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CBedReader Class Reference

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CReaderBase implementation that reads BED data files, either a single object or all objects found. More...

#include <objtools/readers/bed_reader.hpp>

+ Inheritance diagram for CBedReader:
+ Collaboration diagram for CBedReader:

Public Types

enum  EBedFlags { fThreeFeatFormat = 1<<8 , fDirectedFeatureModel = 1<<9 , fAutoSql = 1<<10 , fAddDefaultColumns = 1<<11 }
 
typedef int TFlags
 
- Public Types inherited from CReaderBase
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

 CBedReader (int=fNormal, const string &="", const string &="", CReaderListener *=nullptr)
 
virtual ~CBedReader ()
 
CRef< CSeq_annotReadSeqAnnot (ILineReader &lr, ILineErrorListener *pErrors=nullptr) override
 Read a single object from given line reader containing BED data. More...
 
virtual bool ReadTrackData (ILineReader &, CRawBedTrack &, ILineErrorListener *=nullptr)
 
virtual bool SetAutoSql (const string &)
 
virtual bool SetAutoSql (CNcbiIstream &)
 
- Public Member Functions inherited from CReaderBase
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 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
 

Protected Member Functions

CRef< CSeq_annotxCreateSeqAnnot () override
 
void xGetData (ILineReader &, TReaderData &) override
 
void xProcessData (const TReaderData &, CSeq_annot &) override
 
virtual bool xDetermineLikelyColumnCount (CLinePreBuffer &, ILineErrorListener *)
 
bool xParseTrackLine (const string &) override
 
bool xParseFeature (const SReaderLine &, CSeq_annot &, ILineErrorListener *)
 
bool xParseFeatureAutoSql (const CBedColumnData &, CSeq_annot &, ILineErrorListener *)
 
bool xParseFeatureUserFormat (const CBedColumnData &, CSeq_annot &, ILineErrorListener *)
 
bool xParseFeatureThreeFeatFormat (const CBedColumnData &, CSeq_annot &, ILineErrorListener *)
 
bool xParseFeatureGeneModelFormat (const CBedColumnData &, CSeq_annot &, ILineErrorListener *)
 
bool xAppendFeatureChrom (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
bool xAppendFeatureThick (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
bool xAppendFeatureBlock (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
CRef< CSeq_featxAppendFeatureGene (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
CRef< CSeq_featxAppendFeatureRna (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
CRef< CSeq_featxAppendFeatureCds (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
 
void xSetFeatureLocation (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationChrom (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationGene (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationThick (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationCds (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationBlock (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureLocationRna (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureIdsChrom (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureIdsGene (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureIdsThick (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureIdsCds (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureIdsBlock (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureIdsRna (CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)
 
void xSetFeatureBedData (CRef< CSeq_feat > &, const CBedColumnData &, ILineErrorListener *)
 
void xSetFeatureTitle (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xSetFeatureScore (CRef< CUser_object >, const CBedColumnData &)
 
void xSetFeatureColor (CRef< CUser_object >, const CBedColumnData &, ILineErrorListener *)
 
void xSetFeatureColorFromItemRgb (CRef< CUser_object >, const string &, ILineErrorListener *)
 
void xSetFeatureColorFromScore (CRef< CUser_object >, const string &)
 
void xSetFeatureColorByStrand (CRef< CUser_object >, const string &, ENa_strand, ILineErrorListener *)
 
void xSetFeatureColorDefault (CRef< CUser_object >)
 
bool xContainsThickFeature (const CBedColumnData &) const
 
bool xContainsBlockFeature (const CBedColumnData &) const
 
bool xContainsRnaFeature (const CBedColumnData &) const
 
bool xContainsCdsFeature (const CBedColumnData &) const
 
ENa_strand xGetStrand (const CBedColumnData &) const
 
virtual void xAssignBedColumnCount (CSeq_annot &)
 
void xSetFeatureDisplayData (CRef< CSeq_feat > &, const CBedColumnData &)
 
void xPostProcessAnnot (CSeq_annot &) override
 
bool xReadBedDataRaw (ILineReader &, CRawBedTrack &, ILineErrorListener *)
 
bool xReadBedRecordRaw (const string &, CRawBedRecord &, ILineErrorListener *)
 
- Protected Member Functions inherited from CReaderBase
 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 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 void xSetBrowserRegion (const string &, CAnnot_descr &)
 
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 xCleanColumnValues (vector< string > &)
 
- Static Protected Member Functions inherited from CReaderBase
static void xAddStringFlagsWithMap (const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)
 

Protected Attributes

string m_currentId
 
string mColumnSeparator
 
NStr::TSplitFlags mColumnSplitFlags
 
vector< string >::size_type mRealColumnCount
 
vector< string >::size_type mValidColumnCount
 
bool mAssumeErrorsAreRecordLevel
 
unsigned int m_CurrentFeatureCount
 
bool m_usescore
 
unsigned int m_CurBatchSize
 
const unsigned int m_MaxBatchSize
 
unique_ptr< CLinePreBuffermLinePreBuffer
 
unique_ptr< CBedAutoSqlmpAutoSql
 
- Protected Attributes inherited from CReaderBase
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
 

Additional Inherited Members

- Static Public Member Functions inherited from CReaderBase
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 inherited from CReaderBase
unsigned int mLine
 
string mData
 

Detailed Description

CReaderBase implementation that reads BED data files, either a single object or all objects found.

For the purpose of CBedReader, an object consists of a run of records all with the same ID (BED comlumn 1), and all contained within a single track.

Definition at line 106 of file bed_reader.hpp.

Member Typedef Documentation

◆ TFlags

Definition at line 131 of file bed_reader.hpp.

Member Enumeration Documentation

◆ EBedFlags

Enumerator
fThreeFeatFormat 
fDirectedFeatureModel 
fAutoSql 
fAddDefaultColumns 

Definition at line 125 of file bed_reader.hpp.

Constructor & Destructor Documentation

◆ CBedReader()

CBedReader::CBedReader ( int  flags = fNormal,
const string annotName = "",
const string annotTitle = "",
CReaderListener pRL = nullptr 
)

Definition at line 237 of file bed_reader.cpp.

◆ ~CBedReader()

CBedReader::~CBedReader ( )
virtual

Definition at line 260 of file bed_reader.cpp.

Member Function Documentation

◆ ReadSeqAnnot()

CRef< CSeq_annot > CBedReader::ReadSeqAnnot ( ILineReader lr,
ILineErrorListener pErrors = nullptr 
)
overridevirtual

Read a single object from given line reader containing BED data.

The resulting Seq-annot will contain a feature table.

Parameters
lrline reader to read from.
pErrorspointer to optional error container object.

Reimplemented from CReaderBase.

Definition at line 267 of file bed_reader.cpp.

References m_CurrentFeatureCount, and CReaderBase::ReadSeqAnnot().

Referenced by CMultiReaderApp::xProcessBed().

◆ ReadTrackData()

bool CBedReader::ReadTrackData ( ILineReader lr,
CRawBedTrack rawdata,
ILineErrorListener pMessageListener = nullptr 
)
virtual

◆ SetAutoSql() [1/2]

bool CBedReader::SetAutoSql ( CNcbiIstream istr)
virtual

Definition at line 299 of file bed_reader.cpp.

References CReaderBase::m_pMessageHandler, and mpAutoSql.

◆ SetAutoSql() [2/2]

bool CBedReader::SetAutoSql ( const string fileName)
virtual

Definition at line 278 of file bed_reader.cpp.

References fAutoSql, CException::GetMsg(), and CReaderBase::m_iFlags.

Referenced by CMultiReaderApp::xProcessBed().

◆ xAppendFeatureBlock()

bool CBedReader::xAppendFeatureBlock ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAppendFeatureCds()

CRef< CSeq_feat > CBedReader::xAppendFeatureCds ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAppendFeatureChrom()

bool CBedReader::xAppendFeatureChrom ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAppendFeatureGene()

CRef< CSeq_feat > CBedReader::xAppendFeatureGene ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAppendFeatureRna()

CRef< CSeq_feat > CBedReader::xAppendFeatureRna ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAppendFeatureThick()

bool CBedReader::xAppendFeatureThick ( const CBedColumnData columnData,
CSeq_annot annot,
unsigned int  baseId,
ILineErrorListener pEC 
)
protected

◆ xAssignBedColumnCount()

void CBedReader::xAssignBedColumnCount ( CSeq_annot annot)
protectedvirtual

◆ xCleanColumnValues()

void CBedReader::xCleanColumnValues ( vector< string > &  columns)
staticprotected

Definition at line 1963 of file bed_reader.cpp.

References columns, eDiag_Error, NStr::EqualNocase(), and NStr::Replace().

Referenced by xReadBedRecordRaw().

◆ xContainsBlockFeature()

bool CBedReader::xContainsBlockFeature ( const CBedColumnData columnData) const
protected

◆ xContainsCdsFeature()

bool CBedReader::xContainsCdsFeature ( const CBedColumnData columnData) const
protected

Definition at line 1927 of file bed_reader.cpp.

Referenced by xParseFeatureGeneModelFormat().

◆ xContainsRnaFeature()

bool CBedReader::xContainsRnaFeature ( const CBedColumnData columnData) const
protected

Definition at line 1887 of file bed_reader.cpp.

References eDiag_Error, and NStr::StringToInt().

Referenced by xParseFeatureGeneModelFormat().

◆ xContainsThickFeature()

bool CBedReader::xContainsThickFeature ( const CBedColumnData columnData) const
protected

◆ xCreateSeqAnnot()

CRef< CSeq_annot > CBedReader::xCreateSeqAnnot ( )
overrideprotectedvirtual

◆ xDetermineLikelyColumnCount()

bool CBedReader::xDetermineLikelyColumnCount ( CLinePreBuffer preBuffer,
ILineErrorListener pEc 
)
protectedvirtual

◆ xGetData()

void CBedReader::xGetData ( ILineReader lr,
TReaderData readerData 
)
overrideprotectedvirtual

◆ xGetStrand()

ENa_strand CBedReader::xGetStrand ( const CBedColumnData columnData) const
protected

◆ xParseFeature()

bool CBedReader::xParseFeature ( const SReaderLine &  lineData,
CSeq_annot annot,
ILineErrorListener pEC 
)
protected

◆ xParseFeatureAutoSql()

bool CBedReader::xParseFeatureAutoSql ( const CBedColumnData columnData,
CSeq_annot annot,
ILineErrorListener pEC 
)
protected

◆ xParseFeatureGeneModelFormat()

bool CBedReader::xParseFeatureGeneModelFormat ( const CBedColumnData columnData,
CSeq_annot annot,
ILineErrorListener pEC 
)
protected

◆ xParseFeatureThreeFeatFormat()

bool CBedReader::xParseFeatureThreeFeatFormat ( const CBedColumnData columnData,
CSeq_annot annot,
ILineErrorListener pEC 
)
protected

◆ xParseFeatureUserFormat()

bool CBedReader::xParseFeatureUserFormat ( const CBedColumnData columnData,
CSeq_annot annot,
ILineErrorListener pEC 
)
protected

◆ xParseTrackLine()

bool CBedReader::xParseTrackLine ( const string strLine)
overrideprotectedvirtual

◆ xPostProcessAnnot()

void CBedReader::xPostProcessAnnot ( CSeq_annot annot)
overrideprotectedvirtual

◆ xProcessData()

void CBedReader::xProcessData ( const TReaderData readerData,
CSeq_annot annot 
)
overrideprotectedvirtual

◆ xReadBedDataRaw()

bool CBedReader::xReadBedDataRaw ( ILineReader lr,
CRawBedTrack rawdata,
ILineErrorListener pMessageListener 
)
protected

◆ xReadBedRecordRaw()

bool CBedReader::xReadBedRecordRaw ( const string line,
CRawBedRecord record,
ILineErrorListener pMessageListener 
)
protected

◆ xSetFeatureBedData()

void CBedReader::xSetFeatureBedData ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
ILineErrorListener pEc 
)
protected

◆ xSetFeatureColor()

void CBedReader::xSetFeatureColor ( CRef< CUser_object pDisplayData,
const CBedColumnData columnData,
ILineErrorListener pEC 
)
protected

◆ xSetFeatureColorByStrand()

void CBedReader::xSetFeatureColorByStrand ( CRef< CUser_object pDisplayData,
const string trackColorByStrand,
ENa_strand  strand,
ILineErrorListener pEC 
)
protected

◆ xSetFeatureColorDefault()

void CBedReader::xSetFeatureColorDefault ( CRef< CUser_object pDisplayData)
protected

Definition at line 1487 of file bed_reader.cpp.

References CUser_object::AddField().

Referenced by xSetFeatureColor().

◆ xSetFeatureColorFromItemRgb()

void CBedReader::xSetFeatureColorFromItemRgb ( CRef< CUser_object pDisplayData,
const string itemRgb,
ILineErrorListener pEC 
)
protected

◆ xSetFeatureColorFromScore()

void CBedReader::xSetFeatureColorFromScore ( CRef< CUser_object pDisplayData,
const string featScore 
)
protected

◆ xSetFeatureDisplayData()

void CBedReader::xSetFeatureDisplayData ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureIdsBlock()

void CBedReader::xSetFeatureIdsBlock ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

◆ xSetFeatureIdsCds()

void CBedReader::xSetFeatureIdsCds ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

◆ xSetFeatureIdsChrom()

void CBedReader::xSetFeatureIdsChrom ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

◆ xSetFeatureIdsGene()

void CBedReader::xSetFeatureIdsGene ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

Definition at line 1278 of file bed_reader.cpp.

References CSeq_feat_Base::SetId().

Referenced by xAppendFeatureGene().

◆ xSetFeatureIdsRna()

void CBedReader::xSetFeatureIdsRna ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

◆ xSetFeatureIdsThick()

void CBedReader::xSetFeatureIdsThick ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData,
unsigned int  baseId 
)
protected

◆ xSetFeatureLocation()

void CBedReader::xSetFeatureLocation ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationBlock()

void CBedReader::xSetFeatureLocationBlock ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationCds()

void CBedReader::xSetFeatureLocationCds ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationChrom()

void CBedReader::xSetFeatureLocationChrom ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationGene()

void CBedReader::xSetFeatureLocationGene ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationRna()

void CBedReader::xSetFeatureLocationRna ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureLocationThick()

void CBedReader::xSetFeatureLocationThick ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureScore()

void CBedReader::xSetFeatureScore ( CRef< CUser_object pDisplayData,
const CBedColumnData columnData 
)
protected

◆ xSetFeatureTitle()

void CBedReader::xSetFeatureTitle ( CRef< CSeq_feat > &  feature,
const CBedColumnData columnData 
)
protected

Member Data Documentation

◆ m_CurBatchSize

unsigned int CBedReader::m_CurBatchSize
protected

Definition at line 365 of file bed_reader.hpp.

Referenced by ReadTrackData(), and xReadBedDataRaw().

◆ m_CurrentFeatureCount

unsigned int CBedReader::m_CurrentFeatureCount
protected

◆ m_currentId

string CBedReader::m_currentId
protected

◆ m_MaxBatchSize

const unsigned int CBedReader::m_MaxBatchSize
protected

Definition at line 366 of file bed_reader.hpp.

Referenced by ReadTrackData(), and xReadBedDataRaw().

◆ m_usescore

bool CBedReader::m_usescore
protected

Definition at line 364 of file bed_reader.hpp.

Referenced by xSetFeatureDisplayData().

◆ mAssumeErrorsAreRecordLevel

bool CBedReader::mAssumeErrorsAreRecordLevel
protected

Definition at line 362 of file bed_reader.hpp.

Referenced by xDetermineLikelyColumnCount().

◆ mColumnSeparator

string CBedReader::mColumnSeparator
protected

Definition at line 358 of file bed_reader.hpp.

◆ mColumnSplitFlags

NStr::TSplitFlags CBedReader::mColumnSplitFlags
protected

Definition at line 359 of file bed_reader.hpp.

◆ mLinePreBuffer

unique_ptr<CLinePreBuffer> CBedReader::mLinePreBuffer
protected

Definition at line 367 of file bed_reader.hpp.

Referenced by xGetData().

◆ mpAutoSql

unique_ptr<CBedAutoSql> CBedReader::mpAutoSql
protected

Definition at line 369 of file bed_reader.hpp.

Referenced by SetAutoSql(), xDetermineLikelyColumnCount(), and xParseFeatureAutoSql().

◆ mRealColumnCount

vector<string>::size_type CBedReader::mRealColumnCount
protected

◆ mValidColumnCount

vector<string>::size_type CBedReader::mValidColumnCount
protected

The documentation for this class was generated from the following files:
Modified on Sun Jun 23 05:18:50 2024 by modify_doxy.py rev. 669887