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class CAlnReader supports importing a large variety of text-based alignment formats into standard data structures. More...

#include <objtools/readers/aln_reader.hpp>

Inheritance diagram for CAlnReader:

Collaboration diagram for CAlnReader:

Classes
class	CAlnErrorContainer

Public Types
enum	EAlphabet { eAlpha_Default , eAlpha_Nucleotide , eAlpha_Protein , eAlpha_Dna , eAlpha_Rna , eAlpha_Dna_no_ambiguity , eAlpha_Rna_no_ambiguity }

enum	EReadFlags { fReadDefaults = 0 , fGenerateLocalIDs = 1 }
	Read the file This are the main functions. More...

typedef CAlnErrorContainer	TErrorList

using	TLineInfo = objects::SLineInfo

using	FValidateIds = function< void(const list< CRef< objects::CSeq_id > > &, int, objects::CAlnErrorReporter *)>

using	FIdValidate = function< void(const objects::CSeq_id &, int, objects::CAlnErrorReporter *)>

typedef int	TReadFlags
	binary OR of EReadFlags More...

using	TFastaFlags = objects::CFastaDeflineReader::TFastaFlags

Public Member Functions
	CAlnReader (CNcbiIstream &is, FValidateIds fIdValidate=nullptr)

	CAlnReader (CNcbiIstream &is, FIdValidate fSingleIdValidate)

virtual	~CAlnReader (void)

const string &	GetAlphabet (void) const

void	SetAlphabet (const string &value)

void	SetAlphabet (EAlphabet alpha)

bool	IsAlphabet (EAlphabet alpha) const

const string &	GetBeginningGap (void) const

void	SetBeginningGap (const string &value)

const string &	GetMiddleGap (void) const

void	SetMiddleGap (const string &value)

const string &	GetEndGap (void) const

void	SetEndGap (const string &value)

bool	GetUseNexusInfo () const

void	SetUseNexusInfo (bool useNexusInfo)

void	SetAllGap (const string &value)
	Convenience function for setting beginning, middle, and end gap to the same thing. More...

const string &	GetMissing (void) const

void	SetMissing (const string &value)

const string &	GetMatch (void) const

void	SetMatch (const string &value)

void	SetFastaGap (EAlphabet alpha)
	Alternative & easy way to choose alphabet, etc. More...

void	SetClustal (EAlphabet alpha)

void	SetPhylip (EAlphabet alpha)

void	SetPaup (EAlphabet alpha)

void	Read (bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)

void	Read (TReadFlags=fReadDefaults, objects::ILineErrorListener *pErrorListener=nullptr)

const vector< string > &	GetIds (void) const
	Parsed result data accessors. More...

const vector< string > &	GetSeqs (void) const

const vector< string > &	GetOrganisms (void) const

const vector< string > &	GetDeflines (void) const

const vector< TLineInfo > &	GetDeflineInfo (void) const

int	GetDim (void) const

EAlignFormat	GetLastAlignmentFileFormat (void) const

const TErrorList &	GetErrorList (void) const

CRef< objects::CSeq_align >	GetSeqAlign (TFastaFlags fasta_flags=0, objects::ILineErrorListener *pErrorListener=nullptr)
	Create ASN.1 classes from the parsed alignment. More...

CRef< objects::CSeq_entry >	GetSeqEntry (TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)

objects::CSeq_inst::EMol	GetSequenceMolType (const string &alphabet, const string &seqData, objects::ILineErrorListener *pErrorListener=nullptr)
	Get a sequence's moltype, also considering the alphabet used to read it. More...

Static Public Member Functions
static string	GetAlphabetLetters (EAlphabet)

Protected Types
using	SLineTextAndLoc = objects::CFastaDeflineReader::SLineTextAndLoc

using	TSeqTitles = objects::CFastaDeflineReader::TSeqTitles

using	SDeflineParseInfo = objects::CFastaDeflineReader::SDeflineParseInfo

using	TIgnoredProblems = objects::CFastaDeflineReader::TIgnoredProblems

Protected Member Functions
virtual CRef< objects::CSeq_id >	GenerateID (const string &fasta_defline, const TSeqPos &line_number, TFastaFlags fasta_flags)

void	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)

Protected Attributes
objects::CFastaIdHandler	m_FastaIdHandler

Private Types
using	TIdList = list< CRef< objects::CSeq_id > >
	Parsed result data (analogous to SAlignmentFile) Seqs are upper-case strings representing the sequences, with '-' for a gap. More...

typedef pair< TSeqPos, TSeqPos >	TAlignMiddleInterval
	characters have different contexts, depending on whether they are before the first non-gap character, after the last non-gap character, or between the first and last non-gap character. More...

typedef vector< TAlignMiddleInterval >	TAlignMiddles

typedef objects::CDense_seg::TDim	TNumrow

Private Member Functions
	CAlnReader (const CAlnReader &value)
	Prohibit copy constructor and assignment operator. More...

CAlnReader &	operator= (const CAlnReader &value)

int	x_GetGCD (const int a, const int b) const

bool	x_IsReplicatedSequence (const char *sequence_data, int sequence_length, int repeat_interval) const

void	x_VerifyAlignmentInfo (const ncbi::objects::SAlignmentFile &, TReadFlags readFlags)

CRef< objects::CSeq_inst >	x_GetSeqInst (objects::CSeq_inst::EMol mol, const string &seqData) const

objects::CSeq_inst::EMol	x_GetSequenceMolType (const string &alphabet, const string &seqData, const string &seqId="", objects::ILineErrorListener *pErrorListener=nullptr)

void	x_CalculateMiddleSections ()

bool	x_IsGap (TNumrow row, TSeqPos pos, const string &residue)

void	x_AssignDensegIds (TFastaFlags fasta_flags, objects::CDense_seg &denseg)

void	x_ParseAndValidateSeqIds (const TLineInfo &seqIdInfo, TReadFlags flags, TIdList &ids)

void	x_AddMods (const TLineInfo &defline_info, objects::CBioseq &bioseq, objects::ILineErrorListener *pErrorListener)

void	x_AddTitle (const string &defline, objects::CBioseq &bioseq)

Private Attributes
ncbi::objects::CSequenceInfo	mSequenceInfo

vector< string >	m_IdStrings

vector< TIdList >	m_Ids

vector< string >	m_Seqs

vector< string >	m_Organisms

vector< string >	m_Deflines

vector< TLineInfo >	m_DeflineInfo

FValidateIds	m_fValidateIds =nullptr

EAlignFormat	m_AlignFormat

CNcbiIstream &	m_IS
	Other internal data. More...

bool	m_ReadDone

bool	m_ReadSucceeded

int	m_Dim

CRef< objects::CSeq_align >	m_Aln

CRef< objects::CSeq_entry >	m_Entry

vector< string >	m_SeqVec

vector< TSeqPos >	m_SeqLen

TErrorList	m_Errors

bool	m_UseNexusInfo

TAlignMiddles	m_MiddleSections

Detailed Description

class CAlnReader supports importing a large variety of text-based alignment formats into standard data structures.

Definition at line 99 of file aln_reader.hpp.

Member Typedef Documentation

◆ FIdValidate

using CAlnReader::FIdValidate = function<void(const objects::CSeq_id&, int, objects::CAlnErrorReporter*)>

Definition at line 154 of file aln_reader.hpp.

◆ FValidateIds

using CAlnReader::FValidateIds = function<void(const list<CRef<objects::CSeq_id> >&, int, objects::CAlnErrorReporter*)>

Definition at line 149 of file aln_reader.hpp.

◆ SDeflineParseInfo

using CAlnReader::SDeflineParseInfo = objects::CFastaDeflineReader::SDeflineParseInfo

protected

Definition at line 338 of file aln_reader.hpp.

◆ SLineTextAndLoc

using CAlnReader::SLineTextAndLoc = objects::CFastaDeflineReader::SLineTextAndLoc

protected

Definition at line 336 of file aln_reader.hpp.

◆ TAlignMiddleInterval

typedef pair<TSeqPos, TSeqPos> CAlnReader::TAlignMiddleInterval

private

characters have different contexts, depending on whether they are before the first non-gap character, after the last non-gap character, or between the first and last non-gap character.

This must be precalculated before gap characters can be converted.

Definition at line 310 of file aln_reader.hpp.

◆ TAlignMiddles

typedef vector<TAlignMiddleInterval> CAlnReader::TAlignMiddles

private

Definition at line 311 of file aln_reader.hpp.

◆ TErrorList

typedef CAlnErrorContainer CAlnReader::TErrorList

Definition at line 142 of file aln_reader.hpp.

◆ TFastaFlags

using CAlnReader::TFastaFlags = objects::CFastaDeflineReader::TFastaFlags

Definition at line 236 of file aln_reader.hpp.

◆ TIdList

using CAlnReader::TIdList = list<CRef<objects::CSeq_id> >

private

Parsed result data (analogous to SAlignmentFile) Seqs are upper-case strings representing the sequences, with '-' for a gap.

Ids are ids read from file. Organisms and Deflines may not be set, depending on the file.

Definition at line 282 of file aln_reader.hpp.

◆ TIgnoredProblems

using CAlnReader::TIgnoredProblems = objects::CFastaDeflineReader::TIgnoredProblems

protected

Definition at line 339 of file aln_reader.hpp.

◆ TLineInfo

using CAlnReader::TLineInfo = objects::SLineInfo

Definition at line 148 of file aln_reader.hpp.

◆ TNumrow

typedef objects::CDense_seg::TDim CAlnReader::TNumrow

private

Definition at line 314 of file aln_reader.hpp.

◆ TReadFlags

typedef int CAlnReader::TReadFlags

binary OR of EReadFlags

Definition at line 212 of file aln_reader.hpp.

◆ TSeqTitles

using CAlnReader::TSeqTitles = objects::CFastaDeflineReader::TSeqTitles

protected

Definition at line 337 of file aln_reader.hpp.

Member Enumeration Documentation

◆ EAlphabet

enum CAlnReader::EAlphabet

Enumerator
eAlpha_Default
eAlpha_Nucleotide
eAlpha_Protein
eAlpha_Dna
eAlpha_Rna
eAlpha_Dna_no_ambiguity
eAlpha_Rna_no_ambiguity

Definition at line 103 of file aln_reader.hpp.

◆ EReadFlags

enum CAlnReader::EReadFlags

Read the file This are the main functions.

either would parse the alignment file and create the result data

Enumerator
fReadDefaults
fGenerateLocalIDs

Definition at line 208 of file aln_reader.hpp.

Constructor & Destructor Documentation

◆ CAlnReader() [1/3]

CAlnReader::CAlnReader	(	CNcbiIstream &	is,
		FValidateIds	fIdValidate = `nullptr`
	)

Definition at line 171 of file aln_reader.cpp.

References CAlnReader::CAlnErrorContainer::clear(), eAlpha_Protein, m_Errors, m_fValidateIds, SetAllGap(), and SetAlphabet().

◆ CAlnReader() [2/3]

CAlnReader::CAlnReader	(	CNcbiIstream &	is,
		FIdValidate	fSingleIdValidate
	)

Definition at line 202 of file aln_reader.cpp.

◆ ~CAlnReader()

CAlnReader::~CAlnReader ( void )

virtual

Definition at line 886 of file aln_reader.cpp.

◆ CAlnReader() [3/3]

CAlnReader::CAlnReader ( const CAlnReader & value )

private

Prohibit copy constructor and assignment operator.

Member Function Documentation

◆ GenerateID()

CRef< CSeq_id > CAlnReader::GenerateID	(	const string &	fasta_defline,
		const TSeqPos &	line_number,
		TFastaFlags	fasta_flags
	)

protectedvirtual

Reimplemented in CTextAlnReader.

Definition at line 485 of file aln_reader.cpp.

References _ASSERT, CSeq_id::BestRank(), ctll::empty(), FindBestChoice(), m_Dim, and m_Ids.

Referenced by CTextAlnReader::GenerateID(), and x_AssignDensegIds().

◆ GetAlphabet()

const string & CAlnReader::GetAlphabet ( void ) const

inline

Definition at line 364 of file aln_reader.hpp.

References mSequenceInfo.

Referenced by GetSeqEntry(), and IsAlphabet().

◆ GetAlphabetLetters()

string CAlnReader::GetAlphabetLetters ( EAlphabet alphaId )

static

Definition at line 207 of file aln_reader.cpp.

Referenced by IsAlphabet(), and SetAlphabet().

◆ GetBeginningGap()

const string & CAlnReader::GetBeginningGap ( void ) const

inline

Definition at line 378 of file aln_reader.hpp.

References mSequenceInfo.

Referenced by x_CalculateMiddleSections(), and x_IsGap().

◆ GetDeflineInfo()

const vector<TLineInfo>& CAlnReader::GetDeflineInfo ( void ) const

inline

Definition at line 229 of file aln_reader.hpp.

References m_DeflineInfo.

◆ GetDeflines()

const vector<string>& CAlnReader::GetDeflines ( void ) const

inline

Definition at line 228 of file aln_reader.hpp.

References m_Deflines.

◆ GetDim()

int CAlnReader::GetDim ( void ) const

inline

Definition at line 230 of file aln_reader.hpp.

References m_Dim.

◆ GetEndGap()

const string & CAlnReader::GetEndGap ( void ) const

inline

Definition at line 406 of file aln_reader.hpp.

References mSequenceInfo.

Referenced by x_CalculateMiddleSections(), and x_IsGap().

◆ GetErrorList()

const TErrorList& CAlnReader::GetErrorList ( void ) const

inline

Definition at line 234 of file aln_reader.hpp.

References m_Errors.

Referenced by CUpdateAlign::x_ReadAlign().

◆ GetIds()

const vector<string>& CAlnReader::GetIds ( void ) const

inline

Parsed result data accessors.

Definition at line 225 of file aln_reader.hpp.

References m_IdStrings.

Referenced by CUpdateAlign::x_ReadAlign().

◆ GetLastAlignmentFileFormat()

EAlignFormat CAlnReader::GetLastAlignmentFileFormat ( void ) const

inline

Definition at line 439 of file aln_reader.hpp.

References m_AlignFormat.

◆ GetMatch()

const string& CAlnReader::GetMatch ( void ) const

inline

Definition at line 194 of file aln_reader.hpp.

References mSequenceInfo.

◆ GetMiddleGap()

const string & CAlnReader::GetMiddleGap ( void ) const

inline

Definition at line 392 of file aln_reader.hpp.

References mSequenceInfo.

Referenced by x_IsGap().

◆ GetMissing()

const string& CAlnReader::GetMissing ( void ) const

inline

Definition at line 191 of file aln_reader.hpp.

References mSequenceInfo.

Referenced by x_GetSequenceMolType().

◆ GetOrganisms()

const vector<string>& CAlnReader::GetOrganisms ( void ) const

inline

Definition at line 227 of file aln_reader.hpp.

References m_Organisms.

◆ GetSeqAlign()

CRef< CSeq_align > CAlnReader::GetSeqAlign	(	TFastaFlags	fasta_flags = `0`,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

Create ASN.1 classes from the parsed alignment.

Definition at line 516 of file aln_reader.cpp.

References _ASSERT, CSeq_align_Base::eType_not_set, m_Aln, m_Dim, m_ReadDone, m_ReadSucceeded, m_SeqLen, m_Seqs, m_SeqVec, NCBI_THROW2, CDense_seg_Base::SetDim(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetStarts(), ncbi::grid::netcache::search::fields::size, NStr::ToUpper(), x_AssignDensegIds(), and x_IsGap().

Referenced by GetSeqEntry(), and CUpdateAlign::x_ReadAlign().

◆ GetSeqEntry()

CRef< CSeq_entry > CAlnReader::GetSeqEntry	(	TFastaFlags	fasta_flags = `objects::CFastaReader::fAddMods`,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

◆ GetSeqs()

const vector<string>& CAlnReader::GetSeqs ( void ) const

inline

Definition at line 226 of file aln_reader.hpp.

References m_Seqs.

Referenced by CPsiBlastInputClustalW::x_ReadAsciiMsa().

◆ GetSequenceMolType()

CSeq_inst::EMol CAlnReader::GetSequenceMolType	(	const string &	alphabet,
		const string &	seqData,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

Get a sequence's moltype, also considering the alphabet used to read it.

Definition at line 643 of file aln_reader.cpp.

References x_GetSequenceMolType().

◆ GetUseNexusInfo()

bool CAlnReader::GetUseNexusInfo ( ) const

inline

Definition at line 184 of file aln_reader.hpp.

References m_UseNexusInfo.

◆ IsAlphabet()

bool CAlnReader::IsAlphabet ( EAlphabet alpha ) const

inline

Definition at line 426 of file aln_reader.hpp.

References GetAlphabet(), and GetAlphabetLetters().

◆ operator=()

CAlnReader& CAlnReader::operator= ( const CAlnReader & value )

private

◆ ParseDefline()

void CAlnReader::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
	)

protected

Definition at line 863 of file aln_reader.cpp.

References info, and CFastaDeflineReader::ParseDefline().

◆ Read() [1/2]

void CAlnReader::Read	(	bool	guess,
		bool	generate_local_ids = `false`,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

Referenced by CTextAlignObjectLoader::LoadFromStream(), CMultiReader::ReadAlignment(), CUpdateAlign::x_ReadAlign(), CPsiBlastInputClustalW::x_ReadAsciiMsa(), and CMultiReaderApp::xProcessAlignment().

◆ Read() [2/2]

void CAlnReader::Read	(	TReadFlags	= `fReadDefaults`,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

◆ SetAllGap()

void CAlnReader::SetAllGap ( const string & value )

inline

Convenience function for setting beginning, middle, and end gap to the same thing.

Definition at line 433 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CAlnReader(), CMultiReader::ReadAlignment(), SetClustal(), SetFastaGap(), SetPaup(), and SetPhylip().

◆ SetAlphabet() [1/2]

void CAlnReader::SetAlphabet ( const string & value )

inline

Definition at line 371 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CAlnReader(), CTextAlignObjectLoader::LoadFromStream(), CMultiReader::ReadAlignment(), SetAlphabet(), SetClustal(), SetFastaGap(), SetPaup(), SetPhylip(), CUpdateAlign::x_ReadAlign(), and CMultiReaderApp::xProcessAlignment().

◆ SetAlphabet() [2/2]

void CAlnReader::SetAlphabet ( EAlphabet alpha )

inline

Definition at line 419 of file aln_reader.hpp.

References GetAlphabetLetters(), and SetAlphabet().

◆ SetBeginningGap()

void CAlnReader::SetBeginningGap ( const string & value )

inline

Definition at line 385 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CTextAlignObjectLoader::LoadFromStream(), and CUpdateAlign::x_ReadAlign().

◆ SetClustal()

void CAlnReader::SetClustal ( EAlphabet alpha )

Definition at line 244 of file aln_reader.cpp.

References SetAllGap(), and SetAlphabet().

Referenced by CPsiBlastInputClustalW::x_ReadAsciiMsa().

◆ SetEndGap()

void CAlnReader::SetEndGap ( const string & value )

inline

Definition at line 412 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CTextAlignObjectLoader::LoadFromStream(), and CUpdateAlign::x_ReadAlign().

◆ SetFastaGap()

void CAlnReader::SetFastaGap ( EAlphabet alpha )

Alternative & easy way to choose alphabet, etc.

Definition at line 237 of file aln_reader.cpp.

References SetAllGap(), and SetAlphabet().

◆ SetMatch()

void CAlnReader::SetMatch ( const string & value )

inline

Definition at line 195 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CTextAlignObjectLoader::LoadFromStream(), and CUpdateAlign::x_ReadAlign().

◆ SetMiddleGap()

void CAlnReader::SetMiddleGap ( const string & value )

inline

Definition at line 399 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CTextAlignObjectLoader::LoadFromStream(), and CUpdateAlign::x_ReadAlign().

◆ SetMissing()

void CAlnReader::SetMissing ( const string & value )

inline

Definition at line 192 of file aln_reader.hpp.

References mSequenceInfo, and rapidjson::value.

Referenced by CTextAlignObjectLoader::LoadFromStream(), CMultiReader::ReadAlignment(), and CUpdateAlign::x_ReadAlign().

◆ SetPaup()

void CAlnReader::SetPaup ( EAlphabet alpha )

Definition at line 251 of file aln_reader.cpp.

References SetAllGap(), and SetAlphabet().

◆ SetPhylip()

void CAlnReader::SetPhylip ( EAlphabet alpha )

Definition at line 258 of file aln_reader.cpp.

References SetAllGap(), and SetAlphabet().

◆ SetUseNexusInfo()

void CAlnReader::SetUseNexusInfo ( bool useNexusInfo )

inline

Definition at line 185 of file aln_reader.hpp.

References m_UseNexusInfo.

◆ x_AddMods()

void CAlnReader::x_AddMods	(	const TLineInfo &	defline_info,
		objects::CBioseq &	bioseq,
		objects::ILineErrorListener *	pErrorListener
	)

private

Definition at line 807 of file aln_reader.cpp.

References _ASSERT, CModHandler::AddMods(), CModAdder::Apply(), CTitleParser::Apply(), CModHandler::eAppendReplace, eDiag_Info, CBioseq::GetFirstId(), NStr::IsBlank(), SLineInfo::mData, SLineInfo::mNumLine, s_AppendMods(), IObjtoolsListener::SevEnabled(), NStr::TruncateSpacesInPlace(), and x_AddTitle().

Referenced by GetSeqEntry().

◆ x_AddTitle()

void CAlnReader::x_AddTitle	(	const string &	defline,
		objects::CBioseq &	bioseq
	)

private

Definition at line 852 of file aln_reader.cpp.

References NStr::IsBlank(), Ref(), and CBioseq_Base::SetDescr().

Referenced by GetSeqEntry(), and x_AddMods().

◆ x_AssignDensegIds()

void CAlnReader::x_AssignDensegIds	(	TFastaFlags	fasta_flags,
		objects::CDense_seg &	denseg
	)

private

Definition at line 496 of file aln_reader.cpp.

References GenerateID(), i, m_DeflineInfo, m_Dim, m_Ids, m_IdStrings, and CDense_seg_Base::SetIds().

Referenced by GetSeqAlign().

◆ x_CalculateMiddleSections()

void CAlnReader::x_CalculateMiddleSections ( )

private

Definition at line 433 of file aln_reader.cpp.

References GetBeginningGap(), GetEndGap(), m_Dim, m_MiddleSections, and m_Seqs.

Referenced by x_IsGap().

◆ x_GetGCD()

int CAlnReader::x_GetGCD	(	const int	a,
		const int	b
	)		const

private

◆ x_GetSeqInst()

CRef< CSeq_inst > CAlnReader::x_GetSeqInst	(	objects::CSeq_inst::EMol	mol,
		const string &	seqData
	)		const

private

Definition at line 703 of file aln_reader.cpp.

References data, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, CSeqportUtil::Pack(), and Ref().

Referenced by GetSeqEntry().

◆ x_GetSequenceMolType()

CSeq_inst::EMol CAlnReader::x_GetSequenceMolType	(	const string &	alphabet,
		const string &	seqData,
		const string &	seqId = `""`,
		objects::ILineErrorListener *	pErrorListener = `nullptr`
	)

private

Definition at line 654 of file aln_reader.cpp.

References eAlnSubcode_InconsistentMolType, eDiag_Error, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CFormatGuess::eProtein, eReader_Alignment, CFormatGuess::eUndefined, GetMissing(), remove_if(), CFormatGuess::SequenceType(), and sReportError().

Referenced by GetSeqEntry(), and GetSequenceMolType().

◆ x_IsGap()

bool CAlnReader::x_IsGap	(	TNumrow	row,
		TSeqPos	pos,
		const string &	residue
	)

private

Definition at line 456 of file aln_reader.cpp.

References NStr::Find(), first(), GetBeginningGap(), GetEndGap(), GetMiddleGap(), m_MiddleSections, row, and x_CalculateMiddleSections().

Referenced by GetSeqAlign().

◆ x_IsReplicatedSequence()

bool CAlnReader::x_IsReplicatedSequence	(	const char *	sequence_data,
		int	sequence_length,
		int	repeat_interval
	)		const

private

◆ x_ParseAndValidateSeqIds()

void CAlnReader::x_ParseAndValidateSeqIds	(	const TLineInfo &	seqIdInfo,
		TReadFlags	flags,
		TIdList &	ids
	)

private

Definition at line 342 of file aln_reader.cpp.

References CSeq_id_Base::e_Local, eAlnSubcode_IllegalSequenceId, fGenerateLocalIDs, flags, CSeq_id::fParse_AnyLocal, CSeq_id::fParse_RawText, m_fValidateIds, SLineInfo::mData, SLineInfo::mNumLine, CSeq_id::ParseIDs(), Ref(), and theErrorReporter.

Referenced by x_VerifyAlignmentInfo().

◆ x_VerifyAlignmentInfo()

void CAlnReader::x_VerifyAlignmentInfo	(	const ncbi::objects::SAlignmentFile &	,
		TReadFlags	readFlags
	)

private

Definition at line 372 of file aln_reader.cpp.

References eAlnSubcode_BadSequenceCount, eAlnSubcode_InsufficientDeflineInfo, ErrorPrintf(), flags, i, m_DeflineInfo, m_Ids, m_IdStrings, m_Seqs, SAlignmentFile::mDeflines, SAlignmentFile::mIds, SAlignmentFile::mSequences, SAlignmentFile::NumDeflines(), SAlignmentFile::NumSequences(), theErrorReporter, NStr::TruncateSpaces(), and x_ParseAndValidateSeqIds().

Member Data Documentation

◆ m_AlignFormat

EAlignFormat CAlnReader::m_AlignFormat

private

Definition at line 290 of file aln_reader.hpp.

Referenced by GetLastAlignmentFileFormat().

◆ m_Aln

CRef<objects::CSeq_align> CAlnReader::m_Aln

private

Definition at line 298 of file aln_reader.hpp.

Referenced by GetSeqAlign().

◆ m_DeflineInfo

vector<TLineInfo> CAlnReader::m_DeflineInfo

private

Definition at line 288 of file aln_reader.hpp.

Referenced by GetDeflineInfo(), GetSeqEntry(), x_AssignDensegIds(), and x_VerifyAlignmentInfo().

◆ m_Deflines

vector<string> CAlnReader::m_Deflines

private

Definition at line 287 of file aln_reader.hpp.

Referenced by GetDeflines().

◆ m_Dim

int CAlnReader::m_Dim

private

Definition at line 297 of file aln_reader.hpp.

Referenced by GenerateID(), GetDim(), GetSeqAlign(), GetSeqEntry(), x_AssignDensegIds(), and x_CalculateMiddleSections().

◆ m_Entry

CRef<objects::CSeq_entry> CAlnReader::m_Entry

private

Definition at line 299 of file aln_reader.hpp.

Referenced by GetSeqEntry().

◆ m_Errors

TErrorList CAlnReader::m_Errors

private

Definition at line 302 of file aln_reader.hpp.

Referenced by CAlnReader(), and GetErrorList().

◆ m_FastaIdHandler

objects::CFastaIdHandler CAlnReader::m_FastaIdHandler

protected

Definition at line 353 of file aln_reader.hpp.

◆ m_fValidateIds

FValidateIds CAlnReader::m_fValidateIds =nullptr

private

Definition at line 289 of file aln_reader.hpp.

Referenced by CAlnReader(), and x_ParseAndValidateSeqIds().

◆ m_Ids

vector<TIdList> CAlnReader::m_Ids

private

Definition at line 284 of file aln_reader.hpp.

Referenced by GenerateID(), GetSeqEntry(), x_AssignDensegIds(), and x_VerifyAlignmentInfo().

◆ m_IdStrings

vector<string> CAlnReader::m_IdStrings

private

Definition at line 283 of file aln_reader.hpp.

Referenced by GetIds(), x_AssignDensegIds(), and x_VerifyAlignmentInfo().

◆ m_IS

CNcbiIstream& CAlnReader::m_IS

private

Other internal data.

Definition at line 294 of file aln_reader.hpp.

◆ m_MiddleSections

TAlignMiddles CAlnReader::m_MiddleSections

private

Definition at line 312 of file aln_reader.hpp.

Referenced by x_CalculateMiddleSections(), and x_IsGap().

◆ m_Organisms

vector<string> CAlnReader::m_Organisms

private

Definition at line 286 of file aln_reader.hpp.

Referenced by GetOrganisms().

◆ m_ReadDone

bool CAlnReader::m_ReadDone

private

Definition at line 295 of file aln_reader.hpp.

Referenced by GetSeqAlign(), and GetSeqEntry().

◆ m_ReadSucceeded

bool CAlnReader::m_ReadSucceeded

private

Definition at line 296 of file aln_reader.hpp.

Referenced by GetSeqAlign(), and GetSeqEntry().

◆ m_SeqLen

vector<TSeqPos> CAlnReader::m_SeqLen

private

Definition at line 301 of file aln_reader.hpp.

Referenced by GetSeqAlign().

◆ m_Seqs

vector<string> CAlnReader::m_Seqs

private

Definition at line 285 of file aln_reader.hpp.

Referenced by GetSeqAlign(), GetSeqs(), x_CalculateMiddleSections(), and x_VerifyAlignmentInfo().

◆ m_SeqVec

vector<string> CAlnReader::m_SeqVec

private

Definition at line 300 of file aln_reader.hpp.

Referenced by GetSeqAlign(), and GetSeqEntry().

◆ m_UseNexusInfo

bool CAlnReader::m_UseNexusInfo

private

Definition at line 303 of file aln_reader.hpp.

Referenced by GetUseNexusInfo(), and SetUseNexusInfo().

◆ mSequenceInfo

ncbi::objects::CSequenceInfo CAlnReader::mSequenceInfo

private

Definition at line 274 of file aln_reader.hpp.

Referenced by GetAlphabet(), GetBeginningGap(), GetEndGap(), GetMatch(), GetMiddleGap(), GetMissing(), SetAllGap(), SetAlphabet(), SetBeginningGap(), SetEndGap(), SetMatch(), SetMiddleGap(), and SetMissing().

The documentation for this class was generated from the following files:

include/objtools/readers/aln_reader.hpp
src/objtools/readers/aln_reader.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ FIdValidate

◆ FValidateIds

◆ SDeflineParseInfo

◆ SLineTextAndLoc

◆ TAlignMiddleInterval

◆ TAlignMiddles

◆ TErrorList

◆ TFastaFlags

◆ TIdList

◆ TIgnoredProblems

◆ TLineInfo

◆ TNumrow

◆ TReadFlags

◆ TSeqTitles

Member Enumeration Documentation

◆ EAlphabet

◆ EReadFlags

Constructor & Destructor Documentation

◆ CAlnReader() [1/3]

◆ CAlnReader() [2/3]

◆ ~CAlnReader()

◆ CAlnReader() [3/3]

Member Function Documentation

◆ GenerateID()

◆ GetAlphabet()

◆ GetAlphabetLetters()

◆ GetBeginningGap()

◆ GetDeflineInfo()

◆ GetDeflines()

◆ GetDim()

◆ GetEndGap()

◆ GetErrorList()

◆ GetIds()

◆ GetLastAlignmentFileFormat()

◆ GetMatch()

◆ GetMiddleGap()

◆ GetMissing()

◆ GetOrganisms()

◆ GetSeqAlign()

◆ GetSeqEntry()

◆ GetSeqs()

◆ GetSequenceMolType()

◆ GetUseNexusInfo()

◆ IsAlphabet()

◆ operator=()

◆ ParseDefline()

◆ Read() [1/2]

◆ Read() [2/2]

◆ SetAllGap()

◆ SetAlphabet() [1/2]

◆ SetAlphabet() [2/2]

◆ SetBeginningGap()

◆ SetClustal()

◆ SetEndGap()

◆ SetFastaGap()

◆ SetMatch()

◆ SetMiddleGap()

◆ SetMissing()

◆ SetPaup()

◆ SetPhylip()

◆ SetUseNexusInfo()

◆ x_AddMods()

◆ x_AddTitle()

◆ x_AssignDensegIds()

◆ x_CalculateMiddleSections()

◆ x_GetGCD()

◆ x_GetSeqInst()

◆ x_GetSequenceMolType()