NCBI C++ ToolKit
Classes | Functions
feature_table_reader.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/object_manager.hpp>
#include <objtools/readers/readfeat.hpp>
#include <algo/sequence/orf.hpp>
#include <algo/align/prosplign/prosplign.hpp>
#include <algo/align/util/align_filter.hpp>
#include <objects/seqset/seqset_macros.hpp>
#include <objects/seq/seq_macros.hpp>
#include <algo/align/splign/compart_matching.hpp>
#include <algo/align/util/compartment_finder.hpp>
#include <objtools/readers/fasta.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/annot_selector.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objmgr/annot_ci.hpp>
#include <objtools/edit/gaps_edit.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/edit/feattable_edit.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objmgr/util/feature.hpp>
#include "feature_table_reader.hpp"
#include <objtools/cleanup/cleanup.hpp>
#include "async_token.hpp"
#include "table2asn_context.hpp"
#include "visitors.hpp"
#include "utils.hpp"
#include <common/test_assert.h>
#include <unordered_set>
+ Include dependency graph for feature_table_reader.cpp:

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Classes

struct  SCompareIds
 
struct  SRegionIterators
 

Functions

 USING_SCOPE (objects)
 
static void s_AppendProtRefInfo (CProt_ref &current_ref, const CProt_ref &other_ref)
 
static void s_SetProtRef (const CSeq_feat &cds, CConstRef< CSeq_feat > pMrna, CProt_ref &prot_ref)
 
static bool s_TranslateCds (const CSeq_feat &cds, CScope &scope)
 
static bool s_HasUnprocessedCdregions (const CSeq_entry &nuc_prot)
 
static void s_ReportDuplicateMods (const set< string > &duplicateMods, const string &idString, TSeqPos lineNumber, objects::ILineErrorListener &logger)
 
static CBioseq_Handle s_MatchProteinById (const CBioseq &protein, CSeq_entry_Handle seh)
 
static CBioseq_Handle s_GetSingleNucSeq (CSeq_entry_Handle seh)
 
static CRef< CSeq_locs_GetCDSLoc (CScope &scope, const CSeq_id &proteinId, const CSeq_loc &genomicLoc, TSeqPos bioseqLength, const CTable2AsnContext::SPrtAlnOptions &prtAlnOptions)
 
static CRef< CSeq_feats_MakeCDSFeat (CSeq_loc &loc, bool isPartial, CSeq_id &productId)
 
static bool s_UnknownEstimatedLength (const CSeq_feat &feat)
 
static const CSeq_ids_GetIdFromLocation (const CSeq_loc &loc)
 
static void s_GatherRegionIterators (list< CRef< CSeq_annot >> &annots, list< SRegionIterators > &its)
 
static bool s_MoveProteinSpecificFeats (CSeq_entry &entry)
 

Function Documentation

◆ s_AppendProtRefInfo()

static void s_AppendProtRefInfo ( CProt_ref current_ref,
const CProt_ref other_ref 
)
static

◆ s_GatherRegionIterators()

static void s_GatherRegionIterators ( list< CRef< CSeq_annot >> &  annots,
list< SRegionIterators > &  its 
)
static

Definition at line 1896 of file feature_table_reader.cpp.

References ftable.

Referenced by CFeatureTableReader::MoveRegionsToProteins().

◆ s_GetCDSLoc()

static CRef<CSeq_loc> s_GetCDSLoc ( CScope scope,
const CSeq_id proteinId,
const CSeq_loc genomicLoc,
TSeqPos  bioseqLength,
const CTable2AsnContext::SPrtAlnOptions prtAlnOptions 
)
static

◆ s_GetIdFromLocation()

static const CSeq_id* s_GetIdFromLocation ( const CSeq_loc loc)
static

◆ s_GetSingleNucSeq()

static CBioseq_Handle s_GetSingleNucSeq ( CSeq_entry_Handle  seh)
static

◆ s_HasUnprocessedCdregions()

static bool s_HasUnprocessedCdregions ( const CSeq_entry nuc_prot)
static

◆ s_MakeCDSFeat()

static CRef<CSeq_feat> s_MakeCDSFeat ( CSeq_loc loc,
bool  isPartial,
CSeq_id productId 
)
static

Definition at line 1518 of file feature_table_reader.cpp.

References Ref().

Referenced by CFeatureTableReader::xAddProteinToSeqEntry().

◆ s_MatchProteinById()

static CBioseq_Handle s_MatchProteinById ( const CBioseq protein,
CSeq_entry_Handle  seh 
)
static

◆ s_MoveProteinSpecificFeats()

static bool s_MoveProteinSpecificFeats ( CSeq_entry entry)
static

◆ s_ReportDuplicateMods()

static void s_ReportDuplicateMods ( const set< string > &  duplicateMods,
const string idString,
TSeqPos  lineNumber,
objects::ILineErrorListener &  logger 
)
static

◆ s_SetProtRef()

static void s_SetProtRef ( const CSeq_feat cds,
CConstRef< CSeq_feat pMrna,
CProt_ref prot_ref 
)
static

◆ s_TranslateCds()

static bool s_TranslateCds ( const CSeq_feat cds,
CScope scope 
)
static

◆ s_UnknownEstimatedLength()

static bool s_UnknownEstimatedLength ( const CSeq_feat feat)
static

Definition at line 1636 of file feature_table_reader.cpp.

References CSeq_feat::GetNamedQual().

Referenced by CFeatureTableReader::MakeGap().

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Wed Jul 17 13:17:59 2024 by modify_doxy.py rev. 669887