NCBI C++ ToolKit
Classes
feature.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/mapped_feat.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
+ Include dependency graph for feature.hpp:

Go to the source code of this file.

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Classes

class  CFeatIdRemapper
 
class  CFeatComparatorByLabel
 
class  CFeatTree
 CFeatTree. More...
 
class  CFeatTree::CFeatInfo
 

GetLabel

Returns a label for a CSeq_feat.

Label may be based on just the type of feature, just the content of the feature, or both. If scope is 0, then the label will not include information from feature products.

enum  FFeatLabelFlags {
  fFGL_Type = 1 << 1 , fFGL_Content = 1 << 2 , fFGL_Both = fFGL_Type | fFGL_Content , fFGL_NoComments = 1 << 3 ,
  fFGL_NoQualifiers = 1 << 4
}
 
enum  ELabelType { eType , eContent , eBoth }
 For compatibility with legacy code. More...
 
typedef int TFeatLabelFlags
 binary OR of FFeatLabelFlags More...
 
void GetLabel (const CSeq_feat &feat, string *label, TFeatLabelFlags flags, CScope *scope=0)
 
void GetLabel (const CSeq_feat &feat, string *label, ELabelType label_type, CScope *scope=0)
 
CMappedFeat MapSeq_feat (const CSeq_feat_Handle &feat, const CBioseq_Handle &master_seq, const CRange< TSeqPos > &range)
 
CMappedFeat MapSeq_feat (const CSeq_feat_Handle &feat, const CSeq_id_Handle &master_id, const CRange< TSeqPos > &range)
 
CMappedFeat MapSeq_feat (const CSeq_feat_Handle &feat, const CBioseq_Handle &master_seq)
 
CMappedFeat MapSeq_feat (const CSeq_feat_Handle &feat, const CSeq_id_Handle &master_id)
 

GetParentFeature

Returns a best parent feature for a CMappedFeat.

CSeq_feat_Handle is convertible to a CMappedFeat so it can be used too.

enum  ELocationInFrame {
  eLocationInFrame_InFrame = 0 , eLocationInFrame_BadStart , eLocationInFrame_BadStop , eLocationInFrame_BadStartAndStop ,
  eLocationInFrame_NotIn
}
 
CMappedFeat GetParentFeature (const CMappedFeat &feat)
 
CMappedFeat GetBestGeneForMrna (const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)
 
CMappedFeat GetBestGeneForCds (const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)
 
CMappedFeat GetBestMrnaForCds (const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
CMappedFeat GetBestCdsForMrna (const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
void GetMrnasForGene (const CMappedFeat &gene_feat, list< CMappedFeat > &mrna_feats, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
void GetCdssForGene (const CMappedFeat &gene_feat, list< CMappedFeat > &cds_feats, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
CMappedFeat GetBestGeneForFeat (const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)
 
CMappedFeat GetBestParentForFeat (const CMappedFeat &feat, CSeqFeatData::ESubtype parent_subtype, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
CMappedFeat GetBestOverlappingFeat (const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)
 
CRef< CSeq_loc_MapperCreateSeqLocMapperFromFeat (const CSeq_feat &feat, CSeq_loc_Mapper::EFeatMapDirection dir, CScope *scope=0)
 Create CSeq_loc_Mapper from a feature, check for special cases like exceptions in CDS features. More...
 
void ClearFeatureIds (const CSeq_entry_EditHandle &entry)
 
void ClearFeatureIds (const CSeq_annot_EditHandle &annot)
 
void ReassignFeatureIds (const CSeq_entry_EditHandle &entry)
 
void ReassignFeatureIds (const CSeq_annot_EditHandle &annot)
 
bool GetFeatureGeneBiotype (feature::CFeatTree &ft, CMappedFeat mf, string &biotype)
 
bool GetFeatureGeneBiotypeFaster (feature::CFeatTree &ft, CMappedFeat mf, string &biotype)
 
ELocationInFrame IsLocationInFrame (const CSeq_feat_Handle &cds, const CSeq_loc &loc)
 Determines whether location loc is in frame with coding region cds. More...
 
bool PromoteCDSToNucProtSet (objects::CSeq_feat_Handle &orig_feat)
 Promotes coding region from Seq-annot on nucleotide sequence to Seq-annot on nuc-prot-set if necessary and appropriate. More...
 
bool AdjustFeaturePartialFlagForLocation (CSeq_feat &new_feat)
 AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end of the feature is partial, and clear if neither end of the feature is partial. More...
 
bool CopyFeaturePartials (CSeq_feat &dst, const CSeq_feat &src)
 CopyFeaturePartials A function to copy the start and end partialness from one feature to another. More...
 
bool AdjustProteinMolInfoToMatchCDS (CMolInfo &molinfo, const CSeq_feat &cds)
 AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region. More...
 
bool AdjustForCDSPartials (const CSeq_feat &cds, CSeq_entry_Handle seh)
 AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the partialness of a coding region has been changed. More...
 
bool AdjustForCDSPartials (const CSeq_feat &cds, CScope &scope)
 AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the partialness of a coding region has been changed. More...
 
bool RetranslateCDS (const CSeq_feat &cds, CScope &scope)
 RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current translation of the coding region cds. More...
 
void AddFeatureToBioseq (const CBioseq &seq, const CSeq_feat &f, CScope &scope)
 AddFeatureToBioseq A function to add a feature to a Bioseq - will create a new feature table Seq-annot if necessary. More...
 
void AddProteinFeature (const CBioseq &seq, const string &protein_name, const CSeq_feat &cds, CScope &scope)
 AddProteinFeature A function to create a protein feature with the specified protein name. More...
 
Modified on Sun Jul 14 04:59:38 2024 by modify_doxy.py rev. 669887