NCBI C++ ToolKit
Classes | Macros | Enumerations | Functions
gather_items.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Linkage_evidence.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/annot_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/annot_selector.hpp>
#include <algorithm>
#include <objtools/format/item_ostream.hpp>
#include <objtools/format/flat_expt.hpp>
#include <objtools/format/items/contig_item.hpp>
#include <objtools/format/items/locus_item.hpp>
#include <objtools/format/items/defline_item.hpp>
#include <objtools/format/items/accession_item.hpp>
#include <objtools/format/items/version_item.hpp>
#include <objtools/format/items/keywords_item.hpp>
#include <objtools/format/items/source_item.hpp>
#include <objtools/format/items/reference_item.hpp>
#include <objtools/format/items/comment_item.hpp>
#include <objtools/format/items/basecount_item.hpp>
#include <objtools/format/items/sequence_item.hpp>
#include <objtools/format/items/feature_item.hpp>
#include <objtools/format/items/segment_item.hpp>
#include <objtools/format/items/ctrl_items.hpp>
#include <objtools/format/items/alignment_item.hpp>
#include <objtools/format/items/gap_item.hpp>
#include <objtools/format/items/html_anchor_item.hpp>
#include <objtools/format/gather_items.hpp>
#include <objtools/format/gather_iter.hpp>
#include <objtools/format/genbank_gather.hpp>
#include <objtools/format/embl_gather.hpp>
#include <objtools/format/ftable_gather.hpp>
#include <objtools/format/feature_gather.hpp>
#include <objtools/format/context.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/util/feature_edit.hpp>
#include <objmgr/util/objutil.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <connect/ncbi_socket.hpp>
+ Include dependency graph for gather_items.cpp:

Go to the source code of this file.

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Classes

class  CSubtypeEquals
 
class  CDbEquals
 
class  COrgModEquals
 
struct  SSortSourceByLoc
 
struct  SGapIdxData
 

Macros

#define NCBI_USE_ERRCODE_X   Objtools_Fmt_Gather
 

Enumerations

enum  EEndsOnBioseqOpt { eEndsOnBioseqOpt_LastPartOfSeqLoc = 1 , eEndsOnBioseqOpt_AnyPartOfSeqLoc }
 

Functions

 USING_SCOPE (sequence)
 
static bool s_LocationsTouch (const CSeq_loc &loc1, const CSeq_loc &loc2)
 
static bool s_LocationsOverlap (const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *p_scope)
 
static bool s_IsSegmented (const CBioseq_Handle &seq)
 
static bool s_HasSegments (const CBioseq_Handle &seq)
 
bool s_BioSeqHasContig (const CBioseq_Handle &seq, CFlatFileContext &ctx)
 
bool s_IsJustUids (const CPubdesc &pubdesc)
 
bool s_FilterPubdesc (const CPubdesc &pubdesc, CBioseqContext &ctx)
 
static bool s_IsCircularTopology (CBioseqContext &ctx)
 
static bool s_NsAreGaps (const CBioseq_Handle &seq, CBioseqContext &ctx)
 
bool s_HasRefTrackStatus (const CBioseq_Handle &bsh)
 
static bool s_GiInCSeq_hist_ids (const TGi gi, const CSeq_hist_rec_Base::TIds &ids)
 
static int s_StrucCommOrder (const string &str)
 
static bool s_SeqDescCompare (const CConstRef< CSeqdesc > &desc1, const CConstRef< CSeqdesc > &desc2)
 
static CConstRef< CSeq_loc > s_NormalizeNullsBetween (CConstRef< CSeq_loc > loc, bool force_adding_nulls=false)
 
void s_SetSelection (SAnnotSelector &sel, CBioseqContext &ctx)
 
static bool s_SeqLocEndsOnBioseq (const CSeq_loc &loc, CBioseqContext &ctx, EEndsOnBioseqOpt mode, CSeqFeatData::E_Choice feat_type)
 
static bool s_CopyCDSFromCDNA (CBioseqContext &ctx)
 
CSeqMap_CI s_CreateGapMapIter (const CSeq_loc &loc, CBioseqContext &ctx)
 
static CRef< CGapItem > s_NewGapItem (CSeqMap_CI &gap_it, CBioseqContext &ctx)
 
static CRef< CGapItem > s_NewGapItem (TSeqPos gap_start, TSeqPos gap_end, TSeqPos gap_length, const string &gap_type, const vector< string > &evidence, bool isUnknownLength, bool isAssemblyGap, CBioseqContext &ctx)
 
static bool s_IsDuplicateFeatures (const CSeq_feat_Handle &f1, const CSeq_feat_Handle &f2)
 
static string s_GetFeatDesc (const CSeq_feat_Handle &feat)
 
static void s_CleanCDDFeature (const CSeq_feat &feat)
 
bool s_CoincidingGapFeatures (CFeat_CI it, const TSeqPos gap_start, const TSeqPos gap_end)
 
static CMappedFeat s_GetMappedFeat (CRef< CSeq_feat > &feat, CScope &scope)
 
static CMappedFeat s_GetTrimmedMappedFeat (const CSeq_feat &feat, const CRange< TSeqPos > &range, CScope &scope)
 
static bool s_IsCDD (const CSeq_feat_Handle &feat)
 
static void s_SetGapIdxData (SGapIdxData &gapdat, const vector< CRef< CGapIndex >> &gaps)
 
CRef< CSeq_loc_Mapper > s_MakeSliceMapper (const CSeq_loc &loc, CBioseqContext &ctx)
 
static bool s_ContainsGaps (const CSeq_loc &loc)
 
SAnnotSelector s_GetCdsProductSel (CBioseqContext &ctx)
 
void s_FixIntervalProtToCds (const CSeq_feat &srcFeat, const CSeq_loc &srcLoc, CRef< CSeq_loc > pDestLoc)
 
static void s_GiveOneResidueIntervalsBogusFuzz_Helper (CSeq_interval &interval)
 
static void s_RemoveBogusFuzzFromIntervals_Helper (CSeq_interval &interval)
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Fmt_Gather

Definition at line 114 of file gather_items.cpp.

Enumeration Type Documentation

◆ EEndsOnBioseqOpt

enum EEndsOnBioseqOpt
Enumerator
eEndsOnBioseqOpt_LastPartOfSeqLoc 
eEndsOnBioseqOpt_AnyPartOfSeqLoc 

Definition at line 2548 of file gather_items.cpp.

Function Documentation

◆ s_BioSeqHasContig()

bool s_BioSeqHasContig ( const CBioseq_Handle &  seq,
CFlatFileContext &  ctx 
)

Definition at line 403 of file gather_items.cpp.

References ctx, CSeq_loc_Base::e_not_set, CContigItem::GetLoc(), and CSeq_loc_Base::Which().

Referenced by CFlatGatherer::x_GatherBioseq().

◆ s_CleanCDDFeature()

static void s_CleanCDDFeature ( const CSeq_feat &  feat)
static

Definition at line 2848 of file gather_items.cpp.

References NStr::Equal(), NStr::EqualNocase(), CSeqFeatData_Base::eSite_acetylation, CSeqFeatData_Base::eSite_active, CSeqFeatData_Base::eSite_binding, CSeqFeatData_Base::eSite_cleavage, CSeqFeatData_Base::eSite_dna_binding, CSeqFeatData_Base::eSite_glycosylation, CSeqFeatData_Base::eSite_inhibit, CSeqFeatData_Base::eSite_lipid_binding, CSeqFeatData_Base::eSite_metal_binding, CSeqFeatData_Base::eSite_modified, CSeqFeatData_Base::eSite_other, CSeqFeatData_Base::eSite_phosphorylation, f, NStr::FindNoCase(), first(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeq_feat::GetNamedDbxref(), CSeqFeatData_Base::GetRegion(), CSeqFeatData_Base::GetSite(), NStr::HtmlDecode(), i, CSeqFeatData_Base::IsRegion(), CSeq_feat_Base::IsSetComment(), CSeqFeatData_Base::IsSite(), sc_Pairs, and NStr::TruncateSpaces().

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_CoincidingGapFeatures()

bool s_CoincidingGapFeatures ( CFeat_CI  it,
const TSeqPos  gap_start,
const TSeqPos  gap_end 
)

Definition at line 2930 of file gather_items.cpp.

References eExtreme_Positional, CSeqFeatData::eSubtype_gap, CSeq_feat_Handle::GetFeatSubtype(), CMappedFeat::GetLocation(), CSeq_loc::GetStart(), and CSeq_loc::GetStop().

Referenced by CFlatGatherer::x_GatherFeaturesOnWholeLocation().

◆ s_ContainsGaps()

static bool s_ContainsGaps ( const CSeq_loc &  loc)
static

Definition at line 4036 of file gather_items.cpp.

References CSeq_loc_CI::eEmpty_Allow, and CSeq_loc_CI::IsEmpty().

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ s_CopyCDSFromCDNA()

static bool s_CopyCDSFromCDNA ( CBioseqContext &  ctx)
static

Definition at line 2702 of file gather_items.cpp.

References ctx.

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

◆ s_CreateGapMapIter()

CSeqMap_CI s_CreateGapMapIter ( const CSeq_loc &  loc,
CBioseqContext &  ctx 
)

Definition at line 2707 of file gather_items.cpp.

References CSeqMap::CreateSeqMapForSeq_loc(), ctx, ERR_POST_X, CSeqMap::fFindGap, SSeqMapSelector::SetFlags(), and SSeqMapSelector::SetResolveCount().

Referenced by CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

◆ s_FilterPubdesc()

bool s_FilterPubdesc ( const CPubdesc &  pubdesc,
CBioseqContext &  ctx 
)

Definition at line 566 of file gather_items.cpp.

References CPubdesc_Base::CanGetComment(), ctx, NStr::eNocase, CPubdesc_Base::GetComment(), CFlatFileConfig::HideGeneRIFs(), CFlatFileConfig::LatestGeneRIFs(), CFlatFileConfig::OnlyGeneRIFs(), s_IsJustUids(), and NStr::StartsWith().

Referenced by CFlatGatherer::x_GatherCDSReferences(), and CFlatGatherer::x_GatherReferences().

◆ s_FixIntervalProtToCds()

void s_FixIntervalProtToCds ( const CSeq_feat &  srcFeat,
const CSeq_loc &  srcLoc,
CRef< CSeq_loc >  pDestLoc 
)

Definition at line 4350 of file gather_items.cpp.

References CSerialObject::Assign(), CCdregion_Base::CanGetFrame(), CSeq_interval_Base::CanGetFuzz_from(), CSeq_interval_Base::CanGetFuzz_to(), CSeq_interval_Base::CanGetStrand(), CCdregion_Base::eFrame_not_set, eNa_strand_minus, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_id_Handle::GetHandle(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_loc::SetInt(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().

◆ s_GetCdsProductSel()

SAnnotSelector s_GetCdsProductSel ( CBioseqContext &  ctx)

Definition at line 4335 of file gather_items.cpp.

References ctx, CSeqFeatData::eSubtype_bond, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_propeptide_aa, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_sig_peptide_aa, CSeqFeatData::eSubtype_site, CSeqFeatData::eSubtype_transit_peptide_aa, SAnnotSelector::IncludeFeatSubtype(), and SAnnotSelector::SetFeatSubtype().

Referenced by CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_GetFeatDesc()

static string s_GetFeatDesc ( const CSeq_feat_Handle &  feat)
static

Definition at line 2832 of file gather_items.cpp.

References fFGL_Both, GetLabel(), CSeq_loc::GetLabel(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetScope(), CSeq_feat_Handle::GetSeq_feat(), and NPOS.

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

◆ s_GetMappedFeat()

static CMappedFeat s_GetMappedFeat ( CRef< CSeq_feat > &  feat,
CScope &  scope 
)
static

Definition at line 2959 of file gather_items.cpp.

References CScope::AddSeq_annot(), CScope::GetSeq_featHandle(), Ref(), and CSeq_annot_Base::SetData().

Referenced by s_GetTrimmedMappedFeat().

◆ s_GetTrimmedMappedFeat()

static CMappedFeat s_GetTrimmedMappedFeat ( const CSeq_feat &  feat,
const CRange< TSeqPos > &  range,
CScope &  scope 
)
static

Definition at line 2969 of file gather_items.cpp.

References compile_time_bits::range(), and s_GetMappedFeat().

Referenced by CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_GiInCSeq_hist_ids()

static bool s_GiInCSeq_hist_ids ( const TGi  gi,
const CSeq_hist_rec_Base::TIds &  ids 
)
static

Definition at line 1426 of file gather_items.cpp.

References ITERATE.

Referenced by CFlatGatherer::x_HistoryComments().

◆ s_GiveOneResidueIntervalsBogusFuzz_Helper()

static void s_GiveOneResidueIntervalsBogusFuzz_Helper ( CSeq_interval &  interval)
static

Definition at line 4672 of file gather_items.cpp.

References CInt_fuzz_Base::eLim_circle, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetTo(), CSeq_interval_Base::SetFuzz_from(), and CSeq_interval_Base::SetFuzz_to().

Referenced by CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz().

◆ s_HasRefTrackStatus()

bool s_HasRefTrackStatus ( const CBioseq_Handle &  bsh)

Definition at line 1143 of file gather_items.cpp.

References CSeqdesc_Base::e_User, CCommentItem::eRefTrackStatus_Unknown, and CCommentItem::GetRefTrackStatus().

Referenced by CFlatGatherer::x_IdComments().

◆ s_HasSegments()

static bool s_HasSegments ( const CBioseq_Handle &  seq)
static

Definition at line 388 of file gather_items.cpp.

References CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, and CBioseq_Handle::GetExactComplexityLevel().

Referenced by CFlatGatherer::x_GatherBioseq().

◆ s_IsCDD()

static bool s_IsCDD ( const CSeq_feat_Handle &  feat)
static

Definition at line 2978 of file gather_items.cpp.

References CSeq_feat_Handle::GetAnnot(), CSeq_annot_Handle::GetName(), and CSeq_annot_Handle::IsNamed().

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_IsCircularTopology()

static bool s_IsCircularTopology ( CBioseqContext &  ctx)
static

Definition at line 927 of file gather_items.cpp.

References CBioseq_Handle::CanGetInst_Topology(), ctx, CSeq_inst_Base::eTopology_circular, and CBioseq_Handle::GetInst_Topology().

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ s_IsDuplicateFeatures()

static bool s_IsDuplicateFeatures ( const CSeq_feat_Handle &  f1,
const CSeq_feat_Handle &  f2 
)
static

Definition at line 2803 of file gather_items.cpp.

References _ASSERT, CSerialObject::Equals(), CSeq_feat_Handle::GetAnnot(), CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Handle::IsTableSNP(), and CSeq_annot_Handle::Seq_annot_CanGetDesc().

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_IsJustUids()

bool s_IsJustUids ( const CPubdesc &  pubdesc)

Definition at line 542 of file gather_items.cpp.

References CPub_Base::e_Article, CPub_Base::e_Book, CPub_Base::e_Gen, CPub_Base::e_Journal, CPub_Base::e_Man, CPub_Base::e_Patent, CPub_Base::e_Proc, CPub_Base::e_Sub, CPub_equiv_Base::Get(), CPubdesc_Base::GetPub(), and ITERATE.

Referenced by s_FilterPubdesc().

◆ s_IsSegmented()

static bool s_IsSegmented ( const CBioseq_Handle &  seq)
static

Definition at line 379 of file gather_items.cpp.

References CSeq_inst_Base::eRepr_seg, CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::IsSetInst(), and CBioseq_Handle::IsSetInst_Repr().

Referenced by CFlatGatherer::x_GatherBioseq().

◆ s_LocationsOverlap()

static bool s_LocationsOverlap ( const CSeq_loc &  loc1,
const CSeq_loc &  loc2,
CScope *  p_scope 
)
static

Definition at line 373 of file gather_items.cpp.

References eOverlap_Simple, kInvalidSeqPos, and TestForOverlap().

Referenced by CFlatGatherer::x_BiosourcesEqualForMergingPurposes().

◆ s_LocationsTouch()

static bool s_LocationsTouch ( const CSeq_loc &  loc1,
const CSeq_loc &  loc2 
)
static

Definition at line 359 of file gather_items.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), and CSeq_loc::GetTotalRange().

Referenced by CFlatGatherer::x_BiosourcesEqualForMergingPurposes().

◆ s_MakeSliceMapper()

CRef<CSeq_loc_Mapper> s_MakeSliceMapper ( const CSeq_loc &  loc,
CBioseqContext &  ctx 
)

Definition at line 3517 of file gather_items.cpp.

References CSeq_id::Assign(), ctx, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, GetLength(), CSeq_loc_Mapper_Base::SetFuzzOption(), CSeq_loc::SetInt(), and CSeq_loc_Mapper_Base::TruncateNonmappingRanges().

Referenced by CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_GatherFeaturesOnRange(), and CFlatGatherer::x_GatherFeaturesOnRangeIdx().

◆ s_NewGapItem() [1/2]

static CRef<CGapItem> s_NewGapItem ( CSeqMap_CI &  gap_it,
CBioseqContext &  ctx 
)
static

Definition at line 2739 of file gather_items.cpp.

References ctx, CFastaOstream::SGapModText::gap_linkage_evidences, CFastaOstream::SGapModText::gap_type, CSeqMap_CI::GetData(), CSeqMap_CI::GetEndPosition(), CSeq_data_Base::GetGap(), CFastaOstream::GetGapModText(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefGapLiteral(), CSeq_data_Base::IsGap(), CSeqMap_CI::IsSetData(), and CSeqMap_CI::IsUnknownLength().

Referenced by CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

◆ s_NewGapItem() [2/2]

static CRef<CGapItem> s_NewGapItem ( TSeqPos  gap_start,
TSeqPos  gap_end,
TSeqPos  gap_length,
const string &  gap_type,
const vector< string > &  evidence,
bool  isUnknownLength,
bool  isAssemblyGap,
CBioseqContext &  ctx 
)
static

Definition at line 2782 of file gather_items.cpp.

References ctx, and bm::gap_length().

◆ s_NormalizeNullsBetween()

static CConstRef<CSeq_loc> s_NormalizeNullsBetween ( CConstRef< CSeq_loc >  loc,
bool  force_adding_nulls = false 
)
static

Definition at line 2071 of file gather_items.cpp.

References CSeq_loc::Assign(), CSeq_loc_CI::eEmpty_Allow, CSeq_loc_CI::eEmpty_Skip, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::IsEmpty(), CSeq_loc_Base::IsMix(), CSeq_loc_mix_Base::IsSet(), CSeq_loc::SetMix(), and CSeq_loc::SetNull().

Referenced by CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), and CFlatGatherer::x_SubtractFromFocus().

◆ s_NsAreGaps()

static bool s_NsAreGaps ( const CBioseq_Handle &  seq,
CBioseqContext &  ctx 
)
static

Definition at line 967 of file gather_items.cpp.

References CSeq_literal_Base::CanGetLength(), CSeq_literal_Base::CanGetSeq_data(), ctx, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CBioseq_Handle::GetInst_Ext(), CSeq_literal_Base::GetLength(), CDelta_seq_Base::GetLiteral(), CSeq_ext_Base::IsDelta(), CDelta_seq_Base::IsLiteral(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Ext(), and ITERATE.

◆ s_RemoveBogusFuzzFromIntervals_Helper()

static void s_RemoveBogusFuzzFromIntervals_Helper ( CSeq_interval &  interval)
static

Definition at line 4705 of file gather_items.cpp.

References CInt_fuzz_Base::eLim_circle, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CInt_fuzz_Base::GetLim(), CSeq_interval_Base::GetTo(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetTo(), CSeq_interval_Base::ResetFuzz_from(), and CSeq_interval_Base::ResetFuzz_to().

Referenced by CFlatGatherer::x_RemoveBogusFuzzFromIntervals().

◆ s_SeqDescCompare()

static bool s_SeqDescCompare ( const CConstRef< CSeqdesc > &  desc1,
const CConstRef< CSeqdesc > &  desc2 
)
static

Definition at line 1605 of file gather_items.cpp.

References bool, NStr::CompareCase(), CSeqdesc_Base::e_User, CUser_field_Base::GetData(), CUser_object::GetFieldRef(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_field_Base::IsSetData(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), s_StrucCommOrder(), and CSeqdesc_Base::Which().

Referenced by CFlatGatherer::x_StructuredComments().

◆ s_SeqLocEndsOnBioseq()

static bool s_SeqLocEndsOnBioseq ( const CSeq_loc &  loc,
CBioseqContext &  ctx,
EEndsOnBioseqOpt  mode,
CSeqFeatData::E_Choice  feat_type 
)
static

Definition at line 2556 of file gather_items.cpp.

References ctx, CSeqFeatData_Base::e_Gene, CSeq_loc_CI::eEmpty_Skip, eEndsOnBioseqOpt_AnyPartOfSeqLoc, eExtreme_Biological, eNa_strand_minus, CSeq_loc_CI::eOrder_Biological, first(), CBioseq_Handle::GetBioseqLength(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), CSeq_loc::GetStop(), CSeq_loc_CI::GetStrand(), int, CBioseq_Handle::IsSynonym(), and last().

Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ s_SetGapIdxData()

static void s_SetGapIdxData ( SGapIdxData &  gapdat,
const vector< CRef< CGapIndex >> &  gaps 
)
static

Definition at line 3000 of file gather_items.cpp.

References SGapIdxData::gap_end, SGapIdxData::gap_evidence, SGapIdxData::gap_length, SGapIdxData::gap_start, SGapIdxData::gap_type, SGapIdxData::has_gap, SGapIdxData::is_assembly_gap, SGapIdxData::is_unknown_length, SGapIdxData::next_gap, and sgr().

Referenced by CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

◆ s_SetSelection()

void s_SetSelection ( SAnnotSelector &  sel,
CBioseqContext &  ctx 
)

Definition at line 2474 of file gather_items.cpp.

References ctx, CSeqFeatData_Base::e_Biosrc, CSeqFeatData_Base::e_Bond, CSeqFeatData_Base::e_Comment, CSeqFeatData_Base::e_Het, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Site, eNa_strand_minus, SAnnotSelector::eOverlap_Intervals, SAnnotSelector::eSortOrder_Normal, SAnnotSelector::eSortOrder_Reverse, CSeqFeatData::eSubtype_assembly_gap, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_non_std_residue, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_pub, CSeqFeatData::eSubtype_rsite, CSeqFeatData::eSubtype_seq, SAnnotSelector::ExcludeFeatSubtype(), SAnnotSelector::ExcludeFeatType(), SAnnotSelector::ExcludeNamedAnnots(), GetStrand(), CFlatFileConfig::HideCDDFeatures(), CFlatFileConfig::HideExonFeatures(), CFlatFileConfig::HideGapFeatures(), CFlatFileConfig::HideImpFeatures(), CFlatFileConfig::HideIntronFeatures(), CFlatFileConfig::HideMiscFeatures(), CFlatFileConfig::HideRemoteImpFeatures(), CFlatFileConfig::HideSNPFeatures(), CFlatFileConfig::IsPolicyFtp(), CFlatFileConfig::IsPolicyGenomes(), SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetFeatComparator(), SAnnotSelector::SetLimitTSE(), SAnnotSelector::SetOverlapType(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveTSE(), SAnnotSelector::SetSortOrder(), and CFlatFileConfig::ShowContigFeatures().

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ s_StrucCommOrder()

static int s_StrucCommOrder ( const string &  str)
static

Definition at line 1593 of file gather_items.cpp.

References NStr::StartsWith(), and str().

Referenced by s_SeqDescCompare().

◆ USING_SCOPE()

USING_SCOPE ( sequence  )
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Modified on Fri Sep 20 14:57:20 2024 by modify_doxy.py rev. 669887