#include <ncbi_pch.hpp>#include <objmgr/scope.hpp>#include <objmgr/seqdesc_ci.hpp>#include <objects/seq/Seq_descr.hpp>#include <objects/seq/Bioseq.hpp>#include <serial/iterator.hpp>#include <objects/seq/MolInfo.hpp>#include <objtools/cleanup/cleanup.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/feat_ci.hpp>#include <objmgr/seq_entry_handle.hpp>#include <objmgr/util/sequence.hpp>#include <objmgr/util/feature.hpp>#include <objtools/edit/cds_fix.hpp>#include <objtools/flatfile/flatfile_parse_info.hpp>#include <objtools/flatfile/flatfile_parser.hpp>#include "utilfun.h"#include "loadfeat.h"#include "fcleanup.h"
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Macros | |
| #define | THIS_FILE "fcleanup.cpp" |
Functions | |
| USING_SCOPE (objects) | |
| static void | MoveSourceDescrToTop (CSeq_entry &entry) |
| static bool | IsEmptyMolInfo (const CMolInfo &mol_info) |
| static void | MoveAnnotToTop (CSeq_entry &seq_entry) |
| static void | MoveBiomolToTop (CSeq_entry &seq_entry) |
| static void | LookForProductName (CSeq_feat &feat) |
| static bool | IsConversionPossible (const vector< pair< TSeqPos, TSeqPos >> &ranges) |
| static void | SetNewInterval (const CSeq_interval *first, const CSeq_interval *last, const TSeqPos &from, TSeqPos &to, CSeq_loc &loc) |
| static void | ConvertMixToInterval (CSeq_loc &loc) |
| static void | ConvertPackedIntToInterval (CSeq_loc &loc) |
| void | g_InstantiateMissingProteins (CSeq_entry_Handle entryHandle) |
| void | FinalCleanup (TEntryList &seq_entries) |
Macro Definition Documentation
◆ THIS_FILE
| #define THIS_FILE "fcleanup.cpp" |
Definition at line 61 of file fcleanup.cpp.
Function Documentation
◆ ConvertMixToInterval()
Definition at line 274 of file fcleanup.cpp.
References eExtreme_Biological, CSeq_loc_mix_Base::Get(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetMix(), CSeq_point_Base::GetPoint(), CSeq_interval::GetStart(), CSeq_interval::GetStop(), CSeq_interval_Base::GetTo(), IsConversionPossible(), SetNewInterval(), and ct::sort().
Referenced by FinalCleanup().
◆ ConvertPackedIntToInterval()
Definition at line 318 of file fcleanup.cpp.
References eExtreme_Biological, CSeq_loc_Base::GetPacked_int(), CPacked_seqint::GetStartInt(), CPacked_seqint::GetStopInt(), IsConversionPossible(), SetNewInterval(), and ct::sort().
Referenced by FinalCleanup().
◆ FinalCleanup()
| void FinalCleanup | ( | TEntryList & | seq_entries | ) |
Definition at line 377 of file fcleanup.cpp.
References Begin(), cleanup(), ConvertMixToInterval(), ConvertPackedIntToInterval(), CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::GetBiomol(), CScope::GetBioseqHandle(), CSeq_loc::GetId(), CSeqdesc_Base::GetMolinfo(), GetScope(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CMolInfo_Base::IsSetBiomol(), CSeq_feat_Base::IsSetLocation(), LookForProductName(), MoveAnnotToTop(), MoveBiomolToTop(), MoveSourceDescrToTop(), CSeq_loc::SetId(), CSeq_feat_Base::SetLocation(), and CSeq_id_Base::Which().
Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().
◆ g_InstantiateMissingProteins()
| void g_InstantiateMissingProteins | ( | CSeq_entry_Handle | entryHandle | ) |
Definition at line 335 of file fcleanup.cpp.
References CCleanup::AddProtein(), AddProteinFeature(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData::eSubtype_prot, GetNewProtId(), CCleanup::GetProteinName(), CSeq_entry_Handle::GetScope(), NStr::IsBlank(), IsPseudo(), Ref(), and CSeq_feat_EditHandle::Replace().
Referenced by GenBankAsciiOrig().
◆ IsConversionPossible()
Definition at line 236 of file fcleanup.cpp.
References convert(), first(), and i.
Referenced by ConvertMixToInterval(), and ConvertPackedIntToInterval().
◆ IsEmptyMolInfo()
Definition at line 99 of file fcleanup.cpp.
References CMolInfo_Base::IsSetBiomol(), CMolInfo_Base::IsSetCompleteness(), CMolInfo_Base::IsSetGbmoltype(), CMolInfo_Base::IsSetTech(), and CMolInfo_Base::IsSetTechexp().
Referenced by MoveBiomolToTop().
◆ LookForProductName()
Definition at line 194 of file fcleanup.cpp.
References CSeq_feat_Base::GetData(), CProt_ref_Base::GetName(), CSeq_feat_Base::GetQual(), CSeqFeatData_Base::IsProt(), CSeq_feat_Base::IsSetData(), CProt_ref_Base::IsSetName(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::SetData(), CProt_ref_Base::SetName(), and CSeq_feat_Base::SetQual().
Referenced by FinalCleanup().
◆ MoveAnnotToTop()
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static |
Definition at line 105 of file fcleanup.cpp.
References CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::GetClass(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::ResetAnnot(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
Referenced by FinalCleanup().
◆ MoveBiomolToTop()
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static |
Definition at line 128 of file fcleanup.cpp.
References CMolInfo_Base::eBiomol_unknown, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CSeq_descr_Base::Get(), CBioseq_set_Base::GetClass(), CBioseq_Base::GetDescr(), CSeq_entry::GetDescr(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), IsEmptyMolInfo(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetClass(), CBioseq_Base::IsSetDescr(), CSeq_entry::IsSetDescr(), CMolInfo_Base::SetBiomol(), CSeq_entry::SetDescr(), CBioseq_Base::SetDescr(), CSeqdesc_Base::SetMolinfo(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
Referenced by FinalCleanup().
◆ MoveSourceDescrToTop()
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static |
Definition at line 66 of file fcleanup.cpp.
References Begin(), CSeq_descr_Base::Get(), CBioseq_set_Base::GetDescr(), CSeq_entry_Base::IsSeq(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::SetDescr(), CSeq_entry_Base::SetSet(), and rapidjson::source.
Referenced by FinalCleanup().
◆ SetNewInterval()
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static |
Definition at line 251 of file fcleanup.cpp.
References CSerialObject::Assign(), first(), last(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_loc::SetInt(), and CSeq_interval_Base::SetTo().
Referenced by ConvertMixToInterval(), and ConvertPackedIntToInterval().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
