NCBI C++ ToolKit
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Feature utilities
+ Collaboration diagram for Feature utilities:

Classes

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

Typedefs

typedef pair< int, CTSE_HandleCFeatIdRemapper::TFullId
 
typedef map< TFullId, intCFeatIdRemapper::TIdMap
 
typedef vector< CFeatInfo * > CFeatTree::CFeatInfo::TChildren
 
typedef vector< CFeatInfo * > CFeatTree::TFeatArray
 
typedef vector< CFeatInfo * > CFeatTree::TChildren
 
typedef map< CSeq_feat_Handle, CFeatInfoCFeatTree::TInfoMap
 
typedef vector< CFeatInfo * > CFeatTree::TInfoArray
 

Enumerations

enum  CFeatTree::EFeatIdMode { CFeatTree::eFeatId_ignore , CFeatTree::eFeatId_by_type , CFeatTree::eFeatId_always }
 Mode of processing feature ids. More...
 
enum  CFeatTree::EBestGeneFeatIdMode { CFeatTree::eBestGeneFeatId_ignore , CFeatTree::eBestGeneFeatId_always }
 Mode of processing feature ids. More...
 
enum  CFeatTree::EGeneCheckMode { CFeatTree::eGeneCheck_ignore , CFeatTree::eGeneCheck_match }
 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. More...
 
enum  CFeatTree::ESNPStrandMode { CFeatTree::eSNPStrand_same , CFeatTree::eSNPStrand_both }
 Mode of processing SNP strands. More...
 
enum  CFeatTree::EBestGeneType { CFeatTree::eBestGene_TreeOnly , CFeatTree::eBestGene_AllowOverlapped , CFeatTree::eBestGene_OverlappedOnly }
 
enum  CFeatTree::CFeatInfo::EIsLinkedToRoot { CFeatTree::CFeatInfo::eIsLinkedToRoot_unknown , CFeatTree::CFeatInfo::eIsLinkedToRoot_linked , CFeatTree::CFeatInfo::eIsLinkedToRoot_linking }
 

Functions

void CFeatIdRemapper::Reset (void)
 
size_t CFeatIdRemapper::GetFeatIdsCount (void) const
 
int CFeatIdRemapper::RemapId (int old_id, const CTSE_Handle &tse)
 
bool CFeatIdRemapper::RemapId (CFeat_id &id, const CTSE_Handle &tse)
 
bool CFeatIdRemapper::RemapId (CFeat_id &id, const CFeat_CI &feat_it)
 
bool CFeatIdRemapper::RemapIds (CSeq_feat &feat, const CTSE_Handle &tse)
 
CRef< CSeq_featCFeatIdRemapper::RemapIds (const CFeat_CI &feat_it)
 
virtual bool CFeatComparatorByLabel::Less (const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)
 
EFeatIdMode CFeatTree::GetFeatIdMode (void) const
 
EBestGeneFeatIdMode CFeatTree::GetBestGeneFeatIdMode (void) const
 
void CFeatTree::SetBestGeneFeatIdMode (EBestGeneFeatIdMode mode)
 
EGeneCheckMode CFeatTree::GetGeneCheckMode (void) const
 
bool CFeatTree::GetIgnoreMissingGeneXref (void) const
 Mode for taking into account gene xref to a missing genes. More...
 
ESNPStrandMode CFeatTree::GetSNPStrandMode (void) const
 
vector< CMappedFeatCFeatTree::GetRootFeatures (void)
 Return all root features (w/o parent). More...
 
void CFeatTree::GetRootFeaturesTo (vector< CMappedFeat > &children)
 Store all root features (w/o parent) into a vector. More...
 
bool CFeatTree::CFeatInfo::IsSetParent (void) const
 
bool CFeatTree::CFeatInfo::IsSetGene (void) const
 
CSeqFeatData::ESubtype CFeatTree::CFeatInfo::GetSubtype (void) const
 
bool CFeatTree::CFeatInfo::IsGene (void) const
 
bool CFeatTree::CFeatInfo::GivesGeneToChildren (void) const
 
CFeatInfoCFeatTree::CFeatInfo::GetChildrenGene (void)
 

Variables

TIdMap CFeatIdRemapper::m_IdMap
 
size_t CFeatTree::CFeatInfo::m_AddIndex
 
CMappedFeat CFeatTree::CFeatInfo::m_Feat
 
CRange< TSeqPosCFeatTree::CFeatInfo::m_MasterRange
 
bool CFeatTree::CFeatInfo::m_CanMatchByQual
 
bool CFeatTree::CFeatInfo::m_IsSetParent
 
bool CFeatTree::CFeatInfo::m_IsSetGene
 
bool CFeatTree::CFeatInfo::m_IsSetChildren
 
bool CFeatTree::CFeatInfo::m_MultiId
 
EIsLinkedToRoot CFeatTree::CFeatInfo::m_IsLinkedToRoot
 
CFeatInfoCFeatTree::CFeatInfo::m_Parent
 
CFeatInfoCFeatTree::CFeatInfo::m_Gene
 
TChildren CFeatTree::CFeatInfo::m_Children
 
size_t CFeatTree::m_AssignedParents
 
size_t CFeatTree::m_AssignedGenes
 
TInfoMap CFeatTree::m_InfoMap
 
TInfoArray CFeatTree::m_InfoArray
 
CFeatInfo CFeatTree::m_RootInfo
 
EFeatIdMode CFeatTree::m_FeatIdMode
 
EBestGeneFeatIdMode CFeatTree::m_BestGeneFeatIdMode
 
EGeneCheckMode CFeatTree::m_GeneCheckMode
 
bool CFeatTree::m_IgnoreMissingGeneXref
 
ESNPStrandMode CFeatTree::m_SNPStrandMode
 
CRef< CFeatTreeIndexCFeatTree::m_Index
 

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...
 

GetParentFeature

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 &)
 
CFeatTreeCFeatTree::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 CMappedFeatCFeatTree::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< CMappedFeatCFeatTree::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_HandleCFeatTree::CFeatInfo::GetTSE (void) const
 
void CFeatTree::x_Init (void)
 
CFeatInfoCFeatTree::x_GetInfo (const CSeq_feat_Handle &feat)
 
CFeatInfoCFeatTree::x_GetInfo (const CMappedFeat &feat)
 
CFeatInfoCFeatTree::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)
 
CFeatInfoCFeatTree::x_GetParent (CFeatInfo &info)
 
const TChildrenCFeatTree::x_GetChildren (CFeatInfo &info)
 
void CFeatTree::x_SetGeneRecursive (CFeatInfo &info, CFeatInfo *gene)
 
void CFeatTree::x_SetGene (CFeatInfo &info, CFeatInfo *gene)
 

Detailed Description

Typedef Documentation

◆ TChildren [1/2]

Definition at line 366 of file feature.hpp.

◆ TChildren [2/2]

typedef vector<CFeatInfo*> CFeatTree::TChildren
protected

Definition at line 386 of file feature.hpp.

◆ TFeatArray

typedef vector<CFeatInfo*> CFeatTree::TFeatArray

Definition at line 383 of file feature.hpp.

◆ TFeatLabelFlags

binary OR of FFeatLabelFlags

Definition at line 78 of file feature.hpp.

◆ TFullId

typedef pair<int, CTSE_Handle> CFeatIdRemapper::TFullId
private

Definition at line 115 of file feature.hpp.

◆ TIdMap

Definition at line 116 of file feature.hpp.

◆ TInfoArray

typedef vector<CFeatInfo*> CFeatTree::TInfoArray
protected

Definition at line 415 of file feature.hpp.

◆ TInfoMap

Definition at line 414 of file feature.hpp.

Enumeration Type Documentation

◆ 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

enum 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.

Function Documentation

◆ AddCdsForGene()

void CFeatTree::AddCdsForGene ( const CMappedFeat gene_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get cdregions for a gene feature.

Definition at line 3278 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), CSeqFeatData::eSubtype_cdregion, and CSeqFeatData::eSubtype_gene.

◆ AddCdsForMrna()

void CFeatTree::AddCdsForMrna ( const CMappedFeat mrna_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get cdregions for a mRNA feature.

Definition at line 3240 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), CSeqFeatData::eSubtype_cdregion, and CSeqFeatData::eSubtype_mRNA.

◆ AddFeature()

void CFeatTree::AddFeature ( const CMappedFeat feat)

◆ AddFeatures()

void CFeatTree::AddFeatures ( CFeat_CI  it)

Add all features collected by a CFeat_CI to the tree.

Definition at line 2036 of file feature.cpp.

References CFeatTree::AddFeature().

Referenced by CFeatTree::AddFeaturesFor(), and CFeatTree::CFeatTree().

◆ AddFeaturesFor() [1/3]

void CFeatTree::AddFeaturesFor ( const CMappedFeat feat,
CSeqFeatData::ESubtype  bottom_type,
CSeqFeatData::ESubtype  top_type,
const SAnnotSelector base_sel = 0 
)

◆ AddFeaturesFor() [2/3]

void CFeatTree::AddFeaturesFor ( const CMappedFeat feat,
CSeqFeatData::ESubtype  top_type,
const SAnnotSelector base_sel = 0 
)

◆ AddFeaturesFor() [3/3]

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 
)

◆ AddFeatureToBioseq()

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.

Parameters
seqThe sequence on which to add the feature
fThe feature to add
scopeThe scope that contains the sequence

Definition at line 4169 of file feature.cpp.

References CSeq_annot_EditHandle::AddFeat(), CSerialObject::Assign(), CBioseq_EditHandle::AttachAnnot(), f(), CBioseq_Base::GetAnnot(), CScope::GetBioseqHandle(), CScope::GetSeq_annotHandle(), CBioseq_Base::IsSetAnnot(), ITERATE, and CSeq_annot_Base::SetData().

Referenced by AddProteinFeature().

◆ AddGenesForCds()

void CFeatTree::AddGenesForCds ( const CMappedFeat cds_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get genes for a cdregion feature.

Definition at line 3250 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), and CSeqFeatData::eSubtype_gene.

◆ AddGenesForFeat()

void CFeatTree::AddGenesForFeat ( const CMappedFeat feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get genes for an arbitrary feature.

Definition at line 3288 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), and CSeqFeatData::eSubtype_gene.

◆ AddGenesForMrna()

void CFeatTree::AddGenesForMrna ( const CMappedFeat mrna_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get genes for a mRNA feature.

Definition at line 3231 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), and CSeqFeatData::eSubtype_gene.

◆ AddMrnasForCds()

void CFeatTree::AddMrnasForCds ( const CMappedFeat cds_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get mRNAs for a cdregion feature.

Definition at line 3259 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), and CSeqFeatData::eSubtype_mRNA.

◆ AddMrnasForGene()

void CFeatTree::AddMrnasForGene ( const CMappedFeat gene_feat,
const SAnnotSelector base_sel = 0 
)

Add all necessary features to get mRNAs for a gene feature.

Definition at line 3268 of file feature.cpp.

References CFeatTree::AddFeaturesFor(), CSeqFeatData::eSubtype_gene, and CSeqFeatData::eSubtype_mRNA.

◆ AddProteinFeature()

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.

Parameters
seqThe Bioseq on which to create the protein feature
protein_nameThe protein name
cdsThe coding region for this protein feature
scopeThe scope in which the sequence can be found

Definition at line 4195 of file feature.cpp.

References AddFeatureToBioseq(), CopyFeaturePartials(), CSeq_loc::GetId(), CBioseq::GetLength(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by g_InstantiateMissingProteins(), CCleanup::SetProteinName(), and CCleanup::WGSCleanup().

◆ 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_featThe 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]

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.

Parameters
cdsThe feature for which adjustments are to be made
scopeThe 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]

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.

Parameters
cdsThe feature for which adjustments are to be made
sehThe 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()

bool AdjustProteinMolInfoToMatchCDS ( CMolInfo molinfo,
const CSeq_feat cds 
)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

Parameters
molinfoThe MolInfo to be adjusted (if necessary)
cdsThe CDS to match
Returns
Boolean to indicate whether molinfo was changed

Definition at line 4024 of file feature.cpp.

Referenced by CTruncateCDS::AdjustMolinfo(), CFeatGapInfo::AdjustProteinSeq(), BOOST_AUTO_TEST_CASE(), GetSynchronizeProductMolInfoCommand(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

◆ CFeatInfo()

CFeatTree::CFeatInfo::CFeatInfo ( void  )

Definition at line 3146 of file feature.cpp.

◆ CFeatTree() [1/7]

CFeatTree::CFeatTree ( CFeat_CI  it)
explicit

Construct a tree with features collected by a CFeat_CI.

Definition at line 1929 of file feature.cpp.

References CFeatTree::AddFeatures(), and CFeatTree::x_Init().

◆ CFeatTree() [2/7]

CFeatTree::CFeatTree ( const CFeatTree ft)

Definition at line 1971 of file feature.cpp.

◆ CFeatTree() [3/7]

CFeatTree::CFeatTree ( const CSeq_annot_Handle sah)
explicit

Construct a tree with features from a Seq-annot.

Definition at line 1936 of file feature.cpp.

References CFeatTree::AddFeatures(), and CFeatTree::x_Init().

◆ CFeatTree() [4/7]

CFeatTree::CFeatTree ( const CSeq_annot_Handle sah,
const SAnnotSelector sel 
)
explicit

Construct a tree with features from a Seq-annot, restricted by an annot selector.

Definition at line 1943 of file feature.cpp.

References CFeatTree::AddFeatures(), and CFeatTree::x_Init().

◆ CFeatTree() [5/7]

CFeatTree::CFeatTree ( const CSeq_entry_Handle seh)
explicit

Construct a tree with features from a Seq-entry.

Definition at line 1951 of file feature.cpp.

References CFeatTree::AddFeatures(), and CFeatTree::x_Init().

◆ CFeatTree() [6/7]

CFeatTree::CFeatTree ( const CSeq_entry_Handle seh,
const SAnnotSelector sel 
)
explicit

Construct a tree with features from a Seq-entry, restricted by an annot selector.

Definition at line 1958 of file feature.cpp.

References CFeatTree::AddFeatures(), and CFeatTree::x_Init().

◆ CFeatTree() [7/7]

CFeatTree::CFeatTree ( void  )

Construct empty tree.

Definition at line 1923 of file feature.cpp.

References CFeatTree::x_Init().

◆ ClearFeatureIds() [1/2]

void ClearFeatureIds ( const CSeq_annot_EditHandle annot)

◆ ClearFeatureIds() [2/2]

void ClearFeatureIds ( const CSeq_entry_EditHandle entry)

◆ CopyFeaturePartials()

bool CopyFeaturePartials ( CSeq_feat dst,
const CSeq_feat src 
)

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

Parameters
dstThe feature to be adjusted (if necessary)
srcThe 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()

CRef<CSeq_loc_Mapper> CreateSeqLocMapperFromFeat ( const CSeq_feat feat,
CSeq_loc_Mapper::EFeatMapDirection  dir,
CScope scope = 0 
)

◆ GetBestCdsForMrna()

CMappedFeat GetBestCdsForMrna ( const CMappedFeat mrna_feat,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

◆ GetBestGene()

CMappedFeat CFeatTree::GetBestGene ( const CMappedFeat feat,
EBestGeneType  lookup_type = eBestGene_TreeOnly 
)

◆ GetBestGeneFeatIdMode()

EBestGeneFeatIdMode CFeatTree::GetBestGeneFeatIdMode ( void  ) const
inline

Definition at line 216 of file feature.hpp.

References CFeatTree::m_BestGeneFeatIdMode.

◆ GetBestGeneForCds()

CMappedFeat GetBestGeneForCds ( const CMappedFeat cds_feat,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0,
CFeatTree::EBestGeneType  lookup_type = CFeatTree::eBestGene_TreeOnly 
)

◆ GetBestGeneForFeat()

CMappedFeat GetBestGeneForFeat ( const CMappedFeat feat,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0,
CFeatTree::EBestGeneType  lookup_type = CFeatTree::eBestGene_TreeOnly 
)

◆ GetBestGeneForMrna()

CMappedFeat GetBestGeneForMrna ( const CMappedFeat mrna_feat,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0,
CFeatTree::EBestGeneType  lookup_type = CFeatTree::eBestGene_TreeOnly 
)

◆ GetBestMrnaForCds()

CMappedFeat GetBestMrnaForCds ( const CMappedFeat cds_feat,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

◆ GetBestOverlappingFeat()

CMappedFeat GetBestOverlappingFeat ( const CMappedFeat feat,
CSeqFeatData::ESubtype  need_subtype,
sequence::EOverlapType  overlap_type,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

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()

CMappedFeat GetBestParentForFeat ( const CMappedFeat feat,
CSeqFeatData::ESubtype  parent_subtype,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

◆ GetCdssForGene()

void GetCdssForGene ( const CMappedFeat gene_feat,
list< CMappedFeat > &  cds_feats,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

◆ GetChildren()

vector< CMappedFeat > CFeatTree::GetChildren ( const CMappedFeat feat)

Return all nearest children of a feature.

Will throw an exception if the feature is not in the tree. Will return an empty vector if the feature has no children. If the feat argument is null then all the features without parent are returned.

Definition at line 3100 of file feature.cpp.

References CFeatTree::GetChildrenTo().

Referenced by GetBestCdsForMrna(), GetCdssForGene(), GetMrnasForGene(), CFeatTree::GetRootFeatures(), and s_SetChildrenFeatureIds().

◆ GetChildrenGene()

CFeatInfo* CFeatTree::CFeatInfo::GetChildrenGene ( void  )
inline

Definition at line 362 of file feature.hpp.

References CFeatTree::CFeatInfo::IsGene(), and CFeatTree::CFeatInfo::m_Gene.

Referenced by CFeatTree::x_AssignGenes().

◆ GetChildrenTo()

void CFeatTree::GetChildrenTo ( const CMappedFeat feat,
vector< CMappedFeat > &  children 
)

Store all nearest children of a feature into a vector.

Will throw an exception if the feature is not in the tree. The second argument will become empty if the feature has no children. If the feat argument is null then all the features without parent are returned.

Definition at line 3108 of file feature.cpp.

References ITERATE, CFeatTree::CFeatInfo::m_Children, CFeatTree::m_RootInfo, CFeatTree::x_AssignParents(), CFeatTree::x_GetChildren(), and CFeatTree::x_GetInfo().

Referenced by CFeatTree::GetChildren(), and CFeatTree::GetRootFeaturesTo().

◆ GetFeatIdMode()

EFeatIdMode CFeatTree::GetFeatIdMode ( void  ) const
inline

Definition at line 206 of file feature.hpp.

References CFeatTree::m_FeatIdMode.

◆ GetFeatIdsCount()

size_t CFeatIdRemapper::GetFeatIdsCount ( void  ) const

Definition at line 800 of file feature.cpp.

References CFeatIdRemapper::m_IdMap, and map_checker< Container >::size().

◆ GetFeatureGeneBiotype()

bool GetFeatureGeneBiotype ( feature::CFeatTree &  ft,
CMappedFeat  mf,
string biotype 
)

Definition at line 4495 of file feature.cpp.

References sGetFeatureGeneBiotypeWrapper().

◆ GetFeatureGeneBiotypeFaster()

bool GetFeatureGeneBiotypeFaster ( feature::CFeatTree &  ft,
CMappedFeat  mf,
string biotype 
)

◆ GetGeneCheckMode()

EGeneCheckMode CFeatTree::GetGeneCheckMode ( void  ) const
inline

Definition at line 228 of file feature.hpp.

References CFeatTree::m_GeneCheckMode.

Referenced by CFeatTree::x_AssignParentsByOverlap().

◆ GetIgnoreMissingGeneXref()

bool CFeatTree::GetIgnoreMissingGeneXref ( void  ) const
inline

Mode for taking into account gene xref to a missing genes.

Definition at line 235 of file feature.hpp.

References CFeatTree::m_IgnoreMissingGeneXref.

Referenced by CFeatTree::x_AssignParentByRef().

◆ GetLabel() [1/2]

void GetLabel ( const CSeq_feat feat,
string label,
ELabelType  label_type,
CScope scope = 0 
)

Definition at line 779 of file feature.cpp.

References eBoth, eContent, eType, fFGL_Both, fFGL_Content, fFGL_Type, flags, GetLabel(), and label.

◆ GetLabel() [2/2]

void GetLabel ( const CSeq_feat feat,
string label,
TFeatLabelFlags  flags,
CScope scope = 0 
)

Definition at line 742 of file feature.cpp.

References fFGL_Content, fFGL_Type, flags, label, s_GetContentLabel(), and s_GetTypeLabel().

Referenced by GetLabel(), and CFeatComparatorByLabel::Less().

◆ GetMappedFeat()

const CMappedFeat & CFeatTree::GetMappedFeat ( const CSeq_feat_Handle feat) const

Find a corresponding CMappedFeat for a feature already added to a tree.

Will throw an exception if the feature is not in the tree.

Definition at line 2084 of file feature.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CFeatTree::m_InfoMap, and NCBI_THROW.

◆ GetMrnasForGene()

void GetMrnasForGene ( const CMappedFeat gene_feat,
list< CMappedFeat > &  mrna_feats,
CFeatTree feat_tree = 0,
const SAnnotSelector base_sel = 0 
)

◆ GetParent() [1/3]

CMappedFeat CFeatTree::GetParent ( const CMappedFeat feat)

Return nearest parent of a feature.

Will throw an exception if the feature is not in the tree. Will return null CMappedFeat if the feature has no parent.

Definition at line 3067 of file feature.cpp.

References info, CFeatTree::x_GetInfo(), and CFeatTree::x_GetParent().

Referenced by CCdsMatchInfo::AssignMatch(), CFeatTree::GetBestGene(), GetBestMrnaForCds(), GetBestParentForFeat(), and CFeatTree::GetParent().

◆ GetParent() [2/3]

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.

Will throw an exception if the feature is not in the tree. Will return null CMappedFeat if the feature has no parent of the type.

Definition at line 3078 of file feature.cpp.

References CSeq_feat_Handle::GetFeatType(), and CFeatTree::GetParent().

◆ GetParent() [3/3]

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.

Will throw an exception if the feature is not in the tree. Will return null CMappedFeat if the feature has no parent of the type.

Definition at line 3089 of file feature.cpp.

References CSeq_feat_Handle::GetFeatSubtype(), and CFeatTree::GetParent().

◆ GetParentFeature()

CMappedFeat GetParentFeature ( const CMappedFeat feat)

◆ GetRootFeatures()

vector<CMappedFeat> CFeatTree::GetRootFeatures ( void  )
inline

Return all root features (w/o parent).

Definition at line 322 of file feature.hpp.

References CFeatTree::GetChildren().

◆ GetRootFeaturesTo()

void CFeatTree::GetRootFeaturesTo ( vector< CMappedFeat > &  children)
inline

Store all root features (w/o parent) into a vector.

Definition at line 326 of file feature.hpp.

References CFeatTree::GetChildrenTo().

◆ GetSNPStrandMode()

ESNPStrandMode CFeatTree::GetSNPStrandMode ( void  ) const
inline

Definition at line 245 of file feature.hpp.

References CFeatTree::m_SNPStrandMode.

◆ GetSubtype()

CSeqFeatData::ESubtype CFeatTree::CFeatInfo::GetSubtype ( void  ) const
inline

◆ GetTSE()

const CTSE_Handle & CFeatTree::CFeatInfo::GetTSE ( void  ) const

Definition at line 3165 of file feature.cpp.

◆ GivesGeneToChildren()

bool CFeatTree::CFeatInfo::GivesGeneToChildren ( void  ) const
inline

◆ IsGene()

bool CFeatTree::CFeatInfo::IsGene ( void  ) const
inline

◆ IsLocationInFrame()

ELocationInFrame IsLocationInFrame ( const CSeq_feat_Handle cds,
const CSeq_loc loc 
)

◆ IsSetGene()

bool CFeatTree::CFeatInfo::IsSetGene ( void  ) const
inline

◆ IsSetParent()

bool CFeatTree::CFeatInfo::IsSetParent ( void  ) const
inline

Definition at line 347 of file feature.hpp.

References CFeatTree::CFeatInfo::m_IsSetParent.

◆ Less()

bool CFeatComparatorByLabel::Less ( const CSeq_feat f1,
const CSeq_feat f2,
CScope scope 
)
virtual

◆ MapSeq_feat() [1/4]

CMappedFeat MapSeq_feat ( const CSeq_feat_Handle feat,
const CBioseq_Handle master_seq 
)

Definition at line 1011 of file feature.cpp.

References MapSeq_feat().

◆ MapSeq_feat() [2/4]

CMappedFeat MapSeq_feat ( const CSeq_feat_Handle feat,
const CBioseq_Handle master_seq,
const CRange< TSeqPos > &  range 
)

◆ MapSeq_feat() [3/4]

CMappedFeat MapSeq_feat ( const CSeq_feat_Handle feat,
const CSeq_id_Handle master_id 
)

◆ MapSeq_feat() [4/4]

CMappedFeat MapSeq_feat ( const CSeq_feat_Handle feat,
const CSeq_id_Handle master_id,
const CRange< TSeqPos > &  range 
)

◆ operator=()

CFeatTree & CFeatTree::operator= ( const CFeatTree ft)

◆ PromoteCDSToNucProtSet()

bool PromoteCDSToNucProtSet ( objects::CSeq_feat_Handle &  orig_feat)

◆ ReassignFeatureIds() [1/2]

void ReassignFeatureIds ( const CSeq_annot_EditHandle annot)

Definition at line 3797 of file feature.cpp.

References ClearFeatureIds(), and s_SetChildrenFeatureIds().

◆ ReassignFeatureIds() [2/2]

void ReassignFeatureIds ( const CSeq_entry_EditHandle entry)

Definition at line 3787 of file feature.cpp.

References ClearFeatureIds(), and s_SetChildrenFeatureIds().

◆ RemapId() [1/3]

bool CFeatIdRemapper::RemapId ( CFeat_id id,
const CFeat_CI feat_it 
)

◆ RemapId() [2/3]

bool CFeatIdRemapper::RemapId ( CFeat_id id,
const CTSE_Handle tse 
)

Definition at line 817 of file feature.cpp.

References local, and CFeatIdRemapper::RemapId().

◆ RemapId() [3/3]

int CFeatIdRemapper::RemapId ( int  old_id,
const CTSE_Handle tse 
)

◆ RemapIds() [1/2]

CRef< CSeq_feat > CFeatIdRemapper::RemapIds ( const CFeat_CI feat_it)

◆ RemapIds() [2/2]

bool CFeatIdRemapper::RemapIds ( CSeq_feat feat,
const CTSE_Handle tse 
)

◆ Reset()

void CFeatIdRemapper::Reset ( void  )

Definition at line 794 of file feature.cpp.

References map_checker< Container >::clear(), and CFeatIdRemapper::m_IdMap.

◆ RetranslateCDS()

bool RetranslateCDS ( const CSeq_feat cds,
CScope scope 
)

◆ SetBestGeneFeatIdMode()

void CFeatTree::SetBestGeneFeatIdMode ( EBestGeneFeatIdMode  mode)

◆ SetFeatIdMode()

void CFeatTree::SetFeatIdMode ( EFeatIdMode  mode)

Definition at line 2012 of file feature.cpp.

References CFeatTree::m_FeatIdMode.

◆ SetGeneCheckMode()

void CFeatTree::SetGeneCheckMode ( EGeneCheckMode  mode)

Definition at line 2018 of file feature.cpp.

References CFeatTree::m_GeneCheckMode.

◆ SetIgnoreMissingGeneXref()

void CFeatTree::SetIgnoreMissingGeneXref ( bool  ignore = true)

Definition at line 2024 of file feature.cpp.

References CFeatTree::m_IgnoreMissingGeneXref.

◆ SetSNPStrandMode()

void CFeatTree::SetSNPStrandMode ( ESNPStrandMode  mode)

Definition at line 2030 of file feature.cpp.

References CFeatTree::m_SNPStrandMode.

◆ x_AssignGenes()

void CFeatTree::x_AssignGenes ( void  )
protected

◆ x_AssignGenesByOverlap()

void CFeatTree::x_AssignGenesByOverlap ( TFeatArray features)
protected

◆ x_AssignParentByRef()

bool CFeatTree::x_AssignParentByRef ( CFeatInfo info)
protected

◆ x_AssignParents()

void CFeatTree::x_AssignParents ( void  )
protected

◆ x_AssignParentsByOverlap()

void CFeatTree::x_AssignParentsByOverlap ( TFeatArray features,
const STypeLink link 
)
protected

◆ x_FindInfo()

CFeatTree::CFeatInfo * CFeatTree::x_FindInfo ( const CSeq_feat_Handle feat)
protected

◆ x_GetChildren()

const CFeatTree::TChildren & CFeatTree::x_GetChildren ( CFeatInfo info)
protected

Definition at line 3060 of file feature.cpp.

References info, and CFeatTree::x_AssignParents().

Referenced by CFeatTree::GetChildrenTo().

◆ x_GetInfo() [1/2]

CFeatTree::CFeatInfo & CFeatTree::x_GetInfo ( const CMappedFeat feat)
protected

Definition at line 2067 of file feature.cpp.

References CMappedFeat::GetSeq_feat_Handle(), and CFeatTree::x_GetInfo().

◆ x_GetInfo() [2/2]

CFeatTree::CFeatInfo & CFeatTree::x_GetInfo ( const CSeq_feat_Handle feat)
protected

◆ x_GetParent()

CFeatTree::CFeatInfo * CFeatTree::x_GetParent ( CFeatInfo info)
protected

Definition at line 3051 of file feature.cpp.

References info, and CFeatTree::x_AssignParents().

Referenced by CFeatTree::GetParent().

◆ x_Init()

void CFeatTree::x_Init ( void  )
protected

◆ x_LookupParentByRef()

pair< int, CFeatTree::CFeatInfo * > CFeatTree::x_LookupParentByRef ( CFeatInfo info,
CSeqFeatData::ESubtype  parent_type 
)
protected

◆ x_SetGene()

void CFeatTree::x_SetGene ( CFeatInfo info,
CFeatInfo gene 
)
protected

◆ x_SetGeneRecursive()

void CFeatTree::x_SetGeneRecursive ( CFeatInfo info,
CFeatInfo gene 
)
protected

◆ x_SetNoParent()

void CFeatTree::x_SetNoParent ( CFeatInfo info)
protected

◆ x_SetParent()

void CFeatTree::x_SetParent ( CFeatInfo info,
CFeatInfo parent 
)
protected

◆ x_VerifyLinkedToRoot()

void CFeatTree::x_VerifyLinkedToRoot ( CFeatInfo info)
protected

Definition at line 3000 of file feature.cpp.

References _ASSERT, info, MSerial_AsnText, NCBI_THROW, NcbiCout, and NcbiEndl.

Referenced by CFeatTree::x_AssignParents().

◆ ~CFeatInfo()

CFeatTree::CFeatInfo::~CFeatInfo ( void  )

Definition at line 3160 of file feature.cpp.

◆ ~CFeatTree()

CFeatTree::~CFeatTree ( void  )

Destructor.

Definition at line 1966 of file feature.cpp.

Variable Documentation

◆ m_AddIndex

size_t CFeatTree::CFeatInfo::m_AddIndex

Definition at line 368 of file feature.hpp.

Referenced by PByFeatInfoAddIndex::operator()().

◆ m_AssignedGenes

size_t CFeatTree::m_AssignedGenes
protected

Definition at line 417 of file feature.hpp.

Referenced by CFeatTree::operator=(), CFeatTree::x_AssignGenes(), and CFeatTree::x_Init().

◆ m_AssignedParents

size_t CFeatTree::m_AssignedParents
protected

◆ m_BestGeneFeatIdMode

EBestGeneFeatIdMode CFeatTree::m_BestGeneFeatIdMode
protected

◆ m_CanMatchByQual

bool CFeatTree::CFeatInfo::m_CanMatchByQual

Definition at line 371 of file feature.hpp.

◆ m_Children

TChildren CFeatTree::CFeatInfo::m_Children

◆ m_Feat

CMappedFeat CFeatTree::CFeatInfo::m_Feat

◆ m_FeatIdMode

EFeatIdMode CFeatTree::m_FeatIdMode
protected

◆ m_Gene

CFeatInfo* CFeatTree::CFeatInfo::m_Gene

Definition at line 380 of file feature.hpp.

Referenced by CFeatTree::GetBestGene(), and CFeatTree::CFeatInfo::GetChildrenGene().

◆ m_GeneCheckMode

EGeneCheckMode CFeatTree::m_GeneCheckMode
protected

◆ m_IdMap

TIdMap CFeatIdRemapper::m_IdMap
private

◆ m_IgnoreMissingGeneXref

bool CFeatTree::m_IgnoreMissingGeneXref
protected

◆ m_Index

CRef<CFeatTreeIndex> CFeatTree::m_Index
protected

◆ m_InfoArray

TInfoArray CFeatTree::m_InfoArray
protected

◆ m_InfoMap

TInfoMap CFeatTree::m_InfoMap
protected

◆ m_IsLinkedToRoot

EIsLinkedToRoot CFeatTree::CFeatInfo::m_IsLinkedToRoot

Definition at line 378 of file feature.hpp.

Referenced by CFeatTree::x_SetParent().

◆ m_IsSetChildren

bool CFeatTree::CFeatInfo::m_IsSetChildren

Definition at line 372 of file feature.hpp.

Referenced by CFeatTree::x_SetParent().

◆ m_IsSetGene

bool CFeatTree::CFeatInfo::m_IsSetGene

Definition at line 372 of file feature.hpp.

Referenced by CFeatTree::CFeatInfo::IsSetGene().

◆ m_IsSetParent

bool CFeatTree::CFeatInfo::m_IsSetParent

Definition at line 372 of file feature.hpp.

Referenced by CFeatTree::CFeatInfo::IsSetParent().

◆ m_MasterRange

CRange<TSeqPos> CFeatTree::CFeatInfo::m_MasterRange

Definition at line 370 of file feature.hpp.

◆ m_MultiId

bool CFeatTree::CFeatInfo::m_MultiId

Definition at line 372 of file feature.hpp.

◆ m_Parent

CFeatInfo* CFeatTree::CFeatInfo::m_Parent

Definition at line 379 of file feature.hpp.

◆ m_RootInfo

CFeatInfo CFeatTree::m_RootInfo
protected

◆ m_SNPStrandMode

ESNPStrandMode CFeatTree::m_SNPStrandMode
protected
Modified on Sat May 25 14:20:22 2024 by modify_doxy.py rev. 669887