIds(const TLineInfo &seqIdInfo, TReadFlags flags, TIdList &ids)	CAlnReader	private
x_VerifyAlignmentInfo(const ncbi::objects::SAlignmentFile &, TReadFlags readFlags)	CAlnReader	private
~CAlnReader(void)	CAlnReader	virtual