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NCBI C++ ToolKit: CReaderBase Class Reference

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

#include <objtools/readers/reader_base.hpp>

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 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 CTempString &, CSeq_annot &) virtual bool xParseTrackLine (const CTempString &) virtual void xSetBrowserRegion (const CTempString &, 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 &)

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.

◆ SeqIdResolver ◆ TAnnotCit ◆ TAnnotIt ◆ TAnnotList ◆ TAnnots ◆ TReaderData ◆ TReaderFlags ◆ 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 74 of file reader_base.hpp.

◆ ObjectType Enumerator OT_UNKNOWN OT_SEQANNOT OT_SEQENTRY

Definition at line 86 of file reader_base.hpp.

◆ CReaderBase() [1/3] ◆ CReaderBase() [2/3] ◆ CReaderBase() [3/3] ◆ ~CReaderBase() ◆ GetReader() ◆ IsCanceled() bool CReaderBase::IsCanceled ( void ) const inline ◆ ProcessError() [1/2] ◆ ProcessError() [2/2]

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] ◆ ProcessWarning() [2/2] ◆ ReadObject() [1/2]

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.

References lr().

◆ ReadObject() [2/2]

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 lr(), and ReadSeqAnnot().

◆ ReadSeqAnnot() [1/2]

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.

References lr().

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

◆ ReadSeqAnnot() [2/2]

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

◆ ReadSeqAnnots() [1/2] ◆ ReadSeqAnnots() [2/2]

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

◆ ReadSeqEntry() [1/2]

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.

References lr().

◆ ReadSeqEntry() [2/2]

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 lr(), and xProgressInit().

◆ SetCanceler() ◆ SetProgressReportInterval() void CReaderBase::SetProgressReportInterval ( unsigned int intv ) ◆ xAddConversionInfo()

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() ◆ xAssignTrackData() void CReaderBase::xAssignTrackData ( CSeq_annot & annot ) protectedvirtual ◆ xCreateSeqAnnot() ◆ xGetData() ◆ xGetLine()

Definition at line 762 of file reader_base.cpp.

References lr(), 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() ◆ xGuardedProcessData() ◆ xIsBrowserLine() ◆ xIsCommentLine() ◆ xIsOperationCanceled() bool CReaderBase::xIsOperationCanceled ( ) const protected ◆ xIsReportingProgress() bool CReaderBase::xIsReportingProgress ( ) const protected ◆ xIsTrackLine() ◆ xIsTrackTerminator() ◆ xParseBrowserLine()

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() ◆ xParseTrackLine() ◆ xPostProcessAnnot() void CReaderBase::xPostProcessAnnot ( CSeq_annot & ) protectedvirtual ◆ xProcessData() ◆ xProcessLineError() ◆ xProcessReaderMessage() ◆ xProcessUnknownException() ◆ xProgressInit() ◆ xReadInit() bool CReaderBase::xReadInit ( ) protectedvirtual ◆ xReportProgress() ◆ xSetBrowserRegion()

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() ◆ xValidateAnnot() ◆ m_AnnotName string CReaderBase::m_AnnotName protected ◆ m_AnnotTitle string CReaderBase::m_AnnotTitle protected ◆ m_iFlags

Definition at line 374 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(), 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 ◆ m_PendingLine string CReaderBase::m_PendingLine protected ◆ m_pMessageHandler

Definition at line 383 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(), CPslReader::xProcessData(), CVcfReader::xProcessData(), xProcessReaderMessage(), CMicroArrayReader::xProcessTrackLine(), CVcfReader::xProcessTrackLine(), CBedReader::xReadBedRecordRaw(), xReportProgress(), CBedReader::xSetFeatureColorFromItemRgb(), and CVcfReader::xSetFileFormat().

◆ m_pReader ◆ m_pTrackDefaults unique_ptr<CTrackData> CReaderBase::m_pTrackDefaults protected ◆ m_uDataCount std::atomic<unsigned int> CReaderBase::m_uDataCount = 0 protected ◆ m_uLineNumber unsigned int CReaderBase::m_uLineNumber protected

Definition at line 369 of file reader_base.hpp.

◆ m_uNextProgressReport unsigned int CReaderBase::m_uNextProgressReport protected ◆ m_uProgressReportInterval unsigned int CReaderBase::m_uProgressReportInterval protected ◆ mSeqIdResolve

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

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

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