CWiggleReader Class Reference

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#include <objtools/readers/wiggle_reader.hpp>

Inheritance diagram for CWiggleReader:

Collaboration diagram for CWiggleReader:

Public Types
enum	EWiggleFlags {   fDefaults = 0 , fJoinSame = 1<<8 , fAsByte = 1<<9 , fAsGraph = 1<<10 ,   fDumpStats = 1<<11 , fAsRaw = 1<<12 }
typedef vector< SValueInfo >	TValues
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
	CWiggleReader (int=fDefaults, const string &="", const string &="", CReaderListener *=nullptr)
virtual	~CWiggleReader ()
CRef< CSeq_annot >	ReadSeqAnnot (ILineReader &, ILineErrorListener *=nullptr) override
	Read an object from a given line reader, render it as a single Seq-annot, if possible. More...
virtual bool	ReadTrackData (ILineReader &, CRawWiggleTrack &, ILineErrorListener *=nullptr)
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 Types
enum	ETrackType { eTrackType_invalid , eTrackType_wiggle_0 , eTrackType_bedGraph }

Protected Member Functions
void	xGetData (ILineReader &, TReaderData &) override
void	xProcessData (const TReaderData &, CSeq_annot &) override
void	xPostProcessAnnot (CSeq_annot &) override
bool	xParseBrowserLine (const string &, CSeq_annot &) override
bool	xParseTrackLine (const string &) override
bool	xProcessFixedStepData (TReaderData::const_iterator &, const TReaderData &)
void	xGetFixedStepInfo (const string &, SFixedStepInfo &)
void	xReadFixedStepData (const SFixedStepInfo &, TReaderData::const_iterator &, const TReaderData &)
bool	xReadFixedStepDataRaw (const SFixedStepInfo &, TReaderData::const_iterator &, const TReaderData &, CRawWiggleTrack &)
bool	xProcessVariableStepData (TReaderData::const_iterator &, const TReaderData &)
bool	xProcessBedData (TReaderData::const_iterator &, const TReaderData &)
void	xGetVariableStepInfo (const string &, SVarStepInfo &)
void	xReadVariableStepData (const SVarStepInfo &, TReaderData::const_iterator &, const TReaderData &)
bool	xReadVariableStepDataRaw (const SVarStepInfo &, TReaderData::const_iterator &, const TReaderData &, CRawWiggleTrack &)
string	xGetWord (string &)
bool	xSkipWS (string &)
string	xGetParamName (string &)
string	xGetParamValue (string &)
void	xGetPos (string &, TSeqPos &v)
bool	xTryGetDoubleSimple (string &, double &v)
void	xGetDouble (string &line, double &v)
CRef< CSeq_id >	xMakeChromId ()
CRef< CSeq_table >	xMakeTable ()
CRef< CSeq_graph >	xMakeGraph ()
void	xPreprocessValues (SWiggleStat &)
void	xAddValue (const SValueInfo &value)
double	xEstimateSize (size_t rows, bool fixed_span) const
void	xSetTotalLoc (CSeq_loc &loc, CSeq_id &chrom_id)
void	xDumpChromValues ()
void	xSetChrom (const string &chrom)
bool	xValuesAreFromSingleSequence () const
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 CRef< CSeq_annot >	xCreateSeqAnnot ()
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 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 &)

Protected Attributes
string	m_ChromId
TValues	m_Values
double	m_GapValue
bool	m_SingleAnnot
bool	m_OmitZeros
ETrackType	m_TrackType
CRef< CSeq_annot >	m_Annot
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
Static Protected Member Functions inherited from CReaderBase
static void	xAddStringFlagsWithMap (const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)

Detailed Description

Definition at line 238 of file wiggle_reader.hpp.

Member Typedef Documentation

TFlags

typedef int CWiggleReader::TFlags

Definition at line 266 of file wiggle_reader.hpp.

TValues

typedef vector<SValueInfo> CWiggleReader::TValues

Definition at line 243 of file wiggle_reader.hpp.

Member Enumeration Documentation

ETrackType

enum CWiggleReader::ETrackType

protected

Enumerator
eTrackType_invalid
eTrackType_wiggle_0
eTrackType_bedGraph

Definition at line 435 of file wiggle_reader.hpp.

EWiggleFlags

enum CWiggleReader::EWiggleFlags

Enumerator
fDefaults
fJoinSame
fAsByte
fAsGraph
fDumpStats
fAsRaw

Definition at line 258 of file wiggle_reader.hpp.

Constructor & Destructor Documentation

CWiggleReader()

CWiggleReader::CWiggleReader	(	int	iFlags = fDefaults,
		const string &	name = "",
		const string &	title = "",
		CReaderListener *	pRl = nullptr
	)

Definition at line 70 of file wiggle_reader.cpp.

References m_GapValue, and CReaderBase::m_uLineNumber.

~CWiggleReader()

CWiggleReader::~CWiggleReader ( )

virtual

Definition at line 85 of file wiggle_reader.cpp.

Member Function Documentation

ReadSeqAnnot()

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

overridevirtual

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 from CReaderBase.

Definition at line 92 of file wiggle_reader.cpp.

References fAsGraph, lr(), m_ChromId, CReaderBase::m_iFlags, CReaderBase::m_uDataCount, m_Values, CRef< C, Locker >::Reset(), CReaderBase::xCreateSeqAnnot(), CReaderBase::xGuardedGetData(), CReaderBase::xGuardedProcessData(), xParseTrackLine(), xPostProcessAnnot(), and CReaderBase::xProgressInit().

ReadTrackData()

bool CWiggleReader::ReadTrackData ( ILineReader &  lr, CRawWiggleTrack &  rawdata, ILineErrorListener *  pMessageListener = nullptr  )

virtual

Definition at line 182 of file wiggle_reader.cpp.

References lr(), NStr::StartsWith(), xGetFixedStepInfo(), xGetVariableStepInfo(), CReaderBase::xGuardedGetData(), xReadFixedStepDataRaw(), and xReadVariableStepDataRaw().

Referenced by sRunTest(), sUpdateCase(), and CMultiReaderApp::xProcessWiggleRaw().

xAddValue()

void CWiggleReader::xAddValue ( const SValueInfo &  value )

inlineprotected

Definition at line 399 of file wiggle_reader.hpp.

References m_OmitZeros, m_Values, and rapidjson::value.

Referenced by xProcessBedData(), xReadFixedStepData(), and xReadVariableStepData().

xDumpChromValues()

void CWiggleReader::xDumpChromValues ( void  )

protected

Definition at line 783 of file wiggle_reader.cpp.

References fAsGraph, m_Annot, m_ChromId, CReaderBase::m_iFlags, CSeq_annot_Base::SetData(), CReaderBase::xCreateSeqAnnot(), xMakeGraph(), and xMakeTable().

Referenced by xSetChrom().

xEstimateSize()

double CWiggleReader::xEstimateSize ( size_t  rows, bool  fixed_span  ) const

protected

Definition at line 267 of file wiggle_reader.cpp.

Referenced by xPreprocessValues().

xGetData()

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

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 123 of file wiggle_reader.cpp.

References lr(), CReaderBase::m_uDataCount, CReaderBase::m_uLineNumber, NStr::StartsWith(), CReaderBase::xGetLine(), CReaderBase::xIsBrowserLine(), CReaderBase::xIsTrackLine(), and CReaderBase::xUngetLine().

xGetDouble()

void CWiggleReader::xGetDouble ( string &  line, double &  v  )

inlineprotected

Definition at line 736 of file wiggle_reader.cpp.

References eDiag_Error, CReaderBase::m_uLineNumber, and xTryGetDoubleSimple().

Referenced by xProcessBedData(), xReadFixedStepData(), xReadFixedStepDataRaw(), xReadVariableStepData(), and xReadVariableStepDataRaw().

xGetFixedStepInfo()

void CWiggleReader::xGetFixedStepInfo ( const string &  directive, SFixedStepInfo &  fixedStepInfo  )

protected

Definition at line 892 of file wiggle_reader.cpp.

References eDiag_Error, eDiag_Warning, eTrackType_invalid, eTrackType_wiggle_0, CReaderBase::m_pMessageHandler, m_TrackType, CReaderBase::m_uLineNumber, SFixedStepInfo::mChrom, SFixedStepInfo::mSpan, SFixedStepInfo::mStart, SFixedStepInfo::mStep, SFixedStepInfo::Reset(), NStr::StringToUInt(), NStr::TruncateSpacesInPlace(), rapidjson::value, xGetParamName(), xGetParamValue(), and xSkipWS().

Referenced by ReadTrackData(), and xProcessFixedStepData().

xGetParamName()

string CWiggleReader::xGetParamName ( string &  line )

protected

Definition at line 591 of file wiggle_reader.cpp.

References eDiag_Error, len, and CReaderBase::m_uLineNumber.

Referenced by xGetFixedStepInfo(), and xGetVariableStepInfo().

xGetParamValue()

string CWiggleReader::xGetParamValue ( string &  line )

protected

Definition at line 615 of file wiggle_reader.cpp.

References eDiag_Error, len, CReaderBase::m_uLineNumber, rapidjson::value, and xGetWord().

Referenced by xGetFixedStepInfo(), and xGetVariableStepInfo().

xGetPos()

void CWiggleReader::xGetPos ( string &  line, TSeqPos &  v  )

protected

Definition at line 640 of file wiggle_reader.cpp.

References eDiag_Error, and CReaderBase::m_uLineNumber.

Referenced by xProcessBedData(), xReadVariableStepData(), and xReadVariableStepDataRaw().

xGetVariableStepInfo()

void CWiggleReader::xGetVariableStepInfo ( const string &  directive, SVarStepInfo &  varStepInfo  )

protected

Definition at line 985 of file wiggle_reader.cpp.

References eDiag_Error, eDiag_Warning, eTrackType_invalid, eTrackType_wiggle_0, CReaderBase::m_pMessageHandler, m_TrackType, CReaderBase::m_uLineNumber, SVarStepInfo::mChrom, SVarStepInfo::mSpan, SVarStepInfo::Reset(), NStr::StringToUInt(), rapidjson::value, xGetParamName(), xGetParamValue(), and xSkipWS().

Referenced by ReadTrackData(), and xProcessVariableStepData().

xGetWord()

string CWiggleReader::xGetWord ( string &  line )

protected

Definition at line 567 of file wiggle_reader.cpp.

References eDiag_Error, len, and CReaderBase::m_uLineNumber.

Referenced by xGetParamValue(), and xProcessBedData().

xMakeChromId()

CRef< CSeq_id > CWiggleReader::xMakeChromId ( )

protected

Definition at line 354 of file wiggle_reader.cpp.

References CReadUtil::AsSeqId(), m_ChromId, and CReaderBase::m_iFlags.

Referenced by xMakeGraph(), and xMakeTable().

xMakeGraph()

CRef< CSeq_graph > CWiggleReader::xMakeGraph ( )

protected

Definition at line 494 of file wiggle_reader.cpp.

References _ASSERT, SWiggleStat::AsByte(), i, ITERATE, SWiggleStat::m_FixedSpan, m_GapValue, SWiggleStat::m_Max, SWiggleStat::m_Min, CReaderBase::m_pTrackDefaults, SWiggleStat::m_Span, SWiggleStat::m_Step, m_Values, CSeq_graph_Base::SetA(), CByte_graph_Base::SetAxis(), CSeq_graph_Base::SetB(), CSeq_graph_Base::SetComp(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::SetTitle(), CByte_graph_Base::SetValues(), ncbi::grid::netcache::search::fields::size, xMakeChromId(), xPreprocessValues(), and xSetTotalLoc().

Referenced by xDumpChromValues(), and xPostProcessAnnot().

xMakeTable()

CRef< CSeq_table > CWiggleReader::xMakeTable ( )

protected

Definition at line 378 of file wiggle_reader.cpp.

References SWiggleStat::AsByte(), CReadUtil::AsSeqId(), CSeqTable_column_info_Base::eField_id_location_from, CSeqTable_column_info_Base::eField_id_location_id, fAsByte, ITERATE, SWiggleStat::m_FixedSpan, m_GapValue, SWiggleStat::m_HaveGaps, CReaderBase::m_iFlags, SWiggleStat::m_Min, SWiggleStat::m_Span, SWiggleStat::m_Step, m_Values, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetDefault(), CSeqTable_column_Base::SetHeader(), ncbi::grid::netcache::search::fields::size, table, xMakeChromId(), xPreprocessValues(), xSetTotalLoc(), and xValuesAreFromSingleSequence().

Referenced by xDumpChromValues(), and xPostProcessAnnot().

xParseBrowserLine()

bool CWiggleReader::xParseBrowserLine ( const string &  line, CSeq_annot &    )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 815 of file wiggle_reader.cpp.

References NStr::StartsWith().

Referenced by xProcessData().

xParseTrackLine()

bool CWiggleReader::xParseTrackLine ( const string &  line )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 827 of file wiggle_reader.cpp.

References eDiag_Error, eTrackType_bedGraph, eTrackType_invalid, eTrackType_wiggle_0, CReaderBase::m_pTrackDefaults, m_TrackType, CReaderBase::m_uLineNumber, CReaderBase::xIsTrackLine(), and CReaderBase::xParseTrackLine().

Referenced by ReadSeqAnnot(), and xProcessData().

xPostProcessAnnot()

void CWiggleReader::xPostProcessAnnot ( CSeq_annot &  annot )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 763 of file wiggle_reader.cpp.

References CSeq_annot_Base::C_Data::e_not_set, fAsGraph, CSeq_annot_Base::GetData(), m_ChromId, CReaderBase::m_iFlags, CSeq_annot_Base::SetData(), CSeq_annot_Base::C_Data::Which(), CReaderBase::xAssignTrackData(), xMakeGraph(), and xMakeTable().

Referenced by ReadSeqAnnot().

xPreprocessValues()

void CWiggleReader::xPreprocessValues ( SWiggleStat &  stat )

protected

Definition at line 279 of file wiggle_reader.cpp.

References SWiggleStat::AddSpan(), SWiggleStat::AddValue(), fAsGraph, fJoinSame, i, LOG_POST, SWiggleStat::m_FixedSpan, m_GapValue, SWiggleStat::m_HaveGaps, CReaderBase::m_iFlags, SWiggleStat::m_IntValues, SWiggleStat::m_Max, SWiggleStat::m_Min, SWiggleStat::m_Span, SWiggleStat::m_Step, SWiggleStat::m_StepMul, m_Values, compile_time_bits::range(), SWiggleStat::SetFirstSpan(), SWiggleStat::SetFirstValue(), ncbi::grid::netcache::search::fields::size, ct::sort(), and xEstimateSize().

Referenced by xMakeGraph(), and xMakeTable().

xProcessBedData()

bool CWiggleReader::xProcessBedData ( TReaderData::const_iterator &  curIt, const TReaderData &  readerData  )

protected

Definition at line 1051 of file wiggle_reader.cpp.

References rapidjson::value, xAddValue(), xGetDouble(), xGetPos(), xGetWord(), xSetChrom(), and xSkipWS().

Referenced by xProcessData().

xProcessData()

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

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 154 of file wiggle_reader.cpp.

References xParseBrowserLine(), xParseTrackLine(), xProcessBedData(), xProcessFixedStepData(), and xProcessVariableStepData().

xProcessFixedStepData()

bool CWiggleReader::xProcessFixedStepData ( TReaderData::const_iterator &  curIt, const TReaderData &  readerData  )

protected

Definition at line 853 of file wiggle_reader.cpp.

References NStr::StartsWith(), xGetFixedStepInfo(), and xReadFixedStepData().

Referenced by xProcessData().

xProcessVariableStepData()

bool CWiggleReader::xProcessVariableStepData ( TReaderData::const_iterator &  curIt, const TReaderData &  readerData  )

protected

Definition at line 873 of file wiggle_reader.cpp.

References NStr::StartsWith(), xGetVariableStepInfo(), and xReadVariableStepData().

Referenced by xProcessData().

xReadFixedStepData()

void CWiggleReader::xReadFixedStepData ( const SFixedStepInfo &  fixedStepInfo, TReaderData::const_iterator &  curIt, const TReaderData &  readerData  )

protected

Definition at line 964 of file wiggle_reader.cpp.

References SFixedStepInfo::mChrom, SFixedStepInfo::mSpan, SFixedStepInfo::mStart, SFixedStepInfo::mStep, rapidjson::value, xAddValue(), xGetDouble(), and xSetChrom().

Referenced by xProcessFixedStepData().

xReadFixedStepDataRaw()

bool CWiggleReader::xReadFixedStepDataRaw ( const SFixedStepInfo &  fixedStepInfo, TReaderData::const_iterator &  curIt, const TReaderData &  readerData, CRawWiggleTrack &  rawdata  )

protected

Definition at line 212 of file wiggle_reader.cpp.

References CRawWiggleTrack::AddRecord(), CReadUtil::AsSeqId(), CRawWiggleTrack::HasData(), CReaderBase::m_iFlags, SFixedStepInfo::mChrom, SFixedStepInfo::mSpan, SFixedStepInfo::mStart, SFixedStepInfo::mStep, CRawWiggleTrack::Reset(), rapidjson::value, and xGetDouble().

Referenced by ReadTrackData().

xReadVariableStepData()

void CWiggleReader::xReadVariableStepData ( const SVarStepInfo &  varStepInfo, TReaderData::const_iterator &  curIt, const TReaderData &  readerData  )

protected

Definition at line 1029 of file wiggle_reader.cpp.

References SVarStepInfo::mChrom, SVarStepInfo::mSpan, rapidjson::value, xAddValue(), xGetDouble(), xGetPos(), xSetChrom(), and xSkipWS().

Referenced by xProcessVariableStepData().

xReadVariableStepDataRaw()

bool CWiggleReader::xReadVariableStepDataRaw ( const SVarStepInfo &  varStepInfo, TReaderData::const_iterator &  curIt, const TReaderData &  readerData, CRawWiggleTrack &  rawdata  )

protected

Definition at line 239 of file wiggle_reader.cpp.

References CRawWiggleTrack::AddRecord(), CReadUtil::AsSeqId(), CRawWiggleTrack::HasData(), CReaderBase::m_iFlags, SVarStepInfo::mChrom, SVarStepInfo::mSpan, CRawWiggleTrack::Reset(), rapidjson::value, xGetDouble(), xGetPos(), and xSkipWS().

Referenced by ReadTrackData().

xSetChrom()

void CWiggleReader::xSetChrom ( const string &  chrom )

protected

Definition at line 801 of file wiggle_reader.cpp.

References fAsGraph, m_ChromId, CReaderBase::m_iFlags, m_Values, and xDumpChromValues().

Referenced by xProcessBedData(), xReadFixedStepData(), and xReadVariableStepData().

xSetTotalLoc()

void CWiggleReader::xSetTotalLoc ( CSeq_loc &  loc, CSeq_id &  chrom_id  )

protected

Definition at line 363 of file wiggle_reader.cpp.

References m_Values, CSeq_loc::SetEmpty(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_loc::SetInt(), and CSeq_interval_Base::SetTo().

Referenced by xMakeGraph(), and xMakeTable().

xSkipWS()

bool CWiggleReader::xSkipWS ( string &  line )

protected

Definition at line 550 of file wiggle_reader.cpp.

References len.

Referenced by xGetFixedStepInfo(), xGetVariableStepInfo(), xProcessBedData(), xReadVariableStepData(), and xReadVariableStepDataRaw().

xTryGetDoubleSimple()

bool CWiggleReader::xTryGetDoubleSimple ( string &  line, double &  v  )

protected

Definition at line 673 of file wiggle_reader.cpp.

Referenced by xGetDouble().

xValuesAreFromSingleSequence()

bool CWiggleReader::xValuesAreFromSingleSequence ( ) const

protected

Definition at line 53 of file wiggle_reader.cpp.

References first(), and m_Values.

Referenced by xMakeTable().

Member Data Documentation

m_Annot

CRef<CSeq_annot> CWiggleReader::m_Annot

protected

Definition at line 441 of file wiggle_reader.hpp.

Referenced by xDumpChromValues().

m_ChromId

string CWiggleReader::m_ChromId

protected

Definition at line 429 of file wiggle_reader.hpp.

Referenced by ReadSeqAnnot(), xDumpChromValues(), xMakeChromId(), xPostProcessAnnot(), and xSetChrom().

m_GapValue

double CWiggleReader::m_GapValue

protected

Definition at line 431 of file wiggle_reader.hpp.

Referenced by CWiggleReader(), xMakeGraph(), xMakeTable(), and xPreprocessValues().

m_OmitZeros

bool CWiggleReader::m_OmitZeros

protected

Definition at line 433 of file wiggle_reader.hpp.

Referenced by xAddValue().

m_SingleAnnot

bool CWiggleReader::m_SingleAnnot

protected

Definition at line 432 of file wiggle_reader.hpp.

m_TrackType

ETrackType CWiggleReader::m_TrackType

protected

Definition at line 440 of file wiggle_reader.hpp.

Referenced by xGetFixedStepInfo(), xGetVariableStepInfo(), and xParseTrackLine().

m_Values

TValues CWiggleReader::m_Values

protected

Definition at line 430 of file wiggle_reader.hpp.

Referenced by ReadSeqAnnot(), xAddValue(), xMakeGraph(), xMakeTable(), xPreprocessValues(), xSetChrom(), xSetTotalLoc(), and xValuesAreFromSingleSequence().

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

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