#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:
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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_Mapper > | CreateSeqLocMapperFromFeat (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... | |
