Search Toolkit Book for CObjReaderLineException

#include <objtools/readers/line_error.hpp>

Inheritance diagram for CObjReaderLineException:

Collaboration diagram for CObjReaderLineException:

Public Types
enum	EErrCode

Public Types inherited from ILineError
enum	EProblem { eProblem_Unset = 1 , eProblem_UnrecognizedFeatureName , eProblem_UnrecognizedQualifierName , eProblem_NumericQualifierValueHasExtraTrailingCharacters , eProblem_NumericQualifierValueIsNotANumber , eProblem_FeatureNameNotAllowed , eProblem_NoFeatureProvidedOnIntervals , eProblem_QualifierWithoutFeature , eProblem_IncompleteFeature , eProblem_FeatureBadStartAndOrStop , eProblem_BadFeatureInterval , eProblem_QualifierBadValue , eProblem_BadScoreValue , eProblem_MissingContext , eProblem_BadTrackLine , eProblem_InternalPartialsInFeatLocation , eProblem_FeatMustBeInXrefdGene , eProblem_CreatedGeneFromMultipleFeats , eProblem_UnrecognizedSquareBracketCommand , eProblem_TooLong , eProblem_UnexpectedNucResidues , eProblem_UnexpectedAminoAcids , eProblem_TooManyAmbiguousResidues , eProblem_InvalidResidue , eProblem_ModifierFoundButNoneExpected , eProblem_ExtraModifierFound , eProblem_ExpectedModifierMissing , eProblem_Missing , eProblem_NonPositiveLength , eProblem_ParsingModifiers , eProblem_ContradictoryModifiers , eProblem_InvalidLengthAutoCorrected , eProblem_IgnoredResidue , eProblem_DiscouragedFeatureName , eProblem_DiscouragedQualifierName , eProblem_InvalidQualifier , eProblem_InconsistentQualifiers , eProblem_DuplicateIDs , eProblem_BadInfoLine , eProblem_BadFormatLine , eProblem_BadFilterLine , eProblem_ProgressInfo , eProblem_GeneralParsingError }

typedef vector< unsigned int >	TVecOfLines

Public Types inherited from CObjReaderParseException
enum	EErrCode { eFormat , eEOF , eNoDefline , eNoIDs , eAmbiguous , eBadSegSet , eDuplicateID , eUnusedMods , eIDTooLong , eNoResidues , eWrongGap , eInvalidID }

Public Types inherited from CParseTemplException< CObjReaderException >
enum	EErrCode
	Error types that for exception class. More...

typedef int	TErrCode

Public Member Functions
virtual ILineError *	Clone (void) const
	Use instead of copy constructor, which is protected. More...

void	Throw (void) const
	this function to throw this object. More...

	~CObjReaderLineException (void) noexcept

TErrCode	GetErrCode (void) const

EProblem	Problem (void) const

const std::string &	SeqId (void) const

EDiagSev	Severity (void) const

unsigned int	Line (void) const

const TVecOfLines &	OtherLines (void) const

const std::string &	FeatureName (void) const

const std::string &	QualifierName (void) const

const std::string &	QualifierValue (void) const

const std::string &	ErrorMessage (void) const

std::string	ProblemStr () const

std::string	Message () const

void	SetLineNumber (unsigned int uLineNumber)

void	AddOtherLine (unsigned int uOtherLine)

Public Member Functions inherited from ILineError
virtual	~ILineError (void) noexcept

std::string	SeverityStr (void) const

virtual void	Write (CNcbiOstream &out) const

virtual void	WriteAsXML (CNcbiOstream &out) const

virtual string	GetText (void) const

virtual EDiagSev	GetSeverity (void) const

virtual int	GetCode (void) const

virtual int	GetSubCode (void) const

virtual void	Dump (CNcbiOstream &out) const

virtual std::string	Compose (void) const

virtual void	DumpAsXML (CNcbiOstream &out) const

Public Member Functions inherited from IObjtoolsMessage
virtual	~IObjtoolsMessage (void)=default

Public Member Functions inherited from CObjReaderParseException
virtual const char *	GetErrCodeString (void) const override
	Translate from the error code value to its string representation. More...

	NCBI_EXCEPTION_DEFAULT2 (CObjReaderParseException, CParseTemplException< CObjReaderException >, std::string::size_type)

Public Member Functions inherited from CParseTemplException< CObjReaderException >
	CParseTemplException (const CDiagCompileInfo &info, const CException *prev_exception, EErrCode err_code, const string &message, string::size_type pos, EDiagSev severity=eDiag_Error)
	Constructor. More...

	CParseTemplException (const CParseTemplException< CObjReaderException > &other)
	Constructor. More...

virtual	~CParseTemplException (void) noexcept
	Destructor. More...

virtual void	ReportExtra (ostream &out) const override
	Report error position. More...

virtual const char *	GetType (void) const override
	Get exception class type. More...

TErrCode	GetErrCode (void) const
	Get error code. More...

string::size_type	GetPos (void) const noexcept
	Get error position. More...

Static Public Member Functions
static CObjReaderLineException *	Create (EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())
	Please use this instead of the constructor because the ctor is protected. More...

Static Public Member Functions inherited from ILineError
static std::string	ProblemStr (EProblem eProblem)

Protected Member Functions
	CObjReaderLineException (EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())
	protected instead of public. Please use the Create function instead. More...

	CObjReaderLineException (const CObjReaderLineException &rhs)
	Protected, so use Clone or Throw instead. More...

Protected Member Functions inherited from CParseTemplException< CObjReaderException >
	CParseTemplException (const CDiagCompileInfo &info, const CException *prev_exception, const string &message, string::size_type pos, EDiagSev severity, CException::TFlags flags)

	CParseTemplException (void)
	Constructor. More...

virtual const CException *	x_Clone (void) const override
	Helper clone method. More...

Protected Attributes
EProblem	m_eProblem

std::string	m_strSeqId

unsigned int	m_uLineNumber

std::string	m_strFeatureName

std::string	m_strQualifierName

std::string	m_strQualifierValue

std::string	m_strErrorMessage

TVecOfLines	m_vecOfOtherLines

Detailed Description

Definition at line 609 of file line_error.hpp.

Member Enumeration Documentation

◆ EErrCode

enum CObjReaderParseException::EErrCode

Definition at line 50 of file reader_exception.hpp.

Constructor & Destructor Documentation

◆ ~CObjReaderLineException()

CObjReaderLineException::~CObjReaderLineException ( void )

inlinenoexcept

Definition at line 644 of file line_error.hpp.

◆ CObjReaderLineException() [1/2]

CObjReaderLineException::CObjReaderLineException	(	EDiagSev	eSeverity,
		unsigned int	uLine,
		const std::string &	strMessage,
		EProblem	eProblem = `eProblem_GeneralParsingError`,
		const std::string &	strSeqId = `string("")`,
		const std::string &	strFeatureName = `string("")`,
		const std::string &	strQualifierName = `string("")`,
		const std::string &	strQualifierValue = `string("")`,
		CObjReaderLineException::EErrCode	eErrCode = `eFormat`,
		const TVecOfLines &	vecOfOtherLines = `TVecOfLines()`
	)

protected

protected instead of public. Please use the Create function instead.

Definition at line 227 of file line_error.cpp.

Referenced by Clone(), and Create().

◆ CObjReaderLineException() [2/2]

CObjReaderLineException::CObjReaderLineException ( const CObjReaderLineException & rhs )

protected

Protected, so use Clone or Throw instead.

Definition at line 250 of file line_error.cpp.

References Severity().

Member Function Documentation

◆ AddOtherLine()

void CObjReaderLineException::AddOtherLine ( unsigned int uOtherLine )

inline

Definition at line 677 of file line_error.hpp.

References m_vecOfOtherLines.

◆ Clone()

ILineError * CObjReaderLineException::Clone ( void ) const

virtual

Use instead of copy constructor, which is protected.

Reimplemented from ILineError.

Definition at line 215 of file line_error.cpp.

References CObjReaderLineException().

◆ Create()

CObjReaderLineException * CObjReaderLineException::Create	(	EDiagSev	eSeverity,
		unsigned int	uLine,
		const std::string &	strMessage,
		EProblem	eProblem = `eProblem_GeneralParsingError`,
		const std::string &	strSeqId = `string("")`,
		const std::string &	strFeatureName = `string("")`,
		const std::string &	strQualifierName = `string("")`,
		const std::string &	strQualifierValue = `string("")`,
		CObjReaderLineException::EErrCode	eErrCode = `eFormat`,
		const TVecOfLines &	vecOfOtherLines = `TVecOfLines()`
	)

static

Please use this instead of the constructor because the ctor is protected.

Returns: Caller is responsible for the return value.

Definition at line 194 of file line_error.cpp.

References CObjReaderLineException().

Referenced by CGff2Record::AssignFromGff(), CIdMapper::Map(), CFastaReader::PostWarning(), CReaderBase::ProcessError(), CColumnarVCFReader::ReadData(), CColumnarVCFReader::ReadHeader(), CHgvsReader::ReadSeqAnnot(), CRepeatMaskerReader::ReadSeqAnnot(), CColumnarVCFReader::ReadVariantsForChrs(), CReaderMessageHandler::Report(), s_PostError(), s_PostWarning(), SpecNumber(), SpecType(), CColumnarVCFReader::x_GatherSampleColNames(), CSourceModParser::x_HandleBadModValue(), CSourceModParser::x_HandleUnkModValue(), CColumnarVCFReader::x_ProcessCriticalError(), CSourceModParser::x_ProcessError(), CColumnarVCFReader::x_ProcessError(), CColumnarVCFReader::x_ProcessHeaderLine(), CUCSCRegionReader::x_SetFeatureLocation(), CVcfReader::xNormalizeData(), CVcfReader::xParseData(), CGff3Reader::xParseFeature(), CVcfReader::xProcessMetaLineFilter(), CVcfReader::xProcessMetaLineFormat(), and CVcfReader::xProcessMetaLineInfo().

◆ ErrorMessage()

const std::string& CObjReaderLineException::ErrorMessage ( void ) const

inlinevirtual

Reimplemented from ILineError.

Definition at line 660 of file line_error.hpp.

References m_strErrorMessage.

◆ FeatureName()

const std::string& CObjReaderLineException::FeatureName ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 656 of file line_error.hpp.

References m_strFeatureName.

◆ GetErrCode()

TErrCode CObjReaderLineException::GetErrCode ( void ) const

inline

Definition at line 646 of file line_error.hpp.

◆ Line()

unsigned int CObjReaderLineException::Line ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 654 of file line_error.hpp.

References m_uLineNumber.

◆ Message()

std::string CObjReaderLineException::Message ( void ) const

inlinevirtual

Reimplemented from ILineError.

Definition at line 664 of file line_error.hpp.

References ctll::empty(), and ILineError::Message().

Referenced by CReaderBase::ProcessWarning(), and CColumnarVCFReader::x_ProcessWarning().

◆ OtherLines()

const TVecOfLines& CObjReaderLineException::OtherLines ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 655 of file line_error.hpp.

References m_vecOfOtherLines.

◆ Problem()

EProblem CObjReaderLineException::Problem ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 651 of file line_error.hpp.

References m_eProblem.

◆ ProblemStr()

std::string CObjReaderLineException::ProblemStr ( void ) const

virtual

Reimplemented from ILineError.

Definition at line 263 of file line_error.cpp.

References m_strErrorMessage, and ILineError::ProblemStr().

◆ QualifierName()

const std::string& CObjReaderLineException::QualifierName ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 657 of file line_error.hpp.

References m_strQualifierName.

◆ QualifierValue()

const std::string& CObjReaderLineException::QualifierValue ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 658 of file line_error.hpp.

References m_strQualifierValue.

◆ SeqId()

const std::string& CObjReaderLineException::SeqId ( void ) const

inlinevirtual

Implements ILineError.

Definition at line 652 of file line_error.hpp.

References m_strSeqId.

◆ SetLineNumber()

void CObjReaderLineException::SetLineNumber ( unsigned int uLineNumber )

inline

Definition at line 672 of file line_error.hpp.

References m_uLineNumber.

Referenced by CReaderBase::ProcessError(), and CReaderBase::ProcessWarning().

◆ Severity()

EDiagSev CObjReaderLineException::Severity ( void ) const

inlinevirtual

Reimplemented from ILineError.

Definition at line 653 of file line_error.hpp.

Referenced by CObjReaderLineException().

◆ Throw()

void CObjReaderLineException::Throw ( void ) const

this function to throw this object.

Definition at line 221 of file line_error.cpp.

Referenced by CReaderBase::ProcessError(), CReaderBase::ProcessWarning(), CColumnarVCFReader::x_ProcessCriticalError(), CSourceModParser::x_ProcessError(), CColumnarVCFReader::x_ProcessError(), and CColumnarVCFReader::x_ProcessWarning().

Member Data Documentation

◆ m_eProblem

EProblem CObjReaderLineException::m_eProblem

protected

Definition at line 683 of file line_error.hpp.

Referenced by Problem().

◆ m_strErrorMessage

std::string CObjReaderLineException::m_strErrorMessage

protected

Definition at line 689 of file line_error.hpp.

Referenced by ErrorMessage(), and ProblemStr().

◆ m_strFeatureName

std::string CObjReaderLineException::m_strFeatureName

protected

Definition at line 686 of file line_error.hpp.

Referenced by FeatureName().

◆ m_strQualifierName

std::string CObjReaderLineException::m_strQualifierName

protected

Definition at line 687 of file line_error.hpp.

Referenced by QualifierName().

◆ m_strQualifierValue

std::string CObjReaderLineException::m_strQualifierValue

protected

Definition at line 688 of file line_error.hpp.

Referenced by QualifierValue().

◆ m_strSeqId

std::string CObjReaderLineException::m_strSeqId

protected

Definition at line 684 of file line_error.hpp.

Referenced by SeqId().

◆ m_uLineNumber

unsigned int CObjReaderLineException::m_uLineNumber

protected

Definition at line 685 of file line_error.hpp.

Referenced by Line(), and SetLineNumber().

◆ m_vecOfOtherLines

TVecOfLines CObjReaderLineException::m_vecOfOtherLines

protected

Definition at line 690 of file line_error.hpp.

Referenced by AddOtherLine(), and OtherLines().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ EErrCode

Constructor & Destructor Documentation

◆ ~CObjReaderLineException()

◆ CObjReaderLineException() [1/2]

◆ CObjReaderLineException() [2/2]

Member Function Documentation

◆ AddOtherLine()

◆ Clone()

◆ Create()

◆ ErrorMessage()

◆ FeatureName()

◆ GetErrCode()

◆ Line()

◆ Message()

◆ OtherLines()

◆ Problem()

◆ ProblemStr()

◆ QualifierName()

◆ QualifierValue()

◆ SeqId()

◆ SetLineNumber()

◆ Severity()

◆ Throw()

Member Data Documentation

◆ m_eProblem

◆ m_strErrorMessage

◆ m_strFeatureName

◆ m_strQualifierName

◆ m_strQualifierValue

◆ m_strSeqId

◆ m_uLineNumber

◆ m_vecOfOtherLines