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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__ObjUtilFeature.html below:

NCBI C++ ToolKit: Feature utilities

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)

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...

The algorithm is the following: 1.

Feature types are organized in a tree of possible parent-child relationship: 1.1. operon, gap cannot have a parent, 1.2. gene can have operon as a parent, 1.3. mRNA, VDJ_segment, and C_region can have gene as a parent, 1.4. cdregion can have mRNA, VDJ_segment, or C_region as a parent, 1.5. prot can have cdregion as a parent (by its product location), 1.6. mat_peptide, sig_peptide can have prot as a parent, 1.x. all other feature types can have gene as a parent. 2. If parent of a nearest feature type is not found then the next type in the tree is checked, except prot which will have no parent if no cdregion is found. 3. For each parent type candidate the search is done in several ways: 3.1. first we look for a parent by Seq-feat.xref field, 3.2. then by Gene-ref if current parent type is gene, 3.3. then parent candidates are searched by the best intersection of their locations (product in case of prot -> cdregion link), 3.4. if no candidates are found next parent type is checked.

CFeatTree::CFeatTree (void) Construct empty tree. More...
CFeatTree::CFeatTree (CFeat_CI it) Construct a tree with features collected by a CFeat_CI. More...
CFeatTree::CFeatTree (const CSeq_annot_Handle &sah) Construct a tree with features from a Seq-annot. More...
CFeatTree::CFeatTree (const CSeq_annot_Handle &sah, const SAnnotSelector &sel) Construct a tree with features from a Seq-annot, restricted by an annot selector. More...
CFeatTree::CFeatTree (const CSeq_entry_Handle &seh) Construct a tree with features from a Seq-entry. More...
CFeatTree::CFeatTree (const CSeq_entry_Handle &seh, const SAnnotSelector &sel) Construct a tree with features from a Seq-entry, restricted by an annot selector. More...
CFeatTree::~CFeatTree (void) Destructor. More...
CFeatTree::CFeatTree (const CFeatTree &) CFeatTree & CFeatTree::operator= (const CFeatTree &) void CFeatTree::SetFeatIdMode (EFeatIdMode mode) void CFeatTree::SetGeneCheckMode (EGeneCheckMode mode) void CFeatTree::SetIgnoreMissingGeneXref (bool ignore=true) void CFeatTree::SetSNPStrandMode (ESNPStrandMode mode) void CFeatTree::AddFeatures (CFeat_CI it) Add all features collected by a CFeat_CI to the tree. More...
void CFeatTree::AddFeature (const CMappedFeat &feat) Add a single feature to the tree. More...
void CFeatTree::AddFeaturesFor (CScope &scope, const CSeq_loc &loc, CSeqFeatData::ESubtype bottom_type, CSeqFeatData::ESubtype top_type, const SAnnotSelector *base_sel=0, bool skip_bottom=false) Add all features from bottom_type to top_type for a feature. More...
void CFeatTree::AddFeaturesFor (const CMappedFeat &feat, CSeqFeatData::ESubtype bottom_type, CSeqFeatData::ESubtype top_type, const SAnnotSelector *base_sel=0) void CFeatTree::AddFeaturesFor (const CMappedFeat &feat, CSeqFeatData::ESubtype top_type, const SAnnotSelector *base_sel=0) void CFeatTree::AddGenesForMrna (const CMappedFeat &mrna_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get genes for a mRNA feature. More...
void CFeatTree::AddCdsForMrna (const CMappedFeat &mrna_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get cdregions for a mRNA feature. More...
void CFeatTree::AddMrnasForGene (const CMappedFeat &gene_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get mRNAs for a gene feature. More...
void CFeatTree::AddCdsForGene (const CMappedFeat &gene_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get cdregions for a gene feature. More...
void CFeatTree::AddGenesForCds (const CMappedFeat &cds_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get genes for a cdregion feature. More...
void CFeatTree::AddMrnasForCds (const CMappedFeat &cds_feat, const SAnnotSelector *base_sel=0) Add all necessary features to get mRNAs for a cdregion feature. More...
void CFeatTree::AddGenesForFeat (const CMappedFeat &feat, const SAnnotSelector *base_sel=0) Add all necessary features to get genes for an arbitrary feature. More...
const CMappedFeat & CFeatTree::GetMappedFeat (const CSeq_feat_Handle &feat) const Find a corresponding CMappedFeat for a feature already added to a tree. More...
CMappedFeat CFeatTree::GetParent (const CMappedFeat &feat) Return nearest parent of a feature. More...
CMappedFeat CFeatTree::GetParent (const CMappedFeat &feat, CSeqFeatData::E_Choice type) Return parent of a feature of the specified type, it may be not the nearest parent, but a parent's parent, and so on. More...
CMappedFeat CFeatTree::GetParent (const CMappedFeat &feat, CSeqFeatData::ESubtype subtype) Return parent of a feature of the specified subtype, it may be not the nearest parent, but a parent's parent, and so on. More...
vector< CMappedFeat > CFeatTree::GetChildren (const CMappedFeat &feat) Return all nearest children of a feature. More...
void CFeatTree::GetChildrenTo (const CMappedFeat &feat, vector< CMappedFeat > &children) Store all nearest children of a feature into a vector. More...
CMappedFeat CFeatTree::GetBestGene (const CMappedFeat &feat, EBestGeneType lookup_type=eBestGene_TreeOnly) Return parent gene if exists or best overlapping gene. More...
CFeatTree::CFeatInfo::CFeatInfo (void) CFeatTree::CFeatInfo::~CFeatInfo (void) const CTSE_Handle & CFeatTree::CFeatInfo::GetTSE (void) const void CFeatTree::x_Init (void) CFeatInfo & CFeatTree::x_GetInfo (const CSeq_feat_Handle &feat) CFeatInfo & CFeatTree::x_GetInfo (const CMappedFeat &feat) CFeatInfo * CFeatTree::x_FindInfo (const CSeq_feat_Handle &feat) void CFeatTree::x_AssignParents (void) void CFeatTree::x_AssignParentsByOverlap (TFeatArray &features, const STypeLink &link) bool CFeatTree::x_AssignParentByRef (CFeatInfo &info) void CFeatTree::x_AssignGenesByOverlap (TFeatArray &features) void CFeatTree::x_AssignGenes (void) pair< int, CFeatInfo * > CFeatTree::x_LookupParentByRef (CFeatInfo &info, CSeqFeatData::ESubtype parent_type) void CFeatTree::x_VerifyLinkedToRoot (CFeatInfo &info) void CFeatTree::x_SetParent (CFeatInfo &info, CFeatInfo &parent) void CFeatTree::x_SetNoParent (CFeatInfo &info) CFeatInfo * CFeatTree::x_GetParent (CFeatInfo &info) const TChildren & CFeatTree::x_GetChildren (CFeatInfo &info) void CFeatTree::x_SetGeneRecursive (CFeatInfo &info, CFeatInfo *gene) void CFeatTree::x_SetGene (CFeatInfo &info, CFeatInfo *gene) ◆ TChildren [1/2] ◆ TChildren [2/2] ◆ TFeatArray ◆ TFeatLabelFlags

binary OR of FFeatLabelFlags

Definition at line 78 of file feature.hpp.

◆ TFullId ◆ TIdMap ◆ TInfoArray ◆ TInfoMap ◆ EBestGeneFeatIdMode

Mode of processing feature ids.

Enumerator eBestGeneFeatId_ignore eBestGeneFeatId_always

Definition at line 212 of file feature.hpp.

◆ EBestGeneType Enumerator eBestGene_TreeOnly eBestGene_AllowOverlapped eBestGene_OverlappedOnly

Definition at line 330 of file feature.hpp.

◆ EFeatIdMode

Mode of processing feature ids.

Enumerator eFeatId_ignore eFeatId_by_type eFeatId_always

Definition at line 201 of file feature.hpp.

◆ EGeneCheckMode

Mode for taking into account best gene eGeneCheck_match will try to match a parent feature only if they both match to the same gene.

Enumerator eGeneCheck_ignore eGeneCheck_match

Definition at line 224 of file feature.hpp.

◆ EIsLinkedToRoot Enumerator eIsLinkedToRoot_unknown eIsLinkedToRoot_linked eIsLinkedToRoot_linking

Definition at line 373 of file feature.hpp.

◆ ELabelType

For compatibility with legacy code.

Enumerator eType eContent eBoth

Definition at line 85 of file feature.hpp.

◆ ELocationInFrame Enumerator eLocationInFrame_InFrame eLocationInFrame_BadStart eLocationInFrame_BadStop eLocationInFrame_BadStartAndStop eLocationInFrame_NotIn

Definition at line 531 of file feature.hpp.

◆ ESNPStrandMode

Mode of processing SNP strands.

Enumerator eSNPStrand_same eSNPStrand_both

Definition at line 241 of file feature.hpp.

◆ FFeatLabelFlags Enumerator fFGL_Type

Always include the feature's type.

fFGL_Content

Include its content if there is any.

fFGL_Both fFGL_NoComments

Leave out comments, even as fallbacks.

fFGL_NoQualifiers

Leave out qualifiers.

Definition at line 71 of file feature.hpp.

◆ AddCdsForGene() ◆ AddCdsForMrna() ◆ AddFeature() ◆ AddFeatures() void CFeatTree::AddFeatures ( CFeat_CI it ) ◆ AddFeaturesFor() [1/3] ◆ AddFeaturesFor() [2/3] ◆ AddFeaturesFor() [3/3]

Add all features from bottom_type to top_type for a feature.

Definition at line 3171 of file feature.cpp.

References CFeatTree::AddFeatures(), CSeq_annot_Base::C_Data::e_not_set, CSeqFeatData::eSubtype_bad, STypeLink::GetMultiParentTypes(), SAnnotSelector::IncludeFeatSubtype(), STypeLink::m_ParentType, SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetAnnotType(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetOverlapTotalRange(), and SAnnotSelector::SetResolveAll().

Referenced by CFeatTree::AddCdsForGene(), CFeatTree::AddCdsForMrna(), CFeatTree::AddFeaturesFor(), CFeatTree::AddGenesForCds(), CFeatTree::AddGenesForFeat(), CFeatTree::AddGenesForMrna(), CFeatTree::AddMrnasForCds(), and CFeatTree::AddMrnasForGene().

◆ AddFeatureToBioseq() ◆ AddGenesForCds() ◆ AddGenesForFeat() ◆ AddGenesForMrna() ◆ AddMrnasForCds() ◆ AddMrnasForGene() ◆ AddProteinFeature() ◆ AdjustFeaturePartialFlagForLocation() 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.

Parameters: new_feat The feature to be adjusted (if necessary)

Returns: Boolean to indicate whether the feature was changed

Definition at line 3983 of file feature.cpp.

References eExtreme_Biological, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetPartial(), CSeq_feat_Base::ResetPartial(), and CSeq_feat_Base::SetPartial().

Referenced by CResyncPanel::AddCommand(), AdjustProteinFeaturePartialsToMatchCDS(), CLocationEditPolicy::ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), CopyFeaturePartials(), CSequenceEditingEventHandler::ResynchronizePartials(), and CCleanup::SetCDSPartialsByFrameAndTranslation().

◆ AdjustForCDSPartials() [1/2]

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.

Parameters: cds The feature for which adjustments are to be made scope The scope in which to find the protein sequence

Returns: Boolean to indicate whether the Seq-entry-handle was changed

Definition at line 4062 of file feature.cpp.

References AdjustProteinMolInfoToMatchCDS(), CSerialObject::Assign(), CopyFeaturePartials(), CSeqFeatData::eSubtype_prot, f, CScope::GetBioseqHandle(), CBioseq_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CSeq_annot_Handle::GetParentEntry(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::IsSetProduct(), NON_CONST_ITERATE, CSeq_feat_EditHandle::Replace(), and CBioseq_EditHandle::SetDescr().

Referenced by AdjustForCDSPartials(), and RetranslateCDS().

◆ AdjustForCDSPartials() [2/2]

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.

Parameters: cds The feature for which adjustments are to be made seh The Seq-entry-handle to be adjusted (if necessary)

Returns: Boolean to indicate whether the Seq-entry-handle was changed

Definition at line 4115 of file feature.cpp.

Referenced by ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), and CCleanup::WGSCleanup().

◆ AdjustProteinMolInfoToMatchCDS() ◆ CFeatInfo() CFeatTree::CFeatInfo::CFeatInfo ( void )

Definition at line 3146 of file feature.cpp.

◆ CFeatTree() [1/7] ◆ CFeatTree() [2/7] ◆ CFeatTree() [3/7] ◆ CFeatTree() [4/7] ◆ CFeatTree() [5/7] ◆ CFeatTree() [6/7] ◆ CFeatTree() [7/7] CFeatTree::CFeatTree ( void ) ◆ ClearFeatureIds() [1/2] ◆ ClearFeatureIds() [2/2] ◆ CopyFeaturePartials()

CopyFeaturePartials A function to copy the start and end partialness from one feature to another.

Parameters: dst The feature to be adjusted (if necessary) src The CDS to match

Returns: Boolean to indicate whether the feature was changed

Definition at line 4006 of file feature.cpp.

References AdjustFeaturePartialFlagForLocation(), eExtreme_Biological, CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and CSeq_feat_Base::SetLocation().

Referenced by AddProteinFeature(), AdjustForCDSPartials(), CCleanup::SetGenePartialByLongestContainedFeature(), CCleanup::WGSCleanup(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

◆ CreateSeqLocMapperFromFeat()

Create CSeq_loc_Mapper from a feature, check for special cases like exceptions in CDS features.

Return null on error.

Definition at line 3698 of file feature.cpp.

References eExtreme_Biological, CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetProduct(), CSeq_loc::IsTruncatedStart(), and CRef< C, Locker >::Reset().

◆ GetBestCdsForMrna()

Definition at line 3360 of file feature.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, CFeatTree::GetChildren(), CSeq_feat_Handle::GetFeatSubtype(), ITERATE, and NCBI_THROW.

Referenced by GetBestOverlappingFeat(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CDemoApp::Run(), variation_ref::CVariationUtil::SetVariantProperties(), CAlignedFeatureGraph::x_GatherCluster(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), and CFeatTableEdit::xFeatureAddProteinIdMrna().

◆ GetBestGene() ◆ GetBestGeneFeatIdMode() ◆ GetBestGeneForCds()

Definition at line 3321 of file feature.cpp.

References CSeqFeatData::eSubtype_cdregion, CFeatTree::GetBestGene(), CSeq_feat_Handle::GetFeatSubtype(), and NCBI_THROW.

Referenced by CCreateProteinId::apply(), CCreateLocusTagGene::apply(), CConvertBadCdsAndRnaToMiscFeat::apply(), GetBestOverlappingFeat(), CFixForTransSplicing::GetCommand(), CFeatTableEdit::InferPartials(), MakemRNAforCDS(), TAsyncToken::ParentGene(), CExtendCDSToStop::ResetGenes(), s_GetBestGeneForFeat(), CLinkUtils::x_AddDbxrefFeatureLinks(), CDeflineGenerator::x_GetGeneRefViaCDS(), CGffIdGenerator::xGetIdForCds(), and CFeatTableEdit::xGetLinkedFeature().

◆ GetBestGeneForFeat()

Definition at line 3443 of file feature.cpp.

References CFeatTree::GetBestGene(), and NCBI_THROW.

Referenced by CGffFeatureContext::FindBestGeneParent(), CFeatureIndex::GetBestGene(), GetBestOverlappingFeat(), CGeneXrefsFromFeats::GetCommand(), CDemoApp::Run(), sGetClosestGeneRef(), CGeneFeatTreeProcess::TestFeatureGeneTree(), CFeatTableEdit::xAdjustExistingParentGene(), CGtfWriter::xAssignFeatureAttributeGeneId(), CGffIdGenerator::xExtractGeneLocusTagOrLocus(), CFeatTableEdit::xGenerateMissingMrnaForCds(), CFeatTableEdit::xGetCurrentLocusTagPrefix(), CGffIdGenerator::xGetIdForRna(), CFeatTableEdit::xMakeGeneForFeature(), CFeatTableEdit::xNextProteinId(), and CFeatTableEdit::xNextTranscriptId().

◆ GetBestGeneForMrna()

Definition at line 3301 of file feature.cpp.

References CSeqFeatData::eSubtype_mRNA, CFeatTree::GetBestGene(), CSeq_feat_Handle::GetFeatSubtype(), and NCBI_THROW.

Referenced by CGffFeatureContext::FindBestGeneParent(), GetBestOverlappingFeat(), CDemoApp::Run(), s_GetBestGeneForFeat(), CLinkUtils::x_AddDbxrefFeatureLinks(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), and CGffIdGenerator::xGetIdForRna().

◆ GetBestMrnaForCds()

Definition at line 3341 of file feature.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, CSeq_feat_Handle::GetFeatSubtype(), CFeatTree::GetParent(), and NCBI_THROW.

Referenced by CSplitCDSwithTooManyXs::AdjustSingleCDS(), CExtendCDSToStop::ExtendmRNA(), GetBestOverlappingFeat(), CSeqUtils::GetMrnaForCds(), GetProtAndRnaForCDS(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CFeatTableEdit::InferPartials(), TAsyncToken::ParentMrna(), CFeatTableEdit::xAddTranscriptAndProteinIdsToCdsAndParentMrna(), CGff3Writer::xAssignFeatureAttributeParentMrna(), CFeatTableEdit::xFeatureAddProteinIdCds(), CFeatTableEdit::xFeatureAddTranscriptIdCds(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), CFeatTableEdit::xGetLinkedFeature(), and CExonNumberAssigner::xInitialize().

◆ GetBestOverlappingFeat()

Definition at line 3653 of file feature.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_operon, GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForFeat(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlappingFeat(), GetBestParentForFeat(), CSeq_feat_Handle::GetFeatSubtype(), CMappedFeat::GetLocation(), and CSeq_feat_Handle::GetScope().

Referenced by CSequenceEditingEventHandler::CDSGeneRangeErrorRestore(), CSequenceEditingEventHandler::CDSGeneRangeErrorSuppress(), CConvertImpToProt::Convert(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible_Helper_extremes(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible_Helper_subset(), GetGeneForFeature(), GetmRNAforCDS(), GetProductForCDS(), CmRNACDSLinker::LinkByOverlap(), CDemoApp::Run(), s_GetBestGeneForFeat(), s_GetCDSformRNA(), s_GetmRNAForCDS(), s_GetProductFlagFromCDSProductNames(), s_GetProteinName(), s_TitleFromSegment(), s_VerifyTree(), CMiscFeatValidator::Validate(), CValidError_bioseq::ValidateBadGeneOverlap(), CValidError_bioseq::ValidateSeqDescContext(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CGeneFeatFromOtherFeatDlg::x_AddGeneQuals(), x_GetDivisionProc(), CDeflineGenerator::x_GetLongestProtein(), x_GetSegSeqInfoViaCDS(), x_GetSourceFeatViaCDS(), CValidError_bioseq::x_IsSameAsCDS(), CConvertFeatureBase::x_MoveFeatureToProtein(), CCdregionValidator::x_ValidateBadMRNAOverlap(), CCdregionValidator::x_ValidateCDSPeptides(), CRNAValidator::x_ValidateTrnaOverlap(), and CFeatTableEdit::xGenerateMissingMrnaForCds().

◆ GetBestParentForFeat() ◆ GetCdssForGene() ◆ GetChildren() ◆ GetChildrenGene() CFeatInfo* CFeatTree::CFeatInfo::GetChildrenGene ( void ) inline ◆ GetChildrenTo() ◆ GetFeatIdMode() ◆ GetFeatIdsCount() size_t CFeatIdRemapper::GetFeatIdsCount ( void ) const ◆ GetFeatureGeneBiotype() ◆ GetFeatureGeneBiotypeFaster() ◆ GetGeneCheckMode() ◆ GetIgnoreMissingGeneXref() bool CFeatTree::GetIgnoreMissingGeneXref ( void ) const inline ◆ GetLabel() [1/2] ◆ GetLabel() [2/2] ◆ GetMappedFeat() ◆ GetMrnasForGene() ◆ GetParent() [1/3] ◆ GetParent() [2/3] ◆ GetParent() [3/3] ◆ GetParentFeature() ◆ GetRootFeatures() vector<CMappedFeat> CFeatTree::GetRootFeatures ( void ) inline ◆ GetRootFeaturesTo() void CFeatTree::GetRootFeaturesTo ( vector< CMappedFeat > & children ) inline ◆ GetSNPStrandMode() ◆ GetSubtype() ◆ GetTSE() ◆ GivesGeneToChildren() bool CFeatTree::CFeatInfo::GivesGeneToChildren ( void ) const inline ◆ IsGene() bool CFeatTree::CFeatInfo::IsGene ( void ) const inline ◆ IsLocationInFrame()

Determines whether location loc is in frame with coding region cds.

Parameters: cds coding region feature [in] loc location to compare to coding region

Returns: enumerated return value indicates frame is good or either endpoint is bad

Definition at line 3818 of file feature.cpp.

References Compare(), eContains, eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eLocationInFrame_BadStart, eLocationInFrame_BadStartAndStop, eLocationInFrame_BadStop, eLocationInFrame_InFrame, eLocationInFrame_NotIn, eOffset_FromStart, eSame, fCompareOverlapping, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetScope(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Handle::IsSetData(), LocationOffset(), s_MakePointForLocationStop(), and tmp.

Referenced by BOOST_AUTO_TEST_CASE(), CCleanup::GetProteinLocationFromNucleotideLocation(), s_GetCdsByLocation(), and CPeptideValidator::x_ValidatePeptideOnCodonBoundary().

◆ IsSetGene() bool CFeatTree::CFeatInfo::IsSetGene ( void ) const inline ◆ IsSetParent() bool CFeatTree::CFeatInfo::IsSetParent ( void ) const inline ◆ Less()

Implements IFeatComparator.

Definition at line 891 of file feature.cpp.

References NStr::Compare(), NStr::CompareNocase(), fFGL_Both, CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CObject_id_Base::GetId(), CSeq_feat_Base::GetId(), GetLabel(), CFeat_id_Base::GetLocal(), CGene_ref_Base::GetLocus_tag(), CObject_id_Base::GetStr(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CObject_id_Base::IsId(), CFeat_id_Base::IsLocal(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetId(), CGene_ref_Base::IsSetLocus_tag(), CObject_id_Base::IsStr(), CObject_id_Base::Which(), and CFeat_id_Base::Which().

◆ MapSeq_feat() [1/4] ◆ MapSeq_feat() [2/4]

Definition at line 973 of file feature.cpp.

References depth, CSeq_feat_Handle::GetAnnot(), CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), NCBI_THROW, SAnnotSelector::SetExactDepth(), SAnnotSelector::SetLimitSeqAnnot(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveDepth(), and SAnnotSelector::SetSourceLoc().

Referenced by MapSeq_feat().

◆ MapSeq_feat() [3/4] ◆ MapSeq_feat() [4/4] ◆ operator=()

Definition at line 1977 of file feature.cpp.

References CFeatTree::AddFeature(), map_checker< Container >::clear(), ITERATE, CFeatTree::m_AssignedGenes, CFeatTree::m_AssignedParents, CFeatTree::m_BestGeneFeatIdMode, CFeatTree::m_FeatIdMode, CFeatTree::m_GeneCheckMode, CFeatTree::m_IgnoreMissingGeneXref, CFeatTree::m_Index, CFeatTree::m_InfoArray, CFeatTree::m_InfoMap, CFeatTree::m_RootInfo, and CFeatTree::m_SNPStrandMode.

◆ PromoteCDSToNucProtSet() 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.

Parameters: orig_feat coding region feature [in]

Returns: enumerated return value indicates whether a change was made

Definition at line 3914 of file feature.cpp.

References CSeq_entry_EditHandle::AttachAnnot(), CBioseq_set_Base::eClass_nuc_prot, CSeq_annot_CI::eSearch_entry, ftable, CSeq_feat_EditHandle::GetAnnot(), CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_annot_Base::GetData(), CSeq_annot_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_annot_Handle::GetParentEntry(), CSeq_annot_EditHandle::GetParentEntry(), CBioseq_Handle::GetScope(), CSeq_annot_Handle::GetSeq_annotCore(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), CSeq_annot_EditHandle::Remove(), CSeq_annot_Base::SetData(), and CSeq_annot_EditHandle::TakeFeat().

Referenced by BOOST_AUTO_TEST_CASE(), CCmdChangeSeq_feat::Execute(), and CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot().

◆ ReassignFeatureIds() [1/2] ◆ ReassignFeatureIds() [2/2] ◆ RemapId() [1/3] ◆ RemapId() [2/3] ◆ RemapId() [3/3] ◆ RemapIds() [1/2] ◆ RemapIds() [2/2] ◆ Reset() void CFeatIdRemapper::Reset ( void ) ◆ RetranslateCDS()

RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current translation of the coding region cds.

Parameters: cds The feature for which adjustments are to be made

Returns: Boolean to indicate whether the coding region was retranslated.

Definition at line 4121 of file feature.cpp.

References AdjustForCDSPartials(), CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), CSeqFeatData::eSubtype_prot, f, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Base::GetInst(), CSeq_loc_Base::GetInt(), CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_annot_Handle::GetParentEntry(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeq_entry_Handle(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CBioseq_Base::IsSetInst(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_EditHandle::Replace(), CBioseq_EditHandle::SetInst(), CSeq_feat_Base::SetLocation(), and CSeqTranslator::TranslateToProtein().

Referenced by ApplyPolicyToFeature(), ExtendPartialFeatureEnds(), CCleanup::WGSCleanup(), CCleanupApp::x_BatchExtendCDS(), and CCleanupApp::x_FixCDS().

◆ SetBestGeneFeatIdMode() ◆ SetFeatIdMode() ◆ SetGeneCheckMode() ◆ SetIgnoreMissingGeneXref() void CFeatTree::SetIgnoreMissingGeneXref ( bool ignore = true ) ◆ SetSNPStrandMode() ◆ x_AssignGenes() void CFeatTree::x_AssignGenes ( void ) protected

Definition at line 2862 of file feature.cpp.

References arr, CFeatTree::eBestGeneFeatId_always, CSeqFeatData::eSubtype_gene, CFeatTree::CFeatInfo::GetChildrenGene(), CFeatTree::CFeatInfo::GivesGeneToChildren(), info, CFeatTree::m_AssignedGenes, CFeatTree::m_BestGeneFeatIdMode, CFeatTree::m_InfoArray, swap(), CFeatTree::x_AssignGenesByOverlap(), CFeatTree::x_LookupParentByRef(), CFeatTree::x_SetGene(), and CFeatTree::x_SetGeneRecursive().

Referenced by CFeatTree::GetBestGene().

◆ x_AssignGenesByOverlap() void CFeatTree::x_AssignGenesByOverlap ( TFeatArray & features ) protected

Definition at line 2818 of file feature.cpp.

References _ASSERT, cnt, CSeqFeatData::eSubtype_gene, CFeatTreeIndex::GetIndex(), i, info, CFeatTreeIndex::m_CanonicalIds, CFeatTree::m_Index, CFeatTree::m_InfoArray, s_CollectBestOverlaps(), and CFeatTree::x_SetGene().

Referenced by CFeatTree::x_AssignGenes().

◆ x_AssignParentByRef()

Definition at line 2174 of file feature.cpp.

References _ASSERT, CFeatTree::eBestGeneFeatId_ignore, CFeatTree::eFeatId_always, CFeatTree::eFeatId_by_type, CFeatTree::eFeatId_ignore, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_gene, CFeatTree::GetIgnoreMissingGeneXref(), info, CFeatTree::m_BestGeneFeatIdMode, CFeatTree::m_FeatIdMode, STypeLink::m_ParentType, CFeatTree::x_LookupParentByRef(), CFeatTree::x_SetGene(), and CFeatTree::x_SetParent().

Referenced by CFeatTree::x_AssignParents().

◆ x_AssignParents() void CFeatTree::x_AssignParents ( void ) protected

Definition at line 2931 of file feature.cpp.

References CFeatTree::eFeatId_always, CFeatTree::eFeatId_ignore, CSeqFeatData::eSubtype_max, info, ITERATE, CFeatTree::m_AssignedParents, CFeatTree::m_FeatIdMode, CFeatTree::m_InfoArray, CFeatTree::m_InfoMap, ct::sort(), type, CFeatTree::x_AssignParentByRef(), CFeatTree::x_AssignParentsByOverlap(), CFeatTree::x_SetNoParent(), and CFeatTree::x_VerifyLinkedToRoot().

Referenced by CFeatTree::GetChildrenTo(), CFeatTree::x_GetChildren(), and CFeatTree::x_GetParent().

◆ x_AssignParentsByOverlap()

Definition at line 2731 of file feature.cpp.

References _ASSERT, cnt, CFeatTree::eGeneCheck_match, CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_gene, CFeatTree::GetGeneCheckMode(), CFeatTreeIndex::GetIndex(), STypeLink::GetMultiParentTypes(), CFeatTree::CFeatInfo::GetSubtype(), i, info, ITERATE, STypeLink::m_ByProduct, CFeatTreeIndex::m_CanonicalIds, CFeatTree::m_Index, CFeatTree::m_InfoArray, STypeLink::m_ParentType, s_AllowedParentByOverlap(), s_CollectBestOverlaps(), swap(), CFeatTree::x_SetNoParent(), and CFeatTree::x_SetParent().

Referenced by CFeatTree::x_AssignParents().

◆ x_FindInfo() ◆ x_GetChildren() ◆ x_GetInfo() [1/2] ◆ x_GetInfo() [2/2] ◆ x_GetParent() ◆ x_Init() void CFeatTree::x_Init ( void ) protected

Definition at line 2000 of file feature.cpp.

References CFeatTree::eBestGeneFeatId_always, CFeatTree::eFeatId_by_type, CFeatTree::eGeneCheck_match, CFeatTree::eSNPStrand_both, CFeatTree::m_AssignedGenes, CFeatTree::m_AssignedParents, CFeatTree::m_BestGeneFeatIdMode, CFeatTree::m_FeatIdMode, CFeatTree::m_GeneCheckMode, CFeatTree::m_IgnoreMissingGeneXref, and CFeatTree::m_SNPStrandMode.

Referenced by CFeatTree::CFeatTree().

◆ x_LookupParentByRef()

Definition at line 2106 of file feature.cpp.

References data, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_gene, CSeqFeatXref_Base::GetData(), CTSE_Handle::GetFeaturesWithId(), CTSE_Handle::GetGenesByRef(), CSeqFeatXref_Base::GetId(), CFeatTree::CFeatInfo::GetSubtype(), info, CSeqFeatXref_Base::IsSetData(), CSeqFeatXref_Base::IsSetId(), ITERATE, and CFeatTree::x_FindInfo().

Referenced by CFeatTree::x_AssignGenes(), and CFeatTree::x_AssignParentByRef().

◆ x_SetGene() ◆ x_SetGeneRecursive() ◆ x_SetNoParent() void CFeatTree::x_SetNoParent ( CFeatInfo & info ) protected ◆ x_SetParent() ◆ x_VerifyLinkedToRoot() void CFeatTree::x_VerifyLinkedToRoot ( CFeatInfo & info ) protected ◆ ~CFeatInfo() CFeatTree::CFeatInfo::~CFeatInfo ( void )

Definition at line 3160 of file feature.cpp.

◆ ~CFeatTree() CFeatTree::~CFeatTree ( void ) ◆ m_AddIndex size_t CFeatTree::CFeatInfo::m_AddIndex ◆ m_AssignedGenes size_t CFeatTree::m_AssignedGenes protected ◆ m_AssignedParents size_t CFeatTree::m_AssignedParents protected ◆ m_BestGeneFeatIdMode ◆ m_CanMatchByQual ◆ m_Children ◆ m_Feat ◆ m_FeatIdMode ◆ m_Gene ◆ m_GeneCheckMode ◆ m_IdMap TIdMap CFeatIdRemapper::m_IdMap private ◆ m_IgnoreMissingGeneXref bool CFeatTree::m_IgnoreMissingGeneXref protected ◆ m_Index ◆ m_InfoArray ◆ m_InfoMap ◆ m_IsLinkedToRoot ◆ m_IsSetChildren bool CFeatTree::CFeatInfo::m_IsSetChildren ◆ m_IsSetGene bool CFeatTree::CFeatInfo::m_IsSetGene ◆ m_IsSetParent bool CFeatTree::CFeatInfo::m_IsSetParent ◆ m_MasterRange ◆ m_MultiId ◆ m_Parent ◆ m_RootInfo ◆ m_SNPStrandMode

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