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NCBI C++ ToolKit: src/objtools/edit/seq_entry_edit.cpp File Reference

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CConstRef< CDelta_seq >  GetDeltaSeqForPosition (const unsigned pos, const CBioseq_Handle seq_hl, CScope *scope, unsigned &left_endpoint)   bool  IsDeltaSeqGap (CConstRef< CDelta_seq > delta)   bool  Does5primerAbutGap (const CSeq_feat &feat, CBioseq_Handle seq_hl)   bool  Does3primerAbutGap (const CSeq_feat &feat, CBioseq_Handle seq_hl)   static void  s_AddBioseqToPartsSet (CBioseq_set_EditHandle &parts, CBioseq_EditHandle &seq)   static void  s_AddPartToSegmentedBioseq (const CBioseq_EditHandle &seg, const CBioseq_EditHandle &part)   static void  s_AddBioseqToSegset (CBioseq_set_EditHandle &segset, CBioseq_EditHandle &part)   void  AddSeqEntryToSeqEntry (const CSeq_entry_Handle &target, const CSeq_entry_Handle &insert)   Attach one Seq-entry to another. More...
  static void  s_AddProtToNuc (const CBioseq_EditHandle &nuc, const CBioseq_EditHandle &prot)   static CSeq_id *  s_MakeUniqueLocalId (void)   static void  s_AddBioseqToBioseq (const CBioseq_EditHandle &to, const CBioseq_EditHandle &add)   void  AddBioseqToBioseq (const CBioseq_Handle &to, const CBioseq_Handle &add)   Attach one Bioseq to another. More...
  static void  s_AddBioseqToNucProtSet (CBioseq_set_EditHandle &nuc_prot, CBioseq_EditHandle &seq)   void  AddBioseqToBioseqSet (const CBioseq_set_Handle &set, const CBioseq_Handle &seq)   Add a Bioseq to a Bioseq-set. More...
  bool  IsSeqDescInList (const CSeqdesc &desc, const CSeq_descr &set)   void  AddSeqdescToSeqDescr (const CSeqdesc &desc, CSeq_descr &seq_descr)   void  AddSeqdescToBioseq (const CSeqdesc &desc, CBioseq &seq)   void  AddSeqdescToBioseqSet (const CSeqdesc &desc, CBioseq_set &set)   bool  AddSeqdescToSeqEntryRecursively (CSeq_entry &entry, CSeqdesc &desc)   CRef< CSeq_entry >  SeqEntryFromSeqSubmit (const CSeq_submit &submit)   Create a Seq-entry from a Seq-submit. More...
  static bool  s_IsSingletonSet (const CBioseq_set_Handle &bioseq_set)   static void  s_PromoteSingletonSetsInSet (const CBioseq_set_Handle &bioseq_set_h)   static void  s_MakeGroupsForUniqueValues (const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)   void  SegregateSetsByBioseqList (const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)   Split a Seq-entry, where the second part holds the given bioseqs. More...
  static bool  s_DivvyUpAlignments_ProcessAnnot_Dendiag (const CSeq_align_Handle &align, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapEntryToAlignVec &mapEntryToAlignVec)   static bool  s_DivvyUpAlignments_ProcessAnnot_Denseg (const CSeq_align_Handle &align, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapEntryToAlignVec &mapEntryToAlignVec)   static void  s_DivvyUpAlignments_ProcessAnnot (const CSeq_annot_Handle &annot_h, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapSeqAnnotToDest &mapSeqAnnotToDest, TVecOfSeqAnnotsToErase &vecOfSeqAnnotToErase)   void  DivvyUpAlignments (const TVecOfSeqEntryHandles &vecOfSeqEntryHandles)   Call this if the alignments directly under these seq-entries are all jumbled up between each other. More...
  void  BioseqSetDescriptorPropagateUp (CBioseq_set_Handle set)   Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the descriptor. More...
  void  BioseqSetDescriptorPropagateDown (const CBioseq_set_Handle &bioseq_set_h, const vector< CSeqdesc::E_Choice > &choices_to_delete)   Moves descriptors down to children of the given bioseq-set. More...
  CSeq_id::E_Choice  TypeFromLabel (const string &label)   string  LabelFromType (CSeq_id::E_Choice choice)   string  MakeOriginalLabelForId (const CSeq_id &id)   CRef< CUser_field >  MakeOriginalIdField (const CSeq_id &id)   void  AddLocalIdUserObjects (CSeq_entry &entry)   Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID. More...
  bool  IsMatchingIdMissing (const CUser_field &field, const CBioseq::TId &ids)   bool  HasRepairedIDs (const CUser_object &user, const CBioseq::TId &ids)   bool  HasRepairedIDs (const CSeq_entry &entry)   Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID User-object descriptor. More...
  void  RemoveUserObjectType (CSeq_entry &entry, CUser_object::EObjectType type)   Removes User-object descriptors of a certain type from the seq-entry. More...
  void  HandleCollidingIds (CSeq_entry &entry)   void  s_AddLiteral (CSeq_inst &inst, const string &element)   void  s_AddGap (CSeq_inst &inst, size_t n_len, bool is_unknown, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)   void  ConvertRawToDeltaByNs (CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap, int gap_type, int linkage, int linkage_evidence)   ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to determine the gap location. More...
  TLocAdjustmentVector  NormalizeUnknownLengthGaps (CSeq_inst &inst, TSeqPos unknown_length)   NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific length (100 by default). More...
  void  ConvertRawToDeltaByNs (CBioseq_Handle bsh, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap, int gap_type, int linkage, int linkage_evidence)   void  SetLinkageType (CSeq_ext &ext, CSeq_gap::TType linkage_type)   SetLinkageType A function to set the linkage_type for gaps in a delta sequence. More...
  void  SetLinkageTypeScaffold (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)   SetLinkageTypeScaffold A special case of SetLinkageType. More...
  void  SetLinkageTypeLinkedRepeat (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)   void  AddLinkageEvidence (CSeq_ext &ext, CLinkage_evidence::TType evidence_type)   AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence. More...
  void  ResetLinkageEvidence (CSeq_ext &ext)   ResetLinkageEvidence A function to clear linkage evidence for gaps in a delta sequence. More...
  void  s_BasicValidation (CBioseq_Handle bsh, const TCuts &cuts)   static TRange  s_GetRetainedRange (const TCuts &sorted_merged_cuts, TSeqPos seqLength)   void  TrimSequenceAndAnnotation (CBioseq_Handle bsh, const TCuts &cuts, EInternalTrimType internal_cut_conversion)   Implementation detail: first trim all associated annotation, then trim sequence data. More...
  static void  s_MergeCuts (TCuts &sorted_cuts)   Assumes sorted_cuts are sorted in Ascending order! More...
  static void  s_AdjustInternalCutLocations (TCuts &cuts, TSeqPos seq_length, EInternalTrimType internal_cut_conversion)   Adjust any internal cuts to terminal cuts. More...
  void  GetSortedCuts (CBioseq_Handle bsh, const TCuts &cuts, TCuts &sorted_cuts, EInternalTrimType internal_cut_conversion)   1) Adjust any internal cuts to terminal cuts according to option. More...
  void  UpdateSeqLength (CAutoInitRef< CDelta_ext > &pDeltaExt, CBioseq_Handle &complete_bsh, CSeqMap_CI &seqmap_ci, CSeq_inst_Base::TLength &new_length)   Update sequence length. More...
  void  TrimSeqData (CBioseq_Handle bsh, CRef< CSeq_inst > inst, const TCuts &sorted_cuts)   Trim sequence data. More...
  static void  s_GetTrimCoordinates (CBioseq_Handle bsh, const TCuts &sorted_cuts, TSeqPos &trim_start, TSeqPos &trim_stop)   static void  s_SeqIntervalDelete (CRef< CSeq_interval > interval, TSeqPos cut_from, TSeqPos cut_to, bool &bCompleteCut, bool &bTrimmed)   static void  s_SeqLocDelete (CRef< CSeq_loc > loc, TSeqPos from, TSeqPos to, bool &bCompleteCut, bool &bTrimmed)   static void  s_UpdateSeqGraphLoc (CRef< CSeq_graph > graph, const TCuts &sorted_cuts)   void  TrimSeqGraph (CBioseq_Handle bsh, CRef< CSeq_graph > graph, const TCuts &sorted_cuts)   Trim Seq-graph annotation. More...
  bool  s_FindSegment (const CDense_seg &denseg, CDense_seg::TDim row, TSeqPos pos, CDense_seg::TNumseg &seg, TSeqPos &seg_start)   void  s_CutDensegSegment (CRef< CSeq_align > align, CDense_seg::TDim row, TSeqPos pos)   void  TrimSeqAlign (CBioseq_Handle bsh, CRef< CSeq_align > align, const TCuts &sorted_cuts)   Trim Seq-align annotation. More...
  void  SetPartial (CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)   void  TrimSeqFeat (CRef< CSeq_feat > feat, const TCuts &sorted_cuts, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &partial_start, bool &partial_stop)   Trim Seq-feat annotation. More...
  void  DeleteProteinAndRenormalizeNucProtSet (const CSeq_feat_Handle &feat_h)   Secondary function needed after trimming Seq-feat. More...
  void  AdjustCdregionFrame (TSeqPos original_nuc_len, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)   Secondary function needed after trimming Seq-feat. More...
  CRef< CBioseq >  SetNewProteinSequence (CScope &new_scope, CRef< CSeq_feat > cds, CRef< CSeq_inst > new_inst)   Secondary function needed after trimming Seq-feat. More...
  void  RetranslateCdregion (CBioseq_Handle nuc_bsh, bool isPartialStart, bool isPartialStop, CRef< CSeq_inst > trimmed_nuc_inst, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)   Secondary function needed after trimming Seq-feat. More...
  CRef< CSeqdesc >  FindUnverified (const CBioseq &seq)   bool  IsUnverifiedOrganism (const CBioseq &seq)   bool  IsUnverifiedFeature (const CBioseq &seq)   bool  IsUnverifiedMisassembled (const CBioseq &seq)   bool  IsUnverifiedContaminant (const CBioseq &seq)   void  SortSeqDescr (CSeq_descr &descr)   void  SortSeqDescr (CSeq_entry &entry)   const string &  GetTargetedLocusName (const CGene_ref &gene)   const string &  GetTargetedLocusName (const CProt_ref &prot)   string  GetTargetedLocusName (const CRNA_ref &rna)   string  GetTargetedLocusName (const CSeq_feat &feat)   string  GetTargetedLocusName (const CSeq_feat &cds, CScope &scope)   string  GenerateTargetedLocusName (CBioseq_Handle seq)   void  SetTargetedLocusName (CBioseq_Handle seq, const string &tls)   string  GetTargetedLocusNameConsensus (const string &tls1, const string &tls2)   ◆ TAlignVec ◆ TMapDescendentToInputEntry ◆ TMapEntryToAlignVec ◆ TMapSeqAnnotToDest ◆ TVecOfSeqAnnotsToErase ◆ AddBioseqToBioseq() ◆ AddBioseqToBioseqSet()

Add a Bioseq to a Bioseq-set.

This function will add the Bioseq to the set if: 1. The set is of class 'parts' and the Bioseq has the same molecular type as the other parts. 2.

Parameters
bsst Bioseq to change seq Bioseq to add
See also
AddSeqEntryToSeqEntry()

Definition at line 469 of file seq_entry_edit.cpp.

References CBioseq_set_Base::eClass_conset, CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_equiv, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_gi, CBioseq_set_Base::eClass_gibb, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_other, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_pdb_entry, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pir, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_pub_set, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::eClass_swissprot, CBioseq_set_Base::eClass_wgs_set, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetEditHandle(), CBioseq_EditHandle::MoveTo(), s_AddBioseqToNucProtSet(), s_AddBioseqToPartsSet(), and s_AddBioseqToSegset().

Referenced by AddSeqEntryToSeqEntry().

◆ AddLinkageEvidence() ◆ AddLocalIdUserObjects()

Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID.

Definition at line 1583 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CUser_object_Base::IsSetData(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), ITERATE, MakeOriginalIdField(), NON_CONST_ITERATE, CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetUser().

Referenced by BOOST_AUTO_TEST_CASE(), HandleCollidingIds(), and TestCollidingAccessionFixes().

◆ AddSeqdescToBioseq() ◆ AddSeqdescToBioseqSet() ◆ AddSeqdescToSeqDescr() ◆ AddSeqdescToSeqEntryRecursively()

Definition at line 565 of file seq_entry_edit.cpp.

References AddSeqdescToBioseq(), AddSeqdescToBioseqSet(), CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::GetClass(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::IsSetSeq_set(), NON_CONST_ITERATE, CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by SeqEntryFromSeqSubmit().

◆ AddSeqEntryToSeqEntry() ◆ AdjustCdregionFrame()

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then adjust cdregion frame.

Definition at line 3214 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::CanGetLocation(), eExtreme_Biological, eNa_strand_minus, eNa_strand_unknown, CSeqFeatData::eSubtype_cdregion, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), and CSeq_feat_Base::SetData().

◆ BioseqSetDescriptorPropagateDown()

Moves descriptors down to children of the given bioseq-set.

Each child gets a copy of all the descriptors. It does NOT check for duplicate Seqdescs.

Parameters
bioseq_set_h This is the bioseq_set whose descriptors we're moving. choices_to_delete If non-empty, it indicates the types of CSeqdescs to delete instead of propagating.

Definition at line 1447 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::AddDescr(), CSeqdesc_Base::e_not_set, CSeq_entry_CI::eNonRecursive, CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_set_Handle::GetParentEntry(), CBioseq_set_EditHandle::ResetDescr(), SerialClone(), CSeq_descr_Base::Set(), and CSeqdesc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and s_PromoteSingletonSetsInSet().

◆ BioseqSetDescriptorPropagateUp()

Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the descriptor.

It does NOT check for duplicate Seqdescs. Will not move molinfo, title, or source descriptors.

Parameters
bioseq_set_h This is the bioseq_set whose descriptors we're moving.

Definition at line 1368 of file seq_entry_edit.cpp.

References CBioseq_set_EditHandle::AddSeqdesc(), CSerialObject::Assign(), first(), CSeq_descr_Base::Get(), CBioseq_set_Base::GetSeq_set(), CSeq_descr_Base::IsSet(), ITERATE, CBioseq_EditHandle::RemoveSeqdesc(), CBioseq_set_EditHandle::RemoveSeqdesc(), CSeq_descr_Base::Reset(), CSeq_descr_Base::Set(), CBioseq_EditHandle::SetDescr(), and CBioseq_set_EditHandle::SetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ConvertRawToDeltaByNs() [1/2] void ConvertRawToDeltaByNs ( CBioseq_Handle  bsh, size_t  min_unknown, int  max_unknown, size_t  min_known, int  max_known, bool  is_assembly_gap, int  gap_type, int  linkage, int  linkage_evidence  )

Definition at line 1944 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), ConvertRawToDeltaByNs(), f, FeatureAdjustForInsert(), FeatureAdjustForTrim(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), NormalizeUnknownLengthGaps(), CSeq_feat_EditHandle::Remove(), CSeq_feat_EditHandle::Replace(), and CBioseq_EditHandle::SetInst().

◆ ConvertRawToDeltaByNs() [2/2] void ConvertRawToDeltaByNs ( CSeq_inst &  inst, size_t  min_unknown, int  max_unknown, size_t  min_known, int  max_known, bool  is_assembly_gap, int  gap_type, int  linkage, int  linkage_evidence  )

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to determine the gap location.

The size of the run of Ns determines whether a gap should be created and whether the gap should be of type known or unknown. Note that if the ranges overlap, unknown gaps will be preferred (allowing the user to create known length gaps for 20-forever, but unknown length gaps for 100, for example). Use a negative number for a maximum to indicate that there is no upper limit.

Parameters
inst The Seq-inst to adjust min_unknown The minimum number of Ns to be converted to a gap of unknown length max_unknown The maximum number of Ns to be converted to a gap of unknown length min_known The minimum number of Ns to be converted to a gap of known length max_known The maximum number of Ns to be converted to a gap of known length
Returns
none

Definition at line 1804 of file seq_entry_edit.cpp.

References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi8na, CSeqUtil::e_Ncbi8na, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacna(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbi2na(), CSeq_data_Base::GetNcbi4na(), CSeq_data_Base::GetNcbi8na(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::GetSeq_data(), CSeq_inst_Base::IsSetRepr(), CSeq_inst_Base::IsSetSeq_data(), ITERATE, CSeq_inst_Base::ResetSeq_data(), s_AddGap(), s_AddLiteral(), CSeq_inst_Base::SetRepr(), and CSeq_data_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

◆ DeleteProteinAndRenormalizeNucProtSet()

Secondary function needed after trimming Seq-feat.

If the trim completely covers the feature (boolean reference bFeatureDeleted from TrimSeqFeat() returns true), then delete protein sequence and re-normalize nuc-prot set.

Definition at line 3171 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::ConvertSetToSeq(), CSeqFeatData_Base::e_Cdregion, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetBioseq_setCore(), CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_feat_Handle::GetData(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CMappedFeat::GetProduct(), CSeq_feat_Handle::GetScope(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Handle::IsEmptySeq_set(), CBioseq_Handle::IsProtein(), CBioseq_Handle::IsRemoved(), CBioseq_set_Handle::IsSetClass(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Handle::IsSetProduct(), CBioseq_EditHandle::Remove(), CSeq_feat_EditHandle::Remove(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

◆ DivvyUpAlignments()

Call this if the alignments directly under these seq-entries are all jumbled up between each other.

It will move each Seq-align into the proper location. In particular, it looks at all the seq-ids in each seq-align. If none of them belong to any member of vecOfSeqEntryHandles, then that Seq-align is copied to all members of vecOfSeqEntryHandles. If it belongs to only one member of vecOfSeqEntryHandles, then it goes there. If the align belongs to more than one, it's destroyed.

Parameters
vecOfSeqEntryHandles The Seq-entries we're considering for alignments.

Definition at line 1304 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachAnnot(), CSeq_entry_CI::eRecursive, CSeq_annot_CI::eSearch_entry, CSeq_entry_Handle::GetEditHandle(), ITERATE, and s_DivvyUpAlignments_ProcessAnnot().

Referenced by SegregateSetsByBioseqList().

◆ Does3primerAbutGap() ◆ Does5primerAbutGap() ◆ FindUnverified() ◆ GenerateTargetedLocusName() ◆ GetDeltaSeqForPosition()

Definition at line 197 of file seq_entry_edit.cpp.

References CSeq_inst_Base::CanGetExt(), CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Repr(), GetLength(), CSeq_ext_Base::IsDelta(), CBioseq_Handle::IsNa(), CBioseq_Handle::IsSetInst_Repr(), ITERATE, len, and offset.

◆ GetSortedCuts() ◆ GetTargetedLocusName() [1/5] ◆ GetTargetedLocusName() [2/5] ◆ GetTargetedLocusName() [3/5] ◆ GetTargetedLocusName() [4/5] ◆ GetTargetedLocusName() [5/5]

Definition at line 3558 of file seq_entry_edit.cpp.

References CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, NStr::EqualNocase(), CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mobile_element, NStr::Find(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeqFeatData_Base::GetProt(), CSeq_feat_Base::GetQual(), CSeqFeatData_Base::GetRna(), CSeqFeatData::GetSubtype(), GetTargetedLocusName(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetQual(), NStr::TruncateSpacesInPlace(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetTargetedLocusNameConsensus() ◆ HandleCollidingIds() ◆ HasRepairedIDs() [1/2]

Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID User-object descriptor.

Definition at line 1683 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), HasRepairedIDs(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_Base::IsSetId(), CBioseq_set_Base::IsSetSeq_set(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE(), s_CollidedIds(), and TestCollidingAccessionFixes().

◆ HasRepairedIDs() [2/2] ◆ IsDeltaSeqGap() ◆ IsMatchingIdMissing()

Definition at line 1620 of file seq_entry_edit.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, NStr::Equal(), expected, CUser_field_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), NStr::IsBlank(), CUser_field_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), ITERATE, MakeOriginalLabelForId(), NStr::StartsWith(), and TypeFromLabel().

Referenced by HasRepairedIDs().

◆ IsSeqDescInList() ◆ IsUnverifiedContaminant() ◆ IsUnverifiedFeature() ◆ IsUnverifiedMisassembled() ◆ IsUnverifiedOrganism() ◆ LabelFromType() ◆ MakeOriginalIdField() ◆ MakeOriginalLabelForId() ◆ NormalizeUnknownLengthGaps()

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific length (100 by default).

Parameters
inst The Seq-inst to adjust
Returns
A vector of the adjustments to the sequence, which can be used to fix the locations of features on the sequence.

Definition at line 1907 of file seq_entry_edit.cpp.

References CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetRepr(), NON_CONST_ITERATE, CSeq_inst_Base::SetExt(), and CSeq_inst_Base::SetLength().

Referenced by CRawSeqToDeltaSeqByLoc::apply_impl(), BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

◆ RemoveUserObjectType()

Removes User-object descriptors of a certain type from the seq-entry.

Definition at line 1711 of file seq_entry_edit.cpp.

References EDIT_EACH_SEQDESC_ON_BIOSEQ, EDIT_EACH_SEQDESC_ON_SEQSET, ERASE_SEQDESC_ON_BIOSEQ, ERASE_SEQDESC_ON_SEQSET, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_Base::ResetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by BOOST_AUTO_TEST_CASE(), and HandleCollidingIds().

◆ ResetLinkageEvidence() void ResetLinkageEvidence ( CSeq_ext &  ext ) ◆ RetranslateCdregion()

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then retranslate cdregion.

Definition at line 3304 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, eExtreme_Biological, eNa_strand_unknown, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_loc_Base::GetInt(), CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetScope(), CSeq_loc::GetStrand(), CSeq_loc_Base::IsInt(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_EditHandle::Replace(), CMolInfo_Base::SetBiomol(), CMolInfo_Base::SetCompleteness(), CBioseq_EditHandle::SetDescr(), CBioseq_EditHandle::SetInst(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), SetNewProteinSequence(), SetPartial(), and CSeqFeatData_Base::Which().

Referenced by TrimSequenceAndAnnotation().

◆ s_AddBioseqToBioseq()

Definition at line 384 of file seq_entry_edit.cpp.

References _ASSERT, CSeq_entry_EditHandle::AttachBioseq(), CSeq_entry_EditHandle::ConvertSeqToSet(), CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CSeq_inst_Base::eRepr_seg, CBioseq_Handle::GetInst_Length(), CBioseq_Handle::GetInst_Mol(), CBioseq_EditHandle::GetParentEntry(), CSeq_entry_Handle::IsSet(), s_AddPartToSegmentedBioseq(), s_MakeUniqueLocalId(), CBioseq_Base::SetId(), CBioseq_EditHandle::SetInst_Length(), CBioseq_EditHandle::SetInst_Mol(), CBioseq_EditHandle::SetInst_Repr(), and CSeq_entry_EditHandle::TakeBioseq().

Referenced by AddBioseqToBioseq().

◆ s_AddBioseqToNucProtSet() ◆ s_AddBioseqToPartsSet() ◆ s_AddBioseqToSegset() ◆ s_AddGap() ◆ s_AddLiteral() ◆ s_AddPartToSegmentedBioseq()

Definition at line 286 of file seq_entry_edit.cpp.

References _ASSERT, CBioseq_Handle::CanGetInst_Ext(), copy(), CSeq_inst_Base::eRepr_seg, CSeg_ext_Base::Get(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Repr(), CSeq_ext_Base::GetSeg(), CBioseq_Handle::GetSeqId(), CSeg_ext_Base::Set(), CBioseq_EditHandle::SetInst_Ext(), CSeq_ext_Base::SetSeg(), and CSeq_loc::SetWhole().

Referenced by s_AddBioseqToBioseq(), and s_AddBioseqToSegset().

◆ s_AddProtToNuc() ◆ s_AdjustInternalCutLocations() ◆ s_BasicValidation() ◆ s_CutDensegSegment()

Definition at line 2886 of file seq_entry_edit.cpp.

References eNa_strand_minus, CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CDense_seg_Base::IsSetStrands(), ITERATE, row, s_FindSegment(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and si.

Referenced by TrimSeqAlign().

◆ s_DivvyUpAlignments_ProcessAnnot()

Definition at line 1202 of file seq_entry_edit.cpp.

References _ASSERT, CSerialObject::Assign(), CSeq_annot_Handle::GetCompleteSeq_annot(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_annot_Handle::GetParentEntry(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CAlign_CI::GetSeq_align_Handle(), CSeq_annot_Handle::IsAlign(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), ITERATE, RAW_FIELD_IS_EMPTY, s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), and CSeq_annot_Base::SetData().

Referenced by DivvyUpAlignments().

◆ s_DivvyUpAlignments_ProcessAnnot_Dendiag()

Definition at line 1000 of file seq_entry_edit.cpp.

References _ASSERT, CSerialObject::Assign(), map_checker< Container >::end(), FIELD_EQUALS, map_checker< Container >::find(), CSeq_align_Handle::GetAnnot(), CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDendiag(), CBioseq_Handle::GetParentEntry(), CSeq_annot_Handle::GetParentEntry(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), ITERATE, NON_CONST_ITERATE, CSeq_align_Base::ResetSegs(), and CSeq_align_Base::SetSegs().

Referenced by s_DivvyUpAlignments_ProcessAnnot().

◆ s_DivvyUpAlignments_ProcessAnnot_Denseg()

Definition at line 1123 of file seq_entry_edit.cpp.

References _ASSERT, CSerialObject::Assign(), map_checker< Container >::end(), CDense_seg::ExtractRows(), map_checker< Container >::find(), CSeq_align_Handle::GetAnnot(), CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetIds(), CBioseq_Handle::GetParentEntry(), CSeq_annot_Handle::GetParentEntry(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), ITERATE, and CSeq_align_Base::SetSegs().

Referenced by s_DivvyUpAlignments_ProcessAnnot().

◆ s_FindSegment() ◆ s_GetRetainedRange() ◆ s_GetTrimCoordinates() ◆ s_IsSingletonSet() ◆ s_MakeGroupsForUniqueValues()

Definition at line 758 of file seq_entry_edit.cpp.

References _ASSERT, CBioseq_set_EditHandle::AddSeq_descr(), CBioseq_set_EditHandle::AddSeqdesc(), CBioseq_set_EditHandle::AttachAnnot(), CBioseq_set_EditHandle::AttachEntry(), CSeqdesc_Base::e_not_set, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_not_set, CBioseq_set_Base::eClass_nuc_prot, set< Key, Compare >::end(), CSeq_entry_CI::eNonRecursive, CSeq_annot_CI::eSearch_entry, FIELD_EQUALS, set< Key, Compare >::find(), CBioseq_set_Handle::GetClass(), CSeq_annot_Handle::GetCompleteSeq_annot(), CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::HasParentEntry(), set< Key, Compare >::insert(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), ITERATE, CBioseq_set_EditHandle::ResetDescr(), s_PromoteSingletonSetsInSet(), SerialClone(), CBioseq_set_EditHandle::SetClass(), CBioseq_set_Base::SetClass(), CSeq_entry_Base::SetSet(), and CBioseq_set_EditHandle::TakeEntry().

Referenced by SegregateSetsByBioseqList().

◆ s_MakeUniqueLocalId() ◆ s_MergeCuts() ◆ s_PromoteSingletonSetsInSet()

Definition at line 652 of file seq_entry_edit.cpp.

References _ASSERT, BioseqSetDescriptorPropagateDown(), CSeq_entry_Base::e_Set, CSeqdesc_Base::e_Title, CSeq_entry_CI::eNonRecursive, CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_set_EditHandle::GetParentEntry(), CBioseq_set_Handle::GetSeq_entry_Index(), CSeq_entry_Handle::GetSet(), ITERATE, s_IsSingletonSet(), CSeq_entry_EditHandle::TakeAllAnnots(), and CBioseq_set_EditHandle::TakeEntry().

Referenced by s_MakeGroupsForUniqueValues().

◆ s_SeqIntervalDelete() ◆ s_SeqLocDelete()

Definition at line 2691 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), s_SeqIntervalDelete(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), and CSeq_loc_Base::Which().

Referenced by s_UpdateSeqGraphLoc(), and TrimSeqFeat().

◆ s_UpdateSeqGraphLoc() ◆ SegregateSetsByBioseqList() ◆ SeqEntryFromSeqSubmit()

Create a Seq-entry from a Seq-submit.

Parameters
submit Seq-submit to create Seq-entry from

Definition at line 591 of file seq_entry_edit.cpp.

References AddSeqdescToBioseq(), AddSeqdescToSeqEntryRecursively(), CSerialObject::Assign(), CBioseq_set_Base::eClass_genbank, CSubmit_block_Base::GetCit(), CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CSeq_submit_Base::GetSub(), CSeq_submit::IsEntrys(), CSeq_entry_Base::IsSeq(), CSubmit_block_Base::IsSetCit(), CSeq_submit_Base::IsSetSub(), ITERATE, CBioseq_set_Base::SetClass(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CPub_Base::SetSub().

Referenced by BOOST_AUTO_TEST_CASE(), CLocalFileRestorer::x_AttachNewObject(), CUpdateSeq_Input::x_ReadUpdateSeq_ASN(), and CUpdateMultipleSeq_Input::x_ReadUpdateSeqs_ASN().

◆ SetLinkageType() ◆ SetLinkageTypeLinkedRepeat() ◆ SetLinkageTypeScaffold() ◆ SetNewProteinSequence()

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then make new protein sequence.

Definition at line 3274 of file seq_entry_edit.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbieaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetSeq_data(), and CSeqTranslator::TranslateToProtein().

Referenced by RetranslateCdregion().

◆ SetPartial() ◆ SetTargetedLocusName()

Definition at line 3653 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CUser_object::eObjectType_AutodefOptions, CBioseq_Handle::GetCompleteBioseq(), CAutoDefOptions::InitFromUserObject(), CBioseq_Base::IsSetDescr(), CAutoDefOptions::MakeUserObject(), NON_CONST_ITERATE, CBioseq_EditHandle::SetDescr(), CAutoDefOptions::SetTargetedLocusName(), and CSeqdesc_Base::SetUser().

Referenced by CTLSContigHandler::ProcessBioseq(), and CTLSMasterHandler::ProcessBioseq().

◆ SortSeqDescr() [1/2] ◆ SortSeqDescr() [2/2] ◆ TrimSeqAlign()

Trim Seq-align annotation.

Definition at line 3032 of file seq_entry_edit.cpp.

References CDense_seg_Base::CanGetDim(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CBioseq_Handle::GetSeqId(), CDense_seg_Base::GetStarts(), CRange_Base::GetTo(), row, s_CutDensegSegment(), and CSeq_align_Base::SetSegs().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

◆ TrimSeqData()

Trim sequence data.

Definition at line 2498 of file seq_entry_edit.cpp.

References CScope::AddBioseq(), CSerialObject::Assign(), eNa_strand_plus, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqData, CSeqMap::fFindAny, CSeqMap::fIgnoreUnresolved, CBioseq_Handle::GetCompleteBioseq(), CSeq_inst_Base::GetLength(), CBioseq_Handle::GetScope(), CSeq_entry_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTopLevelEntry(), CSeqMap_CI::GetType(), CBioseq_Handle::IsNucleotide(), CScope::RemoveBioseq(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), and UpdateSeqLength().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

◆ TrimSeqFeat()

Trim Seq-feat annotation.

Definition at line 3114 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetLocation(), CSeq_feat_Base::CanGetProduct(), eExtreme_Positional, eNa_strand_unknown, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), GetStart(), GetStop(), CSeq_loc::GetStrand(), s_SeqLocDelete(), CSeq_feat_Base::SetLocation(), SetPartial(), and CSeq_feat_Base::SetProduct().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

◆ TrimSeqGraph()

Trim Seq-graph annotation.

Definition at line 2815 of file seq_entry_edit.cpp.

References eExtreme_Positional, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CByte_graph_Base::GetValues(), CSeq_graph_Base::C_Graph::IsByte(), s_GetTrimCoordinates(), s_UpdateSeqGraphLoc(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetNumval(), and CByte_graph_Base::SetValues().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

◆ TrimSequenceAndAnnotation()

Implementation detail: first trim all associated annotation, then trim sequence data.

Trim sequence data and all associated annotation.

Definition at line 2147 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CDense_seg_Base::CanGetDim(), CDense_seg_Base::CanGetIds(), CSeq_inst_Base::CanGetLength(), CDense_seg_Base::CanGetLens(), CDense_seg_Base::CanGetNumseg(), CSeq_align_Base::CanGetSegs(), CDense_seg_Base::CanGetStarts(), NStr::CompareNocase(), DeleteProteinAndRenormalizeNucProtSet(), CSeq_annot_Base::C_Data::e_Align, CSeqFeatData_Base::e_Cdregion, CSeq_align_Base::C_Segs::e_Denseg, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CCdregion_Base::eFrame_not_set, CSeq_feat_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_inst_Base::GetLength(), CMappedFeat::GetOriginalFeature(), CMappedGraph::GetOriginalGraph(), CAlign_CI::GetOriginalSeq_align(), CSeq_align_Base::GetSegs(), CAlign_CI::GetSeq_align_Handle(), CMappedGraph::GetSeq_graph_Handle(), GetSortedCuts(), CMappedGraph::GetTitle(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CMappedGraph::IsSetTitle(), CSeq_align_Handle::Replace(), CSeq_feat_EditHandle::Replace(), CSeq_graph_Handle::Replace(), RetranslateCdregion(), s_BasicValidation(), s_GetRetainedRange(), CSeq_feat_Base::SetData(), CBioseq_EditHandle::SetInst(), TrimSeqAlign(), TrimSeqData(), TrimSeqFeat(), TrimSeqGraph(), CSeq_align_Base::C_Segs::Which(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

◆ TypeFromLabel() ◆ UpdateSeqLength()

Update sequence length.

Definition at line 2449 of file seq_entry_edit.cpp.

References CBioseq_Handle::eCoding_Iupac, CInt_fuzz_Base::eLim_unk, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap_CI::GetEndPosition(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefGapLiteral(), CSeqVector::GetSeqData(), CSeqMap_CI::GetType(), CSeqMap_CI::IsUnknownLength(), CSeqportUtil::Pack(), Ref(), CAutoInitRef< T >::Set(), CAliasBase< TPrim >::Set(), and CSeq_data_Base::SetIupacna().

Referenced by TrimSeqData().

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