CReaderBase Class Reference

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Defines and provides stubs for a general interface to a variety of file readers. More...

#include <objtools/readers/reader_base.hpp>

Inheritance diagram for CReaderBase:

Collaboration diagram for CReaderBase:

Public Types
enum	EFlags {   fNormal = 0 , fNumericIdsAsLocal = 1<<0 , fAllIdsAsLocal = 1<<1 , fNextInLine = 1<<2 ,   fAsRaw = 1<<3 }
	Customization flags that are relevant to all CReaderBase derived readers. More...
enum	ObjectType { OT_UNKNOWN , OT_SEQANNOT , OT_SEQENTRY }
using	TReaderLine = struct SReaderLine { SReaderLine(unsigned int line, string data):mLine(line), mData(data) {}
using	TReaderData = vector< TReaderLine >
using	TReaderFlags = long
typedef list< CRef< CSeq_annot > >	TAnnotList
typedef TAnnotList	TAnnots
typedef TAnnots::iterator	TAnnotIt
typedef TAnnots::const_iterator	TAnnotCit
using	SeqIdResolver = CRef< CSeq_id >(*)(const string &, long, bool)

Public Member Functions
virtual	~CReaderBase ()
virtual CRef< CSerialObject >	ReadObject (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as the most appropriate Genbank object. More...
virtual CRef< CSerialObject >	ReadObject (ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given line reader, render it as the most appropriate Genbank object. More...
virtual CRef< CSeq_annot >	ReadSeqAnnot (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as a single Seq-annot. More...
virtual CRef< CSeq_annot >	ReadSeqAnnot (ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given line reader, render it as a single Seq-annot, if possible. More...
virtual void	ReadSeqAnnots (TAnnots &annots, CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...
virtual void	ReadSeqAnnots (TAnnots &annots, ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...
virtual CRef< CSeq_entry >	ReadSeqEntry (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as a single Seq-entry, if possible. More...
virtual CRef< CSeq_entry >	ReadSeqEntry (ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given line reader, render it as a single Seq-entry, if possible. More...
void	SetProgressReportInterval (unsigned int intv)
void	SetCanceler (ICanceled *=nullptr)
bool	IsCanceled () const

Static Public Member Functions
static CReaderBase *	GetReader (CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)
	Allocate a CReaderBase derived reader object based on the given file format. More...

Public Attributes
unsigned int	mLine
string	mData

Protected Member Functions
	CReaderBase (TReaderFlags flags=0, const string &name="", const string &title="", SeqIdResolver seqresolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr)
	Protected constructor. Use GetReader() to get an actual reader object. More...
	CReaderBase (const CReaderBase &)=delete
	CReaderBase (CReaderBase &&)=delete
void	xGuardedGetData (ILineReader &, TReaderData &, ILineErrorListener *)
virtual void	xGuardedProcessData (const TReaderData &, CSeq_annot &, ILineErrorListener *)
virtual CRef< CSeq_annot >	xCreateSeqAnnot ()
virtual void	xGetData (ILineReader &, TReaderData &)
virtual void	xProcessData (const TReaderData &, CSeq_annot &)
virtual void	xValidateAnnot (const CSeq_annot &)
virtual bool	xGetLine (ILineReader &, string &)
virtual bool	xUngetLine (ILineReader &)
virtual bool	xIsCommentLine (const CTempString &)
virtual bool	xIsTrackLine (const CTempString &)
virtual bool	xIsBrowserLine (const CTempString &)
virtual bool	xIsTrackTerminator (const CTempString &)
virtual void	xAssignTrackData (CSeq_annot &)
virtual bool	xParseBrowserLine (const string &, CSeq_annot &)
virtual bool	xParseTrackLine (const string &)
virtual void	xSetBrowserRegion (const string &, CAnnot_descr &)
virtual void	xPostProcessAnnot (CSeq_annot &)
virtual void	xAddConversionInfo (CSeq_annot &, ILineErrorListener *)
bool	xParseComment (const CTempString &, CRef< CSeq_annot > &)
virtual bool	xReadInit ()
virtual bool	xProgressInit (ILineReader &istr)
bool	xIsReportingProgress () const
bool	xIsOperationCanceled () const
void	xReportProgress (ILineErrorListener *=nullptr)
void	ProcessError (CObjReaderLineException &, ILineErrorListener *)
void	ProcessError (CLineError &, ILineErrorListener *)
void	ProcessWarning (CObjReaderLineException &, ILineErrorListener *)
void	ProcessWarning (CLineError &, ILineErrorListener *)
void	xProcessReaderMessage (CReaderMessage &, ILineErrorListener *)
void	xProcessLineError (const ILineError &, ILineErrorListener *)
void	xProcessUnknownException (const CException &)

Static Protected Member Functions
static void	xAddStringFlagsWithMap (const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)

Protected Attributes
unsigned int	m_uLineNumber
unsigned int	m_uDataCount = 0
unsigned int	m_uProgressReportInterval
unsigned int	m_uNextProgressReport
TReaderFlags	m_iFlags
string	m_AnnotName
string	m_AnnotTitle
string	m_PendingLine
unique_ptr< CTrackData >	m_pTrackDefaults
ILineReader *	m_pReader
ICanceled *	m_pCanceler
SeqIdResolver	mSeqIdResolve
unique_ptr< CReaderMessageHandler >	m_pMessageHandler

Detailed Description

Defines and provides stubs for a general interface to a variety of file readers.

These readers are assumed to read information in some foreign format from an input stream, and render it as an NCBI Genbank object.

Definition at line 61 of file reader_base.hpp.

Member Typedef Documentation

SeqIdResolver

using CReaderBase::SeqIdResolver = CRef<CSeq_id> (*)(const string&, long, bool)

Definition at line 95 of file reader_base.hpp.

TAnnotCit

typedef TAnnots::const_iterator CReaderBase::TAnnotCit

Definition at line 93 of file reader_base.hpp.

TAnnotIt

typedef TAnnots::iterator CReaderBase::TAnnotIt

Definition at line 92 of file reader_base.hpp.

TAnnotList

typedef list< CRef< CSeq_annot > > CReaderBase::TAnnotList

Definition at line 90 of file reader_base.hpp.

TAnnots

typedef TAnnotList CReaderBase::TAnnots

Definition at line 91 of file reader_base.hpp.

TReaderData

using CReaderBase::TReaderData = vector<TReaderLine>

Definition at line 70 of file reader_base.hpp.

TReaderFlags

using CReaderBase::TReaderFlags = long

Definition at line 84 of file reader_base.hpp.

TReaderLine

using CReaderBase::TReaderLine = struct SReaderLine { SReaderLine(unsigned int line, string data): mLine(line), mData(data) {}

Definition at line 65 of file reader_base.hpp.

Member Enumeration Documentation

EFlags

enum CReaderBase::EFlags

Customization flags that are relevant to all CReaderBase derived readers.

Enumerator
fNormal
fNumericIdsAsLocal	numeric identifiers are local IDs
fAllIdsAsLocal	all identifiers are local IDs
fNextInLine
fAsRaw

Definition at line 73 of file reader_base.hpp.

ObjectType

enum CReaderBase::ObjectType

Enumerator
OT_UNKNOWN
OT_SEQANNOT
OT_SEQENTRY

Definition at line 85 of file reader_base.hpp.

Constructor & Destructor Documentation

CReaderBase() [1/3]

CReaderBase::CReaderBase ( TReaderFlags  flags = 0, const string &  name = "", const string &  title = "", SeqIdResolver  seqresolver = CReadUtil::AsSeqId, CReaderListener *  pListener = nullptr  )

protected

Protected constructor. Use GetReader() to get an actual reader object.

Definition at line 155 of file reader_base.cpp.

CReaderBase() [2/3]

CReaderBase::CReaderBase ( const CReaderBase &  )

protecteddelete

CReaderBase() [3/3]

CReaderBase::CReaderBase ( CReaderBase &&  )

protecteddelete

~CReaderBase()

CReaderBase::~CReaderBase ( )

virtual

Definition at line 178 of file reader_base.cpp.

Member Function Documentation

GetReader()

CReaderBase * CReaderBase::GetReader ( CFormatGuess::EFormat  format, TReaderFlags  flags = 0, CReaderListener *  pRL = nullptr  )

static

Allocate a CReaderBase derived reader object based on the given file format.

Parameters

format	format specifier as defined in the class CFormatGuess
flags	bit flags as defined in EFlags

Definition at line 117 of file reader_base.cpp.

References CFormatGuess::eBed, CFormatGuess::eBed15, CFormatGuess::eGtf, CFormatGuess::eGtf_POISENED, CFormatGuess::eWiggle, flags, and format.

Referenced by CMultiReaderApp::xProcessDefault().

IsCanceled()

bool CReaderBase::IsCanceled ( void  ) const

inline

Definition at line 243 of file reader_base.hpp.

References ICanceled::IsCanceled(), and m_pCanceler.

Referenced by ReadSeqAnnot().

ProcessError() [1/2]

void CReaderBase::ProcessError ( CLineError &  err, ILineErrorListener *  pContainer  )

protected

Definition at line 430 of file reader_base.cpp.

References ILineErrorListener::PutError(), and CLineError::Throw().

ProcessError() [2/2]

void CReaderBase::ProcessError ( CObjReaderLineException &  err, ILineErrorListener *  pContainer  )

protected

Definition at line 390 of file reader_base.cpp.

References CObjReaderLineException::Create(), eDiag_Critical, ILineError::eProblem_GeneralParsingError, m_uLineNumber, ILineErrorListener::PutError(), CObjReaderLineException::SetLineNumber(), and CObjReaderLineException::Throw().

Referenced by CHgvsReader::ReadSeqAnnot(), CRepeatMaskerReader::ReadSeqAnnot(), CVcfReader::xNormalizeData(), CVcfReader::xParseData(), CGff2Reader::xParseFeature(), CGff3Reader::xParseFeature(), CUCSCRegionReader::xParseFeature(), CVcfReader::xProcessMetaLineFilter(), CVcfReader::xProcessMetaLineFormat(), and CVcfReader::xProcessMetaLineInfo().

ProcessWarning() [1/2]

void CReaderBase::ProcessWarning ( CLineError &  err, ILineErrorListener *  pContainer  )

protected

Definition at line 442 of file reader_base.cpp.

References m_uLineNumber, ILineError::Message(), ILineErrorListener::PutError(), ILineError::SeverityStr(), and CLineError::Throw().

ProcessWarning() [2/2]

void CReaderBase::ProcessWarning ( CObjReaderLineException &  err, ILineErrorListener *  pContainer  )

protected

Definition at line 412 of file reader_base.cpp.

References m_uLineNumber, CObjReaderLineException::Message(), ILineErrorListener::PutError(), CObjReaderLineException::SetLineNumber(), ILineError::SeverityStr(), and CObjReaderLineException::Throw().

Referenced by CHgvsReader::ReadSeqAnnot().

ReadObject() [1/2]

CRef< CSerialObject > CReaderBase::ReadObject ( CNcbiIstream &  istr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given input stream, render it as the most appropriate Genbank object.

Parameters

istr	input stream to read from.
pErrors	pointer to optional error container object.

Definition at line 185 of file reader_base.cpp.

ReadObject() [2/2]

CRef< CSerialObject > CReaderBase::ReadObject ( ILineReader &  lr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given line reader, render it as the most appropriate Genbank object.

This will be Seq-annot by default but may be something else (Bioseq, Seq-entry, ...) in derived classes. This is the only function that does not come with a default implementation. That is, an implementation must be provided in the derived class.

Parameters

lr	line reader to read from.
pErrors	pointer to optional error container object.

Reimplemented in CRepeatMaskerReader, CUCSCRegionReader, CFeature_table_reader, CFastaReader, CGff2Reader, and CHgvsReader.

Definition at line 196 of file reader_base.cpp.

References ReadSeqAnnot().

ReadSeqAnnot() [1/2]

CRef< CSeq_annot > CReaderBase::ReadSeqAnnot ( CNcbiIstream &  istr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given input stream, render it as a single Seq-annot.

Return empty Seq-annot otherwise.

Parameters

istr	input stream to read from.
pErrors	pointer to optional error container object.

Definition at line 208 of file reader_base.cpp.

Referenced by CPslObjectLoader::Execute(), ReadObject(), CGvfReader::ReadSeqAnnot(), CMicroArrayReader::ReadSeqAnnot(), CVcfReader::ReadSeqAnnot(), CBedReader::ReadSeqAnnot(), CGff3Reader::ReadSeqAnnot(), CGtfReader::ReadSeqAnnot(), CGff2Reader::ReadSeqAnnots(), and ReadSeqAnnots().

ReadSeqAnnot() [2/2]

CRef< CSeq_annot > CReaderBase::ReadSeqAnnot ( ILineReader &  lr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given line reader, render it as a single Seq-annot, if possible.

Return empty Seq-annot otherwise.

Parameters

lr	line reader to read from.
pErrors	pointer to optional error container object.

Reimplemented in CRepeatMaskerReader, CGtfReader, CGff3Reader, CBedReader, CFeature_table_reader, CUCSCRegionReader, CWiggleReader, CVcfReader, CMicroArrayReader, CGvfReader, and CHgvsReader.

Definition at line 219 of file reader_base.cpp.

References eDiag_Fatal, IsCanceled(), m_uDataCount, m_uLineNumber, CRef< C, Locker >::Reset(), xCreateSeqAnnot(), xGuardedGetData(), xGuardedProcessData(), xPostProcessAnnot(), xProcessReaderMessage(), xProgressInit(), xReportProgress(), and xValidateAnnot().

ReadSeqAnnots() [1/2]

void CReaderBase::ReadSeqAnnots ( TAnnots &  annots, CNcbiIstream &  istr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read all objects from given insput stream, returning them as a vector of Seq-annots.

Parameters

annots	(out) vector containing read Seq-annots
istr	input stream to read from.
pErrors	pointer to optional error container object.

Reimplemented in CGff2Reader.

Definition at line 338 of file reader_base.cpp.

Referenced by CBedObjectLoader::Execute(), CWigObjectLoader::Execute(), sRunTest(), sUpdateCase(), and CMultiReaderApp::xProcessWiggle().

ReadSeqAnnots() [2/2]

void CReaderBase::ReadSeqAnnots ( TAnnots &  annots, ILineReader &  lr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read all objects from given insput stream, returning them as a vector of Seq-annots.

Parameters

annots	(out) vector containing read Seq-annots
lr	line reader to read from.
pErrors	pointer to optional error container object.

Reimplemented in CGff2Reader.

Definition at line 350 of file reader_base.cpp.

References ReadSeqAnnot(), xProgressInit(), and xReadInit().

ReadSeqEntry() [1/2]

CRef< CSeq_entry > CReaderBase::ReadSeqEntry ( CNcbiIstream &  istr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given input stream, render it as a single Seq-entry, if possible.

Return empty Seq-entry otherwise.

Parameters

istr	input stream to read from.
pErrors	pointer to optional error container object.

Definition at line 367 of file reader_base.cpp.

ReadSeqEntry() [2/2]

CRef< CSeq_entry > CReaderBase::ReadSeqEntry ( ILineReader &  lr, ILineErrorListener *  pErrors = nullptr  )

virtual

Read an object from a given line reader, render it as a single Seq-entry, if possible.

Return empty Seq-entry otherwise.

Parameters

lr	line reader to read from.
pErrors	pointer to optional error container object.

Reimplemented in CFastaReader, and CGff2Reader.

Definition at line 379 of file reader_base.cpp.

References xProgressInit().

SetCanceler()

void CReaderBase::SetCanceler

(

ICanceled *

pCanceler = nullptr

)

Definition at line 704 of file reader_base.cpp.

References m_pCanceler.

Referenced by CAgpObjectLoader::Execute(), CBedObjectLoader::Execute(), CRMObjectLoader::Execute(), CVcfObjectLoader::Execute(), and CWigObjectLoader::Execute().

SetProgressReportInterval()

void CReaderBase::SetProgressReportInterval

(

unsigned int

intv

)

Definition at line 644 of file reader_base.cpp.

References int, m_uNextProgressReport, and m_uProgressReportInterval.

Referenced by CMultiReaderApp::xProcessBed(), CMultiReaderApp::xProcessGff3(), CMultiReaderApp::xProcessGtf(), CMultiReaderApp::xProcessGvf(), and CMultiReaderApp::xProcessWiggle().

xAddConversionInfo()

void CReaderBase::xAddConversionInfo ( CSeq_annot &  annot, ILineErrorListener *  pML  )

protectedvirtual

Definition at line 613 of file reader_base.cpp.

References CUser_object::AddField(), eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, ILineErrorListener::LevelCount(), m_pMessageHandler, CSeq_annot_Base::SetDesc(), CUser_object_Base::SetType(), and CAnnotdesc_Base::SetUser().

Referenced by CRepeatMaskerReader::ReadSeqAnnot(), CBedReader::xPostProcessAnnot(), CGff2Reader::xPostProcessAnnot(), and CGvfReader::xPostProcessAnnot().

xAddStringFlagsWithMap()

void CReaderBase::xAddStringFlagsWithMap ( const list< string > &  stringFlags, const map< string, TReaderFlags >  flagMap, TReaderFlags &  baseFlags  )

staticprotected

Definition at line 459 of file reader_base.cpp.

References map_checker< Container >::end(), eUnknown, map_checker< Container >::find(), and NCBI_THROW.

Referenced by CFastaReader::AddStringFlags(), and CFeature_table_reader::AddStringFlags().

xAssignTrackData()

void CReaderBase::xAssignTrackData ( CSeq_annot &  annot )

protectedvirtual

Definition at line 566 of file reader_base.cpp.

References m_AnnotName, m_AnnotTitle, m_pTrackDefaults, CSeq_annot::SetNameDesc(), and CSeq_annot::SetTitleDesc().

Referenced by CMicroArrayReader::ReadSeqAnnot(), CVcfReader::ReadSeqAnnot(), CBedReader::xPostProcessAnnot(), CGvfReader::xPostProcessAnnot(), and CWiggleReader::xPostProcessAnnot().

xCreateSeqAnnot()

CRef< CSeq_annot > CReaderBase::xCreateSeqAnnot ( )

protectedvirtual

Reimplemented in CVcfReader, CMicroArrayReader, and CBedReader.

Definition at line 255 of file reader_base.cpp.

References m_AnnotName, m_AnnotTitle, CSeq_annot::SetNameDesc(), and CSeq_annot::SetTitleDesc().

Referenced by CWiggleReader::ReadSeqAnnot(), ReadSeqAnnot(), CMicroArrayReader::xCreateSeqAnnot(), CVcfReader::xCreateSeqAnnot(), and CWiggleReader::xDumpChromValues().

xGetData()

void CReaderBase::xGetData ( ILineReader &  lr, TReaderData &  readerData  )

protectedvirtual

Reimplemented in CWiggleReader, CVcfReader, CMicroArrayReader, CGvfReader, CGff2Reader, and CBedReader.

Definition at line 314 of file reader_base.cpp.

References m_uDataCount, m_uLineNumber, and xGetLine().

Referenced by CGvfReader::xGetData(), and xGuardedGetData().

xGetLine()

bool CReaderBase::xGetLine ( ILineReader &  lr, string &  line  )

protectedvirtual

Definition at line 764 of file reader_base.cpp.

References ILineReader::AtEOF(), m_PendingLine, m_uLineNumber, NStr::TruncateSpaces_Unsafe(), and xIsCommentLine().

Referenced by CBedReader::ReadTrackData(), xGetData(), CGff2Reader::xGetData(), CMicroArrayReader::xGetData(), CVcfReader::xGetData(), CWiggleReader::xGetData(), and CBedReader::xReadBedDataRaw().

xGuardedGetData()

void CReaderBase::xGuardedGetData ( ILineReader &  lr, TReaderData &  readerData, ILineErrorListener *  pEL  )

protected

Definition at line 270 of file reader_base.cpp.

References xGetData(), xProcessLineError(), xProcessReaderMessage(), and xProcessUnknownException().

Referenced by CWiggleReader::ReadSeqAnnot(), ReadSeqAnnot(), and CWiggleReader::ReadTrackData().

xGuardedProcessData()

void CReaderBase::xGuardedProcessData ( const TReaderData &  readerData, CSeq_annot &  annot, ILineErrorListener *  pEL  )

protectedvirtual

Definition at line 292 of file reader_base.cpp.

References xProcessData(), xProcessLineError(), xProcessReaderMessage(), and xProcessUnknownException().

Referenced by CWiggleReader::ReadSeqAnnot(), and ReadSeqAnnot().

xIsBrowserLine()

bool CReaderBase::xIsBrowserLine ( const CTempString &  strLine )

protectedvirtual

Definition at line 756 of file reader_base.cpp.

References NStr::StartsWith().

Referenced by CBedReader::xDetermineLikelyColumnCount(), and CWiggleReader::xGetData().

xIsCommentLine()

bool CReaderBase::xIsCommentLine ( const CTempString &  strLine )

protectedvirtual

Reimplemented in CVcfReader.

Definition at line 722 of file reader_base.cpp.

References CTempString::empty().

Referenced by xGetLine(), and CVcfReader::xIsCommentLine().

xIsOperationCanceled()

bool CReaderBase::xIsOperationCanceled ( ) const

protected

Definition at line 712 of file reader_base.cpp.

References ICanceled::IsCanceled(), and m_pCanceler.

xIsReportingProgress()

bool CReaderBase::xIsReportingProgress ( ) const

protected

Definition at line 653 of file reader_base.cpp.

References m_pReader, and m_uProgressReportInterval.

Referenced by xReportProgress().

xIsTrackLine()

bool CReaderBase::xIsTrackLine ( const CTempString &  strLine )

protectedvirtual

Definition at line 733 of file reader_base.cpp.

References NStr::StartsWith().

Referenced by CBedReader::xDetermineLikelyColumnCount(), CBedReader::xGetData(), CGff2Reader::xGetData(), CMicroArrayReader::xGetData(), CVcfReader::xGetData(), CWiggleReader::xGetData(), CWiggleReader::xParseTrackLine(), and CVcfReader::xProcessTrackLine().

xIsTrackTerminator()

bool CReaderBase::xIsTrackTerminator ( const CTempString &  strLine )

protectedvirtual

Definition at line 747 of file reader_base.cpp.

References NStr::TruncateSpaces_Unsafe().

Referenced by CGff2Reader::xGetData(), and CGtfReader::xProcessData().

xParseBrowserLine()

bool CReaderBase::xParseBrowserLine ( const string &  strLine, CSeq_annot &  annot  )

protectedvirtual

Reimplemented in CWiggleReader.

Definition at line 536 of file reader_base.cpp.

References eDiag_Error, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, m_uLineNumber, CSeq_annot_Base::SetDesc(), NStr::Split(), NStr::StartsWith(), and xSetBrowserRegion().

Referenced by CBedReader::xProcessData(), CGff2Reader::xProcessData(), CGff3Reader::xProcessData(), CGtfReader::xProcessData(), CGvfReader::xProcessData(), CMicroArrayReader::xProcessData(), and CVcfReader::xProcessData().

xParseComment()

bool CReaderBase::xParseComment ( const CTempString &  record, CRef< CSeq_annot > &  annot  )

protected

Definition at line 594 of file reader_base.cpp.

References NStr::StartsWith().

Referenced by CUCSCRegionReader::ReadSeqAnnot().

xParseTrackLine()

bool CReaderBase::xParseTrackLine ( const string &  strLine )

protectedvirtual

Reimplemented in CWiggleReader, and CBedReader.

Definition at line 580 of file reader_base.cpp.

References CTrackData::IsTrackData(), m_pTrackDefaults, and CReadUtil::Tokenize().

Referenced by CGff2Reader::xGetData(), CBedReader::xParseTrackLine(), CWiggleReader::xParseTrackLine(), CMicroArrayReader::xProcessTrackLine(), and CVcfReader::xProcessTrackLine().

xPostProcessAnnot()

void CReaderBase::xPostProcessAnnot ( CSeq_annot &  )

protectedvirtual

Reimplemented in CWiggleReader, CGvfReader, CGtfReader, CGff3Reader, CGff2Reader, and CBedReader.

Definition at line 606 of file reader_base.cpp.

Referenced by ReadSeqAnnot().

xProcessData()

void CReaderBase::xProcessData ( const TReaderData &  readerData, CSeq_annot &  annot  )

protectedvirtual

Reimplemented in CWiggleReader, CVcfReader, CMicroArrayReader, CGvfReader, CGtfReader, CGff3Reader, CGff2Reader, CBedReader, and CPslReader.

Definition at line 329 of file reader_base.cpp.

Referenced by xGuardedProcessData().

xProcessLineError()

void CReaderBase::xProcessLineError ( const ILineError &  lineError, ILineErrorListener *  pEL  )

protected

Definition at line 829 of file reader_base.cpp.

References ILineErrorListener::PutMessage().

Referenced by xGuardedGetData(), xGuardedProcessData(), and xProcessReaderMessage().

xProcessReaderMessage()

void CReaderBase::xProcessReaderMessage ( CReaderMessage &  readerMessage, ILineErrorListener *  pEL  )

protected

Definition at line 799 of file reader_base.cpp.

References eDiag_Fatal, m_pMessageHandler, m_uLineNumber, CReaderMessage::SetLineNumber(), CReaderMessage::Severity(), and xProcessLineError().

Referenced by ReadSeqAnnot(), xGuardedGetData(), and xGuardedProcessData().

xProcessUnknownException()

void CReaderBase::xProcessUnknownException ( const CException &  error )

protected

Definition at line 849 of file reader_base.cpp.

References eDiag_Fatal, m_uLineNumber, and terminator.

Referenced by xGuardedGetData(), and xGuardedProcessData().

xProgressInit()

bool CReaderBase::xProgressInit ( ILineReader &  istr )

protectedvirtual

Definition at line 692 of file reader_base.cpp.

References m_pReader, and m_uProgressReportInterval.

Referenced by CWiggleReader::ReadSeqAnnot(), ReadSeqAnnot(), CGff2Reader::ReadSeqAnnots(), ReadSeqAnnots(), CGff2Reader::ReadSeqEntry(), and ReadSeqEntry().

xReadInit()

bool CReaderBase::xReadInit ( )

protectedvirtual

Reimplemented in CGff3Reader.

Definition at line 685 of file reader_base.cpp.

Referenced by ReadSeqAnnots(), and CGff3Reader::xReadInit().

xReportProgress()

void CReaderBase::xReportProgress ( ILineErrorListener *  pProgress = nullptr )

protected

Definition at line 666 of file reader_base.cpp.

References ILineReader::GetPosition(), int, m_pMessageHandler, m_pReader, m_uNextProgressReport, m_uProgressReportInterval, and xIsReportingProgress().

Referenced by ReadSeqAnnot().

xSetBrowserRegion()

void CReaderBase::xSetBrowserRegion ( const string &  strRaw, CAnnot_descr &  desc  )

protectedvirtual

Definition at line 477 of file reader_base.cpp.

References NStr::Compare(), CSeq_id_Base::e_Local, eDiag_Error, eNa_strand_unknown, NStr::fAllowCommas, location, m_uLineNumber, CAnnot_descr_Base::Set(), CSeq_interval_Base::SetFrom(), CAnnotdesc_Base::SetRegion(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), NStr::SplitInTwo(), and NStr::StringToInt().

Referenced by xParseBrowserLine().

xUngetLine()

bool CReaderBase::xUngetLine ( ILineReader &  lr )

protectedvirtual

Definition at line 788 of file reader_base.cpp.

References m_uLineNumber, and ILineReader::UngetLine().

Referenced by CGff2Reader::xGetData(), CMicroArrayReader::xGetData(), CVcfReader::xGetData(), and CWiggleReader::xGetData().

xValidateAnnot()

virtual void CReaderBase::xValidateAnnot ( const CSeq_annot &  )

inlineprotectedvirtual

Reimplemented in CGff3Reader.

Definition at line 266 of file reader_base.hpp.

Referenced by ReadSeqAnnot().

Member Data Documentation

m_AnnotName

string CReaderBase::m_AnnotName

protected

Definition at line 374 of file reader_base.hpp.

Referenced by xAssignTrackData(), xCreateSeqAnnot(), and CBedReader::xCreateSeqAnnot().

m_AnnotTitle

string CReaderBase::m_AnnotTitle

protected

Definition at line 375 of file reader_base.hpp.

Referenced by CGff2Reader::x_ProcessAlignmentsGff(), xAssignTrackData(), xCreateSeqAnnot(), CBedReader::xCreateSeqAnnot(), and CGff3Reader::xProcessAlignmentData().

m_iFlags

TReaderFlags CReaderBase::m_iFlags

protected

Definition at line 373 of file reader_base.hpp.

Referenced by CMicroArrayReader::CMicroArrayReader(), CGff2Reader::IsInGenbankMode(), CWiggleReader::ReadSeqAnnot(), CFeature_table_reader::ReadSeqAnnot(), CBedReader::SetAutoSql(), CFastaReader::x_SetDeflineParseInfo(), CUCSCRegionReader::x_SetFeatureLocation(), CVcfReader::xAssignFeatureLocationSet(), CBedReader::xDetermineLikelyColumnCount(), CWiggleReader::xDumpChromValues(), CGtfReader::xFeatureSetDataCds(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CGff3Reader::xInitializeFeature(), CGff3Reader::xJoinLocationIntoRna(), CWiggleReader::xMakeChromId(), CWiggleReader::xMakeTable(), CBedReader::xParseFeature(), CWiggleReader::xPostProcessAnnot(), CWiggleReader::xPreprocessValues(), CGtfReader::xProcessQualifierSpecialCase(), CGff3Reader::xProcessSequenceRegionPragma(), CMicroArrayReader::xProcessTrackLine(), CBedReader::xReadBedRecordRaw(), CWiggleReader::xReadFixedStepDataRaw(), CWiggleReader::xReadVariableStepDataRaw(), CGtfReader::xSetAncestorXrefs(), CWiggleReader::xSetChrom(), CMicroArrayReader::xSetFeatureDisplayData(), CBedReader::xSetFeatureLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationCds(), CBedReader::xSetFeatureLocationRna(), CBedReader::xSetFeatureLocationThick(), CGff3Reader::xUpdateAnnotCds(), CGff3Reader::xUpdateAnnotExon(), CGff2Reader::xUpdateAnnotFeature(), CGff3Reader::xUpdateAnnotGene(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRegion(), CGff3Reader::xUpdateAnnotRna(), and CGff3Reader::xVerifyExonLocation().

m_pCanceler

ICanceled* CReaderBase::m_pCanceler

protected

Definition at line 380 of file reader_base.hpp.

Referenced by IsCanceled(), SetCanceler(), and xIsOperationCanceled().

m_PendingLine

string CReaderBase::m_PendingLine

protected

Definition at line 376 of file reader_base.hpp.

Referenced by CGff2Reader::xGetData(), xGetLine(), and CGff2Reader::xNeedsNewSeqAnnot().

m_pMessageHandler

unique_ptr<CReaderMessageHandler> CReaderBase::m_pMessageHandler

protected

Definition at line 382 of file reader_base.hpp.

Referenced by CBedReader::SetAutoSql(), xAddConversionInfo(), CVcfReader::xAssignVariantProps(), CVcfReader::xAssignVariantSource(), CGtfReader::xCheckForGeneIdConflict(), CGvfReader::xFeatureSetExt(), CWiggleReader::xGetFixedStepInfo(), CWiggleReader::xGetVariableStepInfo(), CBedReader::xParseFeatureAutoSql(), CBedReader::xParseTrackLine(), CGff3Reader::xPostProcessAnnot(), CPslReader::xProcessData(), CVcfReader::xProcessData(), xProcessReaderMessage(), CMicroArrayReader::xProcessTrackLine(), CVcfReader::xProcessTrackLine(), CBedReader::xReadBedRecordRaw(), xReportProgress(), CBedReader::xSetFeatureColorFromItemRgb(), and CVcfReader::xSetFileFormat().

m_pReader

ILineReader* CReaderBase::m_pReader

protected

Definition at line 379 of file reader_base.hpp.

Referenced by xIsReportingProgress(), xProgressInit(), and xReportProgress().

m_pTrackDefaults

unique_ptr<CTrackData> CReaderBase::m_pTrackDefaults

protected

Definition at line 378 of file reader_base.hpp.

Referenced by CGff2Reader::xAssignAnnotId(), xAssignTrackData(), CWiggleReader::xMakeGraph(), xParseTrackLine(), CWiggleReader::xParseTrackLine(), CBedReader::xSetFeatureColor(), and CBedReader::xSetFeatureScore().

m_uDataCount

unsigned int CReaderBase::m_uDataCount = 0

protected

Definition at line 369 of file reader_base.hpp.

Referenced by CWiggleReader::ReadSeqAnnot(), ReadSeqAnnot(), xGetData(), CBedReader::xGetData(), CGff2Reader::xGetData(), CMicroArrayReader::xGetData(), CVcfReader::xGetData(), CWiggleReader::xGetData(), and CVcfReader::xProcessData().

m_uLineNumber

unsigned int CReaderBase::m_uLineNumber

protected

Definition at line 368 of file reader_base.hpp.

Referenced by CWiggleReader::CWiggleReader(), ProcessError(), ProcessWarning(), CHgvsReader::ReadSeqAnnot(), CUCSCRegionReader::ReadSeqAnnot(), ReadSeqAnnot(), CGvfReader::x_CreateRecord(), CUCSCRegionReader::x_SetFeatureLocation(), CVcfReader::xAssignVariantProps(), CVcfReader::xAssignVariantSource(), CGtfReader::xCheckForGeneIdConflict(), CGvfReader::xFeatureSetExt(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CGff3Reader::xFindFeatureUnderConstruction(), xGetData(), CBedReader::xGetData(), CGff2Reader::xGetData(), CMicroArrayReader::xGetData(), CVcfReader::xGetData(), CWiggleReader::xGetData(), CWiggleReader::xGetDouble(), CWiggleReader::xGetFixedStepInfo(), xGetLine(), CWiggleReader::xGetParamName(), CWiggleReader::xGetParamValue(), CWiggleReader::xGetPos(), CWiggleReader::xGetVariableStepInfo(), CWiggleReader::xGetWord(), xParseBrowserLine(), CBedReader::xParseFeature(), CGvfReader::xParseFeature(), CUCSCRegionReader::xParseFeature(), CBedReader::xParseTrackLine(), CWiggleReader::xParseTrackLine(), CGff3Reader::xPostProcessAnnot(), CVcfReader::xProcessData(), CMicroArrayReader::xProcessFeature(), xProcessReaderMessage(), CGff3Reader::xProcessSequenceRegionPragma(), CMicroArrayReader::xProcessTrackLine(), CVcfReader::xProcessTrackLine(), xProcessUnknownException(), CBedReader::xReadBedRecordRaw(), xSetBrowserRegion(), CBedReader::xSetFeatureColorByStrand(), CBedReader::xSetFeatureColorFromItemRgb(), CBedReader::xSetFeatureColorFromScore(), CBedReader::xSetFeatureLocationCds(), CBedReader::xSetFeatureLocationThick(), CBedReader::xSetFeatureTitle(), CVcfReader::xSetFileFormat(), xUngetLine(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRna(), CGvfReader::xVariationMakeCNV(), CGff3Reader::xVerifyCdsParents(), and CGff3Reader::xVerifyExonLocation().

m_uNextProgressReport

unsigned int CReaderBase::m_uNextProgressReport

protected

Definition at line 371 of file reader_base.hpp.

Referenced by SetProgressReportInterval(), and xReportProgress().

m_uProgressReportInterval

unsigned int CReaderBase::m_uProgressReportInterval

protected

Definition at line 370 of file reader_base.hpp.

Referenced by SetProgressReportInterval(), xIsReportingProgress(), xProgressInit(), and xReportProgress().

mData

string CReaderBase::mData

Definition at line 68 of file reader_base.hpp.

mLine

unsigned int CReaderBase::mLine

Definition at line 67 of file reader_base.hpp.

mSeqIdResolve

SeqIdResolver CReaderBase::mSeqIdResolve

protected

Definition at line 381 of file reader_base.hpp.

Referenced by CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGtfReader::xFeatureSetDataCds(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CPslReader::xProcessData(), CGff3Reader::xProcessSequenceRegionPragma(), CGff3Reader::xUpdateAnnotGeneric(), and CGff3Reader::xVerifyExonLocation().

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

• include/objtools/readers/reader_base.hpp
• src/objtools/readers/reader_base.cpp