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NCBI C++ ToolKit: include/objmgr/util/feature.hpp Source File

SetFeatIdMode(EFeatIdMode

);

eBestGeneFeatId_always

m_BestGeneFeatIdMode;

m_GeneCheckMode;

SetGeneCheckMode(EGeneCheckMode

);

m_IgnoreMissingGeneXref;

SetIgnoreMissingGeneXref(

ignore =

);

m_SNPStrandMode;

SetSNPStrandMode(ESNPStrandMode

);

skip_bottom =

);

AddGenesForMrna(

& mrna_feat,

AddMrnasForGene(

& gene_feat,

vector<CMappedFeat> GetChildren(

& feat);

GetChildrenTo(

& feat, vector<CMappedFeat>& children);

eBestGene_OverlappedOnly

EBestGeneType lookup_type = eBestGene_TreeOnly);

m_IsSetParent;

m_Feat.GetFeatSubtype();

IsGene() || IsSetGene();

IsGene()?

: m_Gene;

m_IsSetParent, m_IsSetGene, m_IsSetChildren,

;

eIsLinkedToRoot_linking

x_AssignParents(

);

x_AssignParentsByOverlap(

& features,

x_AssignGenesByOverlap(

& features);

x_AssignGenes(

);

pair<int, CFeatInfo*>

list< CMappedFeat >& mrna_feats,

list< CMappedFeat >& cds_feats,

@Gb_qual.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

Include a standard set of the NCBI C++ Toolkit most basic headers.

int GetSubtype(CFieldNamePanel *field_name_panel, string &ncRNA_class)

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

EGeneCheckMode m_GeneCheckMode

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 necessar...

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

bool m_IgnoreMissingGeneXref

CRef< CFeatTreeIndex > m_Index

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

CRange< TSeqPos > m_MasterRange

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

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

map< CSeq_feat_Handle, CFeatInfo > TInfoMap

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

bool RetranslateCDS(const CSeq_feat &cds, CScope &scope)

RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current tr...

void ClearFeatureIds(const CSeq_entry_EditHandle &entry)

bool IsSetParent(void) const

CFeatInfo * GetChildrenGene(void)

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

pair< int, CTSE_Handle > TFullId

vector< CFeatInfo * > TChildren

bool CopyFeaturePartials(CSeq_feat &dst, const CSeq_feat &src)

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

ESNPStrandMode

Mode of processing SNP strands.

map< TFullId, int > TIdMap

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

EBestGeneFeatIdMode GetBestGeneFeatIdMode(void) const

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.

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-anno...

ELabelType

For compatibility with legacy code.

void SetBestGeneFeatIdMode(EBestGeneFeatIdMode mode)

EBestGeneFeatIdMode m_BestGeneFeatIdMode

EFeatIdMode GetFeatIdMode(void) const

ESNPStrandMode m_SNPStrandMode

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

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

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

vector< CFeatInfo * > TFeatArray

EIsLinkedToRoot m_IsLinkedToRoot

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.

bool GetIgnoreMissingGeneXref(void) const

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

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end o...

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

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

vector< CMappedFeat > GetRootFeatures(void)

Return all root features (w/o parent).

ESNPStrandMode GetSNPStrandMode(void) const

vector< CFeatInfo * > TChildren

CMappedFeat GetParentFeature(const CMappedFeat &feat)

EGeneCheckMode

Mode for taking into account best gene eGeneCheck_match will try to match a parent feature only if th...

bool IsSetGene(void) const

size_t GetFeatIdsCount(void) const

CSeqFeatData::ESubtype GetSubtype(void) const

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

EBestGeneFeatIdMode

Mode of processing feature ids.

vector< CFeatInfo * > TInfoArray

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...

int RemapId(int old_id, const CTSE_Handle &tse)

EGeneCheckMode GetGeneCheckMode(void) const

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

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

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

void ReassignFeatureIds(const CSeq_entry_EditHandle &entry)

EFeatIdMode

Mode of processing feature ids.

void GetRootFeaturesTo(vector< CMappedFeat > &children)

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

int TFeatLabelFlags

binary OR of FFeatLabelFlags

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

bool GivesGeneToChildren(void) const

@ eBestGene_AllowOverlapped

@ eIsLinkedToRoot_unknown

@ eLocationInFrame_InFrame

@ eLocationInFrame_BadStart

@ eLocationInFrame_BadStop

@ eLocationInFrame_BadStartAndStop

@ fFGL_NoComments

Leave out comments, even as fallbacks.

@ fFGL_NoQualifiers

Leave out qualifiers.

@ fFGL_Content

Include its content if there is any.

@ fFGL_Type

Always include the feature's type.

EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

virtual bool Less(const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)=0

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

int8_t Int1

1-byte (8-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJUTIL_EXPORT

static const char label[]

E_Choice

Choice variants.

#define NCBI_PACKED_ENUM_END()

#define NCBI_PACKED_ENUM_TYPE(type)

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