NCBI C++ ToolKit
CBedReader Member List

This is the complete list of members for CBedReader, including all inherited members.

CBedReader(int=fNormal, const string &="", const string &="", CReaderListener *=nullptr)CBedReader
CReaderBase(TReaderFlags flags=0, const string &name="", const string &title="", SeqIdResolver seqresolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr)CReaderBaseprotected
CReaderBase(const CReaderBase &)=deleteCReaderBaseprotected
CReaderBase(CReaderBase &&)=deleteCReaderBaseprotected
EBedFlags enum nameCBedReader
EFlags enum nameCReaderBase
fAddDefaultColumns enum valueCBedReader
fAllIdsAsLocal enum valueCReaderBase
fAsRaw enum valueCReaderBase
fAutoSql enum valueCBedReader
fDirectedFeatureModel enum valueCBedReader
fNextInLine enum valueCReaderBase
fNormal enum valueCReaderBase
fNumericIdsAsLocal enum valueCReaderBase
fThreeFeatFormat enum valueCBedReader
GetReader(CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)CReaderBasestatic
IsCanceled() constCReaderBaseinline
m_AnnotNameCReaderBaseprotected
m_AnnotTitleCReaderBaseprotected
m_CurBatchSizeCBedReaderprotected
m_CurrentFeatureCountCBedReaderprotected
m_currentIdCBedReaderprotected
m_iFlagsCReaderBaseprotected
m_MaxBatchSizeCBedReaderprotected
m_pCancelerCReaderBaseprotected
m_PendingLineCReaderBaseprotected
m_pMessageHandlerCReaderBaseprotected
m_pReaderCReaderBaseprotected
m_pTrackDefaultsCReaderBaseprotected
m_uDataCountCReaderBaseprotected
m_uLineNumberCReaderBaseprotected
m_uNextProgressReportCReaderBaseprotected
m_uProgressReportIntervalCReaderBaseprotected
m_usescoreCBedReaderprotected
mAssumeErrorsAreRecordLevelCBedReaderprotected
mColumnSeparatorCBedReaderprotected
mColumnSplitFlagsCBedReaderprotected
mDataCReaderBase
mLineCReaderBase
mLinePreBufferCBedReaderprotected
mpAutoSqlCBedReaderprotected
mRealColumnCountCBedReaderprotected
mSeqIdResolveCReaderBaseprotected
mValidColumnCountCBedReaderprotected
ObjectType enum nameCReaderBase
OT_SEQANNOT enum valueCReaderBase
OT_SEQENTRY enum valueCReaderBase
OT_UNKNOWN enum valueCReaderBase
ProcessError(CObjReaderLineException &, ILineErrorListener *)CReaderBaseprotected
ProcessError(CLineError &, ILineErrorListener *)CReaderBaseprotected
ProcessWarning(CObjReaderLineException &, ILineErrorListener *)CReaderBaseprotected
ProcessWarning(CLineError &, ILineErrorListener *)CReaderBaseprotected
ReadObject(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadObject(ILineReader &lr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadSeqAnnot(ILineReader &lr, ILineErrorListener *pErrors=nullptr) overrideCBedReadervirtual
CReaderBase::ReadSeqAnnot(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadSeqAnnots(TAnnots &annots, CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadSeqAnnots(TAnnots &annots, ILineReader &lr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadSeqEntry(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadSeqEntry(ILineReader &lr, ILineErrorListener *pErrors=nullptr)CReaderBasevirtual
ReadTrackData(ILineReader &, CRawBedTrack &, ILineErrorListener *=nullptr)CBedReadervirtual
SeqIdResolver typedefCReaderBase
SetAutoSql(const string &)CBedReadervirtual
SetAutoSql(CNcbiIstream &)CBedReadervirtual
SetCanceler(ICanceled *=nullptr)CReaderBase
SetProgressReportInterval(unsigned int intv)CReaderBase
TAnnotCit typedefCReaderBase
TAnnotIt typedefCReaderBase
TAnnotList typedefCReaderBase
TAnnots typedefCReaderBase
TFlags typedefCBedReader
TReaderData typedefCReaderBase
TReaderFlags typedefCReaderBase
TReaderLine typedefCReaderBase
xAddConversionInfo(CSeq_annot &, ILineErrorListener *)CReaderBaseprotectedvirtual
xAddStringFlagsWithMap(const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)CReaderBaseprotectedstatic
xAppendFeatureBlock(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAppendFeatureCds(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAppendFeatureChrom(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAppendFeatureGene(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAppendFeatureRna(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAppendFeatureThick(const CBedColumnData &, CSeq_annot &, unsigned int, ILineErrorListener *)CBedReaderprotected
xAssignBedColumnCount(CSeq_annot &)CBedReaderprotectedvirtual
xAssignTrackData(CSeq_annot &)CReaderBaseprotectedvirtual
xCleanColumnValues(vector< string > &)CBedReaderprotectedstatic
xContainsBlockFeature(const CBedColumnData &) constCBedReaderprotected
xContainsCdsFeature(const CBedColumnData &) constCBedReaderprotected
xContainsRnaFeature(const CBedColumnData &) constCBedReaderprotected
xContainsThickFeature(const CBedColumnData &) constCBedReaderprotected
xCreateSeqAnnot() overrideCBedReaderprotectedvirtual
xDetermineLikelyColumnCount(CLinePreBuffer &, ILineErrorListener *)CBedReaderprotectedvirtual
xGetData(ILineReader &, TReaderData &) overrideCBedReaderprotectedvirtual
xGetLine(ILineReader &, string &)CReaderBaseprotectedvirtual
xGetStrand(const CBedColumnData &) constCBedReaderprotected
xGuardedGetData(ILineReader &, TReaderData &, ILineErrorListener *)CReaderBaseprotected
xGuardedProcessData(const TReaderData &, CSeq_annot &, ILineErrorListener *)CReaderBaseprotectedvirtual
xIsBrowserLine(const CTempString &)CReaderBaseprotectedvirtual
xIsCommentLine(const CTempString &)CReaderBaseprotectedvirtual
xIsOperationCanceled() constCReaderBaseprotected
xIsReportingProgress() constCReaderBaseprotected
xIsTrackLine(const CTempString &)CReaderBaseprotectedvirtual
xIsTrackTerminator(const CTempString &)CReaderBaseprotectedvirtual
xParseBrowserLine(const string &, CSeq_annot &)CReaderBaseprotectedvirtual
xParseComment(const CTempString &, CRef< CSeq_annot > &)CReaderBaseprotected
xParseFeature(const SReaderLine &, CSeq_annot &, ILineErrorListener *)CBedReaderprotected
xParseFeatureAutoSql(const CBedColumnData &, CSeq_annot &, ILineErrorListener *)CBedReaderprotected
xParseFeatureGeneModelFormat(const CBedColumnData &, CSeq_annot &, ILineErrorListener *)CBedReaderprotected
xParseFeatureThreeFeatFormat(const CBedColumnData &, CSeq_annot &, ILineErrorListener *)CBedReaderprotected
xParseFeatureUserFormat(const CBedColumnData &, CSeq_annot &, ILineErrorListener *)CBedReaderprotected
xParseTrackLine(const string &) overrideCBedReaderprotectedvirtual
xPostProcessAnnot(CSeq_annot &) overrideCBedReaderprotectedvirtual
xProcessData(const TReaderData &, CSeq_annot &) overrideCBedReaderprotectedvirtual
xProcessLineError(const ILineError &, ILineErrorListener *)CReaderBaseprotected
xProcessReaderMessage(CReaderMessage &, ILineErrorListener *)CReaderBaseprotected
xProcessUnknownException(const CException &)CReaderBaseprotected
xProgressInit(ILineReader &istr)CReaderBaseprotectedvirtual
xReadBedDataRaw(ILineReader &, CRawBedTrack &, ILineErrorListener *)CBedReaderprotected
xReadBedRecordRaw(const string &, CRawBedRecord &, ILineErrorListener *)CBedReaderprotected
xReadInit()CReaderBaseprotectedvirtual
xReportProgress(ILineErrorListener *=nullptr)CReaderBaseprotected
xSetBrowserRegion(const string &, CAnnot_descr &)CReaderBaseprotectedvirtual
xSetFeatureBedData(CRef< CSeq_feat > &, const CBedColumnData &, ILineErrorListener *)CBedReaderprotected
xSetFeatureColor(CRef< CUser_object >, const CBedColumnData &, ILineErrorListener *)CBedReaderprotected
xSetFeatureColorByStrand(CRef< CUser_object >, const string &, ENa_strand, ILineErrorListener *)CBedReaderprotected
xSetFeatureColorDefault(CRef< CUser_object >)CBedReaderprotected
xSetFeatureColorFromItemRgb(CRef< CUser_object >, const string &, ILineErrorListener *)CBedReaderprotected
xSetFeatureColorFromScore(CRef< CUser_object >, const string &)CBedReaderprotected
xSetFeatureDisplayData(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureIdsBlock(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureIdsCds(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureIdsChrom(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureIdsGene(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureIdsRna(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureIdsThick(CRef< CSeq_feat > &, const CBedColumnData &, unsigned int)CBedReaderprotected
xSetFeatureLocation(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationBlock(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationCds(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationChrom(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationGene(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationRna(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureLocationThick(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xSetFeatureScore(CRef< CUser_object >, const CBedColumnData &)CBedReaderprotected
xSetFeatureTitle(CRef< CSeq_feat > &, const CBedColumnData &)CBedReaderprotected
xUngetLine(ILineReader &)CReaderBaseprotectedvirtual
xValidateAnnot(const CSeq_annot &)CReaderBaseinlineprotectedvirtual
~CBedReader()CBedReadervirtual
~CReaderBase()CReaderBasevirtual
Modified on Thu Feb 29 12:19:05 2024 by modify_doxy.py rev. 669887