CBedReader Class Reference

Search Toolkit Book for CBedReader

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_annot >	ReadSeqAnnot (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< 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 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

Protected Member Functions
CRef< CSeq_annot >	xCreateSeqAnnot () 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_feat >	xAppendFeatureGene (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
CRef< CSeq_feat >	xAppendFeatureRna (const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)
CRef< CSeq_feat >	xAppendFeatureCds (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< CLinePreBuffer >	mLinePreBuffer
unique_ptr< CBedAutoSql >	mpAutoSql
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< CTrackData >	m_pTrackDefaults
ILineReader *	m_pReader
ICanceled *	m_pCanceler
SeqIdResolver	mSeqIdResolve
unique_ptr< CReaderMessageHandler >	m_pMessageHandler

Additional Inherited Members
Static Public Member Functions inherited from CReaderBase
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 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

typedef int CBedReader::TFlags

Definition at line 131 of file bed_reader.hpp.

Member Enumeration Documentation

EBedFlags

enum CBedReader::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

lr	line reader to read from.
pErrors	pointer 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

Definition at line 1735 of file bed_reader.cpp.

References lr(), m_CurBatchSize, m_MaxBatchSize, NStr::StartsWith(), CReaderBase::xGetLine(), and xReadBedDataRaw().

Referenced by CMultiReaderApp::xProcessBedRaw().

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

Definition at line 750 of file bed_reader.cpp.

References ftable, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsBlock(), and xSetFeatureLocationBlock().

Referenced by xParseFeatureThreeFeatFormat().

xAppendFeatureCds()

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

protected

Definition at line 730 of file bed_reader.cpp.

References ftable, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsCds(), and xSetFeatureLocationCds().

Referenced by xParseFeatureGeneModelFormat().

xAppendFeatureChrom()

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

protected

Definition at line 668 of file bed_reader.cpp.

References ftable, m_currentId, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsChrom(), and xSetFeatureLocationChrom().

Referenced by xParseFeatureThreeFeatFormat().

xAppendFeatureGene()

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

protected

Definition at line 689 of file bed_reader.cpp.

References ftable, m_currentId, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsGene(), and xSetFeatureLocationGene().

Referenced by xParseFeatureGeneModelFormat().

xAppendFeatureRna()

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

protected

Definition at line 770 of file bed_reader.cpp.

References ftable, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsRna(), and xSetFeatureLocationRna().

Referenced by xParseFeatureGeneModelFormat().

xAppendFeatureThick()

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

protected

Definition at line 710 of file bed_reader.cpp.

References ftable, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureBedData(), xSetFeatureIdsThick(), and xSetFeatureLocationThick().

Referenced by xParseFeatureThreeFeatFormat().

xAssignBedColumnCount()

void CBedReader::xAssignBedColumnCount ( CSeq_annot &  annot )

protectedvirtual

Definition at line 2008 of file bed_reader.cpp.

References CUser_object::AddField(), CSerialObject::Assign(), mValidColumnCount, CSeq_annot_Base::SetDesc(), CUser_object_Base::SetType(), and CAnnotdesc_Base::SetUser().

Referenced by xPostProcessAnnot().

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

Definition at line 1917 of file bed_reader.cpp.

Referenced by xParseFeatureThreeFeatFormat(), xSetFeatureIdsCds(), xSetFeatureIdsChrom(), and xSetFeatureIdsThick().

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

Definition at line 1857 of file bed_reader.cpp.

References eDiag_Error, and NStr::StringToInt().

Referenced by xParseFeatureThreeFeatFormat(), xSetFeatureIdsBlock(), and xSetFeatureIdsChrom().

xCreateSeqAnnot()

CRef< CSeq_annot > CBedReader::xCreateSeqAnnot ( )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 308 of file bed_reader.cpp.

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

xDetermineLikelyColumnCount()

bool CBedReader::xDetermineLikelyColumnCount ( CLinePreBuffer &  preBuffer, ILineErrorListener *  pEc  )

protectedvirtual

Definition at line 376 of file bed_reader.cpp.

References CLinePreBuffer::begin(), CBedColumnData::ColumnCount(), eDiag_Fatal, CLinePreBuffer::end(), NStr::EndsWith(), fAutoSql, NStr::fDS_ProhibitFractions, CLinePreBuffer::FillBuffer(), NStr::fSplit_MergeDelimiters, CLinePreBuffer::IsCommentLine(), CReaderBase::m_iFlags, mAssumeErrorsAreRecordLevel, mpAutoSql, mRealColumnCount, mValidColumnCount, CReaderMessage::SetLineNumber(), NStr::Split(), NStr::StringToInt(), NStr::StringToULong(), CReaderBase::xIsBrowserLine(), and CReaderBase::xIsTrackLine().

Referenced by xGetData().

xGetData()

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

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 325 of file bed_reader.cpp.

References lr(), CReaderBase::m_uDataCount, CReaderBase::m_uLineNumber, mLinePreBuffer, mRealColumnCount, NStr::StartsWith(), xDetermineLikelyColumnCount(), and CReaderBase::xIsTrackLine().

xGetStrand()

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

protected

Definition at line 1040 of file bed_reader.cpp.

References eDiag_Error, eNa_strand_minus, and eNa_strand_plus.

Referenced by xSetFeatureLocationBlock(), xSetFeatureLocationCds(), xSetFeatureLocationRna(), and xSetFeatureLocationThick().

xParseFeature()

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

protected

Definition at line 576 of file bed_reader.cpp.

References CBedColumnData::ColumnCount(), eDiag_Error, fAutoSql, fDirectedFeatureModel, fThreeFeatFormat, CReaderBase::m_iFlags, CReaderBase::m_uLineNumber, mRealColumnCount, xParseFeatureAutoSql(), xParseFeatureGeneModelFormat(), xParseFeatureThreeFeatFormat(), and xParseFeatureUserFormat().

Referenced by xProcessData().

xParseFeatureAutoSql()

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

protected

Definition at line 812 of file bed_reader.cpp.

References ftable, m_currentId, CReaderBase::m_pMessageHandler, mpAutoSql, and CSeq_annot_Base::SetData().

Referenced by xParseFeature().

xParseFeatureGeneModelFormat()

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

protected

Definition at line 630 of file bed_reader.cpp.

References CSeq_feat_Base::GetLocation(), CSeq_loc::Intersect(), m_CurrentFeatureCount, CSeq_feat_Base::SetLocation(), xAppendFeatureCds(), xAppendFeatureGene(), xAppendFeatureRna(), xContainsCdsFeature(), and xContainsRnaFeature().

Referenced by xParseFeature().

xParseFeatureThreeFeatFormat()

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

protected

Definition at line 607 of file bed_reader.cpp.

References m_CurrentFeatureCount, xAppendFeatureBlock(), xAppendFeatureChrom(), xAppendFeatureThick(), xContainsBlockFeature(), and xContainsThickFeature().

Referenced by xParseFeature().

xParseFeatureUserFormat()

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

protected

Definition at line 791 of file bed_reader.cpp.

References ftable, m_currentId, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), xSetFeatureDisplayData(), xSetFeatureLocation(), and xSetFeatureTitle().

Referenced by xParseFeature().

xParseTrackLine()

bool CBedReader::xParseTrackLine ( const string &  strLine )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 543 of file bed_reader.cpp.

References eDiag_Warning, m_currentId, CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, NStr::StartsWith(), CReadUtil::Tokenize(), and CReaderBase::xParseTrackLine().

Referenced by xProcessData().

xPostProcessAnnot()

void CBedReader::xPostProcessAnnot ( CSeq_annot &  annot )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 532 of file bed_reader.cpp.

References CReaderBase::xAddConversionInfo(), xAssignBedColumnCount(), and CReaderBase::xAssignTrackData().

xProcessData()

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

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 357 of file bed_reader.cpp.

References m_CurrentFeatureCount, CReaderBase::xParseBrowserLine(), xParseFeature(), and xParseTrackLine().

xReadBedDataRaw()

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

protected

Definition at line 1937 of file bed_reader.cpp.

References CRawBedTrack::AddRecord(), CRawBedTrack::HasData(), lr(), m_CurBatchSize, m_MaxBatchSize, CRawBedTrack::Reset(), CReaderBase::xGetLine(), and xReadBedRecordRaw().

Referenced by ReadTrackData().

xReadBedRecordRaw()

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

protected

Definition at line 1764 of file bed_reader.cpp.

References CReadUtil::AsSeqId(), columns, eDiag_Error, eNa_strand_minus, eNa_strand_plus, NStr::fAllowTrailingSymbols, NStr::fConvErr_NoThrow, NStr::fSplit_MergeDelimiters, CReaderBase::m_iFlags, CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, mRealColumnCount, mValidColumnCount, CRawBedRecord::SetInterval(), CRawBedRecord::SetScore(), NStr::Split(), NStr::StartsWith(), NStr::StringToInt(), NStr::TruncateSpacesInPlace(), and xCleanColumnValues().

Referenced by xReadBedDataRaw().

xSetFeatureBedData()

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

protected

Definition at line 1632 of file bed_reader.cpp.

References CBedColumnData::ColumnCount(), data, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExts(), CUser_object_Base::SetType(), xSetFeatureColor(), and xSetFeatureScore().

Referenced by xAppendFeatureBlock(), xAppendFeatureCds(), xAppendFeatureChrom(), xAppendFeatureGene(), xAppendFeatureRna(), and xAppendFeatureThick().

xSetFeatureColor()

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

protected

Definition at line 1439 of file bed_reader.cpp.

References CBedColumnData::ColumnCount(), eNa_strand_minus, eNa_strand_plus, CReaderBase::m_pTrackDefaults, xSetFeatureColorByStrand(), xSetFeatureColorDefault(), xSetFeatureColorFromItemRgb(), and xSetFeatureColorFromScore().

Referenced by xSetFeatureBedData().

xSetFeatureColorByStrand()

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

protected

Definition at line 1496 of file bed_reader.cpp.

References eDiag_Error, eNa_strand_minus, CReaderBase::m_uLineNumber, NStr::SplitInTwo(), and xSetFeatureColorFromItemRgb().

Referenced by xSetFeatureColor().

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

Definition at line 1546 of file bed_reader.cpp.

References CUser_object::AddField(), eDiag_Warning, NStr::fDS_ProhibitFractions, i, NStr::IntToString(), CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, NStr::Split(), NStr::StartsWith(), NStr::StringToInt(), NStr::StringToULong(), and test.

Referenced by xSetFeatureColor(), and xSetFeatureColorByStrand().

xSetFeatureColorFromScore()

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

protected

Definition at line 1519 of file bed_reader.cpp.

References CUser_object::AddField(), NStr::DoubleToString(), eDiag_Error, NStr::Join(), CReaderBase::m_uLineNumber, and NStr::StringToDouble().

Referenced by xSetFeatureColor().

xSetFeatureDisplayData()

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

protected

Definition at line 830 of file bed_reader.cpp.

References CUser_object::AddField(), CSeq_feat::AddOrReplaceQualifier(), NStr::fAllowTrailingSymbols, NStr::fConvErr_NoThrow, NStr::fDS_ProhibitFractions, m_usescore, mValidColumnCount, CSeq_feat_Base::SetData(), CUser_object_Base::SetType(), and NStr::StringToInt().

Referenced by xParseFeatureUserFormat().

xSetFeatureIdsBlock()

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

protected

Definition at line 1340 of file bed_reader.cpp.

References CSeq_feat_Base::SetId(), CObject_id_Base::SetId(), CFeat_id_Base::SetLocal(), CSeq_feat_Base::SetXref(), and xContainsThickFeature().

Referenced by xAppendFeatureBlock().

xSetFeatureIdsCds()

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

protected

Definition at line 1314 of file bed_reader.cpp.

References CSeq_feat_Base::SetId(), CObject_id_Base::SetId(), CFeat_id_Base::SetLocal(), CSeq_feat_Base::SetXref(), and xContainsBlockFeature().

Referenced by xAppendFeatureCds().

xSetFeatureIdsChrom()

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

protected

Definition at line 1251 of file bed_reader.cpp.

References CSeq_feat_Base::SetId(), CObject_id_Base::SetId(), CFeat_id_Base::SetLocal(), CSeq_feat_Base::SetXref(), xContainsBlockFeature(), and xContainsThickFeature().

Referenced by xAppendFeatureChrom().

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

Definition at line 1365 of file bed_reader.cpp.

References CSeq_feat_Base::SetId(), CObject_id_Base::SetId(), CFeat_id_Base::SetLocal(), and CSeq_feat_Base::SetXref().

Referenced by xAppendFeatureRna().

xSetFeatureIdsThick()

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

protected

Definition at line 1289 of file bed_reader.cpp.

References CSeq_feat_Base::SetId(), CObject_id_Base::SetId(), CFeat_id_Base::SetLocal(), CSeq_feat_Base::SetXref(), and xContainsBlockFeature().

Referenced by xAppendFeatureThick().

xSetFeatureLocation()

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

protected

Definition at line 1657 of file bed_reader.cpp.

References CReadUtil::AsSeqId(), CBedColumnData::ColumnCount(), eDiag_Error, eNa_strand_minus, eNa_strand_plus, CBedColumnData::LineNo(), location, CReaderBase::m_iFlags, CSeq_feat_Base::SetLocation(), and NStr::StringToInt().

Referenced by xParseFeatureUserFormat(), xSetFeatureLocationChrom(), and xSetFeatureLocationGene().

xSetFeatureLocationBlock()

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

protected

Definition at line 1063 of file bed_reader.cpp.

References CUser_object::AddField(), CReadUtil::AsSeqId(), blocks, eDiag_Error, i, CBedColumnData::LineNo(), location, CReaderBase::m_iFlags, negative(), CSeq_feat_Base::SetExts(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), CUser_object_Base::SetType(), NStr::Split(), NStr::StringToUInt(), and xGetStrand().

Referenced by xAppendFeatureBlock().

xSetFeatureLocationCds()

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

protected

Definition at line 980 of file bed_reader.cpp.

References CUser_object::AddField(), CReadUtil::AsSeqId(), eDiag_Error, location, CReaderBase::m_iFlags, CReaderBase::m_uLineNumber, CSeq_feat_Base::SetExts(), CSeq_feat_Base::SetLocation(), CUser_object_Base::SetType(), NStr::StringToInt(), and xGetStrand().

Referenced by xAppendFeatureCds().

xSetFeatureLocationChrom()

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

protected

Definition at line 890 of file bed_reader.cpp.

References CUser_object::AddField(), CSeq_feat_Base::SetExts(), CUser_object_Base::SetType(), and xSetFeatureLocation().

Referenced by xAppendFeatureChrom().

xSetFeatureLocationGene()

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

protected

Definition at line 905 of file bed_reader.cpp.

References CUser_object::AddField(), CSeq_feat_Base::SetExts(), CUser_object_Base::SetType(), and xSetFeatureLocation().

Referenced by xAppendFeatureGene().

xSetFeatureLocationRna()

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

protected

Definition at line 1157 of file bed_reader.cpp.

References CUser_object::AddField(), CReadUtil::AsSeqId(), blocks, eDiag_Error, i, CBedColumnData::LineNo(), location, CReaderBase::m_iFlags, negative(), CSeq_feat_Base::SetExts(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), CUser_object_Base::SetType(), NStr::Split(), NStr::StringToUInt(), and xGetStrand().

Referenced by xAppendFeatureRna().

xSetFeatureLocationThick()

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

protected

Definition at line 920 of file bed_reader.cpp.

References CUser_object::AddField(), CReadUtil::AsSeqId(), eDiag_Error, location, CReaderBase::m_iFlags, CReaderBase::m_uLineNumber, CSeq_feat_Base::SetExts(), CSeq_feat_Base::SetLocation(), CUser_object_Base::SetType(), NStr::StringToInt(), and xGetStrand().

Referenced by xAppendFeatureThick().

xSetFeatureScore()

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

protected

Definition at line 1398 of file bed_reader.cpp.

References CUser_object::AddField(), CBedColumnData::ColumnCount(), eDiag_Error, NStr::fConvErr_NoThrow, CBedColumnData::LineNo(), CReaderBase::m_pTrackDefaults, NStr::StringToDouble(), and NStr::StringToInt().

Referenced by xSetFeatureBedData().

xSetFeatureTitle()

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

protected

Definition at line 1382 of file bed_reader.cpp.

References CBedColumnData::ColumnCount(), NStr::IntToString(), CReaderBase::m_uLineNumber, and CSeq_feat_Base::SetTitle().

Referenced by xParseFeatureUserFormat().

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

Definition at line 363 of file bed_reader.hpp.

Referenced by ReadSeqAnnot(), xParseFeatureGeneModelFormat(), xParseFeatureThreeFeatFormat(), and xProcessData().

m_currentId

string CBedReader::m_currentId

protected

Definition at line 357 of file bed_reader.hpp.

Referenced by xAppendFeatureChrom(), xAppendFeatureGene(), xParseFeatureAutoSql(), xParseFeatureUserFormat(), and xParseTrackLine().

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

Definition at line 360 of file bed_reader.hpp.

Referenced by xDetermineLikelyColumnCount(), xGetData(), xParseFeature(), and xReadBedRecordRaw().

mValidColumnCount

vector<string>::size_type CBedReader::mValidColumnCount

protected

Definition at line 361 of file bed_reader.hpp.

Referenced by xAssignBedColumnCount(), xDetermineLikelyColumnCount(), xReadBedRecordRaw(), and xSetFeatureDisplayData().

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

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