CAutoSqlStandardFields Struct Reference

Search Toolkit Book for CAutoSqlStandardFields

#include "bed_autosql_standard.hpp"
(Private to src/objtools/readers.)

Collaboration diagram for CAutoSqlStandardFields:

Public Member Functions
	CAutoSqlStandardFields ()
bool	SetLocation (const CBedColumnData &, int bedFlags, CSeq_feat &, CReaderMessageHandler &) const
bool	SetTitle (const CBedColumnData &, CSeq_feat &, CReaderMessageHandler &) const
bool	SetRegion (const CBedColumnData &columnData, CSeq_feat &feat, CReaderMessageHandler &messageHandler) const
bool	SetDisplayData (const CBedColumnData &columnData, int bedFlags, CSeq_feat &feat, CReaderMessageHandler &messageHandler) const
bool	ProcessTableRow (size_t, const string &, const string &)
bool	Validate (CReaderMessageHandler &) const
size_t	NumFields () const

Private Member Functions
bool	ContainsInfo () const

Private Attributes
int	mColChrom
int	mColSeqStart
int	mColSeqStop
int	mColStrand
int	mColName
int	mColScore
size_t	mNumFields

Detailed Description

Definition at line 44 of file bed_autosql_standard.hpp.

Constructor & Destructor Documentation

CAutoSqlStandardFields()

CAutoSqlStandardFields::CAutoSqlStandardFields

(

)

Definition at line 47 of file bed_autosql_standard.cpp.

Member Function Documentation

ContainsInfo()

bool CAutoSqlStandardFields::ContainsInfo ( ) const

inlineprivate

Definition at line 97 of file bed_autosql_standard.hpp.

References mColChrom, mColName, mColScore, mColSeqStart, mColSeqStop, and mColStrand.

NumFields()

size_t CAutoSqlStandardFields::NumFields ( ) const

inline

Definition at line 86 of file bed_autosql_standard.hpp.

References mNumFields.

Referenced by CBedAutoSql::Load().

ProcessTableRow()

bool CAutoSqlStandardFields::ProcessTableRow	(	size_t	colIndex,
		const string &	colName,
		const string &	colFormat
	)

Definition at line 55 of file bed_autosql_standard.cpp.

References mColChrom, mColName, mColScore, mColSeqStart, mColSeqStop, mColStrand, and mNumFields.

Referenced by CBedAutoSql::xProcessLine().

SetDisplayData()

bool CAutoSqlStandardFields::SetDisplayData	(	const CBedColumnData &	columnData,
		int	bedFlags,
		CSeq_feat &	feat,
		CReaderMessageHandler &	messageHandler
	)		const

Definition at line 190 of file bed_autosql_standard.cpp.

References NStr::fAllowTrailingSymbols, NStr::fConvErr_NoThrow, mColScore, Ref(), CSeq_feat_Base::SetExts(), and NStr::StringToInt().

SetLocation()

bool CAutoSqlStandardFields::SetLocation	(	const CBedColumnData &	columnData,
		int	bedFlags,
		CSeq_feat &	feat,
		CReaderMessageHandler &	messageHandler
	)		const

Definition at line 92 of file bed_autosql_standard.cpp.

References CReadUtil::AsSeqId(), eDiag_Error, eDiag_Warning, eNa_strand_minus, eNa_strand_plus, location, and NStr::StringToUInt().

SetRegion()

bool CAutoSqlStandardFields::SetRegion	(	const CBedColumnData &	columnData,
		CSeq_feat &	feat,
		CReaderMessageHandler &	messageHandler
	)		const

Definition at line 170 of file bed_autosql_standard.cpp.

References mColChrom, mColName, and CSeq_feat_Base::SetData().

SetTitle()

bool CAutoSqlStandardFields::SetTitle	(	const CBedColumnData &	columnData,
		CSeq_feat &	feat,
		CReaderMessageHandler &	messageHandler
	)		const

Definition at line 155 of file bed_autosql_standard.cpp.

Validate()

bool CAutoSqlStandardFields::Validate

(

CReaderMessageHandler &

messageHandler

)

const

Definition at line 212 of file bed_autosql_standard.cpp.

References eDiag_Error, and fatal().

Member Data Documentation

mColChrom

int CAutoSqlStandardFields::mColChrom

private

Definition at line 89 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), ProcessTableRow(), and SetRegion().

mColName

int CAutoSqlStandardFields::mColName

private

Definition at line 93 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), ProcessTableRow(), and SetRegion().

mColScore

int CAutoSqlStandardFields::mColScore

private

Definition at line 94 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), ProcessTableRow(), and SetDisplayData().

mColSeqStart

int CAutoSqlStandardFields::mColSeqStart

private

Definition at line 90 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), and ProcessTableRow().

mColSeqStop

int CAutoSqlStandardFields::mColSeqStop

private

Definition at line 91 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), and ProcessTableRow().

mColStrand

int CAutoSqlStandardFields::mColStrand

private

Definition at line 92 of file bed_autosql_standard.hpp.

Referenced by ContainsInfo(), and ProcessTableRow().

mNumFields

size_t CAutoSqlStandardFields::mNumFields

private

Definition at line 95 of file bed_autosql_standard.hpp.

Referenced by NumFields(), and ProcessTableRow().

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

• src/objtools/readers/bed_autosql_standard.hpp
• src/objtools/readers/bed_autosql_standard.cpp