NCBI C++ ToolKit
Functions | Variables
sequpd.cpp File Reference
#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_ids_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()

static void s_FixCollidingIDs_Annot ( CBioseq bseq,
CSeq_entry::TAnnot annot,
const vector< CRef< CSeq_id >> &  upd_ids 
)
static

◆ s_GetMatchingSequence()

static CBioseq_Handle s_GetMatchingSequence ( CSeq_inst::EMol  type,
CSeq_entry_Handle oldSeq,
const CBioseq upd_bseq,
bool collide,
const sequpd::TSeqIdHMap matches 
)
static

◆ s_GetOriginalId()

static CConstRef< CSeq_id > s_GetOriginalId ( const CBioseq_Handle bsh)
static

◆ s_MatchSeqIds()

static bool s_MatchSeqIds ( CScope scope,
const CSeq_id old_id,
const CSeq_id upd_id,
bool collide 
)
static

◆ s_RunBlast2AASeq()

static vector< CConstRef< CSeq_align > > s_RunBlast2AASeq ( const CBioseq_Handle sh,
const CBioseq_Handle qh 
)
static

◆ s_RunBlast2NASeq()

static vector< CConstRef< CSeq_align > > s_RunBlast2NASeq ( const CBioseq_Handle sh,
const CBioseq_Handle qh,
bool  accept_atleast_one,
ICanceled canceled 
)
static

◆ s_RunBlast2NWSeq()

static vector< CConstRef< CSeq_align > > s_RunBlast2NWSeq ( const CBioseq_Handle sh,
const CBioseq_Handle qh 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kUpdateSuffix

const char* kUpdateSuffix = "_update"
static

Definition at line 137 of file sequpd.cpp.

Referenced by sequpd::FixCollidingIDs_Bioseq().

Modified on Sat May 18 11:35:37 2024 by modify_doxy.py rev. 669887