NCBI C++ ToolKit
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Search Toolkit Book for CGffBaseColumns
#include <objtools/readers/gff_base_columns.hpp>
Public Types | |
using | TFrame = CCdregion::EFrame |
using | TReaderFlags = long |
using | SeqIdResolver = CRef< CSeq_id >(*)(const string &, TReaderFlags, bool) |
Static Public Member Functions | |
static unsigned int | NextId () |
static void | ResetId () |
Protected Attributes | |
string | mSeqId |
TSeqPos | m_uSeqStart |
TSeqPos | m_uSeqStop |
string | m_strSource |
string | m_strType |
string | m_strNormalizedType |
double * | m_pdScore |
ENa_strand * | m_peStrand |
TFrame * | m_pePhase |
Static Protected Attributes | |
static unsigned int | msNextId = 0 |
Definition at line 42 of file gff_base_columns.hpp.
using CGffBaseColumns::SeqIdResolver = CRef<CSeq_id> (*)(const string&, TReaderFlags, bool) |
Definition at line 48 of file gff_base_columns.hpp.
Definition at line 46 of file gff_base_columns.hpp.
using CGffBaseColumns::TReaderFlags = long |
Definition at line 47 of file gff_base_columns.hpp.
CGffBaseColumns::CGffBaseColumns | ( | ) |
Definition at line 55 of file gff_base_columns.cpp.
CGffBaseColumns::CGffBaseColumns | ( | const CGffBaseColumns & | rhs | ) |
Definition at line 70 of file gff_base_columns.cpp.
References m_pdScore, m_pePhase, m_peStrand, Phase(), Score(), and Strand().
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Definition at line 95 of file gff_base_columns.cpp.
References m_pdScore, m_pePhase, and m_peStrand.
CRef< CSeq_id > CGffBaseColumns::GetSeqId | ( | TReaderFlags | flags, |
SeqIdResolver | seqidresolve = nullptr |
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) | const |
Definition at line 104 of file gff_base_columns.cpp.
References CReadUtil::AsSeqId(), and flags.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), and CGtfLocationRecord::CGtfLocationRecord().
CRef< CSeq_loc > CGffBaseColumns::GetSeqLoc | ( | TReaderFlags | flags, |
SeqIdResolver | seqidresolve = nullptr |
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) | const |
Definition at line 116 of file gff_base_columns.cpp.
References flags, GetSeqId(), and CSeq_loc::SetInt().
Referenced by CGff3Reader::xVerifyExonLocation().
Definition at line 59 of file gff_base_columns.hpp.
References mSeqId.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), CGffIdTracker::CheckAndIndexRecord(), CGff3LocationMerger::VerifyRecordLocation(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CGff3Reader::xInitializeFeature(), CGff3Reader::xUpdateAnnotGeneric(), and CGff3Reader::xUpdateAnnotRegion().
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Reimplemented in CGff2Record.
Definition at line 132 of file gff_base_columns.cpp.
References flags.
Referenced by CGff2Record::InitializeFeature().
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Definition at line 96 of file gff_base_columns.hpp.
References m_pdScore.
Referenced by Score(), CGff2Reader::xAlignmentSetScore(), and CGvfReader::xFeatureSetExt().
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Definition at line 100 of file gff_base_columns.hpp.
References m_peStrand.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), CGtfLocationRecord::CGtfLocationRecord(), Strand(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), and CGff3Reader::xUpdateAnnotGeneric().
Definition at line 149 of file gff_base_columns.hpp.
References msNextId.
Definition at line 79 of file gff_base_columns.hpp.
References m_strNormalizedType.
Referenced by CGff3LocationMerger::AddRecord(), CGff3LocationRecord::CGff3LocationRecord(), CGffIdTracker::CheckAndIndexRecord(), CGtfLocationMerger::GetFeatureIdFor(), CGtfLocationRecord::GetRecordType(), CGtfReader::xCreateParentGene(), CGtfReader::xCreateParentMrna(), CGvfReader::xFeatureSetVariation(), CGff3LocationMerger::xGetLocationIds(), CGff3Reader::xMakeRecordId(), CGff3Reader::xUpdateAnnotFeature(), CGtfReader::xUpdateAnnotFeature(), CGtfReader::xUpdateAnnotParent(), and CGvfReader::xVariationMakeCNV().
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Definition at line 92 of file gff_base_columns.hpp.
References CCdregion_Base::eFrame_not_set, IsSetPhase(), and m_pePhase.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), and CGffBaseColumns().
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Definition at line 153 of file gff_base_columns.hpp.
References msNextId.
Referenced by CGff3Reader::CGff3Reader().
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Definition at line 84 of file gff_base_columns.hpp.
References IsSetScore(), and m_pdScore.
Referenced by CGffBaseColumns(), CGff2Reader::xAlignmentSetScore(), and CGvfReader::xFeatureSetExt().
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Definition at line 63 of file gff_base_columns.hpp.
References m_uSeqStart.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), CGtfLocationRecord::CGtfLocationRecord(), CGff3LocationMerger::VerifyRecordLocation(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetLocation(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), CGff2Reader::xSetDensegStarts(), and CGff3Reader::xUpdateAnnotGeneric().
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Definition at line 67 of file gff_base_columns.hpp.
References m_uSeqStop.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), CGtfLocationRecord::CGtfLocationRecord(), CGff3LocationMerger::VerifyRecordLocation(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetLocation(), CGvfReader::xFeatureSetLocationInterval(), CGff2Reader::xSetDensegStarts(), and CGff3Reader::xUpdateAnnotGeneric().
Definition at line 122 of file gff_base_columns.hpp.
References m_uSeqStart, and m_uSeqStop.
Definition at line 129 of file gff_base_columns.hpp.
References m_strNormalizedType, m_strType, and NStr::ToLower().
Referenced by CGff3ReadRecord::AssignFromGff().
Definition at line 71 of file gff_base_columns.hpp.
References m_strSource.
Referenced by CGvfReader::xFeatureSetExt(), CGvfReader::xVariationSetId(), and CGvfReader::xVariationSetParent().
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Definition at line 88 of file gff_base_columns.hpp.
References eNa_strand_unknown, IsSetStrand(), and m_peStrand.
Referenced by CGff3LocationRecord::CGff3LocationRecord(), CGffBaseColumns(), CGtfLocationRecord::CGtfLocationRecord(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CGvfReader::xFeatureSetLocationInterval(), CGvfReader::xFeatureSetLocationPoint(), and CGff3Reader::xUpdateAnnotGeneric().
Definition at line 75 of file gff_base_columns.hpp.
References m_strType.
Referenced by CGtfReadRecord::FeatureKey(), CGff2Record::IsAlignmentRecord(), CGff2Reader::xAlignmentSetSegment(), CGff2Reader::xAlignmentSetSpliced_seg(), CGtfReader::xCreateParentGene(), CGvfReader::xFeatureSetExt(), CGvfReader::xFeatureSetLocationPoint(), CGff3Reader::xFindFeatureUnderConstruction(), CGff3LocationMerger::xGetLocationIds(), CGff3Reader::xUpdateAnnotGeneric(), and CGff3Reader::xVerifyExonLocation().
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Reimplemented in CGff2Record.
Definition at line 172 of file gff_base_columns.cpp.
References CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, and CSeqFeatData::eSubtype_cdregion.
Referenced by CGff2Record::xInitFeatureData().
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Definition at line 148 of file gff_base_columns.cpp.
References CObject_id_Base::SetId(), and CFeat_id_Base::SetLocal().
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Definition at line 161 of file gff_base_columns.cpp.
References flags.
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Definition at line 165 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), CGffBaseColumns(), IsSetScore(), Score(), and ~CGffBaseColumns().
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Definition at line 167 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), CGffBaseColumns(), IsSetPhase(), Phase(), and ~CGffBaseColumns().
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Definition at line 166 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), CGffBaseColumns(), IsSetStrand(), Strand(), and ~CGffBaseColumns().
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Definition at line 164 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), NormalizedType(), and SetType().
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Definition at line 162 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), and Source().
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Definition at line 163 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), CGff3ReadRecord::AssignFromGff(), SetType(), and Type().
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Definition at line 160 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), SeqStart(), and SetExtent().
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Definition at line 161 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), SeqStop(), and SetExtent().
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Definition at line 159 of file gff_base_columns.hpp.
Referenced by CGff2Record::AssignFromGff(), and Id().
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Definition at line 169 of file gff_base_columns.hpp.