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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< CSerialObjectReadObject (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
 Read an object from a given input stream, render it as the most appropriate Genbank object. More...
 
virtual CRef< CSerialObjectReadObject (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_annotReadSeqAnnot (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
 Read an object from a given input stream, render it as a single Seq-annot. More...
 
virtual CRef< CSeq_annotReadSeqAnnot (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_entryReadSeqEntry (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_entryReadSeqEntry (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 CReaderBaseGetReader (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_annotxCreateSeqAnnot ()
 
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< CTrackDatam_pTrackDefaults
 
ILineReaderm_pReader
 
ICanceledm_pCanceler
 
SeqIdResolver mSeqIdResolve
 
unique_ptr< CReaderMessageHandlerm_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

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

Definition at line 90 of file reader_base.hpp.

◆ TAnnots

Definition at line 91 of file reader_base.hpp.

◆ TReaderData

Definition at line 70 of file reader_base.hpp.

◆ TReaderFlags

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

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

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
formatformat specifier as defined in the class CFormatGuess
flagsbit 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

◆ ProcessWarning() [1/2]

void CReaderBase::ProcessWarning ( CLineError err,
ILineErrorListener pContainer 
)
protected

◆ ProcessWarning() [2/2]

void CReaderBase::ProcessWarning ( CObjReaderLineException err,
ILineErrorListener pContainer 
)
protected

◆ 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
istrinput stream to read from.
pErrorspointer 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
lrline reader to read from.
pErrorspointer 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
istrinput stream to read from.
pErrorspointer 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
lrline reader to read from.
pErrorspointer 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
istrinput stream to read from.
pErrorspointer 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
lrline reader to read from.
pErrorspointer 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
istrinput stream to read from.
pErrorspointer 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
lrline reader to read from.
pErrorspointer 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)

◆ SetProgressReportInterval()

void CReaderBase::SetProgressReportInterval ( unsigned int  intv)

◆ xAddConversionInfo()

void CReaderBase::xAddConversionInfo ( CSeq_annot annot,
ILineErrorListener pML 
)
protectedvirtual

◆ xAddStringFlagsWithMap()

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

◆ xAssignTrackData()

void CReaderBase::xAssignTrackData ( CSeq_annot annot)
protectedvirtual

◆ xCreateSeqAnnot()

CRef< CSeq_annot > CReaderBase::xCreateSeqAnnot ( )
protectedvirtual

◆ xGetData()

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

◆ xGetLine()

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

◆ xGuardedGetData()

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

◆ xGuardedProcessData()

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

◆ xIsBrowserLine()

bool CReaderBase::xIsBrowserLine ( const CTempString strLine)
protectedvirtual

◆ 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

◆ 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

◆ xParseComment()

bool CReaderBase::xParseComment ( const CTempString record,
CRef< CSeq_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

◆ 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 ,
CSeq_annot  
)
protectedvirtual

◆ xProcessLineError()

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

◆ xProcessReaderMessage()

void CReaderBase::xProcessReaderMessage ( CReaderMessage readerMessage,
ILineErrorListener pEL 
)
protected

◆ 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

◆ 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 = nullptr)
protected

◆ xSetBrowserRegion()

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

◆ xUngetLine()

bool CReaderBase::xUngetLine ( ILineReader lr)
protectedvirtual

◆ 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

◆ 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

◆ m_pMessageHandler

unique_ptr<CReaderMessageHandler> CReaderBase::m_pMessageHandler
protected

◆ 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

◆ m_uDataCount

unsigned int CReaderBase::m_uDataCount = 0
protected

◆ 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(), 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

◆ 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

The documentation for this class was generated from the following files:
Modified on Tue Jun 18 13:36:58 2024 by modify_doxy.py rev. 669887