#include <objtools/readers/gff2_reader.hpp>

Inheritance diagram for CGff2Reader:

Collaboration diagram for CGff2Reader:

Public Types
enum	TFlags { fNormal = 0 , fGenbankMode = 1 << 4 , fRetainLocusIds = 1 << 5 , fAssumeCircularSequence = 1 << 6 }

using	IdToFeatureMap = map< string, CRef< CSeq_feat > >

using	TScoreValueMap = map< string, CRef< CScore::TValue > >

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
	CGff2Reader (TReaderFlags iFlags, const string &name="", const string &title="", SeqIdResolver resolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr)

virtual	~CGff2Reader ()

unsigned int	ObjectType () const

CRef< CSeq_entry >	ReadSeqEntry (ILineReader &, ILineErrorListener *=nullptr) override
	Read an object from a given line reader, render it as a single Seq-entry, if possible. More...

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

void	ReadSeqAnnots (TAnnotList &, CNcbiIstream &, ILineErrorListener *=nullptr) override
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...

void	ReadSeqAnnots (TAnnotList &, ILineReader &, ILineErrorListener *=nullptr) override
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...

bool	AtSequenceData () const

void	xGetData (ILineReader &, TReaderData &) override

void	xProcessData (const TReaderData &, CSeq_annot &) override

bool	IsInGenbankMode () const

virtual bool	xParseStructuredComment (const string &)

virtual bool	xParseFeature (const string &, CSeq_annot &, ILineErrorListener *)

virtual bool	xIsCurrentDataType (const string &)

void	xPostProcessAnnot (CSeq_annot &) override

virtual void	xAssignAnnotId (CSeq_annot &, const string &="")

virtual bool	x_ParseAlignmentGff (const string &strLine, list< string > &id_list, map< string, list< CRef< CSeq_align >>> &alignments)

void	x_GetAlignmentScores (const CSeq_align &alignment, TScoreValueMap &score_values) const

void	x_FindMatchingScores (const TScoreValueMap &scores_1, const TScoreValueMap &scores_2, set< string > &matching_scores) const

virtual bool	x_CreateAlignment (const CGff2Record &gff, CRef< CSeq_align > &pAlign)

bool	x_MergeAlignments (const list< CRef< CSeq_align >> &alignment_list, CRef< CSeq_align > &processed)

void	x_InitializeScoreSums (const TScoreValueMap score_values, map< string, TSeqPos > &summed_scores) const

void	x_ProcessAlignmentScores (const CSeq_align &alignment, map< string, TSeqPos > &summed_scores, TScoreValueMap &common_scores) const

void	x_ProcessAlignmentsGff (const list< string > &id_list, const map< string, list< CRef< CSeq_align >>> &alignments, CRef< CSeq_annot > pAnnot)

virtual bool	xUpdateAnnotFeature (const CGff2Record &, CSeq_annot &, ILineErrorListener *=0)

virtual bool	x_UpdateAnnotAlignment (const CGff2Record &, CSeq_annot &, ILineErrorListener *=0)

virtual bool	xAddFeatureToAnnot (CRef< CSeq_feat >, CSeq_annot &)

bool	xFeatureSetQualifier (const string &, const string &, CRef< CSeq_feat >)

virtual bool	x_ProcessQualifierSpecialCase (CGff2Record::TAttrCit, CRef< CSeq_feat >)

bool	x_GetFeatureById (const string &, CRef< CSeq_feat > &)

bool	xAlignmentSetScore (const CGff2Record &, CRef< CSeq_align >)

bool	xSetDensegStarts (const vector< string > &gapParts, ENa_strand identStrand, ENa_strand targetStrand, const TSeqPos targetStart, const TSeqPos targetEnd, const CGff2Record &gff, CSeq_align::C_Segs::TDenseg &denseg)

bool	xGetStartsOnMinusStrand (TSeqPos offset, const vector< string > &gapParts, bool isTarget, vector< int > &starts) const

bool	xGetStartsOnPlusStrand (TSeqPos offset, const vector< string > &gapParts, bool isTarget, vector< int > &starts) const

virtual bool	xAnnotPostProcess (CSeq_annot &)

virtual bool	xGenerateParentChildXrefs (CSeq_annot &)

bool	xUpdateSplicedAlignment (const CGff2Record &gff, CRef< CSeq_align > pAlign) const

bool	xUpdateSplicedSegment (const CGff2Record &gff, CSpliced_seg &segment) const

bool	xSetSplicedExon (const CGff2Record &gff, CRef< CSpliced_exon > pExon) const

bool	xGetTargetParts (const CGff2Record &gff, vector< string > &targetParts) const

bool	xAlignmentSetSegment (const CGff2Record &, CRef< CSeq_align >)

bool	xAlignmentSetDenseg (const CGff2Record &, CRef< CSeq_align >)

bool	xAlignmentSetSpliced_seg (const CGff2Record &, CRef< CSeq_align >)

virtual bool	xIsIgnoredFeatureType (const string &)

virtual bool	xIsIgnoredFeatureId (const string &)

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 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 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...

void	SetProgressReportInterval (unsigned int intv)

void	SetCanceler (ICanceled *=nullptr)

bool	IsCanceled () const

Static Public Member Functions
static bool	IsAlignmentData (const string &)

static CRef< CDbtag >	x_ParseDbtag (const string &)

static bool	xIsSequenceRegion (const string &line)

static bool	xIsFastaMarker (const string &line)

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
CMessageListenerLenient	m_ErrorsPrivate

IdToFeatureMap	m_MapIdToFeature

Public Attributes inherited from CReaderBase
unsigned int	mLine

string	mData

Protected Member Functions
virtual CGff2Record *	x_CreateRecord ()

void	xSetAncestryLine (CSeq_feat &, const string &)

virtual void	xSetAncestorXrefs (CSeq_feat &, CSeq_feat &)

void	xSetXrefFromTo (CSeq_feat &, CSeq_feat &)

bool	xNeedsNewSeqAnnot (const string &)

virtual void	xProcessSequenceRegionPragma (const string &)

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 bool	xParseBrowserLine (const string &, CSeq_annot &)

virtual bool	xParseTrackLine (const string &)

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_CurrentSeqId

ILineErrorListener *	m_pErrors

unsigned int	mCurrentFeatureCount

bool	mParsingAlignment

CRef< CAnnotdesc >	m_CurrentBrowserInfo

CRef< CAnnotdesc >	m_CurrentTrackInfo

bool	mAtSequenceData

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 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 52 of file gff2_reader.hpp.

Member Typedef Documentation

◆ IdToFeatureMap

using CGff2Reader::IdToFeatureMap = map<string, CRef<CSeq_feat> >

Definition at line 64 of file gff2_reader.hpp.

◆ TScoreValueMap

using CGff2Reader::TScoreValueMap = map<string, CRef<CScore::TValue> >

Definition at line 65 of file gff2_reader.hpp.

Member Enumeration Documentation

◆ TFlags

enum CGff2Reader::TFlags

Enumerator
fNormal
fGenbankMode
fRetainLocusIds
fAssumeCircularSequence

Definition at line 57 of file gff2_reader.hpp.

Constructor & Destructor Documentation

◆ CGff2Reader()

CGff2Reader::CGff2Reader	(	TReaderFlags	iFlags,
		const string &	name = `""`,
		const string &	title = `""`,
		SeqIdResolver	resolver = `CReadUtil::AsSeqId`,
		CReaderListener *	pListener = `nullptr`
	)

Definition at line 79 of file gff2_reader.cpp.

◆ ~CGff2Reader()

CGff2Reader::~CGff2Reader ( )

virtual

Definition at line 95 of file gff2_reader.cpp.

Member Function Documentation

◆ AtSequenceData()

bool CGff2Reader::AtSequenceData ( ) const

inline

Definition at line 112 of file gff2_reader.hpp.

References mAtSequenceData.

Referenced by CMultiReader::xReadGFF3().

◆ IsAlignmentData()

bool CGff2Reader::IsAlignmentData ( const string & line )

static

Definition at line 1395 of file gff2_reader.cpp.

References columns, NStr::EndsWith(), NStr::StartsWith(), and CGff2Record::TokenizeGFF().

Referenced by xIsCurrentDataType(), xParseFeature(), and CGff3Reader::xParseFeature().

◆ IsInGenbankMode()

bool CGff2Reader::IsInGenbankMode ( ) const

Definition at line 1451 of file gff2_reader.cpp.

References fGenbankMode, and CReaderBase::m_iFlags.

Referenced by xAssignAnnotId(), CGff3Reader::xIsIgnoredFeatureType(), xNeedsNewSeqAnnot(), CGff3Reader::xParseAlignment(), and xPostProcessAnnot().

◆ ObjectType()

unsigned int CGff2Reader::ObjectType ( ) const

inline

Definition at line 87 of file gff2_reader.hpp.

References CReaderBase::OT_SEQENTRY.

◆ ReadObject()

CRef< CSerialObject > CGff2Reader::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 163 of file gff2_reader.cpp.

References lr(), and ReadSeqEntry().

◆ ReadSeqAnnots() [1/2]

void CGff2Reader::ReadSeqAnnots	(	TAnnotList &	annots,
		CNcbiIstream &	istr,
		ILineErrorListener *	pErrors = `nullptr`
	)

overridevirtual

Read all objects from given insput stream, returning them as a vector of Seq-annots.

Parameters

annots	(out) vector containing read Seq-annots
istr	input stream to read from.
pErrors	pointer to optional error container object.

Reimplemented from CReaderBase.

Definition at line 102 of file gff2_reader.cpp.

References lr().

Referenced by ReadSeqEntry(), sRunTest(), sUpdateCase(), CGBProjectTool::x_LoadGffData(), CMultiReaderApp::xProcessGff2(), CMultiReaderApp::xProcessGff3(), CMultiReaderApp::xProcessGtf(), CMultiReaderApp::xProcessGvf(), CMultiReader::xReadGFF3(), and CMultiReader::xReadGTF().

◆ ReadSeqAnnots() [2/2]

void CGff2Reader::ReadSeqAnnots	(	TAnnotList &	annots,
		ILineReader &	lr,
		ILineErrorListener *	pErrors = `nullptr`
	)

overridevirtual

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 from CReaderBase.

Definition at line 114 of file gff2_reader.cpp.

References lr(), mAtSequenceData, CReaderBase::ReadSeqAnnot(), and CReaderBase::xProgressInit().

◆ ReadSeqEntry()

CRef< CSeq_entry > CGff2Reader::ReadSeqEntry	(	ILineReader &	lr,
		ILineErrorListener *	pErrors = `nullptr`
	)

overridevirtual

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 from CReaderBase.

Definition at line 132 of file gff2_reader.cpp.

References CSeq_id_Base::e_Local, CSeq_inst_Base::eMol_not_set, CSeq_inst_Base::eRepr_not_set, lr(), ReadSeqAnnots(), CBioseq_Base::SetAnnot(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CReaderBase::xProgressInit().

Referenced by ReadObject().

◆ x_CreateAlignment()

bool CGff2Reader::x_CreateAlignment	(	const CGff2Record &	gff,
		CRef< CSeq_align > &	pAlign
	)

virtual

Definition at line 641 of file gff2_reader.cpp.

References CSeq_align_Base::eType_partial, Ref(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetType(), xAlignmentSetScore(), and xAlignmentSetSegment().

Referenced by x_ParseAlignmentGff(), and CGff3Reader::xParseAlignment().

◆ x_CreateRecord()

virtual CGff2Record* CGff2Reader::x_CreateRecord ( )

inlineprotectedvirtual

Reimplemented in CGvfReader, CGtfReader, and CGff3Reader.

Definition at line 290 of file gff2_reader.hpp.

Referenced by x_ParseAlignmentGff(), and xParseFeature().

◆ x_FindMatchingScores()

void CGff2Reader::x_FindMatchingScores	(	const TScoreValueMap &	scores_1,
		const TScoreValueMap &	scores_2,
		set< string > &	matching_scores
	)		const

Definition at line 368 of file gff2_reader.cpp.

References s_CompareValues(), and rapidjson::value.

◆ x_GetAlignmentScores()

void CGff2Reader::x_GetAlignmentScores	(	const CSeq_align &	alignment,
		TScoreValueMap &	score_values
	)		const

Definition at line 319 of file gff2_reader.cpp.

References Ref(), and rapidjson::value.

Referenced by x_MergeAlignments().

◆ x_GetFeatureById()

bool CGff2Reader::x_GetFeatureById	(	const string &	,
		CRef< CSeq_feat > &
	)

Definition at line 1203 of file gff2_reader.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_MapIdToFeature.

Referenced by CGtfReader::xPostProcessAnnot(), xSetAncestryLine(), and CGff3Reader::xUpdateAnnotExon().

◆ x_InitializeScoreSums()

void CGff2Reader::x_InitializeScoreSums	(	const TScoreValueMap	score_values,
		map< string, TSeqPos > &	summed_scores
	)		const

Definition at line 455 of file gff2_reader.cpp.

Referenced by x_MergeAlignments().

◆ x_MergeAlignments()

bool CGff2Reader::x_MergeAlignments	(	const list< CRef< CSeq_align >> &	alignment_list,
		CRef< CSeq_align > &	processed
	)

Definition at line 503 of file gff2_reader.cpp.

References CSerialObject::Assign(), map_checker< Container >::begin(), map_checker< Container >::empty(), map_checker< Container >::end(), CSeq_align_Base::eType_disc, CSeq_align_Base::eType_global, map_checker< Container >::find(), Ref(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), x_GetAlignmentScores(), x_InitializeScoreSums(), and x_ProcessAlignmentScores().

Referenced by x_ProcessAlignmentsGff(), and CGff3Reader::xProcessAlignmentData().

◆ x_ParseAlignmentGff()

bool CGff2Reader::x_ParseAlignmentGff	(	const string &	strLine,
		list< string > &	id_list,
		map< string, list< CRef< CSeq_align >>> &	alignments
	)

virtual

Definition at line 419 of file gff2_reader.cpp.

References mCurrentFeatureCount, mParsingAlignment, x_CreateAlignment(), and x_CreateRecord().

◆ x_ParseDbtag()

CRef< CDbtag > CGff2Reader::x_ParseDbtag ( const string & str )

static

Definition at line 1229 of file gff2_reader.cpp.

References CDbtag_Base::SetDb(), CDbtag_Base::SetTag(), NStr::SplitInTwo(), str(), and NStr::StringToUInt().

Referenced by CGff2Record::xMigrateAttributes(), and CGtfReader::xProcessQualifierSpecialCase().

◆ x_ProcessAlignmentScores()

void CGff2Reader::x_ProcessAlignmentScores	(	const CSeq_align &	alignment,
		map< string, TSeqPos > &	summed_scores,
		TScoreValueMap &	common_scores
	)		const

Definition at line 470 of file gff2_reader.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), and Ref().

Referenced by x_MergeAlignments().

◆ x_ProcessAlignmentsGff()

void CGff2Reader::x_ProcessAlignmentsGff	(	const list< string > &	id_list,
		const map< string, list< CRef< CSeq_align >>> &	alignments,
		CRef< CSeq_annot >	pAnnot
	)

Definition at line 389 of file gff2_reader.cpp.

References CRef< C, Locker >::IsNull(), CReaderBase::m_AnnotTitle, m_CurrentBrowserInfo, Ref(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_annot::SetNameDesc(), CSeq_annot::SetTitleDesc(), and x_MergeAlignments().

◆ x_ProcessQualifierSpecialCase()

bool CGff2Reader::x_ProcessQualifierSpecialCase	(	CGff2Record::TAttrCit	it,
		CRef< CSeq_feat >	pFeature
	)

virtual

Definition at line 1180 of file gff2_reader.cpp.

◆ x_UpdateAnnotAlignment()

bool CGff2Reader::x_UpdateAnnotAlignment	(	const CGff2Record &	gff,
		CSeq_annot &	annot,
		ILineErrorListener *	pEC = `0`
	)

virtual

Definition at line 663 of file gff2_reader.cpp.

References CSeq_align_Base::eType_partial, CSeq_annot_Base::SetData(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetType(), xAlignmentSetScore(), and xAlignmentSetSegment().

◆ xAddFeatureToAnnot()

bool CGff2Reader::xAddFeatureToAnnot	(	CRef< CSeq_feat >	pFeature,
		CSeq_annot &	annot
	)

virtual

Reimplemented in CGff3Reader.

Definition at line 1218 of file gff2_reader.cpp.

References CSeq_annot_Base::SetData().

Referenced by CGtfReader::xCreateParentCds(), CGtfReader::xCreateParentGene(), CGtfReader::xCreateParentMrna(), and xUpdateAnnotFeature().

◆ xAlignmentSetDenseg()

bool CGff2Reader::xAlignmentSetDenseg	(	const CGff2Record &	gff,
		CRef< CSeq_align >	pAlign
	)

◆ xAlignmentSetScore()

bool CGff2Reader::xAlignmentSetScore	(	const CGff2Record &	gff,
		CRef< CSeq_align >	pAlign
	)

Definition at line 1110 of file gff2_reader.cpp.

References CSeq_align::eScore_Score, CGff2Record::GetAttribute(), i, CGffBaseColumns::IsSetScore(), CGffBaseColumns::Score(), CSeq_align::SetNamedScore(), and NStr::StringToDouble().

Referenced by x_CreateAlignment(), and x_UpdateAnnotAlignment().

◆ xAlignmentSetSegment()

bool CGff2Reader::xAlignmentSetSegment	(	const CGff2Record &	gff,
		CRef< CSeq_align >	pAlign
	)

Definition at line 930 of file gff2_reader.cpp.

References CGffBaseColumns::Type(), xAlignmentSetDenseg(), and xAlignmentSetSpliced_seg().

Referenced by x_CreateAlignment(), and x_UpdateAnnotAlignment().

◆ xAlignmentSetSpliced_seg()

bool CGff2Reader::xAlignmentSetSpliced_seg	(	const CGff2Record &	gff,
		CRef< CSeq_align >	pAlign
	)

◆ xAnnotPostProcess()

bool CGff2Reader::xAnnotPostProcess ( CSeq_annot & annot )

virtual

Definition at line 1262 of file gff2_reader.cpp.

References xGenerateParentChildXrefs().

◆ xAssignAnnotId()

void CGff2Reader::xAssignAnnotId	(	CSeq_annot &	annot,
		const string &	givenId = `""`
	)

virtual

Definition at line 239 of file gff2_reader.cpp.

References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsAlign(), IsInGenbankMode(), CReaderBase::m_pTrackDefaults, and CSeq_annot_Base::SetId().

Referenced by xPostProcessAnnot(), and CGvfReader::xPostProcessAnnot().

◆ xFeatureSetQualifier()

bool CGff2Reader::xFeatureSetQualifier	(	const string &	key,
		const string &	value,
		CRef< CSeq_feat >	pTargetFeature
	)

Definition at line 1189 of file gff2_reader.cpp.

References CSeq_feat::AddOrReplaceQualifier(), ncbi::grid::netcache::search::fields::key, and rapidjson::value.

Referenced by CGff3Reader::xUpdateAnnotCds().

◆ xGenerateParentChildXrefs()

bool CGff2Reader::xGenerateParentChildXrefs ( CSeq_annot & annot )

virtual

Definition at line 1273 of file gff2_reader.cpp.

References ftable, CSeq_feat::GetNamedQual(), CSeq_annot::IsFtable(), CSeq_annot_Base::SetData(), NStr::Split(), and xSetAncestryLine().

Referenced by xAnnotPostProcess(), and xPostProcessAnnot().

◆ xGetData()

void CGff2Reader::xGetData	(	ILineReader &	lr,
		TReaderData &	readerData
	)

overridevirtual

Reimplemented from CReaderBase.

Reimplemented in CGvfReader.

Definition at line 188 of file gff2_reader.cpp.

References lr(), CReaderBase::m_PendingLine, CReaderBase::m_uDataCount, CReaderBase::m_uLineNumber, mAtSequenceData, mCurrentFeatureCount, CReaderBase::xGetLine(), xIsCurrentDataType(), xIsFastaMarker(), xIsSequenceRegion(), CReaderBase::xIsTrackLine(), CReaderBase::xIsTrackTerminator(), xNeedsNewSeqAnnot(), CReaderBase::xParseTrackLine(), xProcessSequenceRegionPragma(), and CReaderBase::xUngetLine().

◆ xGetStartsOnMinusStrand()

bool CGff2Reader::xGetStartsOnMinusStrand	(	TSeqPos	offset,
		const vector< string > &	gapParts,
		bool	isTarget,
		vector< int > &	starts
	)		const

Definition at line 778 of file gff2_reader.cpp.

References i, offset, and NStr::StringToInt().

Referenced by xSetDensegStarts().

◆ xGetStartsOnPlusStrand()

bool CGff2Reader::xGetStartsOnPlusStrand	(	TSeqPos	offset,
		const vector< string > &	gapParts,
		bool	isTarget,
		vector< int > &	starts
	)		const

Definition at line 823 of file gff2_reader.cpp.

References i, offset, and NStr::StringToInt().

Referenced by xSetDensegStarts().

◆ xGetTargetParts()

bool CGff2Reader::xGetTargetParts	(	const CGff2Record &	gff,
		vector< string > &	targetParts
	)		const

Definition at line 760 of file gff2_reader.cpp.

References NStr::Split().

Referenced by xAlignmentSetDenseg(), and xAlignmentSetSpliced_seg().

◆ xIsCurrentDataType()

bool CGff2Reader::xIsCurrentDataType ( const string & line )

virtual

Definition at line 617 of file gff2_reader.cpp.

References IsAlignmentData(), mCurrentFeatureCount, and mParsingAlignment.

Referenced by xGetData().

◆ xIsFastaMarker()

bool CGff2Reader::xIsFastaMarker ( const string & line )

static

Definition at line 1468 of file gff2_reader.cpp.

References NStr::StartsWith(), and NStr::ToLower().

Referenced by xGetData().

◆ xIsIgnoredFeatureId()

bool CGff2Reader::xIsIgnoredFeatureId ( const string & type )

virtual

Definition at line 1420 of file gff2_reader.cpp.

Referenced by xParseFeature(), and CGff3Reader::xParseFeature().

◆ xIsIgnoredFeatureType()

bool CGff2Reader::xIsIgnoredFeatureType ( const string & type )

virtual

Reimplemented in CGff3Reader.

Definition at line 1412 of file gff2_reader.cpp.

Referenced by xParseFeature().

◆ xIsSequenceRegion()

bool CGff2Reader::xIsSequenceRegion ( const string & line )

static

Definition at line 1458 of file gff2_reader.cpp.

References NStr::StartsWith(), and NStr::ToLower().

Referenced by xGetData().

◆ xNeedsNewSeqAnnot()

bool CGff2Reader::xNeedsNewSeqAnnot ( const string & line )

protected

Definition at line 1429 of file gff2_reader.cpp.

References columns, NStr::eMergeDelims, IsInGenbankMode(), m_CurrentSeqId, CReaderBase::m_PendingLine, mCurrentFeatureCount, and NStr::Split().

Referenced by xGetData().

◆ xParseFeature()

bool CGff2Reader::xParseFeature	(	const string &	line,
		CSeq_annot &	annot,
		ILineErrorListener *	pEC
	)

virtual

Reimplemented in CGvfReader, and CGff3Reader.

Definition at line 277 of file gff2_reader.cpp.

References IsAlignmentData(), mCurrentFeatureCount, mParsingAlignment, CReaderBase::ProcessError(), x_CreateRecord(), xIsIgnoredFeatureId(), xIsIgnoredFeatureType(), and xUpdateAnnotFeature().

Referenced by xProcessData(), and CGtfReader::xProcessData().

◆ xParseStructuredComment()

bool CGff2Reader::xParseStructuredComment ( const string & strLine )

virtual

Reimplemented in CGvfReader.

Definition at line 262 of file gff2_reader.cpp.

References NStr::StartsWith().

Referenced by CGvfReader::xParseStructuredComment(), xProcessData(), CGff3Reader::xProcessData(), and CGtfReader::xProcessData().

◆ xPostProcessAnnot()

void CGff2Reader::xPostProcessAnnot ( CSeq_annot & annot )

overridevirtual

Reimplemented from CReaderBase.

Reimplemented in CGvfReader, CGtfReader, and CGff3Reader.

Definition at line 174 of file gff2_reader.cpp.

References IsInGenbankMode(), CReaderBase::xAddConversionInfo(), xAssignAnnotId(), and xGenerateParentChildXrefs().

Referenced by CGff3Reader::xPostProcessAnnot(), and CGtfReader::xPostProcessAnnot().

◆ xProcessData()

void CGff2Reader::xProcessData	(	const TReaderData &	readerData,
		CSeq_annot &	annot
	)

overridevirtual

Reimplemented from CReaderBase.

Reimplemented in CGvfReader, CGtfReader, and CGff3Reader.

Definition at line 1479 of file gff2_reader.cpp.

References CReaderBase::xParseBrowserLine(), xParseFeature(), and xParseStructuredComment().

◆ xProcessSequenceRegionPragma()

virtual void CGff2Reader::xProcessSequenceRegionPragma ( const string & )

inlineprotectedvirtual

Reimplemented in CGff3Reader.

Definition at line 307 of file gff2_reader.hpp.

Referenced by xGetData().

◆ xSetAncestorXrefs()

void CGff2Reader::xSetAncestorXrefs	(	CSeq_feat &	descendent,
		CSeq_feat &	ancestor
	)

protectedvirtual

Reimplemented in CGtfReader.

Definition at line 1385 of file gff2_reader.cpp.

References xSetXrefFromTo().

Referenced by xSetAncestryLine().

◆ xSetAncestryLine()

void CGff2Reader::xSetAncestryLine	(	CSeq_feat &	feat,
		const string &	directParentStr
	)

protected

Definition at line 1298 of file gff2_reader.cpp.

References CSeq_feat::GetNamedQual(), NStr::Split(), x_GetFeatureById(), and xSetAncestorXrefs().

Referenced by xGenerateParentChildXrefs().

◆ xSetDensegStarts()

bool CGff2Reader::xSetDensegStarts	(	const vector< string > &	gapParts,
		ENa_strand	identStrand,
		ENa_strand	targetStrand,
		const TSeqPos	targetStart,
		const TSeqPos	targetEnd,
		const CGff2Record &	gff,
		CSeq_align::C_Segs::TDenseg &	denseg
	)

Definition at line 868 of file gff2_reader.cpp.

References eNa_strand_minus, i, CGffBaseColumns::SeqStart(), CGffBaseColumns::SeqStop(), xGetStartsOnMinusStrand(), and xGetStartsOnPlusStrand().

Referenced by xAlignmentSetDenseg().

◆ xSetSplicedExon()

bool CGff2Reader::xSetSplicedExon	(	const CGff2Record &	gff,
		CRef< CSpliced_exon >	pExon
	)		const

Definition at line 724 of file gff2_reader.cpp.

References eNa_strand_minus, eNa_strand_plus, and NStr::StringToInt().

Referenced by xUpdateSplicedSegment().

◆ xSetXrefFromTo()

void CGff2Reader::xSetXrefFromTo	(	CSeq_feat &	from,
		CSeq_feat &	to
	)

protected

Definition at line 1370 of file gff2_reader.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::GetId(), CSeq_feat_Base::SetXref(), and sFeatureHasXref().

Referenced by xSetAncestorXrefs(), and CGtfReader::xSetAncestorXrefs().

◆ xUpdateAnnotFeature()

bool CGff2Reader::xUpdateAnnotFeature	(	const CGff2Record &	record,
		CSeq_annot &	annot,
		ILineErrorListener *	= `0`
	)

virtual

Reimplemented in CGtfReader, and CGff3Reader.

Definition at line 628 of file gff2_reader.cpp.

References CGff2Record::InitializeFeature(), CReaderBase::m_iFlags, and xAddFeatureToAnnot().

Referenced by xParseFeature().

◆ xUpdateSplicedAlignment()

bool CGff2Reader::xUpdateSplicedAlignment	(	const CGff2Record &	gff,
		CRef< CSeq_align >	pAlign
	)		const

Definition at line 686 of file gff2_reader.cpp.

References CSeq_align_Base::eType_partial, CSeq_align_Base::IsSetType(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), and xUpdateSplicedSegment().

◆ xUpdateSplicedSegment()

bool CGff2Reader::xUpdateSplicedSegment	(	const CGff2Record &	gff,
		CSpliced_seg &	segment
	)		const

Definition at line 703 of file gff2_reader.cpp.

References CSpliced_seg_Base::eProduct_type_transcript, CSpliced_seg_Base::IsSetProduct_type(), Ref(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetProduct_type(), and xSetSplicedExon().

Referenced by xUpdateSplicedAlignment().

Member Data Documentation

◆ m_CurrentBrowserInfo

CRef<CAnnotdesc> CGff2Reader::m_CurrentBrowserInfo

protected

Definition at line 317 of file gff2_reader.hpp.

Referenced by x_ProcessAlignmentsGff(), and CGff3Reader::xProcessAlignmentData().

◆ m_CurrentSeqId

string CGff2Reader::m_CurrentSeqId

protected

Definition at line 313 of file gff2_reader.hpp.

Referenced by xNeedsNewSeqAnnot().

◆ m_CurrentTrackInfo

CRef<CAnnotdesc> CGff2Reader::m_CurrentTrackInfo

protected

Definition at line 318 of file gff2_reader.hpp.

◆ m_ErrorsPrivate

CMessageListenerLenient CGff2Reader::m_ErrorsPrivate

Definition at line 277 of file gff2_reader.hpp.

◆ m_MapIdToFeature

IdToFeatureMap CGff2Reader::m_MapIdToFeature

Definition at line 278 of file gff2_reader.hpp.

Referenced by x_GetFeatureById(), CGtfReader::xCreateParentCds(), CGtfReader::xCreateParentGene(), CGtfReader::xCreateParentMrna(), CGff3Reader::xFeatureSetXrefGrandParent(), CGff3Reader::xFeatureSetXrefParent(), CGtfReader::xFindFeatById(), CGff3Reader::xFindFeatureUnderConstruction(), CGff3Reader::xPostProcessAnnot(), CGtfReader::xPostProcessAnnot(), CGff3Reader::xUpdateAnnotCds(), CGff3Reader::xUpdateAnnotExon(), CGff3Reader::xUpdateAnnotGene(), CGff3Reader::xUpdateAnnotGeneric(), CGff3Reader::xUpdateAnnotRegion(), and CGff3Reader::xUpdateAnnotRna().

◆ m_pErrors

ILineErrorListener* CGff2Reader::m_pErrors

protected

Definition at line 314 of file gff2_reader.hpp.

◆ mAtSequenceData

bool CGff2Reader::mAtSequenceData

protected

Definition at line 320 of file gff2_reader.hpp.

Referenced by AtSequenceData(), ReadSeqAnnots(), and xGetData().

◆ mCurrentFeatureCount

unsigned int CGff2Reader::mCurrentFeatureCount

protected

Definition at line 315 of file gff2_reader.hpp.

Referenced by CGff3Reader::ReadSeqAnnot(), CGtfReader::ReadSeqAnnot(), x_ParseAlignmentGff(), xGetData(), xIsCurrentDataType(), xNeedsNewSeqAnnot(), CGff3Reader::xParseAlignment(), xParseFeature(), CGff3Reader::xParseFeature(), CGvfReader::xParseFeature(), and CGff3Reader::xPostProcessAnnot().

◆ mParsingAlignment

bool CGff2Reader::mParsingAlignment

protected

Definition at line 316 of file gff2_reader.hpp.

Referenced by CGff3Reader::ReadSeqAnnot(), x_ParseAlignmentGff(), xIsCurrentDataType(), CGff3Reader::xParseAlignment(), xParseFeature(), and CGff3Reader::xParseFeature().

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

include/objtools/readers/gff2_reader.hpp
src/objtools/readers/gff2_reader.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IdToFeatureMap

◆ TScoreValueMap

Member Enumeration Documentation

◆ TFlags

Constructor & Destructor Documentation

◆ CGff2Reader()

◆ ~CGff2Reader()

Member Function Documentation

◆ AtSequenceData()

◆ IsAlignmentData()

◆ IsInGenbankMode()

◆ ObjectType()

◆ ReadObject()

◆ ReadSeqAnnots() [1/2]

◆ ReadSeqAnnots() [2/2]

◆ ReadSeqEntry()

◆ x_CreateAlignment()

◆ x_CreateRecord()

◆ x_FindMatchingScores()

◆ x_GetAlignmentScores()

◆ x_GetFeatureById()

◆ x_InitializeScoreSums()

◆ x_MergeAlignments()

◆ x_ParseAlignmentGff()

◆ x_ParseDbtag()

◆ x_ProcessAlignmentScores()

◆ x_ProcessAlignmentsGff()

◆ x_ProcessQualifierSpecialCase()

◆ x_UpdateAnnotAlignment()

◆ xAddFeatureToAnnot()

◆ xAlignmentSetDenseg()

◆ xAlignmentSetScore()

◆ xAlignmentSetSegment()

◆ xAlignmentSetSpliced_seg()

◆ xAnnotPostProcess()

◆ xAssignAnnotId()

◆ xFeatureSetQualifier()

◆ xGenerateParentChildXrefs()

◆ xGetData()

◆ xGetStartsOnMinusStrand()

◆ xGetStartsOnPlusStrand()

◆ xGetTargetParts()

◆ xIsCurrentDataType()

◆ xIsFastaMarker()

◆ xIsIgnoredFeatureId()

◆ xIsIgnoredFeatureType()

◆ xIsSequenceRegion()

◆ xNeedsNewSeqAnnot()

◆ xParseFeature()

◆ xParseStructuredComment()

◆ xPostProcessAnnot()

◆ xProcessData()

◆ xProcessSequenceRegionPragma()

◆ xSetAncestorXrefs()

◆ xSetAncestryLine()

◆ xSetDensegStarts()

◆ xSetSplicedExon()

◆ xSetXrefFromTo()

◆ xUpdateAnnotFeature()

◆ xUpdateSplicedAlignment()

◆ xUpdateSplicedSegment()

Member Data Documentation

◆ m_CurrentBrowserInfo

◆ m_CurrentSeqId

◆ m_CurrentTrackInfo

◆ m_ErrorsPrivate

◆ m_MapIdToFeature

◆ m_pErrors

◆ mAtSequenceData

◆ mCurrentFeatureCount

◆ mParsingAlignment