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CFastaIdValidate Class Reference

Search Toolkit Book for CFastaIdValidate

#include <objtools/readers/seqid_validate.hpp>

+ Collaboration diagram for CFastaIdValidate:

Public Types

enum  EErrCode {
  eUnexpectedNucResidues , eUnexpectedAminoAcids , eIDTooLong , eBadLocalID ,
  eOther
}
 
using TFastaFlags = long
 
using FReportError = function< void(EDiagSev severity, int lineNum, const string &idString, EErrCode errCode, const string &msg)>
 
using TIds = list< CRef< CSeq_id > >
 

Public Member Functions

 CFastaIdValidate (TFastaFlags flags)
 
virtual ~CFastaIdValidate ()=default
 
virtual void operator() (const TIds &ids, int lineNum, FReportError fReportError)
 
void SetMaxLocalIDLength (size_t length)
 
void SetMaxGeneralTagLength (size_t length)
 
void SetMaxAccessionLength (size_t length)
 

Protected Member Functions

void CheckIDLength (const CSeq_id &id, int lineNum, FReportError fReportError) const
 
bool IsValidLocalID (const CSeq_id &id) const
 
virtual bool IsValidLocalString (const CTempString &idString) const
 
void CheckForExcessiveNucData (const CSeq_id &id, int lineNum, FReportError fReportError) const
 
void CheckForExcessiveProtData (const CSeq_id &id, int lineNum, FReportError fReportError) const
 

Static Protected Member Functions

static size_t CountPossibleNucResidues (const string &idString)
 
static size_t CountPossibleAminoAcids (const string &idString)
 

Protected Attributes

size_t kWarnNumNucCharsAtEnd = 20
 
size_t kErrNumNucCharsAtEnd = 25
 
size_t kWarnNumAminoAcidCharsAtEnd = 50
 
size_t kMaxLocalIDLength = CSeq_id::kMaxLocalIDLength
 
size_t kMaxGeneralTagLength = CSeq_id::kMaxGeneralTagLength
 
size_t kMaxAccessionLength = CSeq_id::kMaxAccessionLength
 
TFastaFlags m_Flags
 

Detailed Description

Definition at line 61 of file seqid_validate.hpp.

Member Typedef Documentation

◆ FReportError

using CFastaIdValidate::FReportError = function<void(EDiagSev severity, int lineNum, const string& idString, EErrCode errCode, const string& msg)>

Definition at line 79 of file seqid_validate.hpp.

◆ TFastaFlags

using CFastaIdValidate::TFastaFlags = long

Definition at line 65 of file seqid_validate.hpp.

◆ TIds

using CFastaIdValidate::TIds = list<CRef<CSeq_id> >

Definition at line 86 of file seqid_validate.hpp.

Member Enumeration Documentation

◆ EErrCode

enum CFastaIdValidate::EErrCode
Enumerator
eUnexpectedNucResidues 
eUnexpectedAminoAcids 
eIDTooLong 
eBadLocalID 
eOther 

Definition at line 71 of file seqid_validate.hpp.

Constructor & Destructor Documentation

◆ CFastaIdValidate()

CFastaIdValidate::CFastaIdValidate ( TFastaFlags  flags)

Definition at line 103 of file seqid_validate.cpp.

◆ ~CFastaIdValidate()

virtual CFastaIdValidate::~CFastaIdValidate ( )
virtualdefault

Member Function Documentation

◆ CheckForExcessiveNucData()

void CFastaIdValidate::CheckForExcessiveNucData ( const CSeq_id &  id,
int  lineNum,
FReportError  fReportError 
) const
protected

Definition at line 240 of file seqid_validate.cpp.

References CountPossibleNucResidues(), eDiag_Error, eDiag_Warning, eUnexpectedNucResidues, kErrNumNucCharsAtEnd, kWarnNumNucCharsAtEnd, and NStr::NumericToString().

Referenced by operator()().

◆ CheckForExcessiveProtData()

void CFastaIdValidate::CheckForExcessiveProtData ( const CSeq_id &  id,
int  lineNum,
FReportError  fReportError 
) const
protected

Definition at line 296 of file seqid_validate.cpp.

References CountPossibleAminoAcids(), eDiag_Warning, eUnexpectedAminoAcids, kWarnNumAminoAcidCharsAtEnd, and NStr::NumericToString().

Referenced by operator()().

◆ CheckIDLength()

void CFastaIdValidate::CheckIDLength ( const CSeq_id &  id,
int  lineNum,
FReportError  fReportError 
) const
protected

Definition at line 169 of file seqid_validate.cpp.

References eDiag_Error, eIDTooLong, GetSeqIdString(), kMaxAccessionLength, kMaxGeneralTagLength, kMaxLocalIDLength, msg(), and s_GetIDLengthErrorString().

Referenced by operator()().

◆ CountPossibleAminoAcids()

size_t CFastaIdValidate::CountPossibleAminoAcids ( const string &  idString)
staticprotected

Definition at line 318 of file seqid_validate.cpp.

Referenced by CheckForExcessiveProtData().

◆ CountPossibleNucResidues()

size_t CFastaIdValidate::CountPossibleNucResidues ( const string &  idString)
staticprotected

Definition at line 286 of file seqid_validate.cpp.

References s_IsPossibleNuc().

Referenced by CheckForExcessiveNucData().

◆ IsValidLocalID()

bool CFastaIdValidate::IsValidLocalID ( const CSeq_id &  id) const
protected

Definition at line 215 of file seqid_validate.cpp.

References IsValidLocalString().

Referenced by operator()().

◆ IsValidLocalString()

bool CFastaIdValidate::IsValidLocalString ( const CTempString &  idString) const
protectedvirtual

Definition at line 229 of file seqid_validate.cpp.

References CSeq_id::CheckLocalID(), CSeq_id::fInvalidChar, CFastaReader::fQuickIDCheck, m_Flags, and CTempString::substr().

Referenced by IsValidLocalID().

◆ operator()()

void CFastaIdValidate::operator() ( const TIds &  ids,
int  lineNum,
FReportError  fReportError 
)
virtual

Definition at line 107 of file seqid_validate.cpp.

References CheckForExcessiveNucData(), CheckForExcessiveProtData(), CheckIDLength(), eBadLocalID, eDiag_Error, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, IsValidLocalID(), m_Flags, and msg().

◆ SetMaxAccessionLength()

void CFastaIdValidate::SetMaxAccessionLength ( size_t  length)

Definition at line 148 of file seqid_validate.cpp.

References kMaxAccessionLength.

Referenced by CSeqIdCheck::operator()().

◆ SetMaxGeneralTagLength()

void CFastaIdValidate::SetMaxGeneralTagLength ( size_t  length)

Definition at line 142 of file seqid_validate.cpp.

References kMaxGeneralTagLength.

Referenced by CSeqIdCheck::operator()().

◆ SetMaxLocalIDLength()

void CFastaIdValidate::SetMaxLocalIDLength ( size_t  length)

Definition at line 136 of file seqid_validate.cpp.

References kMaxLocalIDLength.

Referenced by CSeqIdCheck::operator()().

Member Data Documentation

◆ kErrNumNucCharsAtEnd

size_t CFastaIdValidate::kErrNumNucCharsAtEnd = 25
protected

Definition at line 123 of file seqid_validate.hpp.

Referenced by CheckForExcessiveNucData().

◆ kMaxAccessionLength

size_t CFastaIdValidate::kMaxAccessionLength = CSeq_id::kMaxAccessionLength
protected

Definition at line 127 of file seqid_validate.hpp.

Referenced by CheckIDLength(), and SetMaxAccessionLength().

◆ kMaxGeneralTagLength

size_t CFastaIdValidate::kMaxGeneralTagLength = CSeq_id::kMaxGeneralTagLength
protected

Definition at line 126 of file seqid_validate.hpp.

Referenced by CheckIDLength(), and SetMaxGeneralTagLength().

◆ kMaxLocalIDLength

size_t CFastaIdValidate::kMaxLocalIDLength = CSeq_id::kMaxLocalIDLength
protected

Definition at line 125 of file seqid_validate.hpp.

Referenced by CheckIDLength(), and SetMaxLocalIDLength().

◆ kWarnNumAminoAcidCharsAtEnd

size_t CFastaIdValidate::kWarnNumAminoAcidCharsAtEnd = 50
protected

Definition at line 124 of file seqid_validate.hpp.

Referenced by CheckForExcessiveProtData().

◆ kWarnNumNucCharsAtEnd

size_t CFastaIdValidate::kWarnNumNucCharsAtEnd = 20
protected

Definition at line 122 of file seqid_validate.hpp.

Referenced by CheckForExcessiveNucData().

◆ m_Flags

TFastaFlags CFastaIdValidate::m_Flags
protected

Definition at line 129 of file seqid_validate.hpp.

Referenced by IsValidLocalString(), and operator()().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:57:24 2024 by modify_doxy.py rev. 669887