#include <ncbi_pch.hpp>#include <gui/packages/pkg_sequence_edit/sequpd.hpp>#include <gui/packages/pkg_sequence_edit/sequpd_except.hpp>#include <objects/general/User_object.hpp>#include <objects/general/User_field.hpp>#include <objects/general/Object_id.hpp>#include <objects/seqalign/Seq_align_set.hpp>#include <serial/iterator.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/seqdesc_ci.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/impl/synonyms.hpp>#include <objmgr/scope.hpp>#include <objmgr/seq_vector.hpp>#include <algo/align/ngalign/ngalign.hpp>#include <algo/align/ngalign/sequence_set.hpp>#include <algo/align/ngalign/merge_aligner.hpp>#include <algo/align/ngalign/blast_aligner.hpp>#include <algo/align/ngalign/alignment_scorer.hpp>#include <algo/align/ngalign/alignment_filterer.hpp>#include <algo/align/nw/nw_aligner.hpp>#include <algo/align/nw/nw_formatter.hpp>#include <algo/blast/api/blast_prot_options.hpp>
Include dependency graph for sequpd.cpp:
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Functions | |
| USING_SCOPE (objects) | |
| static void | s_FixCollidingIDs_Annot (CBioseq &bseq, CSeq_entry::TAnnot &annot, const vector< CRef< CSeq_id >> &upd_ids) |
| static CBioseq_Handle | s_GetMatchingSequence (CSeq_inst::EMol type, CSeq_entry_Handle &oldSeq, const CBioseq &upd_bseq, bool &collide, const sequpd::TSeqIdHMap &matches) |
| static bool | s_MatchSeqIds (CScope &scope, const CSeq_id &old_id, const CSeq_id &upd_id, bool &collide) |
| static CConstRef< CSeq_id > | s_GetOriginalId (const CBioseq_Handle &bsh) |
| static vector< CConstRef< CSeq_align > > | s_RunBlast2NASeq (const CBioseq_Handle &sh, const CBioseq_Handle &qh, bool accept_atleast_one, ICanceled *canceled) |
| static vector< CConstRef< CSeq_align > > | s_RunBlast2NWSeq (const CBioseq_Handle &sh, const CBioseq_Handle &qh) |
| static vector< CConstRef< CSeq_align > > | s_RunBlast2AASeq (const CBioseq_Handle &sh, const CBioseq_Handle &qh) |
Variables | |
| static const char * | kUpdateSuffix = "_update" |
Function Documentation
◆ s_FixCollidingIDs_Annot()
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static |
Definition at line 121 of file sequpd.cpp.
References CSeq_id::Assign(), Compare(), CSeq_id::e_YES, CBioseq_Base::GetId(), and NON_CONST_ITERATE.
Referenced by sequpd::FixCollidingIDs_Bioseq().
◆ s_GetMatchingSequence()
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Definition at line 264 of file sequpd.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), sequpd::GetGoodSeqIdHandle(), CBioseq_Base::GetId(), CSeq_entry_Handle::GetScope(), CBioseq_Base::IsSetId(), and s_MatchSeqIds().
Referenced by sequpd::FindMatches().
◆ s_GetOriginalId()
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Definition at line 320 of file sequpd.cpp.
References CSeq_id_Base::e_Local, CSeqdesc_Base::e_User, CUser_object::eObjectType_OriginalId, NStr::EqualNocase(), CUser_object_Base::GetData(), CBioseq_Handle::GetLocalIdOrNull(), CUser_object::GetObjectType(), CBioseq_Handle::IsAa(), ITERATE, and CConstRef< C, Locker >::Reset().
Referenced by s_MatchSeqIds().
◆ s_MatchSeqIds()
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Definition at line 286 of file sequpd.cpp.
References CSeq_id::Compare(), CSeq_id::e_DIFF, CSeq_id::e_NO, CSeq_id::e_YES, CSeq_id::eContent, NStr::EqualCase(), NStr::Find(), CScope::GetBioseqHandle(), CSeq_id::GetLabel(), CSeq_id_Base::IsLocal(), kEmptyStr, NPOS, and s_GetOriginalId().
Referenced by s_GetMatchingSequence().
◆ s_RunBlast2AASeq()
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Definition at line 576 of file sequpd.cpp.
References eNa_strand_plus, ERR_POST, Error(), CRef< C, Locker >::GetPointerOrNull(), CBioseq_Handle::GetRangeSeq_loc(), CBioseq_Handle::GetScope(), ITERATE, NCBI_THROW, query, and subject.
◆ s_RunBlast2NASeq()
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Definition at line 452 of file sequpd.cpp.
References CNgAligner::AddAligner(), CNgAligner::AddFilter(), CNgAligner::AddScorer(), CNgAligner::Align(), Error(), CBlastScorer::eSkipUnsupportedAlignments, CMergeAligner::eTreeAlignMerger, CSeq_align_set_Base::Get(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetRangeSeq_loc(), CBioseq_Handle::GetScope(), CRef< C, Locker >::IsNull(), CSeq_align_set_Base::IsSet(), ITERATE, LOG_POST, prog, query, CNgAligner::SetQuery(), CNgAligner::SetSubject(), and subject.
Referenced by sequpd::RunBlast2Seq().
◆ s_RunBlast2NWSeq()
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Definition at line 548 of file sequpd.cpp.
References CNWFormatter::AsSeqAlign(), CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqVector(), NCBISM_Blosum62, CSeq_align_Base::SetSegs(), CSeqVector::size(), and NStr::ToUpper().
Referenced by sequpd::RunBlast2Seq().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ kUpdateSuffix
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static |
Definition at line 137 of file sequpd.cpp.
Referenced by sequpd::FixCollidingIDs_Bioseq().
