Search Toolkit Book for CUCSCRegionReader

#include <objtools/readers/ucscregion_reader.hpp>

Inheritance diagram for CUCSCRegionReader:

Collaboration diagram for CUCSCRegionReader:

Public Member Functions
	CUCSCRegionReader (unsigned int=fNormal)

virtual	~CUCSCRegionReader ()

CRef< CSeq_annot >	ReadSeqAnnot (ILineReader &lr, ILineErrorListener *pEC) override
	Read an object from a given line reader, render it as a single Seq-annot, if possible. More...

CRef< CSerialObject >	ReadObject (ILineReader &lr, ILineErrorListener *pErrors=nullptr) override
	Read an object from a given line reader, render it as the most appropriate Genbank object. More...

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< 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_feat >	xParseFeatureUCSCFormat (const string &Line, int Number)

void	x_SetFeatureLocation (CRef< CSeq_feat > &feature, const vector< string > &fields)

void	xSmartFieldSplit (vector< string > &fields, CTempString line)

bool	xParseFeature (const vector< string > &, CSeq_annot &, 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 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 string &, CSeq_annot &)

virtual bool	xParseTrackLine (const string &)

virtual void	xSetBrowserRegion (const string &, CAnnot_descr &)

virtual void	xPostProcessAnnot (CSeq_annot &)

virtual void	xAddConversionInfo (CSeq_annot &, ILineErrorListener *)

bool	xParseComment (const CTempString &, CRef< CSeq_annot > &)

virtual bool	xReadInit ()

virtual bool	xProgressInit (ILineReader &istr)

bool	xIsReportingProgress () const

bool	xIsOperationCanceled () const

void	xReportProgress (ILineErrorListener *=nullptr)

void	ProcessError (CObjReaderLineException &, ILineErrorListener *)

void	ProcessError (CLineError &, ILineErrorListener *)

void	ProcessWarning (CObjReaderLineException &, ILineErrorListener *)

void	ProcessWarning (CLineError &, ILineErrorListener *)

void	xProcessReaderMessage (CReaderMessage &, ILineErrorListener *)

void	xProcessLineError (const ILineError &, ILineErrorListener *)

void	xProcessUnknownException (const CException &)

Additional Inherited Members
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)

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)

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

Detailed Description

Definition at line 50 of file ucscregion_reader.hpp.

Constructor & Destructor Documentation

◆ CUCSCRegionReader()

CUCSCRegionReader::CUCSCRegionReader ( unsigned int iflags = fNormal )

Definition at line 99 of file ucscregion_reader.cpp.

◆ ~CUCSCRegionReader()

CUCSCRegionReader::~CUCSCRegionReader ( )

virtual

Definition at line 104 of file ucscregion_reader.cpp.

Member Function Documentation

◆ ReadObject()

CRef< CSerialObject > CUCSCRegionReader::ReadObject	(	ILineReader &	lr,
		ILineErrorListener *	pErrors = `nullptr`
	)

overridevirtual

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 from CReaderBase.

Definition at line 320 of file ucscregion_reader.cpp.

References lr(), and ReadSeqAnnot().

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

◆ ReadSeqAnnot()

CRef< CSeq_annot > CUCSCRegionReader::ReadSeqAnnot	(	ILineReader &	lr,
		ILineErrorListener *	pErrors
	)

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 328 of file ucscregion_reader.cpp.

References ctll::empty(), lr(), CReaderBase::m_uLineNumber, CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), NStr::TruncateSpaces_Unsafe(), CReaderBase::xParseComment(), xParseFeature(), and xSmartFieldSplit().

Referenced by ReadObject().

◆ x_SetFeatureLocation()

void CUCSCRegionReader::x_SetFeatureLocation	(	CRef< CSeq_feat > &	feature,
		const vector< string > &	fields
	)

protected

Definition at line 226 of file ucscregion_reader.cpp.

References CReadUtil::AsSeqId(), CObjReaderLineException::Create(), eDiag_Error, eNa_strand_minus, eNa_strand_plus, NStr::fAllowCommas, location, CReaderBase::m_iFlags, CReaderBase::m_uLineNumber, CSeq_feat_Base::SetLocation(), and NStr::StringToInt().

Referenced by xParseFeature().

◆ xParseFeature()

bool CUCSCRegionReader::xParseFeature	(	const vector< string > &	fields,
		CSeq_annot &	annot,
		ILineErrorListener *	pEC
	)

protected

Definition at line 202 of file ucscregion_reader.cpp.

References CSeq_feat_Base::CanGetTitle(), ftable, NStr::IntToString(), CReaderBase::m_uLineNumber, CReaderBase::ProcessError(), CRef< C, Locker >::Reset(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetTitle(), and x_SetFeatureLocation().

Referenced by ReadSeqAnnot().

◆ xParseFeatureUCSCFormat()

CRef< objects::CSeq_feat > CUCSCRegionReader::xParseFeatureUCSCFormat	(	const string &	Line,
		int	Number
	)

protected

◆ xSmartFieldSplit()

void CUCSCRegionReader::xSmartFieldSplit	(	vector< string > &	fields,
		CTempString	line
	)

protected

Definition at line 180 of file ucscregion_reader.cpp.

References CTempString::erase(), NStr::fSplit_Tokenize, len, CTempString::length(), and NStr::Split().

Referenced by ReadSeqAnnot().

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

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

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CUCSCRegionReader()

◆ ~CUCSCRegionReader()

Member Function Documentation

◆ ReadObject()

◆ ReadSeqAnnot()

◆ x_SetFeatureLocation()

◆ xParseFeature()

◆ xParseFeatureUCSCFormat()

◆ xSmartFieldSplit()