Feature utilities

Collaboration diagram for Feature utilities:

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

Typedefs
typedef pair< int, CTSE_Handle >	CFeatIdRemapper::TFullId
typedef map< TFullId, int >	CFeatIdRemapper::TIdMap
typedef vector< CFeatInfo * >	CFeatTree::CFeatInfo::TChildren
typedef vector< CFeatInfo * >	CFeatTree::TFeatArray
typedef vector< CFeatInfo * >	CFeatTree::TChildren
typedef map< CSeq_feat_Handle, CFeatInfo >	CFeatTree::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_feat >	CFeatIdRemapper::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< CMappedFeat >	CFeatTree::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
CFeatInfo *	CFeatTree::CFeatInfo::GetChildrenGene (void)

Variables
TIdMap	CFeatIdRemapper::m_IdMap
size_t	CFeatTree::CFeatInfo::m_AddIndex
CMappedFeat	CFeatTree::CFeatInfo::m_Feat
CRange< TSeqPos >	CFeatTree::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
CFeatInfo *	CFeatTree::CFeatInfo::m_Parent
CFeatInfo *	CFeatTree::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< CFeatTreeIndex >	CFeatTree::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_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...

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 &)
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)

Detailed Description

Typedef Documentation

TChildren [1/2]

typedef vector<CFeatInfo*> CFeatTree::CFeatInfo::TChildren

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

typedef int 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

typedef map<TFullId, int> CFeatIdRemapper::TIdMap

private

Definition at line 116 of file feature.hpp.

TInfoArray

typedef vector<CFeatInfo*> CFeatTree::TInfoArray

protected

Definition at line 415 of file feature.hpp.

TInfoMap

typedef map<CSeq_feat_Handle, CFeatInfo> CFeatTree::TInfoMap

protected

Definition at line 414 of file feature.hpp.

Enumeration Type Documentation

EBestGeneFeatIdMode

enum CFeatTree::EBestGeneFeatIdMode

Mode of processing feature ids.

Enumerator
eBestGeneFeatId_ignore
eBestGeneFeatId_always

Definition at line 212 of file feature.hpp.

EBestGeneType

enum CFeatTree::EBestGeneType

Enumerator
eBestGene_TreeOnly
eBestGene_AllowOverlapped
eBestGene_OverlappedOnly

Definition at line 330 of file feature.hpp.

EFeatIdMode

enum CFeatTree::EFeatIdMode

Mode of processing feature ids.

Enumerator
eFeatId_ignore
eFeatId_by_type
eFeatId_always

Definition at line 201 of file feature.hpp.

EGeneCheckMode

enum CFeatTree::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

enum CFeatTree::CFeatInfo::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

enum ELocationInFrame

Enumerator
eLocationInFrame_InFrame
eLocationInFrame_BadStart
eLocationInFrame_BadStop
eLocationInFrame_BadStartAndStop
eLocationInFrame_NotIn

Definition at line 531 of file feature.hpp.

ESNPStrandMode

enum CFeatTree::ESNPStrandMode

Mode of processing SNP strands.

Enumerator
eSNPStrand_same
eSNPStrand_both

Definition at line 241 of file feature.hpp.

FFeatLabelFlags

enum 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

)

Add a single feature to the tree.

Definition at line 2044 of file feature.cpp.

References _ASSERT, CMappedFeat::GetSeq_feat_Handle(), info, CFeatTree::m_InfoArray, CFeatTree::m_InfoMap, NCBI_THROW, and map_checker< Container >::size().

Referenced by CFeatTree::AddFeatures(), CFeatTree::AddFeaturesFor(), and CFeatTree::operator=().

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
	)

Definition at line 3210 of file feature.cpp.

References CFeatTree::AddFeature(), CFeatTree::AddFeaturesFor(), CMappedFeat::GetLocation(), and CSeq_feat_Handle::GetScope().

AddFeaturesFor() [2/3]

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

Definition at line 3221 of file feature.cpp.

References CFeatTree::AddFeature(), CFeatTree::AddFeaturesFor(), CSeq_feat_Handle::GetFeatSubtype(), CMappedFeat::GetLocation(), and CSeq_feat_Handle::GetScope().

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
	)

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()

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

seq	The sequence on which to add the feature
f	The feature to add
scope	The 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

seq	The Bioseq on which to create the protein feature
protein_name	The protein name
cds	The coding region for this protein feature
scope	The 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_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]

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

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]

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

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()

bool AdjustProteinMolInfoToMatchCDS	(	CMolInfo &	molinfo,
		const CSeq_feat &	cds
	)

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

Parameters

molinfo	The MolInfo to be adjusted (if necessary)
cds	The 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

)

Definition at line 3727 of file feature.cpp.

References CSeq_feat_EditHandle::ClearFeatIds(), and CSeq_feat_EditHandle::ClearFeatXrefs().

Referenced by ReassignFeatureIds().

ClearFeatureIds() [2/2]

void ClearFeatureIds

(

const CSeq_entry_EditHandle &

entry

)

Definition at line 3737 of file feature.cpp.

References CSeq_feat_EditHandle::ClearFeatIds(), and CSeq_feat_EditHandle::ClearFeatXrefs().

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

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()

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.

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()

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

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()

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

Return parent gene if exists or best overlapping gene.

Definition at line 3127 of file feature.cpp.

References CFeatTree::eBestGene_AllowOverlapped, CFeatTree::eBestGene_TreeOnly, CSeqFeatData::eSubtype_gene, CFeatTree::GetParent(), CFeatTree::CFeatInfo::m_Feat, CFeatTree::CFeatInfo::m_Gene, CFeatTree::x_AssignGenes(), and CFeatTree::x_GetInfo().

Referenced by GetBestGeneForCds(), GetBestGeneForFeat(), and GetBestGeneForMrna().

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
	)

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()

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

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()

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

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()

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

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()

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
	)

Definition at line 3462 of file feature.cpp.

References CFeatTree::GetParent(), and NCBI_THROW.

Referenced by GetBestOverlappingFeat(), CFeatureIndex::GetBestParent(), s_VerifyTree(), CGff3Writer::xAssignFeatureAttributeParentCds(), CGff3Writer::xAssignFeatureAttributeParentMrna(), CGff3Writer::xAssignFeatureAttributeParentpreRNA(), CGff3Writer::xAssignFeatureAttributeParentRegion(), and CGff3Writer::xAssignFeatureAttributeParentVDJsegmentCregion().

GetCdssForGene()

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

Definition at line 3409 of file feature.cpp.

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

Referenced by GetRelatedFeatures(), CAlignedFeatureGraph::x_GatherCluster(), and CFlatFeatureRetrieveJob::x_Run().

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
	)

Definition at line 4485 of file feature.cpp.

References sGetFeatureGeneBiotypeWrapper().

Referenced by CGff2Writer::xAssignFeatureAttributeGeneBiotype().

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
	)

Definition at line 3384 of file feature.cpp.

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

Referenced by CAlignedFeatureGraph::x_GatherCluster(), and CFlatFeatureRetrieveJob::x_Run().

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

)

Definition at line 1615 of file feature.cpp.

References CSeq_feat_Handle::GetFeatSubtype(), CMappedFeat::GetLocation(), and CSeq_feat_Handle::GetScope().

Referenced by CGtfWriter::xAssignFeatureAttributeTranscriptId().

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

Definition at line 353 of file feature.hpp.

References CSeq_feat_Handle::GetFeatSubtype(), and CFeatTree::CFeatInfo::m_Feat.

Referenced by CDisambiguator::Add(), CFeatTree::CFeatInfo::IsGene(), CFeatTree::x_AssignParentsByOverlap(), and CFeatTree::x_LookupParentByRef().

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

Definition at line 359 of file feature.hpp.

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

Referenced by CFeatTree::x_AssignGenes().

IsGene()

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

inline

Definition at line 356 of file feature.hpp.

References CSeqFeatData::eSubtype_gene, and CFeatTree::CFeatInfo::GetSubtype().

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

IsLocationInFrame()

ELocationInFrame IsLocationInFrame	(	const CSeq_feat_Handle &	cds,
		const CSeq_loc &	loc
	)

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

Definition at line 350 of file feature.hpp.

References CFeatTree::CFeatInfo::m_IsSetGene.

Referenced by CFeatTree::CFeatInfo::GivesGeneToChildren(), and CFeatTree::x_SetGeneRecursive().

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

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]

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
	)

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, compile_time_bits::range(), SAnnotSelector::SetExactDepth(), SAnnotSelector::SetLimitSeqAnnot(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveDepth(), and SAnnotSelector::SetSourceLoc().

Referenced by MapSeq_feat().

MapSeq_feat() [3/4]

CMappedFeat MapSeq_feat	(	const CSeq_feat_Handle &	feat,
		const CSeq_id_Handle &	master_id
	)

Definition at line 1019 of file feature.cpp.

References CScope::GetBioseqHandle(), CSeq_feat_Handle::GetScope(), MapSeq_feat(), and NCBI_THROW.

MapSeq_feat() [4/4]

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

Definition at line 997 of file feature.cpp.

References CScope::GetBioseqHandle(), CSeq_feat_Handle::GetScope(), MapSeq_feat(), NCBI_THROW, and compile_time_bits::range().

operator=()

CFeatTree & CFeatTree::operator=

(

const CFeatTree &

ft

)

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]

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
	)

Definition at line 835 of file feature.cpp.

References CAnnotTypes_CI::GetAnnot(), CSeq_annot_Handle::GetTSE_Handle(), local, and CFeatIdRemapper::RemapId().

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
	)

Definition at line 806 of file feature.cpp.

References int, ncbi::grid::netcache::search::fields::key, CFeatIdRemapper::m_IdMap, and map_checker< Container >::size().

Referenced by CFeatIdRemapper::RemapId(), and CFeatIdRemapper::RemapIds().

RemapIds() [1/2]

CRef< CSeq_feat > CFeatIdRemapper::RemapIds

(

const CFeat_CI &

feat_it

)

Definition at line 873 of file feature.cpp.

References CMappedFeat::GetMappedFeature(), CSeq_feat_Base::IsSetId(), CSeqFeatXref_Base::IsSetId(), CSeq_feat_Base::IsSetXref(), NON_CONST_ITERATE, CFeatIdRemapper::RemapId(), SerialClone(), CSeq_feat_Base::SetId(), CSeqFeatXref_Base::SetId(), and CSeq_feat_Base::SetXref().

RemapIds() [2/2]

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

Definition at line 853 of file feature.cpp.

References CSeq_feat_Base::IsSetId(), CSeqFeatXref_Base::IsSetId(), CSeq_feat_Base::IsSetXref(), NON_CONST_ITERATE, CFeatIdRemapper::RemapId(), CSeq_feat_Base::SetId(), CSeqFeatXref_Base::SetId(), and CSeq_feat_Base::SetXref().

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
	)

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()

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

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()

bool CFeatTree::x_AssignParentByRef ( CFeatInfo &  info )

protected

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()

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

protected

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()

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

protected

Definition at line 2095 of file feature.cpp.

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

Referenced by CFeatTree::x_LookupParentByRef().

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

Definition at line 2073 of file feature.cpp.

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

Referenced by CFeatTree::GetBestGene(), CFeatTree::GetChildrenTo(), CFeatTree::GetParent(), and CFeatTree::x_GetInfo().

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

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()

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

protected

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()

void CFeatTree::x_SetGene ( CFeatInfo &  info, CFeatInfo *  gene  )

protected

Definition at line 3043 of file feature.cpp.

References _ASSERT, and info.

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

x_SetGeneRecursive()

void CFeatTree::x_SetGeneRecursive ( CFeatInfo &  info, CFeatInfo *  gene  )

protected

Definition at line 2850 of file feature.cpp.

References info, CFeatTree::CFeatInfo::IsSetGene(), ITERATE, and CFeatTree::x_SetGene().

Referenced by CFeatTree::x_AssignGenes().

x_SetNoParent()

void CFeatTree::x_SetNoParent ( CFeatInfo &  info )

protected

Definition at line 3033 of file feature.cpp.

References _ASSERT, info, CFeatTree::CFeatInfo::m_Children, and CFeatTree::m_RootInfo.

Referenced by CFeatTree::x_AssignParents(), and CFeatTree::x_AssignParentsByOverlap().

x_SetParent()

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

protected

Definition at line 3020 of file feature.cpp.

References _ASSERT, info, CFeatTree::CFeatInfo::m_Children, CFeatTree::CFeatInfo::m_IsLinkedToRoot, and CFeatTree::CFeatInfo::m_IsSetChildren.

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

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

Definition at line 417 of file feature.hpp.

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

m_BestGeneFeatIdMode

EBestGeneFeatIdMode CFeatTree::m_BestGeneFeatIdMode

protected

Definition at line 422 of file feature.hpp.

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

m_CanMatchByQual

bool CFeatTree::CFeatInfo::m_CanMatchByQual

Definition at line 371 of file feature.hpp.

m_Children

TChildren CFeatTree::CFeatInfo::m_Children

Definition at line 381 of file feature.hpp.

Referenced by CDisambiguator::Add(), CFeatTree::GetChildrenTo(), CFeatTree::x_SetNoParent(), and CFeatTree::x_SetParent().

m_Feat

CMappedFeat CFeatTree::CFeatInfo::m_Feat

Definition at line 369 of file feature.hpp.

Referenced by CFeatTree::GetBestGene(), CFeatTree::CFeatInfo::GetSubtype(), and s_CollectBestOverlaps().

m_FeatIdMode

EFeatIdMode CFeatTree::m_FeatIdMode

protected

Definition at line 421 of file feature.hpp.

Referenced by CFeatTree::GetFeatIdMode(), CFeatTree::operator=(), CFeatTree::SetFeatIdMode(), CFeatTree::x_AssignParentByRef(), CFeatTree::x_AssignParents(), and CFeatTree::x_Init().

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

Definition at line 423 of file feature.hpp.

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

m_IdMap

TIdMap CFeatIdRemapper::m_IdMap

private

Definition at line 117 of file feature.hpp.

Referenced by CFeatIdRemapper::GetFeatIdsCount(), CFeatIdRemapper::RemapId(), and CFeatIdRemapper::Reset().

m_IgnoreMissingGeneXref

bool CFeatTree::m_IgnoreMissingGeneXref

protected

Definition at line 424 of file feature.hpp.

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

m_Index

CRef<CFeatTreeIndex> CFeatTree::m_Index

protected

Definition at line 426 of file feature.hpp.

Referenced by CFeatTree::operator=(), CFeatTree::x_AssignGenesByOverlap(), and CFeatTree::x_AssignParentsByOverlap().

m_InfoArray

TInfoArray CFeatTree::m_InfoArray

protected

Definition at line 419 of file feature.hpp.

Referenced by CFeatTree::AddFeature(), CFeatTree::operator=(), CFeatTree::x_AssignGenes(), CFeatTree::x_AssignGenesByOverlap(), CFeatTree::x_AssignParents(), and CFeatTree::x_AssignParentsByOverlap().

m_InfoMap

TInfoMap CFeatTree::m_InfoMap

protected

Definition at line 418 of file feature.hpp.

Referenced by CFeatTree::AddFeature(), CFeatTree::GetMappedFeat(), CFeatTree::operator=(), CFeatTree::x_AssignParents(), CFeatTree::x_FindInfo(), and CFeatTree::x_GetInfo().

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

Definition at line 420 of file feature.hpp.

Referenced by CFeatTree::GetChildrenTo(), CFeatTree::operator=(), and CFeatTree::x_SetNoParent().

m_SNPStrandMode

ESNPStrandMode CFeatTree::m_SNPStrandMode

protected

Definition at line 425 of file feature.hpp.

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