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CGff2Reader Class Reference

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#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_entryReadSeqEntry (ILineReader &, ILineErrorListener *=nullptr) override
 Read an object from a given line reader, render it as a single Seq-entry, if possible. More...
 
CRef< CSerialObjectReadObject (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< CSerialObjectReadObject (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
 Read an object from a given input stream, render it as the most appropriate Genbank object. More...
 
virtual CRef< CSeq_annotReadSeqAnnot (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
 Read an object from a given input stream, render it as a single Seq-annot. More...
 
virtual CRef< CSeq_annotReadSeqAnnot (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_entryReadSeqEntry (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< CDbtagx_ParseDbtag (const string &)
 
static bool xIsSequenceRegion (const string &line)
 
static bool xIsFastaMarker (const string &line)
 
- Static Public Member Functions inherited from CReaderBase
static CReaderBaseGetReader (CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)
 Allocate a CReaderBase derived reader object based on the given file format. More...
 

Public Attributes

CMessageListenerLenient m_ErrorsPrivate
 
IdToFeatureMap m_MapIdToFeature
 
- Public Attributes inherited from CReaderBase
unsigned int mLine
 
string mData
 

Protected Member Functions

virtual CGff2Recordx_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_annotxCreateSeqAnnot ()
 
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
 
ILineErrorListenerm_pErrors
 
unsigned int mCurrentFeatureCount
 
bool mParsingAlignment
 
CRef< CAnnotdescm_CurrentBrowserInfo
 
CRef< CAnnotdescm_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< CTrackDatam_pTrackDefaults
 
ILineReaderm_pReader
 
ICanceledm_pCanceler
 
SeqIdResolver mSeqIdResolve
 
unique_ptr< CReaderMessageHandlerm_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

Definition at line 64 of file gff2_reader.hpp.

◆ TScoreValueMap

Definition at line 65 of file gff2_reader.hpp.

Member Enumeration Documentation

◆ 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

◆ IsInGenbankMode()

bool CGff2Reader::IsInGenbankMode ( ) const

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

Reimplemented from CReaderBase.

Definition at line 163 of file gff2_reader.cpp.

References 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
istrinput stream to read from.
pErrorspointer to optional error container object.

Reimplemented from CReaderBase.

Definition at line 102 of file gff2_reader.cpp.

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

Reimplemented from CReaderBase.

Definition at line 114 of file gff2_reader.cpp.

References ILineReader::AtEOF(), 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
lrline reader to read from.
pErrorspointer 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, 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

◆ 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 > &   
)

◆ 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 
)

◆ x_ParseAlignmentGff()

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

◆ x_ParseDbtag()

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

◆ x_ProcessAlignmentScores()

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

◆ x_ProcessAlignmentsGff()

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

◆ 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

◆ xAddFeatureToAnnot()

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

◆ xAlignmentSetDenseg()

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

◆ xAlignmentSetScore()

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

◆ xAlignmentSetSegment()

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

◆ 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

◆ xFeatureSetQualifier()

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

◆ xGenerateParentChildXrefs()

bool CGff2Reader::xGenerateParentChildXrefs ( CSeq_annot annot)
virtual

◆ xGetData()

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

◆ 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

◆ xParseFeature()

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

◆ xParseStructuredComment()

bool CGff2Reader::xParseStructuredComment ( const string strLine)
virtual

◆ xPostProcessAnnot()

void CGff2Reader::xPostProcessAnnot ( CSeq_annot annot)
overridevirtual

◆ 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

◆ 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 
)

◆ 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

◆ 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

◆ xUpdateSplicedSegment()

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

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

◆ 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

◆ mParsingAlignment

bool CGff2Reader::mParsingAlignment
protected

The documentation for this class was generated from the following files:
Modified on Mon May 27 04:37:31 2024 by modify_doxy.py rev. 669887