NCBI C++ ToolKit
Classes | Namespaces | Functions
variation_util2.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Prot_pos.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Variation_ref.hpp>
#include <objects/seqfeat/Phenotype.hpp>
#include <objects/seqfeat/Variation_inst.hpp>
#include <objects/seqfeat/VariantProperties.hpp>
#include <objects/seqfeat/Delta_item.hpp>
#include <objects/seqfeat/Ext_loc.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/pub/Pub_set.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/biblio/Cit_art.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/variation/VariationMethod.hpp>
#include <objects/variation/VariationException.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <serial/iterator.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <misc/hgvs/variation_util2.hpp>
#include <objects/seqloc/Na_strand.hpp>
+ Include dependency graph for variation_util2.cpp:

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Classes

class  variation::SFastLocSubtract
 Note: this is strand-agnostic. More...
 

Namespaces

 variation
 

Functions

static CRef< CVariationExceptionvariation::CreateException (const string &message, CVariationException::ECode code=static_cast< CVariationException::ECode >(0))
 
template<typename T >
static void variation::ChangeIdsInPlace (T &container, sequence::EGetIdType id_type, CScope &scope)
 
static bool variation::ValidExonTerminal (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, TSeqPos exon_anchor_pos, int offset_pos)
 
static int variation::GetFuzzSign (const CInt_fuzz &fuzz, int loc_sign)
 
static bool variation::ValidExonTerminals (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, const CVariantPlacement &p)
 
static void variation::SwapLtGtFuzz (CInt_fuzz &fuzz)
 
static void variation::ApplyOffsetFuzz (CSeq_loc &loc, const CInt_fuzz &offset_fuzz, bool is_start)
 
static CRef< CSeq_alignvariation::CreateSplicedSeqAlignFromFeat (const CSeq_feat &rna_feat)
 
template<typename T >
static bool variation::ContainsIupacNaAmbiguities (const T &obj)
 
static bool variation::IsRightPartial (CBioseq_Handle bsh)
 
static string variation::Translate (const string &nuc_str, bool is_mito)
 
CVariation_inst::EType variation::CalcInstTypeForAA (const string &prot_ref_str, const string &prot_delta_str)
 
static CVariantProperties::TEffect variation::CalcEffectForProt (const string &prot_ref_str, const string &prot_delta_str)
 
static CVariationUtil::TSOTerms variation::CalcSOTermsForProt (TSignedSeqPos nuc_delta_len, const string &prot_ref_str, const string &prot_variant_str)
 
static bool variation::Contains (const CSeq_loc &a, const CSeq_loc &b, CScope *scope)
 
static CRef< CVariationvariation::CreateUnknownProtConsequenceVariation (const CVariantPlacement &nuc_p, const CSeq_feat &cds_feat, bool is_frameshifting, CScope &scope)
 
static size_t variation::GetCommonPrefixLen (const string &a, const string &b)
 
static size_t variation::GetCommonSuffixLen (const string &a, const string &b)
 
static bool variation::HasProblematicExceptions (const CSeq_feat &cds_feat)
 
static bool variation::Equals (const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)
 
static bool variation::IsRefSeqGene (const CBioseq_Handle &bsh)
 
static set< intvariation::GetFocusLocusIDs (const CBioseq_Handle &bsh)
 
CRef< CVariationvariation::InheritParentAttributes (const CVariation &child, const CVariation &parent)
 
static CRef< CDelta_itemvariation::CreateDeltaForOffset (int offset, const CInt_fuzz *fuzz)
 
static int variation::GetSignedOffset (const CDelta_item &delta)
 
static const CInt_fuzzvariation::GetFuzz (const CDelta_item &delta)
 
Modified on Thu Feb 29 12:16:57 2024 by modify_doxy.py rev. 669887