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CAlnReader Class Reference

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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 stringGetAlphabet (void) const
 
void SetAlphabet (const string &value)
 
void SetAlphabet (EAlphabet alpha)
 
bool IsAlphabet (EAlphabet alpha) const
 
const stringGetBeginningGap (void) const
 
void SetBeginningGap (const string &value)
 
const stringGetMiddleGap (void) const
 
void SetMiddleGap (const string &value)
 
const stringGetEndGap (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 stringGetMissing (void) const
 
void SetMissing (const string &value)
 
const stringGetMatch (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 TErrorListGetErrorList (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, TSeqPosTAlignMiddleInterval
 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< TAlignMiddleIntervalTAlignMiddles
 
typedef objects::CDense_seg::TDim TNumrow
 

Private Member Functions

 CAlnReader (const CAlnReader &value)
 Prohibit copy constructor and assignment operator. More...
 
CAlnReaderoperator= (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< stringm_IdStrings
 
vector< TIdListm_Ids
 
vector< stringm_Seqs
 
vector< stringm_Organisms
 
vector< stringm_Deflines
 
vector< TLineInfom_DeflineInfo
 
FValidateIds m_fValidateIds =nullptr
 
EAlignFormat m_AlignFormat
 
CNcbiIstreamm_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< stringm_SeqVec
 
vector< TSeqPosm_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

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

Definition at line 311 of file aln_reader.hpp.

◆ 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

Definition at line 148 of file aln_reader.hpp.

◆ TNumrow

Definition at line 314 of file aln_reader.hpp.

◆ 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

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

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 
)

◆ 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 
)

◆ 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 
)

◆ 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

◆ 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

◆ 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

◆ 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

◆ SetMiddleGap()

void CAlnReader::SetMiddleGap ( const string value)
inline

◆ SetMissing()

void CAlnReader::SetMissing ( const string value)
inline

◆ 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

◆ 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

◆ x_IsGap()

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

◆ 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

◆ x_VerifyAlignmentInfo()

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

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

◆ 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

◆ 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

◆ 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

The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:26:05 2024 by modify_doxy.py rev. 669887