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string PrintBestSeqId (const CSeq_id &sid, CScope &scope) string PrintSeqIntUseBestID (const CSeq_interval &seq_int, CScope &scope, bool range_only) string PrintPntAndPntsUseBestID (const CSeq_loc &seq_loc, CScope &scope, bool range_only) string SeqLocPrintUseBestID (const CSeq_loc &seq_loc, CScope &scope, bool range_only) CRef< CSeq_loc > SeqLocExtend5 (const CSeq_loc &loc, TSeqPos pos, CScope *scope) CRef< CSeq_loc > SeqLocExtend3 (const CSeq_loc &loc, TSeqPos pos, CScope *scope) CRef< CSeq_loc > SeqLocExtend (const CSeq_loc &loc, size_t pos, CScope *scope) void AdjustFrameFor5Extension (CSeq_feat &feat, size_t diff) bool ApplyPolicyToFeature (const CLocationEditPolicy &policy, const CSeq_feat &orig_feat, CScope &scope, bool adjust_gene, bool retranslate_cds) void ReverseComplementLocation (CSeq_interval &interval, CScope &scope) void ReverseComplementLocation (CSeq_point &pnt, CScope &scope) void ReverseComplementLocation (CPacked_seqpnt &ppnt, CScope &scope) void ReverseComplementLocation (CSeq_loc &loc, CScope &scope) void ReverseComplementCDRegion (CCdregion &cdr, CScope &scope) void ReverseComplementTrna (CTrna_ext &trna, CScope &scope) void ReverseComplementFeature (CSeq_feat &feat, CScope &scope) bool OkToAdjustLoc (const CSeq_interval &interval, const CSeq_id *seqid) bool OkToAdjustLoc (const CSeq_point &pnt, const CSeq_id *seqid) bool OkToAdjustLoc (const CPacked_seqpnt &pack, const CSeq_id *seqid) void NormalizeLoc (CSeq_loc &loc) void SeqLocAdjustForTrim (CSeq_interval &interval, TSeqPos cut_from, TSeqPos cut_to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CPacked_seqint &packint, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CSeq_loc_mix &mix, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CSeq_point &pnt, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CPacked_seqpnt &pack, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CSeq_bond &bond, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CSeq_loc_equiv &equiv, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForTrim (CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted) void SeqLocAdjustForInsert (CSeq_interval &interval, TSeqPos insert_from, TSeqPos insert_to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CPacked_seqint &packint, TSeqPos insert_from, TSeqPos insert_to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CSeq_loc_mix &mix, TSeqPos insert_from, TSeqPos insert_to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CSeq_point &pnt, TSeqPos insert_from, TSeqPos insert_to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CPacked_seqpnt &packpnt, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CSeq_bond &bond, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CSeq_loc_equiv &equiv, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void SeqLocAdjustForInsert (CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid) CRef< CSeq_interval > SplitLocationForGap (CSeq_interval &before, TSeqPos start, TSeqPos stop, const CSeq_id *seqid, bool &cut, unsigned int options) void SplitLocationForGap (CSeq_loc::TPacked_int &before_intervals, CSeq_loc::TPacked_int &after_intervals, TSeqPos start, TSeqPos stop, const CSeq_id *seqid, unsigned int options) void SplitLocationForGap (CSeq_loc &loc1, CSeq_loc &loc2, size_t start, size_t stop, const CSeq_id *seqid, unsigned int options) void CdregionAdjustForTrim (CCdregion &cdr, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void TrnaAdjustForTrim (CTrna_ext &trna, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void FeatureAdjustForTrim (CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed) void CdregionAdjustForInsert (CCdregion &cdr, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void TrnaAdjustForInsert (CTrna_ext &trna, TSeqPos from, TSeqPos to, const CSeq_id *seqid) void FeatureAdjustForInsert (CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid) bool s_PPntComparePlus (const TSeqPos &p1, const TSeqPos &p2) bool s_PPntCompareMinus (const TSeqPos &p1, const TSeqPos &p2) bool CorrectIntervalOrder (CPacked_seqpnt &ppnt) bool s_StrandsConsistent (const CSeq_interval &a, const CSeq_interval &b) bool CorrectIntervalOrder (CPacked_seqint &pint) bool OneIdOneStrand (const CSeq_loc &loc, const CSeq_id **id, ENa_strand &strand) bool CorrectIntervalOrder (CSeq_loc::TMix::Tdata &mix) bool CorrectIntervalOrder (CSeq_loc &loc) Correct the order of consecutive intervals with the same Seq-id on the same strand. More...Definition at line 2503 of file loc_edit.cpp.
References eExtreme_Biological, eNa_strand_minus, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStop(), CSeq_loc_CI::GetStrand(), IsExtendableLeft(), IsExtendableRight(), CSeq_loc::IsPartialStop(), CSeq_loc_CI::IsSetStrand(), SeqLocExtend3(), CSeq_feat_Base::SetLocation(), and CSeq_loc_CI::SetPos().
Referenced by ExtendPartialFeatureEnds().
◆ AdjustFeatureEnd5()Definition at line 2447 of file loc_edit.cpp.
References AdjustFrameFor5Extension(), eExtreme_Biological, eNa_strand_minus, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_feat_Base::GetData(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetSeq_id(), CSeq_loc::GetStart(), CSeq_loc_CI::GetStrand(), CSeqFeatData_Base::IsCdregion(), IsExtendableLeft(), IsExtendableRight(), CSeq_loc::IsPartialStart(), CSeq_feat_Base::IsSetData(), CSeq_loc_CI::IsSetStrand(), SeqLocExtend5(), and CSeq_feat_Base::SetLocation().
Referenced by ExtendPartialFeatureEnds().
◆ AdjustFrameFor5Extension() void AdjustFrameFor5Extension ( CSeq_feat & feat, size_t diff ) ◆ ApplyPolicyToFeature()Definition at line 835 of file loc_edit.cpp.
References AdjustForCDSPartials(), CLocationEditPolicy::ApplyPolicyToFeature(), CSerialObject::Assign(), eExtreme_Biological, CSeq_feat_Handle::GetAnnot(), CSeq_feat_Base::GetData(), CSeq_entry_Handle::GetEditHandle(), CSeq_feat_Base::GetLocation(), GetOverlappingGene(), CSeq_annot_Handle::GetParentEntry(), CScope::GetSeq_featHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetProduct(), l(), CSeq_feat_EditHandle::Replace(), RetranslateCDS(), SeqLocExtend3(), SeqLocExtend5(), and CSeq_feat_Base::SetLocation().
Referenced by BOOST_AUTO_TEST_CASE().
◆ CdregionAdjustForInsert() ◆ CdregionAdjustForTrim() ◆ CorrectIntervalOrder() [1/4] ◆ CorrectIntervalOrder() [2/4]Definition at line 2174 of file loc_edit.cpp.
References eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::IsSetPoints(), CPacked_seqpnt_Base::IsSetStrand(), s_PPntCompareMinus(), s_PPntComparePlus(), seq_mac_is_sorted(), and CPacked_seqpnt_Base::SetPoints().
Referenced by CorrectIntervalOrder().
◆ CorrectIntervalOrder() [3/4]Correct the order of consecutive intervals with the same Seq-id on the same strand.
Definition at line 2346 of file loc_edit.cpp.
References CorrectIntervalOrder(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), and CSeq_loc_Base::Which().
Referenced by CCorrectIntervalOrder::ApplyToCSeq_entry(), and BOOST_AUTO_TEST_CASE().
◆ CorrectIntervalOrder() [4/4]Definition at line 2290 of file loc_edit.cpp.
References a, b, CorrectIntervalOrder(), eExtreme_Biological, eNa_strand_minus, eNa_strand_plus, CSerialObject::Equals(), CRef< C, Locker >::GetPointer(), NON_CONST_ITERATE, and OneIdOneStrand().
◆ ExtendPartialFeatureEnds()Definition at line 2585 of file loc_edit.cpp.
References AdjustFeatureEnd3(), AdjustFeatureEnd5(), CSerialObject::Assign(), CSeqFeatData::eSubtype_mRNA, f, CSeq_feat_Handle::GetOriginalSeq_feat(), CBioseq_Handle::GetScope(), CSeq_feat_EditHandle::Replace(), and RetranslateCDS().
Referenced by CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), and CTable2AsnValidator::Cleanup().
◆ FeatureAdjustForInsert() ◆ FeatureAdjustForTrim() ◆ IsExtendable()Definition at line 2555 of file loc_edit.cpp.
References eExtreme_Positional, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStop(), IsExtendableLeft(), IsExtendableRight(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and CSeq_loc_CI::SetPos().
Referenced by CheckAdjustStart(), CheckAdjustStartAndStop(), and CheckAdjustStop().
◆ IsExtendableLeft()Definition at line 2375 of file loc_edit.cpp.
References CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), GetLength(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetRepr(), ITERATE, and offset.
Referenced by AdjustFeatureEnd3(), AdjustFeatureEnd5(), and IsExtendable().
◆ IsExtendableRight()Definition at line 2411 of file loc_edit.cpp.
References CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), GetLength(), CBioseq::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetRepr(), ITERATE, and offset.
Referenced by AdjustFeatureEnd3(), AdjustFeatureEnd5(), and IsExtendable().
◆ NormalizeLoc()Definition at line 1124 of file loc_edit.cpp.
References CSeq_loc::Assign(), CSerialObject::Assign(), CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetEquiv(), CPacked_seqpnt_Base::GetFuzz(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::IsSetId(), CPacked_seqpnt_Base::IsSetStrand(), CSeq_loc_Base::Reset(), CSeq_loc::SetEquiv(), CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPnt(), CSeq_point_Base::SetPoint(), CSeq_point_Base::SetStrand(), and CSeq_loc_Base::Which().
Referenced by SeqLocAdjustForTrim(), and SplitLocationForGap().
◆ OkToAdjustLoc() [1/3] ◆ OkToAdjustLoc() [2/3] ◆ OkToAdjustLoc() [3/3] ◆ OneIdOneStrand() ◆ PrintBestSeqId() ◆ PrintPntAndPntsUseBestID()Definition at line 131 of file loc_edit.cpp.
References CPacked_seqpnt_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc::GetLabel(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), kEmptyStr, location, PrintBestSeqId(), and strtmp.
Referenced by SeqLocPrintUseBestID().
◆ PrintSeqIntUseBestID()Definition at line 82 of file loc_edit.cpp.
References CSeq_interval_Base::CanGetFuzz_from(), CSeq_interval_Base::CanGetFuzz_to(), CSeq_interval_Base::CanGetStrand(), eNa_strand_both_rev, eNa_strand_minus, eNa_strand_unknown, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CInt_fuzz::GetLabel(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), int, NStr::IntToString(), kEmptyStr, location, PrintBestSeqId(), and strand_symbol.
Referenced by SeqLocPrintUseBestID().
◆ ReverseComplementCDRegion() ◆ ReverseComplementFeature()Definition at line 1068 of file loc_edit.cpp.
References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_tRNA, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), ReverseComplementCDRegion(), ReverseComplementLocation(), ReverseComplementTrna(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().
Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CMixedStrands::GetCommand(), GetReverseComplimentSequenceCommand(), and CRevCompSequencesDlg::RevCompBioSeq().
◆ ReverseComplementLocation() [1/4] ◆ ReverseComplementLocation() [2/4]Definition at line 893 of file loc_edit.cpp.
References CSeq_interval::FlipStrand(), CScope::GetBioseqHandle(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CBioseq_Handle::GetInst_Length(), CSeq_interval_Base::GetTo(), CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetId(), CSeq_interval_Base::IsSetTo(), CSeq_interval_Base::ResetFrom(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::ResetTo(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetTo(), and swap().
Referenced by ReverseComplementCDRegion(), ReverseComplementFeature(), ReverseComplementLocation(), and ReverseComplementTrna().
◆ ReverseComplementLocation() [3/4]Definition at line 991 of file loc_edit.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::GetBond(), CSeq_loc::InvalidateCache(), CSeq_bond_Base::IsSetA(), CSeq_bond_Base::IsSetB(), NON_CONST_ITERATE, ReverseComplementLocation(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().
Referenced by BOOST_AUTO_TEST_CASE(), and CRevCompSequencesDlg::RevCompBioSeq().
◆ ReverseComplementLocation() [4/4] ◆ ReverseComplementTrna() ◆ s_PPntCompareMinus() ◆ s_PPntComparePlus() ◆ s_StrandsConsistent() ◆ SeqLocAdjustForInsert() [1/8] ◆ SeqLocAdjustForInsert() [2/8] ◆ SeqLocAdjustForInsert() [3/8] ◆ SeqLocAdjustForInsert() [4/8] ◆ SeqLocAdjustForInsert() [5/8]Definition at line 1682 of file loc_edit.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, SeqLocAdjustForInsert(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().
Referenced by BOOST_AUTO_TEST_CASE().
◆ SeqLocAdjustForInsert() [6/8] ◆ SeqLocAdjustForInsert() [7/8] ◆ SeqLocAdjustForInsert() [8/8] ◆ SeqLocAdjustForTrim() [1/8] ◆ SeqLocAdjustForTrim() [2/8] ◆ SeqLocAdjustForTrim() [3/8] ◆ SeqLocAdjustForTrim() [4/8]Definition at line 1207 of file loc_edit.cpp.
References CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::CanGetTo(), eNa_strand_minus, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_interval_Base::IsSetStrand(), OkToAdjustLoc(), CSeq_interval_Base::SetFrom(), and CSeq_interval_Base::SetTo().
Referenced by CdregionAdjustForTrim(), FeatureAdjustForTrim(), SeqLocAdjustForTrim(), and TrnaAdjustForTrim().
◆ SeqLocAdjustForTrim() [5/8]Definition at line 1489 of file loc_edit.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, NormalizeLoc(), SeqLocAdjustForTrim(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().
Referenced by CFeatGapInfo::AdjustProteinSeq(), and BOOST_AUTO_TEST_CASE().
◆ SeqLocAdjustForTrim() [6/8] ◆ SeqLocAdjustForTrim() [7/8] ◆ SeqLocAdjustForTrim() [8/8] ◆ SeqLocExtend()Definition at line 546 of file loc_edit.cpp.
References eExtreme_Positional, CSeq_loc::fMerge_AbuttingOnly, CSeq_loc::fSort, CSeq_loc::GetId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), Seq_loc_Add(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().
Referenced by AdjustGene(), CEditSequenceEnds::Extend3(), CEditSequenceEnds::Extend5(), and ExtendCDSToStopCodon().
◆ SeqLocExtend3()Definition at line 517 of file loc_edit.cpp.
References eExtreme_Biological, eExtreme_Positional, eNa_strand_minus, eNa_strand_plus, CSeq_loc::fMerge_AbuttingOnly, CSeq_loc::fSort, CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStop(), CSeq_loc::IsSetStrand(), Seq_loc_Add(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), and CSeq_loc_CI::SetPos().
Referenced by AdjustFeatureEnd3(), ApplyPolicyToFeature(), and CLocationEditPolicy::Extend3().
◆ SeqLocExtend5()Definition at line 491 of file loc_edit.cpp.
References eExtreme_Biological, eExtreme_Positional, eNa_strand_minus, eNa_strand_plus, CSeq_loc::fMerge_AbuttingOnly, CSeq_loc::fSort, CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsSetStrand(), Seq_loc_Add(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().
Referenced by AdjustFeatureEnd5(), ApplyPolicyToFeature(), and CLocationEditPolicy::Extend5().
◆ SeqLocPrintUseBestID()Definition at line 153 of file loc_edit.cpp.
References CSeq_bond_Base::CanGetB(), CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetInt(), CSeq_loc::GetLabel(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::IsBond(), CSeq_loc_Base::IsEquiv(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), ITERATE, kEmptyStr, location, PrintPntAndPntsUseBestID(), PrintSeqIntUseBestID(), and CSeq_loc::SetBond().
Referenced by BOOST_AUTO_TEST_CASE().
◆ SplitLocationForGap() [1/3]Definition at line 1728 of file loc_edit.cpp.
References CSerialObject::Assign(), CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::CanGetTo(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eSplitLocOption_make_partial, eSplitLocOption_split_in_exon, eSplitLocOption_split_in_intron, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), OkToAdjustLoc(), CRef< C, Locker >::Reset(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), and CSeq_interval_Base::SetTo().
Referenced by SplitLocationForGap().
◆ SplitLocationForGap() [2/3]Definition at line 1833 of file loc_edit.cpp.
References CSeq_loc::Add(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, eExtreme_Positional, CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc::GetStart(), CSeq_loc_mix::IsReverseStrand(), CSeq_loc_equiv_Base::IsSet(), CSeq_loc_mix_Base::IsSet(), NormalizeLoc(), OkToAdjustLoc(), Ref(), CSeq_loc_Base::Reset(), CPacked_seqint_Base::Set(), CSeq_loc_equiv_Base::Set(), CSeq_loc_mix_Base::Set(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), SplitLocationForGap(), and CSeq_loc_Base::Which().
Referenced by BOOST_AUTO_TEST_CASE(), CFeatGapInfo::Split(), and CFeatGapInfo::Trim().
◆ SplitLocationForGap() [3/3] ◆ TrnaAdjustForInsert() ◆ TrnaAdjustForTrim() ◆ strand_symbolRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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