CSeqFeatData Class Reference

Search Toolkit Book for CSeqFeatData

#include <objects/seqfeat/SeqFeatData.hpp>

Inheritance diagram for CSeqFeatData:

Collaboration diagram for CSeqFeatData:

Classes
struct	SFeatDataInfo

Public Types
enum	EVocabulary { eVocabulary_full , eVocabulary_genbank }
	ASCII representation of subtype (GenBank feature key, e.g.) More...
enum	ESubtype {   eSubtype_bad = 0 , eSubtype_gene = 1 , eSubtype_org = 2 , eSubtype_cdregion = 3 ,   eSubtype_prot = 4 , eSubtype_preprotein = 5 , eSubtype_mat_peptide_aa = 6 , eSubtype_sig_peptide_aa = 7 ,   eSubtype_transit_peptide_aa = 8 , eSubtype_preRNA = 9 , eSubtype_mRNA = 10 , eSubtype_tRNA = 11 ,   eSubtype_rRNA = 12 , eSubtype_snRNA = 13 , eSubtype_scRNA = 14 , eSubtype_snoRNA = 15 ,   eSubtype_otherRNA = 16 , eSubtype_pub = 17 , eSubtype_seq = 18 , eSubtype_imp = 19 ,   eSubtype_allele = 20 , eSubtype_attenuator = 21 , eSubtype_C_region = 22 , eSubtype_CAAT_signal = 23 ,   eSubtype_Imp_CDS = 24 , eSubtype_conflict = 25 , eSubtype_D_loop = 26 , eSubtype_D_segment = 27 ,   eSubtype_enhancer = 28 , eSubtype_exon = 29 , eSubtype_EC_number = 30 , eSubtype_GC_signal = 31 ,   eSubtype_iDNA = 32 , eSubtype_intron = 33 , eSubtype_J_segment = 34 , eSubtype_LTR = 35 ,   eSubtype_mat_peptide = 36 , eSubtype_misc_binding = 37 , eSubtype_misc_difference = 38 , eSubtype_misc_feature = 39 ,   eSubtype_misc_recomb = 40 , eSubtype_misc_RNA = 41 , eSubtype_misc_signal = 42 , eSubtype_misc_structure = 43 ,   eSubtype_modified_base = 44 , eSubtype_mutation = 45 , eSubtype_N_region = 46 , eSubtype_old_sequence = 47 ,   eSubtype_polyA_signal = 48 , eSubtype_polyA_site = 49 , eSubtype_precursor_RNA = 50 , eSubtype_prim_transcript = 51 ,   eSubtype_primer_bind = 52 , eSubtype_promoter = 53 , eSubtype_protein_bind = 54 , eSubtype_RBS = 55 ,   eSubtype_repeat_region = 56 , eSubtype_repeat_unit = 57 , eSubtype_rep_origin = 58 , eSubtype_S_region = 59 ,   eSubtype_satellite = 60 , eSubtype_sig_peptide = 61 , eSubtype_source = 62 , eSubtype_stem_loop = 63 ,   eSubtype_STS = 64 , eSubtype_TATA_signal = 65 , eSubtype_terminator = 66 , eSubtype_transit_peptide = 67 ,   eSubtype_unsure = 68 , eSubtype_V_region = 69 , eSubtype_V_segment = 70 , eSubtype_variation = 71 ,   eSubtype_virion = 72 , eSubtype_3clip = 73 , eSubtype_3UTR = 74 , eSubtype_5clip = 75 ,   eSubtype_5UTR = 76 , eSubtype_10_signal = 77 , eSubtype_35_signal = 78 , eSubtype_gap = 79 ,   eSubtype_operon = 80 , eSubtype_oriT = 81 , eSubtype_site_ref = 82 , eSubtype_region = 83 ,   eSubtype_comment = 84 , eSubtype_bond = 85 , eSubtype_site = 86 , eSubtype_rsite = 87 ,   eSubtype_user = 88 , eSubtype_txinit = 89 , eSubtype_num = 90 , eSubtype_psec_str = 91 ,   eSubtype_non_std_residue = 92 , eSubtype_het = 93 , eSubtype_biosrc = 94 , eSubtype_ncRNA = 95 ,   eSubtype_tmRNA = 96 , eSubtype_clone = 97 , eSubtype_variation_ref = 98 , eSubtype_mobile_element = 99 ,   eSubtype_centromere = 100 , eSubtype_telomere = 101 , eSubtype_assembly_gap = 102 , eSubtype_regulatory = 103 ,   eSubtype_propeptide = 104 , eSubtype_propeptide_aa = 105 , eSubtype_max = 106 , eSubtype_any = 255 }
enum	EQualifier {   eQual_bad = 0 , eQual_allele , eQual_altitude , eQual_anticodon ,   eQual_artificial_location , eQual_bio_material , eQual_bond_type , eQual_bound_moiety ,   eQual_calculated_mol_wt , eQual_cell_line , eQual_cell_type , eQual_chloroplast ,   eQual_chromoplast , eQual_chromosome , eQual_circular_RNA , eQual_citation ,   eQual_clone , eQual_clone_lib , eQual_coded_by , eQual_codon ,   eQual_codon_start , eQual_collected_by , eQual_collection_date , eQual_compare ,   eQual_cons_splice , eQual_country , eQual_cultivar , eQual_culture_collection ,   eQual_cyanelle , eQual_db_xref , eQual_derived_from , eQual_dev_stage ,   eQual_direction , eQual_EC_number , eQual_ecotype , eQual_environmental_sample ,   eQual_estimated_length , eQual_evidence , eQual_exception , eQual_experiment ,   eQual_feat_class , eQual_focus , eQual_frequency , eQual_function ,   eQual_gap_type , eQual_gdb_xref , eQual_gene , eQual_gene_synonym ,   eQual_germline , eQual_haplogroup , eQual_haplotype , eQual_heterogen ,   eQual_host , eQual_identified_by , eQual_inference , eQual_insertion_seq ,   eQual_isolate , eQual_isolation_source , eQual_kinetoplast , eQual_lab_host ,   eQual_label , eQual_lat_lon , eQual_linkage_evidence , eQual_linkage_group ,   eQual_locus_tag , eQual_macronuclear , eQual_map , eQual_mating_type ,   eQual_metagenome_source , eQual_metagenomic , eQual_mitochondrion , eQual_mobile_element ,   eQual_mobile_element_type , eQual_mod_base , eQual_mol_type , eQual_name ,   eQual_nomenclature , eQual_non_std_residue , eQual_ncRNA_class , eQual_note ,   eQual_number , eQual_old_locus_tag , eQual_operon , eQual_organelle ,   eQual_organism , eQual_partial , eQual_PCR_conditions , eQual_PCR_primers ,   eQual_phenotype , eQual_plasmid , eQual_pop_variant , eQual_product ,   eQual_protein_id , eQual_proviral , eQual_pseudo , eQual_pseudogene ,   eQual_rearranged , eQual_recombination_class , eQual_region_name , eQual_regulatory_class ,   eQual_replace , eQual_ribosomal_slippage , eQual_rpt_family , eQual_rpt_type ,   eQual_rpt_unit , eQual_rpt_unit_range , eQual_rpt_unit_seq , eQual_satellite ,   eQual_sec_str_type , eQual_segment , eQual_sequenced_mol , eQual_serotype ,   eQual_serovar , eQual_sex , eQual_site_type , eQual_SO_type ,   eQual_specimen_voucher , eQual_standard_name , eQual_strain , eQual_submitter_seqid ,   eQual_sub_clone , eQual_sub_species , eQual_sub_strain , eQual_tag_peptide ,   eQual_tissue_lib , eQual_tissue_type , eQual_trans_splicing , eQual_transcript_id ,   eQual_transgenic , eQual_translation , eQual_transl_except , eQual_transl_table ,   eQual_transposon , eQual_type_material , eQual_UniProtKB_evidence , eQual_usedin ,   eQual_variety , eQual_virion , eQual_whole_replicon }
	List of available qualifiers for feature keys. More...
enum	EFeatureLocationAllowed { eFeatureLocationAllowed_Any = 0 , eFeatureLocationAllowed_Error , eFeatureLocationAllowed_NucOnly , eFeatureLocationAllowed_ProtOnly }
using	TLegalQualifiers = ct::const_bitset< eQual_whole_replicon+1, EQualifier >
using	TSubtypes = ct::const_bitset< eSubtype_max, ESubtype >
using	TQualifiers = TLegalQualifiers
using	TSubTypeQualifiersMap = ct::const_map< ESubtype, TQualifiers >
Public Types inherited from CSeqFeatData_Base
enum	EBond {   eBond_disulfide = 1 , eBond_thiolester = 2 , eBond_xlink = 3 , eBond_thioether = 4 ,   eBond_other = 255 }
enum	ESite {   eSite_active = 1 , eSite_binding = 2 , eSite_cleavage = 3 , eSite_inhibit = 4 ,   eSite_modified = 5 , eSite_glycosylation = 6 , eSite_myristoylation = 7 , eSite_mutagenized = 8 ,   eSite_metal_binding = 9 , eSite_phosphorylation = 10 , eSite_acetylation = 11 , eSite_amidation = 12 ,   eSite_methylation = 13 , eSite_hydroxylation = 14 , eSite_sulfatation = 15 , eSite_oxidative_deamination = 16 ,   eSite_pyrrolidone_carboxylic_acid = 17 , eSite_gamma_carboxyglutamic_acid = 18 , eSite_blocked = 19 , eSite_lipid_binding = 20 ,   eSite_np_binding = 21 , eSite_dna_binding = 22 , eSite_signal_peptide = 23 , eSite_transit_peptide = 24 ,   eSite_transmembrane_region = 25 , eSite_nitrosylation = 26 , eSite_other = 255 }
enum	EPsec_str { ePsec_str_helix = 1 , ePsec_str_sheet = 2 , ePsec_str_turn = 3 }
	protein secondary structure More...
enum	E_Choice {   e_not_set = 0 , e_Gene , e_Org , e_Cdregion ,   e_Prot , e_Rna , e_Pub , e_Seq ,   e_Imp , e_Region , e_Comment , e_Bond ,   e_Site , e_Rsite , e_User , e_Txinit ,   e_Num , e_Psec_str , e_Non_std_residue , e_Het ,   e_Biosrc , e_Clone , e_Variation }
	Choice variants. More...
enum	E_ChoiceStopper { e_MaxChoice = 23 }
	Maximum+1 value of the choice variant enumerator. More...
typedef CGene_ref	TGene
typedef COrg_ref	TOrg
typedef CCdregion	TCdregion
typedef CProt_ref	TProt
typedef CRNA_ref	TRna
typedef CPubdesc	TPub
typedef CSeq_loc	TSeq
typedef CImp_feat	TImp
typedef string	TRegion
typedef EBond	TBond
typedef ESite	TSite
typedef CRsite_ref	TRsite
typedef CUser_object	TUser
typedef CTxinit	TTxinit
typedef CNumbering	TNum
typedef EPsec_str	TPsec_str
typedef string	TNon_std_residue
typedef CHeterogen	THet
typedef CBioSource	TBiosrc
typedef CClone_ref	TClone
typedef CVariation_ref	TVariation
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CSeqFeatData (void)
	constructor More...
	~CSeqFeatData (void)
	destructor More...
string	GetKey (EVocabulary vocab=eVocabulary_full) const
ESubtype	GetSubtype (void) const
void	InvalidateSubtype (void) const
	Call after changes that could affect the subtype. More...
void	InvalidateCache (void) const
	Combine invalidation of all cached values. More...
void	SetGene (TGene &v)
TGene &	SetGene (void)
void	SetOrg (TOrg &v)
TOrg &	SetOrg (void)
void	SetCdregion (TCdregion &v)
TCdregion &	SetCdregion (void)
void	SetProt (TProt &v)
TProt &	SetProt (void)
void	SetRna (TRna &v)
TRna &	SetRna (void)
void	SetPub (TPub &v)
TPub &	SetPub (void)
void	SetSeq (TSeq &v)
TSeq &	SetSeq (void)
void	SetImp (TImp &v)
TImp &	SetImp (void)
void	SetRegion (const TRegion &v)
TRegion &	SetRegion (void)
void	SetComment (void)
void	SetBond (const TBond &v)
TBond &	SetBond (void)
void	SetSite (const TSite &v)
TSite &	SetSite (void)
void	SetRsite (TRsite &v)
TRsite &	SetRsite (void)
void	SetUser (TUser &v)
TUser &	SetUser (void)
void	SetTxinit (TTxinit &v)
TTxinit &	SetTxinit (void)
void	SetNum (TNum &v)
TNum &	SetNum (void)
void	SetPsec_str (const TPsec_str &v)
TPsec_str &	SetPsec_str (void)
void	SetNon_std_residue (const TNon_std_residue &v)
TNon_std_residue &	SetNon_std_residue (void)
void	SetHet (THet &v)
THet &	SetHet (void)
void	SetBiosrc (TBiosrc &v)
TBiosrc &	SetBiosrc (void)
void	SetClone (TClone &v)
TClone &	SetClone (void)
void	SetVariation (TVariation &v)
TVariation &	SetVariation (void)
virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Override Assign() to incorporate cache invalidation. More...
void	PostRead (void) const
	Invalidate subtype cache after deserialization. More...
bool	IsLegalQualifier (EQualifier qual) const
	Test wheather a certain qualifier is legal for the feature. More...
const TLegalQualifiers &	GetLegalQualifiers (void) const
	Get a list of all the legal qualifiers for the feature. More...
const TQualifiers &	GetMandatoryQualifiers (void) const
	Get the list of all mandatory qualifiers for the feature. More...
Public Member Functions inherited from CSeqFeatData_Base
	CSeqFeatData_Base (void)
virtual	~CSeqFeatData_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
virtual void	Reset (void)
	Reset the whole object. More...
virtual void	ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	Which (void) const
	Which variant is currently selected. More...
void	CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
void	Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	IsGene (void) const
	Check if variant Gene is selected. More...
const TGene &	GetGene (void) const
	Get the variant data. More...
TGene &	SetGene (void)
	Select the variant. More...
void	SetGene (TGene &value)
	Select the variant and set its data. More...
bool	IsOrg (void) const
	Check if variant Org is selected. More...
const TOrg &	GetOrg (void) const
	Get the variant data. More...
TOrg &	SetOrg (void)
	Select the variant. More...
void	SetOrg (TOrg &value)
	Select the variant and set its data. More...
bool	IsCdregion (void) const
	Check if variant Cdregion is selected. More...
const TCdregion &	GetCdregion (void) const
	Get the variant data. More...
TCdregion &	SetCdregion (void)
	Select the variant. More...
void	SetCdregion (TCdregion &value)
	Select the variant and set its data. More...
bool	IsProt (void) const
	Check if variant Prot is selected. More...
const TProt &	GetProt (void) const
	Get the variant data. More...
TProt &	SetProt (void)
	Select the variant. More...
void	SetProt (TProt &value)
	Select the variant and set its data. More...
bool	IsRna (void) const
	Check if variant Rna is selected. More...
const TRna &	GetRna (void) const
	Get the variant data. More...
TRna &	SetRna (void)
	Select the variant. More...
void	SetRna (TRna &value)
	Select the variant and set its data. More...
bool	IsPub (void) const
	Check if variant Pub is selected. More...
const TPub &	GetPub (void) const
	Get the variant data. More...
TPub &	SetPub (void)
	Select the variant. More...
void	SetPub (TPub &value)
	Select the variant and set its data. More...
bool	IsSeq (void) const
	Check if variant Seq is selected. More...
const TSeq &	GetSeq (void) const
	Get the variant data. More...
TSeq &	SetSeq (void)
	Select the variant. More...
void	SetSeq (TSeq &value)
	Select the variant and set its data. More...
bool	IsImp (void) const
	Check if variant Imp is selected. More...
const TImp &	GetImp (void) const
	Get the variant data. More...
TImp &	SetImp (void)
	Select the variant. More...
void	SetImp (TImp &value)
	Select the variant and set its data. More...
bool	IsRegion (void) const
	Check if variant Region is selected. More...
const TRegion &	GetRegion (void) const
	Get the variant data. More...
TRegion &	SetRegion (void)
	Select the variant. More...
void	SetRegion (const TRegion &value)
	Select the variant and set its data. More...
bool	IsComment (void) const
	Check if variant Comment is selected. More...
void	SetComment (void)
	Select the variant. More...
bool	IsBond (void) const
	Check if variant Bond is selected. More...
TBond	GetBond (void) const
	Get the variant data. More...
TBond &	SetBond (void)
	Select the variant. More...
void	SetBond (TBond value)
	Select the variant and set its data. More...
bool	IsSite (void) const
	Check if variant Site is selected. More...
TSite	GetSite (void) const
	Get the variant data. More...
TSite &	SetSite (void)
	Select the variant. More...
void	SetSite (TSite value)
	Select the variant and set its data. More...
bool	IsRsite (void) const
	Check if variant Rsite is selected. More...
const TRsite &	GetRsite (void) const
	Get the variant data. More...
TRsite &	SetRsite (void)
	Select the variant. More...
void	SetRsite (TRsite &value)
	Select the variant and set its data. More...
bool	IsUser (void) const
	Check if variant User is selected. More...
const TUser &	GetUser (void) const
	Get the variant data. More...
TUser &	SetUser (void)
	Select the variant. More...
void	SetUser (TUser &value)
	Select the variant and set its data. More...
bool	IsTxinit (void) const
	Check if variant Txinit is selected. More...
const TTxinit &	GetTxinit (void) const
	Get the variant data. More...
TTxinit &	SetTxinit (void)
	Select the variant. More...
void	SetTxinit (TTxinit &value)
	Select the variant and set its data. More...
bool	IsNum (void) const
	Check if variant Num is selected. More...
const TNum &	GetNum (void) const
	Get the variant data. More...
TNum &	SetNum (void)
	Select the variant. More...
void	SetNum (TNum &value)
	Select the variant and set its data. More...
bool	IsPsec_str (void) const
	Check if variant Psec_str is selected. More...
TPsec_str	GetPsec_str (void) const
	Get the variant data. More...
TPsec_str &	SetPsec_str (void)
	Select the variant. More...
void	SetPsec_str (TPsec_str value)
	Select the variant and set its data. More...
bool	IsNon_std_residue (void) const
	Check if variant Non_std_residue is selected. More...
const TNon_std_residue &	GetNon_std_residue (void) const
	Get the variant data. More...
TNon_std_residue &	SetNon_std_residue (void)
	Select the variant. More...
void	SetNon_std_residue (const TNon_std_residue &value)
	Select the variant and set its data. More...
bool	IsHet (void) const
	Check if variant Het is selected. More...
const THet &	GetHet (void) const
	Get the variant data. More...
THet &	SetHet (void)
	Select the variant. More...
void	SetHet (const THet &value)
	Select the variant and set its data. More...
bool	IsBiosrc (void) const
	Check if variant Biosrc is selected. More...
const TBiosrc &	GetBiosrc (void) const
	Get the variant data. More...
TBiosrc &	SetBiosrc (void)
	Select the variant. More...
void	SetBiosrc (TBiosrc &value)
	Select the variant and set its data. More...
bool	IsClone (void) const
	Check if variant Clone is selected. More...
const TClone &	GetClone (void) const
	Get the variant data. More...
TClone &	SetClone (void)
	Select the variant. More...
void	SetClone (TClone &value)
	Select the variant and set its data. More...
bool	IsVariation (void) const
	Check if variant Variation is selected. More...
const TVariation &	GetVariation (void) const
	Get the variant data. More...
TVariation &	SetVariation (void)
	Select the variant. More...
void	SetVariation (TVariation &value)
	Select the variant and set its data. More...
Public Member Functions inherited from CSerialObject
	CSerialObject (void)
virtual	~CSerialObject (void)
virtual const CTypeInfo *	GetThisTypeInfo (void) const =0
virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
void	ThrowUnassigned (TMemberIndex index) const
void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...
const string &	GetNamespaceName (void) const
	Get namespace name. More...
bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...
const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Static Public Member Functions
static E_Choice	GetTypeFromSubtype (ESubtype subtype)
static CTempString	SubtypeValueToName (ESubtype eSubtype)
	Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum. More...
static ESubtype	SubtypeNameToValue (CTempString sName)
	Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum. More...
static bool	CanHaveGene (ESubtype subtype)
static bool	IsLegalQualifier (ESubtype subtype, EQualifier qual)
static const TLegalQualifiers &	GetLegalQualifiers (ESubtype subtype)
static const TQualifiers &	GetMandatoryQualifiers (ESubtype subtype)
static CTempString	GetQualifierAsString (EQualifier qual)
	Convert a qualifier from an enumerated value to a string representation or empty if not found. More...
static EQualifier	GetQualifierType (CTempString qual)
	convert qual string to enumerated value More...
static std::pair< EQualifier, CTempString >	GetQualifierTypeAndValue (CTempString qual)
static const CFeatList *	GetFeatList ()
static const CBondList *	GetBondList ()
static const CSiteList *	GetSiteList ()
static bool	IsRegulatory (ESubtype subtype)
static const string &	GetRegulatoryClass (ESubtype subtype)
static ESubtype	GetRegulatoryClass (const string &class_name)
static const vector< string > &	GetRegulatoryClassList ()
static bool	FixRegulatoryClassValue (string &val)
static const vector< string > &	GetRecombinationClassList ()
static bool	IsDiscouragedSubtype (ESubtype subtype)
static bool	IsDiscouragedQual (EQualifier qual)
static EFeatureLocationAllowed	AllowedFeatureLocation (ESubtype subtype)
static bool	AllowStrandBoth (ESubtype subtype)
static bool	RequireLocationIntervalsInBiologicalOrder (ESubtype subtype)
static bool	AllowAdjacentIntervals (ESubtype subtype)
static bool	ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, const CGb_qual &qual)
static bool	ShouldRepresentAsGbqual (CSeqFeatData::ESubtype feat_subtype, CSeqFeatData::EQualifier qual_type)
static void	s_InitXrefAllowedSubtypesTable (void)
static void	s_InitXrefProhibitedSubtypesTable (void)
static bool	AllowXref (CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
static bool	ProhibitXref (CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
static bool	FixImportKey (string &key)
static bool	IsLegalProductNameForRibosomalSlippage (const string &product_name)
Static Public Member Functions inherited from CSeqFeatData_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EBond (void)
	Access to EBond's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ESite (void)
	Access to ESite's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EPsec_str (void)
	Access to EPsec_str's attributes (values, names) as defined in spec. More...
static string	SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)
static void	SetVerifyDataGlobal (ESerialVerifyData verify)
static string	UnassignedString (void)
static CStringUTF8	UnassignedStringUTF8 (void)
static char	UnassignedByte (void)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Private Types
typedef CSeqFeatData_Base	Tparent
typedef CStaticArraySet< ESubtype >	TSubtypeSet

Private Member Functions
void	x_InitFeatDataInfo (void) const
	CSeqFeatData (const CSeqFeatData &value)
CSeqFeatData &	operator= (const CSeqFeatData &value)

Static Private Member Functions
static void	s_InitSubtypesTable (void)
static const TSubTypeQualifiersMap &	s_GetLegalQualMap () noexcept
static const TSubtypeSet &	GetSetOfRegulatorySubtypes ()

Private Attributes
SFeatDataInfo	m_FeatDataInfo

Additional Inherited Members
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<*unassigned*>"
static const char	ms_UnassignedByte = char(0xcd)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 112 of file SeqFeatData.hpp.

Member Typedef Documentation

TLegalQualifiers

using CSeqFeatData::TLegalQualifiers = ct::const_bitset<eQual_whole_replicon + 1, EQualifier>

Definition at line 468 of file SeqFeatData.hpp.

Tparent

typedef CSeqFeatData_Base CSeqFeatData::Tparent

private

Definition at line 114 of file SeqFeatData.hpp.

TQualifiers

using CSeqFeatData::TQualifiers = TLegalQualifiers

Definition at line 470 of file SeqFeatData.hpp.

TSubTypeQualifiersMap

using CSeqFeatData::TSubTypeQualifiersMap = ct::const_map<ESubtype, TQualifiers>

Definition at line 471 of file SeqFeatData.hpp.

TSubtypes

using CSeqFeatData::TSubtypes = ct::const_bitset<eSubtype_max, ESubtype>

Definition at line 469 of file SeqFeatData.hpp.

TSubtypeSet

typedef CStaticArraySet<ESubtype> CSeqFeatData::TSubtypeSet

private

Definition at line 551 of file SeqFeatData.hpp.

Member Enumeration Documentation

EFeatureLocationAllowed

enum CSeqFeatData::EFeatureLocationAllowed

Enumerator
eFeatureLocationAllowed_Any
eFeatureLocationAllowed_Error
eFeatureLocationAllowed_NucOnly
eFeatureLocationAllowed_ProtOnly

Definition at line 508 of file SeqFeatData.hpp.

EQualifier

enum CSeqFeatData::EQualifier

List of available qualifiers for feature keys.

For more information see: The DDBJ/EMBL/GenBank Feature Table: Definition (http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html)

Enumerator
eQual_bad
eQual_allele
eQual_altitude
eQual_anticodon
eQual_artificial_location
eQual_bio_material
eQual_bond_type
eQual_bound_moiety
eQual_calculated_mol_wt
eQual_cell_line
eQual_cell_type
eQual_chloroplast
eQual_chromoplast
eQual_chromosome
eQual_circular_RNA
eQual_citation
eQual_clone
eQual_clone_lib
eQual_coded_by
eQual_codon
eQual_codon_start
eQual_collected_by
eQual_collection_date
eQual_compare
eQual_cons_splice
eQual_country
eQual_cultivar
eQual_culture_collection
eQual_cyanelle
eQual_db_xref
eQual_derived_from
eQual_dev_stage
eQual_direction
eQual_EC_number
eQual_ecotype
eQual_environmental_sample
eQual_estimated_length
eQual_evidence
eQual_exception
eQual_experiment
eQual_feat_class
eQual_focus
eQual_frequency
eQual_function
eQual_gap_type
eQual_gdb_xref
eQual_gene
eQual_gene_synonym
eQual_germline
eQual_haplogroup
eQual_haplotype
eQual_heterogen
eQual_host
eQual_identified_by
eQual_inference
eQual_insertion_seq
eQual_isolate
eQual_isolation_source
eQual_kinetoplast
eQual_lab_host
eQual_label
eQual_lat_lon
eQual_linkage_evidence
eQual_linkage_group
eQual_locus_tag
eQual_macronuclear
eQual_map
eQual_mating_type
eQual_metagenome_source
eQual_metagenomic
eQual_mitochondrion
eQual_mobile_element
eQual_mobile_element_type
eQual_mod_base
eQual_mol_type
eQual_name
eQual_nomenclature
eQual_non_std_residue
eQual_ncRNA_class
eQual_note
eQual_number
eQual_old_locus_tag
eQual_operon
eQual_organelle
eQual_organism
eQual_partial
eQual_PCR_conditions
eQual_PCR_primers
eQual_phenotype
eQual_plasmid
eQual_pop_variant
eQual_product
eQual_protein_id
eQual_proviral
eQual_pseudo
eQual_pseudogene
eQual_rearranged
eQual_recombination_class
eQual_region_name
eQual_regulatory_class
eQual_replace
eQual_ribosomal_slippage
eQual_rpt_family
eQual_rpt_type
eQual_rpt_unit
eQual_rpt_unit_range
eQual_rpt_unit_seq
eQual_satellite
eQual_sec_str_type
eQual_segment
eQual_sequenced_mol
eQual_serotype
eQual_serovar
eQual_sex
eQual_site_type
eQual_SO_type
eQual_specimen_voucher
eQual_standard_name
eQual_strain
eQual_submitter_seqid
eQual_sub_clone
eQual_sub_species
eQual_sub_strain
eQual_tag_peptide
eQual_tissue_lib
eQual_tissue_type
eQual_trans_splicing
eQual_transcript_id
eQual_transgenic
eQual_translation
eQual_transl_except
eQual_transl_table
eQual_transposon
eQual_type_material
eQual_UniProtKB_evidence
eQual_usedin
eQual_variety
eQual_virion
eQual_whole_replicon

Definition at line 325 of file SeqFeatData.hpp.

ESubtype

enum CSeqFeatData::ESubtype

Enumerator
eSubtype_bad	These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.
eSubtype_gene
eSubtype_org
eSubtype_cdregion
eSubtype_prot
eSubtype_preprotein
eSubtype_mat_peptide_aa
eSubtype_sig_peptide_aa
eSubtype_transit_peptide_aa
eSubtype_preRNA
eSubtype_mRNA
eSubtype_tRNA
eSubtype_rRNA
eSubtype_snRNA
eSubtype_scRNA
eSubtype_snoRNA
eSubtype_otherRNA
eSubtype_pub
eSubtype_seq
eSubtype_imp
eSubtype_allele
eSubtype_attenuator
eSubtype_C_region
eSubtype_CAAT_signal
eSubtype_Imp_CDS
eSubtype_conflict
eSubtype_D_loop
eSubtype_D_segment
eSubtype_enhancer
eSubtype_exon
eSubtype_EC_number
eSubtype_GC_signal
eSubtype_iDNA
eSubtype_intron
eSubtype_J_segment
eSubtype_LTR
eSubtype_mat_peptide
eSubtype_misc_binding
eSubtype_misc_difference
eSubtype_misc_feature
eSubtype_misc_recomb
eSubtype_misc_RNA
eSubtype_misc_signal
eSubtype_misc_structure
eSubtype_modified_base
eSubtype_mutation
eSubtype_N_region
eSubtype_old_sequence
eSubtype_polyA_signal
eSubtype_polyA_site
eSubtype_precursor_RNA
eSubtype_prim_transcript
eSubtype_primer_bind
eSubtype_promoter
eSubtype_protein_bind
eSubtype_RBS
eSubtype_repeat_region
eSubtype_repeat_unit
eSubtype_rep_origin
eSubtype_S_region
eSubtype_satellite
eSubtype_sig_peptide
eSubtype_source
eSubtype_stem_loop
eSubtype_STS
eSubtype_TATA_signal
eSubtype_terminator
eSubtype_transit_peptide
eSubtype_unsure
eSubtype_V_region
eSubtype_V_segment
eSubtype_variation
eSubtype_virion
eSubtype_3clip
eSubtype_3UTR
eSubtype_5clip
eSubtype_5UTR
eSubtype_10_signal
eSubtype_35_signal
eSubtype_gap
eSubtype_operon
eSubtype_oriT
eSubtype_site_ref
eSubtype_region
eSubtype_comment
eSubtype_bond
eSubtype_site
eSubtype_rsite
eSubtype_user
eSubtype_txinit
eSubtype_num
eSubtype_psec_str
eSubtype_non_std_residue
eSubtype_het
eSubtype_biosrc
eSubtype_ncRNA
eSubtype_tmRNA
eSubtype_clone
eSubtype_variation_ref
eSubtype_mobile_element
eSubtype_centromere
eSubtype_telomere
eSubtype_assembly_gap
eSubtype_regulatory
eSubtype_propeptide
eSubtype_propeptide_aa
eSubtype_max
eSubtype_any

Definition at line 128 of file SeqFeatData.hpp.

EVocabulary

enum CSeqFeatData::EVocabulary

ASCII representation of subtype (GenBank feature key, e.g.)

Enumerator
eVocabulary_full
eVocabulary_genbank

Definition at line 122 of file SeqFeatData.hpp.

Constructor & Destructor Documentation

CSeqFeatData() [1/2]

CSeqFeatData::CSeqFeatData

(

void

)

constructor

Definition at line 60 of file SeqFeatData.cpp.

References InvalidateCache().

~CSeqFeatData()

CSeqFeatData::~CSeqFeatData

(

void

)

destructor

Definition at line 345 of file SeqFeatData.cpp.

CSeqFeatData() [2/2]

CSeqFeatData::CSeqFeatData ( const CSeqFeatData &  value )

private

Member Function Documentation

AllowAdjacentIntervals()

bool CSeqFeatData::AllowAdjacentIntervals ( CSeqFeatData::ESubtype  feat_subtype )

static

Definition at line 4537 of file SeqFeatData.cpp.

References eSubtype_het, eSubtype_misc_recomb, eSubtype_primer_bind, and eSubtype_pub.

Referenced by CValidError_imp::ValidateSeqLoc().

AllowedFeatureLocation()

CSeqFeatData::EFeatureLocationAllowed CSeqFeatData::AllowedFeatureLocation ( ESubtype  subtype )

static

Definition at line 4453 of file SeqFeatData.cpp.

References eFeatureLocationAllowed_Any, eFeatureLocationAllowed_Error, eFeatureLocationAllowed_NucOnly, eFeatureLocationAllowed_ProtOnly, eSubtype_any, eSubtype_bad, eSubtype_bond, eSubtype_mat_peptide_aa, eSubtype_max, eSubtype_non_std_residue, eSubtype_preprotein, eSubtype_propeptide_aa, eSubtype_prot, eSubtype_psec_str, eSubtype_pub, eSubtype_region, eSubtype_sig_peptide_aa, eSubtype_site, and eSubtype_transit_peptide_aa.

Referenced by BOOST_AUTO_TEST_CASE(), CSequenceEditingEventHandler::GetFeatureLocation(), CAlignmentAssistant::IsSelectionAndClean(), CEditSequence::IsSelectionAndClean(), CDiscrepancyVisitorImpl< _Name >::Summarize(), and CSequenceEditingEventHandler::x_IsLocationOkForFeatCmd().

AllowStrandBoth()

bool CSeqFeatData::AllowStrandBoth ( ESubtype  subtype )

static

Definition at line 4487 of file SeqFeatData.cpp.

References eSubtype_assembly_gap, eSubtype_centromere, eSubtype_LTR, eSubtype_misc_binding, eSubtype_misc_difference, eSubtype_misc_feature, eSubtype_misc_recomb, eSubtype_misc_structure, eSubtype_mobile_element, eSubtype_protein_bind, eSubtype_regulatory, eSubtype_rep_origin, eSubtype_repeat_region, eSubtype_S_region, eSubtype_telomere, and eSubtype_variation.

Referenced by CNewCleanup_imp::SeqfeatBC(), and CSingleFeatValidator::x_ValidateBothStrands().

AllowXref()

bool CSeqFeatData::AllowXref ( CSeqFeatData::ESubtype  subtype1, CSeqFeatData::ESubtype  subtype2  )

static

Definition at line 3745 of file SeqFeatData.cpp.

References grid::netschedule::limits::Check().

Referenced by CFeatureGenePanel::AddReciprocicalXref(), BOOST_AUTO_TEST_CASE(), CCleanup::RepairXrefs(), and CValidError_feat::ValidateOneFeatXrefPair().

Assign()

void CSeqFeatData::Assign ( const CSerialObject &  source, ESerialRecursionMode  how = eRecursive  )

virtual

Override Assign() to incorporate cache invalidation.

Reimplemented from CSerialObject.

Definition at line 370 of file SeqFeatData.cpp.

References CSerialObject::Assign(), InvalidateCache(), and rapidjson::source.

CanHaveGene()

bool CSeqFeatData::CanHaveGene ( CSeqFeatData::ESubtype  subtype )

static

Definition at line 522 of file SeqFeatData.cpp.

References eSubtype_assembly_gap, eSubtype_biosrc, eSubtype_centromere, eSubtype_gap, eSubtype_operon, eSubtype_rep_origin, and eSubtype_telomere.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature().

FixImportKey()

bool CSeqFeatData::FixImportKey ( string &  key )

static

Definition at line 4664 of file SeqFeatData.cpp.

References NStr::Equal(), NStr::EqualNocase(), ncbi::grid::netcache::search::fields::key, kImportTable, kImportTableEnd, and SImportEntry::m_Name.

Referenced by BOOST_AUTO_TEST_CASE(), and CNewCleanup_imp::ImpFeatBC().

FixRegulatoryClassValue()

bool CSeqFeatData::FixRegulatoryClassValue ( string &  val )

static

Definition at line 3943 of file SeqFeatData.cpp.

References NStr::FindNoCase(), GetRegulatoryClassList(), and val.

Referenced by CNewCleanup_imp::GBQualBC().

GetBondList()

const CBondList * CSeqFeatData::GetBondList ( )

static

Definition at line 3771 of file SeqFeatData.cpp.

References DEFINE_STATIC_MUTEX().

Referenced by CMacroEditorContext::GetBondTypes(), and CFeatureTableReader_Imp::x_AddQualifierToFeature().

GetFeatList()

const CFeatList * CSeqFeatData::GetFeatList ( )

static

Definition at line 3757 of file SeqFeatData.cpp.

References DEFINE_STATIC_MUTEX().

Referenced by CFieldChoicePanel::AutoMatchFeat(), CFeatureGraph::CFeatureGraph(), CGeneModelTrack::CGeneModelTrack(), CFeatureTrackFactory::CloneTrack(), CTrackConfigManager::CreateTrackConfig(), CFeatureTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), CSearchFormBase::CSearchFormBase(), CDataTrackUtils::FeatSubtypes2TrackSubtypes(), CSeqTextPaneConfig::GetCaseFeature(), CSeqTextPaneConfig::GetCaseFeatureSubtype(), CFuseFeaturesDlg::GetCommand(), CRmDupFeaturesDlg::GetCommand(), CSeqGraphicConfig::GetFeatParams(), CSettingsSet::GetFeatReadKey(), NMacroUtil::GetFeatSubtype(), CSeqGraphicPane::GetFeatureNames(), CSettingsSet::GetFeatWriteKey(), CHistParamsManager::GetHistParams(), CHistogramGlyph::GetHTMLActiveAreas(), CGeneModelFactory::GetMatchedAnnots(), CAllOtherFeaturesTrackFactory::GetSettings(), CFeatureTrackFactory::GetSettings(), GetSortedFeatList(), CGuiObjectInfoSeq_feat::GetSubtype(), CHistogramGlyph::GetTooltip(), CHistParamsManager::HasSettings(), CwxTrackSettingsDlg::InitTrackTypes(), CHistogramGlyph::IsClickable(), CAlignmentTrack::OnChangeProjectedFeats(), CFeatureTypeSubpanel::OnSelectButton(), CAllOtherFeaturesTrack::ReinitNASubtracks(), CHistogramGlyph::RunSettingsDialog(), s_GetFeatSubtypeStr(), CSeqTextPaneConfig::SetCaseFeature(), CFeatureTypeSubpanel::SetClusters(), CFeatureTrack::SetFeatSubtype(), CFeatureTrack::x_AddHistogram(), CAlignedFeatureGraph::x_GetTooltip(), CFeatureCreateDialog::x_InitFeatTypes(), CFeatureCheckPanel::x_InitTree(), CFeatureSearchForm::x_LoadSettings(), and CAllOtherFeaturesTrack::x_ReinitSubtracks().

GetKey()

string CSeqFeatData::GetKey

(

EVocabulary

vocab = eVocabulary_full

)

const

Definition at line 351 of file SeqFeatData.cpp.

References eSubtype_any, eVocabulary_genbank, m_FeatDataInfo, CSeqFeatData::SFeatDataInfo::m_Key_full, CSeqFeatData::SFeatDataInfo::m_Key_gb, CSeqFeatData::SFeatDataInfo::m_Subtype, and x_InitFeatDataInfo().

Referenced by CGffRecord::AssignType(), CEditObjectSeq_feat::CreateWindowImpl(), CAnnotCompareDS::DumpTextReport(), CFeatureItemBase::GetKey(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CBioseqEditor::OnCreateFeature(), CGffFeatureRecord::SetGbKeyFrom(), CValidError_feat::ValidateOneFeatXrefPair(), CFastaOstreamEx::x_AddGBkeyAttribute(), CSingleFeatValidator::x_ValidateGbquals(), and CSingleFeatValidator::x_ValidateNonImpFeat().

GetLegalQualifiers() [1/2]

const CSeqFeatData::TLegalQualifiers & CSeqFeatData::GetLegalQualifiers ( ESubtype  subtype )

static

Definition at line 2997 of file SeqFeatData.cpp.

References compile_time_bits::const_set_map_base< _Traits, _Backend, _Duplicates >::find(), and s_GetLegalQualMap().

GetLegalQualifiers() [2/2]

const CSeqFeatData::TLegalQualifiers & CSeqFeatData::GetLegalQualifiers ( void  ) const

inline

Get a list of all the legal qualifiers for the feature.

Definition at line 580 of file SeqFeatData.hpp.

References GetSubtype().

Referenced by BOOST_AUTO_TEST_CASE(), CGBQualPanel::CreateControls(), CMacroEditorContext::GetLegalQualifiers(), CFeatureTypePanel::ListPresentFeaturesFirst(), CFeatureFieldNamePanel::s_FillFeatQualList(), CMacroFeatsOnSeqPanel::x_GetFeatureChoices(), and CFeatureCreateDialog::x_UpdateQualifiers().

GetMandatoryQualifiers() [1/2]

const CSeqFeatData::TQualifiers & CSeqFeatData::GetMandatoryQualifiers ( ESubtype  subtype )

static

Definition at line 544 of file SeqFeatData.cpp.

References eQual_bound_moiety, eQual_citation, eQual_estimated_length, eQual_gap_type, eQual_mobile_element_type, eQual_mod_base, eQual_ncRNA_class, eQual_operon, eQual_organism, eQual_regulatory_class, eSubtype_assembly_gap, eSubtype_conflict, eSubtype_gap, eSubtype_misc_binding, eSubtype_mobile_element, eSubtype_modified_base, eSubtype_ncRNA, eSubtype_old_sequence, eSubtype_operon, eSubtype_protein_bind, eSubtype_regulatory, eSubtype_source, and MAKE_CONST_MAP.

GetMandatoryQualifiers() [2/2]

const CSeqFeatData::TQualifiers & CSeqFeatData::GetMandatoryQualifiers ( void  ) const

inline

Get the list of all mandatory qualifiers for the feature.

Definition at line 587 of file SeqFeatData.hpp.

References GetSubtype().

Referenced by BOOST_AUTO_TEST_CASE(), CEditObjectSeq_feat::CanClose(), CGBQualPanel::CreateControls(), ParseFeatureBlock(), CSingleFeatValidator::x_ValidateImpFeatQuals(), CSingleFeatValidator::x_ValidateNonImpFeat(), XGBFeatKeyQualValid(), and XMLParseFeatureBlock().

GetQualifierAsString()

static CTempString CSeqFeatData::GetQualifierAsString ( EQualifier  qual )

static

Convert a qualifier from an enumerated value to a string representation or empty if not found.

Referenced by CFieldChoicePanel::AutoMatchFeat(), BOOST_AUTO_TEST_CASE(), CEditObjectSeq_feat::CanClose(), CGBQualPanel::CreateControls(), CMacroEditorContext::GetLegalQualifiers(), ParseFeatureBlock(), CFeatureFieldNamePanel::s_FillFeatQualList(), CFeatureTableReader_Imp::x_AddGBQualToFeature(), CFeatureCreateDialog::x_UpdateQualifiers(), CSingleFeatValidator::x_ValidateImpFeatQuals(), CSingleFeatValidator::x_ValidateNonImpFeat(), XGBFeatKeyQualValid(), and XMLParseFeatureBlock().

GetQualifierType()

CSeqFeatData::EQualifier CSeqFeatData::GetQualifierType ( CTempString  qual )

static

convert qual string to enumerated value

Definition at line 3170 of file SeqFeatData.cpp.

References eQual_bad.

Referenced by CEditObjectSeq_feat::CanClose(), CheckLegalQual(), CConvertCDSToMiscFeat::Convert(), CGBQualPanel::CreateControls(), CFeatTableEdit::EliminateBadQualifiers(), GBQualSemanticValid(), NMItemData::GetEditableFieldForPair(), CMacroEditorContext::GetGUIFieldName(), NMItemData::GetMemberNames(), CWrongIllegalQuals::IllegalQualsToNote(), CGBQualPanel::PanelNeeded(), CGBQualPanel::PopulateGBQuals(), CWrongIllegalQuals::RmIllegalQuals(), CWrongIllegalQuals::RmWrongOrIllegalQuals(), CWrongIllegalQuals::RmWrongQuals(), ScanEmbedQual(), ShouldRepresentAsGbqual(), CWrongIllegalQuals::WrongQualsToNote(), CFeatureTableReader_Imp::x_AddGBQualToFeature(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CSingleFeatValidator::x_ValidateImpFeatQuals(), CSingleFeatValidator::x_ValidateNonImpFeat(), and XGBFeatKeyQualValid().

GetQualifierTypeAndValue()

std::pair< CSeqFeatData::EQualifier, CTempString > CSeqFeatData::GetQualifierTypeAndValue ( CTempString  qual )

static

Definition at line 3179 of file SeqFeatData.cpp.

References eQual_bad, kEmptyStr, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), and CSingleFeatValidator::x_ValidateGbquals().

GetRecombinationClassList()

const vector< string > & CSeqFeatData::GetRecombinationClassList ( )

static

Definition at line 3960 of file SeqFeatData.cpp.

Referenced by s_IsValidRecombinationClass(), and CGff3Writer::xAssignFeatureAttributeNote().

GetRegulatoryClass() [1/2]

CSeqFeatData::ESubtype CSeqFeatData::GetRegulatoryClass ( const string &  class_name )

static

Definition at line 3874 of file SeqFeatData.cpp.

References _ASSERT, eSubtype_bad, GetRegulatoryClass(), GetSetOfRegulatorySubtypes(), ITERATE, AutoPtr< X, Del >::release(), and CStaticArraySearchBase< KeyValueGetter, KeyCompare >::size().

GetRegulatoryClass() [2/2]

const string & CSeqFeatData::GetRegulatoryClass ( ESubtype  subtype )

static

Definition at line 3809 of file SeqFeatData.cpp.

References _ASSERT, ArraySize(), eSubtype_10_signal, eSubtype_35_signal, eSubtype_misc_signal, eSubtype_polyA_signal, eSubtype_RBS, eSubtype_TATA_signal, GetSetOfRegulatorySubtypes(), IsRegulatory(), ITERATE, ITERATE_0_IDX, kEmptyStr, AutoPtr< X, Del >::release(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::size(), and SubtypeValueToName().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRegulatoryFeature(), GetRegulatoryClass(), CNewCleanup_imp::ImpFeatBC(), and IsRBS().

GetRegulatoryClassList()

const vector< string > & CSeqFeatData::GetRegulatoryClassList ( )

static

Definition at line 3910 of file SeqFeatData.cpp.

Referenced by CSingleGbQualSubPanel::CreateControls(), FixRegulatoryClassValue(), s_IsValidRegulatoryClass(), CImpFeatValidator::Validate(), CFeatureTableReader_Imp::x_AddQualifierToImp(), and CGff3Writer::xAssignFeatureAttributeNote().

GetSetOfRegulatorySubtypes()

const CSeqFeatData::TSubtypeSet & CSeqFeatData::GetSetOfRegulatorySubtypes ( void  )

staticprivate

Definition at line 4428 of file SeqFeatData.cpp.

References DEFINE_STATIC_ARRAY_MAP_WITH_COPY, eSubtype_10_signal, eSubtype_35_signal, eSubtype_attenuator, eSubtype_CAAT_signal, eSubtype_enhancer, eSubtype_GC_signal, eSubtype_LTR, eSubtype_misc_signal, eSubtype_polyA_signal, eSubtype_promoter, eSubtype_RBS, eSubtype_TATA_signal, and eSubtype_terminator.

Referenced by GetRegulatoryClass(), and IsRegulatory().

GetSiteList()

const CSiteList * CSeqFeatData::GetSiteList ( )

static

Definition at line 3786 of file SeqFeatData.cpp.

References DEFINE_STATIC_MUTEX().

Referenced by CMacroEditorContext::GetSiteTypes(), and CFeatureTableReader_Imp::x_AddQualifierToFeature().

GetSubtype()

CSeqFeatData::ESubtype CSeqFeatData::GetSubtype

(

void

)

const

Definition at line 361 of file SeqFeatData.cpp.

References eSubtype_any, m_FeatDataInfo, CSeqFeatData::SFeatDataInfo::m_Subtype, and x_InitFeatDataInfo().

Referenced by AddColumnsToFeatureTable(), CFlatFileFactoryBuilder::AddItem(), CAutoDefFeatureClause::AddmRNA(), CFeatureGenePanel::AddReciprocicalXref(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CNcrnaClassColumn::AddToFeature(), AddtRNAAndOther(), AdjustCdregionFrame(), CEditSequence::AdjustFeatureLocations(), CFeatTrim::Apply(), ApplyFeatureSeqTableToSeqEntry(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CGffRecord::AssignAttributesCore(), CGvfWriteRecord::AssignSource(), CGvfWriteRecord::AssignType(), CGffRecord::AssignType(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CSpliceProblems::CalculateSpliceProblems(), CEditObjectSeq_feat::CanClose(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CheckPropagatedCDSLocation(), CNcrnaClassColumn::ClearInFeature(), CDiscrepancyContext::CollectFeature(), CAnnotObject_SplitInfo::Compare(), CSeq_feat::CompareNonLocation(), CmRNACDSLinker::CompleteHalfFormedXrefPairs(), ConvertRegulatoryFeature(), CGBQualPanel::CreateControls(), CGuiObjectInfoSeq_feat::CreateObject(), CEditObjectSeq_feat::CreateWindowImpl(), DoesFeatureHaveUnnecessaryException(), CFeatTableEdit::EliminateBadQualifiers(), FeatureAdjustForInsert(), FeatureAdjustForTrim(), FeatureClauseFactory(), FeaturePairIsTwoTypes(), FeatValidatorFactory(), CCdsToMatPeptide::FindAnnot(), CGeneFinder::GetAssociatedGeneInfo(), GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlappingFeat(), GetCdssForGene(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CValidErrorFormat::GetFeatureContentLabel(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CNcrnaClassColumn::GetFromFeat(), CFeatFindContext::GetIndexRange(), CFeatureItem::GetKey(), CSeq_featHandler::GetLabel(), GetLegalQualifiers(), CAutoDefFeatureClause::GetMainFeatureSubtype(), GetMandatoryQualifiers(), CSeqUtils::GetMappingInfo(), GetMrnasForGene(), CAnnotObject_SplitInfo::GetPriority(), CmRNACDSLinker::GetReferencedmRNA_CDS(), CMiscSeqTableColumn::GetRelatedApplyObjects(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), GetSeqFeatLabel(), GetSortedFeatList(), GetTargetedLocusName(), IEditingAction::GetUpdateMRNAProductNameCmd(), CNewCleanup_imp::ImpFeatBC(), CGff3ImportData::Initialize(), CAutoDefFeatureClause::IsControlRegion(), IsDuplicate(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), CAutoDefFeatureClause::IsExonWithNumber(), CAutoDefFeatureClause::IsGeneCluster(), CAutoDefFeatureClause::IsInsertionSequence(), CValidError_feat::IsIntronShort(), IsLegalQualifier(), CAutoDefFeatureClause::IsLTR(), IsMicroSatellite(), CAutoDefFeatureClause::IsMobileElement(), CSelectionVisitor::IsObjectSelected(), CAutoDefFeatureClause::IsPromoter(), CAutoDefPromoterAnd5UTRClause::IsPromoterAnd5UTR(), CAutoDefFeatureClause::IsRecognizedFeature(), CCompareFeats::IsSameSubtype(), CAutoDefFeatureClause::IsSatellite(), NSnp::IsSnp(), CmRNACDSLinker::LinkByLabelAndLocation(), CmRNACDSLinker::LinkSelectedFeatures(), CAutoDefFeatureClause::OkToGroupUnderByLocation(), CAutoDefFeatureClause::OkToGroupUnderByType(), CBioseqEditor::OnDeleteSelection(), CGBQualPanel::PanelNeeded(), CCdsForMrnaPlugin::processMainLoop(), C5ColAnnotAssembler::ProcessRecord(), CFeaturePropagator::Propagate(), CGlimmerReader::Read(), CGFFReader::Read(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RepairXrefs(), ReverseComplementFeature(), CWrongIllegalQuals::RmIllegalQuals(), CWrongIllegalQuals::RmWrongOrIllegalQuals(), CWrongIllegalQuals::RmWrongQuals(), CFeatureLoadingJob::Run(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CFeatTreeSampleApp::Run(), s_AreDifferentVariations(), s_AreLinkedToDifferentFeats(), s_CheckMandatoryQuals(), s_CompareFtables(), s_GetBestGeneForFeat(), NSearchFeatPanel::s_GetCustomLabel(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetFeatureLabel(), s_GetFeaturesForRange(), s_GetImpLabel(), s_GetMappedFeat(), s_GetmRNAName(), s_IsOperon(), s_LocIsFuzz(), CSequenceUpdater::s_OffsetFeature(), s_Render_SeqFeat(), s_SetUpXrefPairs(), s_SkipFeature(), s_TreatAsRna(), NSearchFeatPanel::s_UseCustomLabel(), CNewCleanup_imp::SeqfeatBC(), C5ColImportData::Serialize(), CFeatureGenerator::SImplementation::SetFeatureExceptions(), CTextSelHandler::STGH_GetSelectedFeatureSubtypes(), TestCds(), TestCdsFromLastBioseq(), CGeneFeatTreeProcess::TestFeatureGeneTree(), TestTwoIntCdsFromLastBioseqOutsideAlign(), CMacroFunction_SwapRelFeatQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_AddParsedToFeatQual::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_RemoveOutside::TheFunction(), CMacroFunction_RmvOutsideRelFeatQual::TheFunction(), CMacroFunction_ConvertFeature::TheFunction(), CCrossRefFeatsDlg::TransferDataToWindow(), UpdatemRNAProduct(), CSingleFeatValidator::Validate(), CImpFeatValidator::Validate(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_feat::ValidateOneFeatXrefPair(), CValidError_imp::ValidateSeqLoc(), CCleanup::WGSCleanup(), CWrongIllegalQuals::WrongQualsToNote(), CLinkUtils::x_AddDbxrefFeatureLinks(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureTableReader_Imp::x_AddQualifierToImp(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsRna(), CSingleFeatValidator::x_AllowFeatureToMatchGapExactly(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeName(), CGvfWriteRecord::x_AssignAttributeParent(), CFeaturePropagator::x_CdsCleanupPartials(), CFeaturePropagator::x_CdsStopAtStopCodon(), CFeatureGenerator::SImplementation::x_CheckInconsistentDbxrefs(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeature1(), CGFFReader::x_CreateGeneFeatures(), CValidError_bioseq::x_DupFeatSeverity(), x_FeatIsCDS(), x_FeatIsVDJC(), CTSE_Info::x_FindSeq_feat(), CFeatureItem::x_GatherInfoWithParent(), CSeq_featHandler::x_GetCustomLabel(), CAutoDefFeatureClause::x_GetDescription(), CAutoDefFeatureClause::x_GetFeatureTypeWord(), CAutoDefFeatureClause::x_GetProductName(), CCompareSeqRegions::x_GetPutativeMatches(), CAlignedFeatureGraph::x_GetTooltip(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CAutoDef::x_Is5SList(), CIntronValidator::x_IsIntronShort(), CValidError_bioseq::x_IsSameAsCDS(), CAutoDef::x_IsSingleMiscFeat(), CAlignedFeatureGraph::x_LinkedLayout(), CPromote::x_MakeMolinfoDesc(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CGeneModelTrack::x_NeedHighlight(), CSequenceUpdater::x_RemoveNewIDInFeature(), CAlignedFeatureGraph::x_RenderFeature(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CSingleFeatValidator::x_ReportPseudogeneConflict(), CValidError_bioseq::x_ReportStartStopPartialProblem(), CReportEntry::x_SetFeature(), CAnnotObject_Info::x_SetObject(), CGFFReader::x_SetProducts(), CSequenceUpdater::x_ShouldImportFeature(), CSeq_featHandler::x_UseCustomLabel(), CSingleFeatValidator::x_ValidateBothStrands(), CSingleFeatValidator::x_ValidateGbquals(), CSingleFeatValidator::x_ValidateGeneId(), CSingleFeatValidator::x_ValidateGeneXRef(), CSingleFeatValidator::x_ValidateImpFeatQuals(), CSingleFeatValidator::x_ValidateNonImpFeat(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), CGff3Reader::xFindFeatureUnderConstruction(), CGtfReader::xPostProcessAnnot(), CGff3AnnotAssembler::xProcessFeatureDefault(), and CGff3Reader::xUpdateAnnotGeneric().

GetTypeFromSubtype()

CSeqFeatData::E_Choice CSeqFeatData::GetTypeFromSubtype ( ESubtype  subtype )

static

Definition at line 391 of file SeqFeatData.cpp.

References s_InitSubtypesTable(), sx_SubtypesTable, and sx_SubtypesTableInitialized.

Referenced by CConvertFeatureBase::CConvertFeatureBase(), CFeatureSeqTableColumnBaseFactory::Create(), CreateAction(), CreateActionCdsGeneProt(), CProductColumn::GetApplyObjects(), CCodonStartColumn::GetApplyObjects(), GetBestOverlapForSNP(), GetBestOverlappingFeat(), CMacroEditorContext::GetFeatureTypes(), CFeatureSeqTableColumnBase::GetObjects(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), NSearchFeatPanel::GetSubtypesForType(), SAnnotSelector::IncludedFeatSubtype(), CDemoApp::Run(), CMacroFunction_NumberOfFeatures::s_GetFeatTypeCount(), s_InitSubtypesTable(), CFeatureTrack::SetFeatSubtype(), SAnnotTypeSelector::SetFeatSubtype(), CFeatureTrack::x_AddHistogram(), x_HasFeatIds(), x_HasFeatType(), CFeatList::x_Init(), CAnnotType_Index::x_InitIndexTables(), CConvertFeatureBase::x_IsImportSubtype(), CConvertFeatureBase::x_IsProtSubtype(), CConvertFeatureBase::x_IsRnaSubtype(), CMacroChoiceTypePanel::x_PopulateList(), CMacroFunction_ConvertFeature::x_SetConvertOptions(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

InvalidateCache()

void CSeqFeatData::InvalidateCache ( void  ) const

inline

Combine invalidation of all cached values.

Definition at line 566 of file SeqFeatData.hpp.

References InvalidateSubtype().

Referenced by Assign(), CSeqFeatData(), PostRead(), and SetComment().

InvalidateSubtype()

void CSeqFeatData::InvalidateSubtype ( void  ) const

inline

Call after changes that could affect the subtype.

Definition at line 559 of file SeqFeatData.hpp.

References eSubtype_any, m_FeatDataInfo, and CSeqFeatData::SFeatDataInfo::m_Subtype.

Referenced by InvalidateCache().

IsDiscouragedQual()

bool CSeqFeatData::IsDiscouragedQual ( EQualifier  qual )

static

Definition at line 4006 of file SeqFeatData.cpp.

References eQual_insertion_seq, eQual_mobile_element, eQual_rpt_unit, and eQual_transposon.

Referenced by BOOST_AUTO_TEST_CASE(), CFeatureFieldNamePanel::s_FillFeatQualList(), and CFeatureTableReader_Imp::x_AddQualifierToFeature().

IsDiscouragedSubtype()

bool CSeqFeatData::IsDiscouragedSubtype ( ESubtype  subtype )

static

Definition at line 3972 of file SeqFeatData.cpp.

References eSubtype_10_signal, eSubtype_35_signal, eSubtype_allele, eSubtype_attenuator, eSubtype_CAAT_signal, eSubtype_conflict, eSubtype_enhancer, eSubtype_GC_signal, eSubtype_LTR, eSubtype_misc_binding, eSubtype_mutation, eSubtype_polyA_signal, eSubtype_promoter, eSubtype_RBS, eSubtype_repeat_unit, eSubtype_satellite, eSubtype_scRNA, eSubtype_site_ref, eSubtype_snoRNA, eSubtype_snRNA, eSubtype_TATA_signal, eSubtype_terminator, and eSubtype_virion.

Referenced by BOOST_AUTO_TEST_CASE(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

IsLegalProductNameForRibosomalSlippage()

bool CSeqFeatData::IsLegalProductNameForRibosomalSlippage ( const string &  product_name )

static

Definition at line 4697 of file SeqFeatData.cpp.

IsLegalQualifier() [1/2]

bool CSeqFeatData::IsLegalQualifier ( EQualifier  qual ) const

inline

Test wheather a certain qualifier is legal for the feature.

Definition at line 573 of file SeqFeatData.hpp.

References GetSubtype().

Referenced by BOOST_AUTO_TEST_CASE(), CConvertCDSToMiscFeat::Convert(), CFeatTableEdit::EliminateBadQualifiers(), CWrongIllegalQuals::RmIllegalQuals(), CWrongIllegalQuals::RmWrongOrIllegalQuals(), CWrongIllegalQuals::RmWrongQuals(), CWrongIllegalQuals::WrongQualsToNote(), CFastaOstreamEx::x_AddPseudoGeneAttribute(), CSingleFeatValidator::x_ValidateGbquals(), CGff2Writer::xAssignFeatureAttributePseudoGene(), and XGBFeatKeyQualValid().

IsLegalQualifier() [2/2]

bool CSeqFeatData::IsLegalQualifier ( ESubtype  subtype, EQualifier  qual  )

static

Definition at line 3006 of file SeqFeatData.cpp.

References compile_time_bits::const_set_map_base< _Traits, _Backend, _Duplicates >::find(), and s_GetLegalQualMap().

IsRegulatory()

bool CSeqFeatData::IsRegulatory ( ESubtype  subtype )

static

Definition at line 3800 of file SeqFeatData.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), and GetSetOfRegulatorySubtypes().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRegulatoryFeature(), CMacroEditorContext::GetFeatureTypes(), GetRegulatoryClass(), CNewCleanup_imp::ImpFeatBC(), CFeatureTypePanel::ListPresentFeaturesFirst(), CFeatureTableReader_Imp::x_AddQualifierToImp(), CMacroFeatsOnSeqPanel::x_GetFeatureChoices(), CAddFeatureBetweenDlg::x_ListFeatures(), CBulkOtherAddPanel::x_ListFeatures(), and CAlignOtherAddPanel::x_ListFeatures().

operator=()

CSeqFeatData& CSeqFeatData::operator= ( const CSeqFeatData &  value )

private

PostRead()

void CSeqFeatData::PostRead

(

void

)

const

Invalidate subtype cache after deserialization.

Definition at line 378 of file SeqFeatData.cpp.

References InvalidateCache().

ProhibitXref()

bool CSeqFeatData::ProhibitXref ( CSeqFeatData::ESubtype  subtype1, CSeqFeatData::ESubtype  subtype2  )

static

Definition at line 3749 of file SeqFeatData.cpp.

References grid::netschedule::limits::Check().

Referenced by BOOST_AUTO_TEST_CASE(), and CValidError_feat::ValidateOneFeatXrefPair().

RequireLocationIntervalsInBiologicalOrder()

bool CSeqFeatData::RequireLocationIntervalsInBiologicalOrder ( CSeqFeatData::ESubtype  feat_subtype )

static

Definition at line 4519 of file SeqFeatData.cpp.

References eSubtype_het, eSubtype_misc_recomb, eSubtype_primer_bind, and eSubtype_pub.

Referenced by CValidError_imp::ValidateSeqLoc().

s_GetLegalQualMap()

const CSeqFeatData::TSubTypeQualifiersMap & CSeqFeatData::s_GetLegalQualMap ( )

staticprivatenoexcept

Definition at line 778 of file SeqFeatData.cpp.

References eQual_allele, eQual_altitude, eQual_anticodon, eQual_artificial_location, eQual_bio_material, eQual_bond_type, eQual_bound_moiety, eQual_calculated_mol_wt, eQual_cell_line, eQual_cell_type, eQual_chloroplast, eQual_chromoplast, eQual_chromosome, eQual_citation, eQual_clone, eQual_clone_lib, eQual_coded_by, eQual_codon, eQual_codon_start, eQual_collected_by, eQual_collection_date, eQual_compare, eQual_cons_splice, eQual_country, eQual_cultivar, eQual_culture_collection, eQual_cyanelle, eQual_db_xref, eQual_derived_from, eQual_dev_stage, eQual_direction, eQual_EC_number, eQual_ecotype, eQual_environmental_sample, eQual_estimated_length, eQual_evidence, eQual_exception, eQual_experiment, eQual_feat_class, eQual_focus, eQual_frequency, eQual_function, eQual_gap_type, eQual_gdb_xref, eQual_gene, eQual_gene_synonym, eQual_germline, eQual_haplogroup, eQual_haplotype, eQual_heterogen, eQual_host, eQual_identified_by, eQual_inference, eQual_insertion_seq, eQual_isolate, eQual_isolation_source, eQual_kinetoplast, eQual_lab_host, eQual_label, eQual_lat_lon, eQual_linkage_evidence, eQual_linkage_group, eQual_locus_tag, eQual_macronuclear, eQual_map, eQual_mating_type, eQual_metagenome_source, eQual_metagenomic, eQual_mitochondrion, eQual_mobile_element, eQual_mobile_element_type, eQual_mod_base, eQual_mol_type, eQual_name, eQual_ncRNA_class, eQual_nomenclature, eQual_non_std_residue, eQual_note, eQual_number, eQual_old_locus_tag, eQual_operon, eQual_organelle, eQual_organism, eQual_partial, eQual_PCR_conditions, eQual_PCR_primers, eQual_phenotype, eQual_plasmid, eQual_pop_variant, eQual_product, eQual_protein_id, eQual_proviral, eQual_pseudo, eQual_pseudogene, eQual_rearranged, eQual_recombination_class, eQual_region_name, eQual_regulatory_class, eQual_replace, eQual_ribosomal_slippage, eQual_rpt_family, eQual_rpt_type, eQual_rpt_unit, eQual_rpt_unit_range, eQual_rpt_unit_seq, eQual_satellite, eQual_sec_str_type, eQual_segment, eQual_sequenced_mol, eQual_serotype, eQual_serovar, eQual_sex, eQual_site_type, eQual_SO_type, eQual_specimen_voucher, eQual_standard_name, eQual_strain, eQual_sub_clone, eQual_sub_species, eQual_sub_strain, eQual_submitter_seqid, eQual_tag_peptide, eQual_tissue_lib, eQual_tissue_type, eQual_trans_splicing, eQual_transcript_id, eQual_transgenic, eQual_transl_except, eQual_transl_table, eQual_translation, eQual_transposon, eQual_type_material, eQual_UniProtKB_evidence, eQual_usedin, eQual_variety, eQual_virion, eQual_whole_replicon, eSubtype_10_signal, eSubtype_35_signal, eSubtype_3clip, eSubtype_3UTR, eSubtype_5clip, eSubtype_5UTR, eSubtype_any, eSubtype_assembly_gap, eSubtype_attenuator, eSubtype_biosrc, eSubtype_bond, eSubtype_C_region, eSubtype_CAAT_signal, eSubtype_cdregion, eSubtype_centromere, eSubtype_comment, eSubtype_conflict, eSubtype_D_loop, eSubtype_D_segment, eSubtype_enhancer, eSubtype_exon, eSubtype_gap, eSubtype_GC_signal, eSubtype_gene, eSubtype_het, eSubtype_iDNA, eSubtype_Imp_CDS, eSubtype_intron, eSubtype_J_segment, eSubtype_LTR, eSubtype_mat_peptide, eSubtype_mat_peptide_aa, eSubtype_misc_binding, eSubtype_misc_difference, eSubtype_misc_feature, eSubtype_misc_recomb, eSubtype_misc_RNA, eSubtype_misc_signal, eSubtype_misc_structure, eSubtype_mobile_element, eSubtype_modified_base, eSubtype_mRNA, eSubtype_N_region, eSubtype_ncRNA, eSubtype_non_std_residue, eSubtype_old_sequence, eSubtype_operon, eSubtype_oriT, eSubtype_otherRNA, eSubtype_polyA_signal, eSubtype_polyA_site, eSubtype_precursor_RNA, eSubtype_preprotein, eSubtype_preRNA, eSubtype_prim_transcript, eSubtype_primer_bind, eSubtype_promoter, eSubtype_propeptide, eSubtype_propeptide_aa, eSubtype_prot, eSubtype_protein_bind, eSubtype_psec_str, eSubtype_RBS, eSubtype_region, eSubtype_regulatory, eSubtype_rep_origin, eSubtype_repeat_region, eSubtype_repeat_unit, eSubtype_rRNA, eSubtype_S_region, eSubtype_satellite, eSubtype_scRNA, eSubtype_sig_peptide, eSubtype_sig_peptide_aa, eSubtype_site, eSubtype_snoRNA, eSubtype_snRNA, eSubtype_source, eSubtype_stem_loop, eSubtype_STS, eSubtype_TATA_signal, eSubtype_telomere, eSubtype_terminator, eSubtype_tmRNA, eSubtype_transit_peptide, eSubtype_transit_peptide_aa, eSubtype_tRNA, eSubtype_unsure, eSubtype_V_region, eSubtype_V_segment, eSubtype_variation, eSubtype_variation_ref, MAKE_CONST_MAP, and compile_time_bits::const_bitset< _Bits, T >::set_range().

Referenced by GetLegalQualifiers(), and IsLegalQualifier().

s_InitSubtypesTable()

void CSeqFeatData::s_InitSubtypesTable ( void  )

staticprivate

Definition at line 697 of file SeqFeatData.cpp.

References _ASSERT, CSeqFeatData_Base::e_Biosrc, CSeqFeatData_Base::e_Bond, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Clone, CSeqFeatData_Base::e_Comment, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Het, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Non_std_residue, CSeqFeatData_Base::e_not_set, CSeqFeatData_Base::e_Num, CSeqFeatData_Base::e_Org, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Psec_str, CSeqFeatData_Base::e_Pub, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Rna, CSeqFeatData_Base::e_Rsite, CSeqFeatData_Base::e_Seq, CSeqFeatData_Base::e_Site, CSeqFeatData_Base::e_Txinit, CSeqFeatData_Base::e_User, CSeqFeatData_Base::e_Variation, eSubtype_any, eSubtype_biosrc, eSubtype_bond, eSubtype_cdregion, eSubtype_clone, eSubtype_comment, eSubtype_gene, eSubtype_het, eSubtype_imp, eSubtype_ncRNA, eSubtype_non_std_residue, eSubtype_num, eSubtype_org, eSubtype_otherRNA, eSubtype_preRNA, eSubtype_propeptide, eSubtype_propeptide_aa, eSubtype_prot, eSubtype_psec_str, eSubtype_pub, eSubtype_region, eSubtype_rsite, eSubtype_seq, eSubtype_site, eSubtype_site_ref, eSubtype_tmRNA, eSubtype_transit_peptide_aa, eSubtype_txinit, eSubtype_user, eSubtype_variation_ref, GetTypeFromSubtype(), i, info, kImportTable, kImportTableEnd, NcbiCout, NcbiEndl, NStr::ReplaceInPlace(), s_subtype_count, s_subtype_info, CSeqFeatData_Base::SelectionName(), sx_SubtypesTable, sx_SubtypesTableInitialized, table, toupper(), and type.

Referenced by GetTypeFromSubtype().

s_InitXrefAllowedSubtypesTable()

static void CSeqFeatData::s_InitXrefAllowedSubtypesTable ( void  )

static

s_InitXrefProhibitedSubtypesTable()

static void CSeqFeatData::s_InitXrefProhibitedSubtypesTable ( void  )

static

SetBiosrc() [1/2]

void CSeqFeatData::SetBiosrc ( TBiosrc &  v )

inline

Definition at line 290 of file SeqFeatData.hpp.

Referenced by CBioseqEditor::OnCreateBiosourceFeat(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData().

SetBiosrc() [2/2]

TBiosrc& CSeqFeatData::SetBiosrc ( void  )

inline

Definition at line 290 of file SeqFeatData.hpp.

SetBond() [1/2]

void CSeqFeatData::SetBond ( const TBond &  v )

inline

Definition at line 281 of file SeqFeatData.hpp.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetBond() [2/2]

TBond& CSeqFeatData::SetBond ( void  )

inline

Definition at line 281 of file SeqFeatData.hpp.

SetCdregion() [1/2]

void CSeqFeatData::SetCdregion ( TCdregion &  v )

inline

Definition at line 270 of file SeqFeatData.hpp.

Referenced by CSeq_loc_Conversion::ConvertCdregion(), CSeq_loc_Conversion_Set::ConvertCdregion(), CEditObjectSeq_feat::CreateWindowImpl(), CFeatureTableReader_Imp::x_AddQualifierToCdregion(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC().

SetCdregion() [2/2]

TCdregion& CSeqFeatData::SetCdregion ( void  )

inline

Definition at line 270 of file SeqFeatData.hpp.

SetClone() [1/2]

void CSeqFeatData::SetClone ( TClone &  v )

inline

Definition at line 291 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC().

SetClone() [2/2]

TClone& CSeqFeatData::SetClone ( void  )

inline

Definition at line 291 of file SeqFeatData.hpp.

SetComment()

void CSeqFeatData::SetComment ( void  )

inline

Definition at line 277 of file SeqFeatData.hpp.

References InvalidateCache(), and CSeqFeatData_Base::SetComment().

SetGene() [1/2]

void CSeqFeatData::SetGene ( TGene &  v )

inline

Definition at line 268 of file SeqFeatData.hpp.

Referenced by CEditObjectSeq_feat::CreateWindowImpl(), CFeatureTableReader_Imp::x_AddQualifierToGene(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData().

SetGene() [2/2]

TGene& CSeqFeatData::SetGene ( void  )

inline

Definition at line 268 of file SeqFeatData.hpp.

SetHet() [1/2]

void CSeqFeatData::SetHet ( THet &  v )

inline

Definition at line 289 of file SeqFeatData.hpp.

SetHet() [2/2]

THet& CSeqFeatData::SetHet ( void  )

inline

Definition at line 289 of file SeqFeatData.hpp.

SetImp() [1/2]

void CSeqFeatData::SetImp ( TImp &  v )

inline

Definition at line 275 of file SeqFeatData.hpp.

Referenced by CRepeatToFeat::operator()(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetImp() [2/2]

TImp& CSeqFeatData::SetImp ( void  )

inline

Definition at line 275 of file SeqFeatData.hpp.

SetNon_std_residue() [1/2]

void CSeqFeatData::SetNon_std_residue ( const TNon_std_residue &  v )

inline

Definition at line 288 of file SeqFeatData.hpp.

SetNon_std_residue() [2/2]

TNon_std_residue& CSeqFeatData::SetNon_std_residue ( void  )

inline

Definition at line 288 of file SeqFeatData.hpp.

SetNum() [1/2]

void CSeqFeatData::SetNum ( TNum &  v )

inline

Definition at line 286 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC().

SetNum() [2/2]

TNum& CSeqFeatData::SetNum ( void  )

inline

Definition at line 286 of file SeqFeatData.hpp.

SetOrg() [1/2]

void CSeqFeatData::SetOrg ( TOrg &  v )

inline

Definition at line 269 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData().

SetOrg() [2/2]

TOrg& CSeqFeatData::SetOrg ( void  )

inline

Definition at line 269 of file SeqFeatData.hpp.

SetProt() [1/2]

void CSeqFeatData::SetProt ( TProt &  v )

inline

Definition at line 271 of file SeqFeatData.hpp.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetProt() [2/2]

TProt& CSeqFeatData::SetProt ( void  )

inline

Definition at line 271 of file SeqFeatData.hpp.

SetPsec_str() [1/2]

void CSeqFeatData::SetPsec_str ( const TPsec_str &  v )

inline

Definition at line 287 of file SeqFeatData.hpp.

SetPsec_str() [2/2]

TPsec_str& CSeqFeatData::SetPsec_str ( void  )

inline

Definition at line 287 of file SeqFeatData.hpp.

SetPub() [1/2]

void CSeqFeatData::SetPub ( TPub &  v )

inline

Definition at line 273 of file SeqFeatData.hpp.

Referenced by CEditObjectSeq_feat::CreateWindowImpl(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData().

SetPub() [2/2]

TPub& CSeqFeatData::SetPub ( void  )

inline

Definition at line 273 of file SeqFeatData.hpp.

SetRegion() [1/2]

void CSeqFeatData::SetRegion ( const TRegion &  v )

inline

Definition at line 276 of file SeqFeatData.hpp.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data().

SetRegion() [2/2]

TRegion& CSeqFeatData::SetRegion ( void  )

inline

Definition at line 276 of file SeqFeatData.hpp.

SetRna() [1/2]

void CSeqFeatData::SetRna ( TRna &  v )

inline

Definition at line 272 of file SeqFeatData.hpp.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToRna(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetRna() [2/2]

TRna& CSeqFeatData::SetRna ( void  )

inline

Definition at line 272 of file SeqFeatData.hpp.

SetRsite() [1/2]

void CSeqFeatData::SetRsite ( TRsite &  v )

inline

Definition at line 283 of file SeqFeatData.hpp.

SetRsite() [2/2]

TRsite& CSeqFeatData::SetRsite ( void  )

inline

Definition at line 283 of file SeqFeatData.hpp.

SetSeq() [1/2]

void CSeqFeatData::SetSeq ( TSeq &  v )

inline

Definition at line 274 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC().

SetSeq() [2/2]

TSeq& CSeqFeatData::SetSeq ( void  )

inline

Definition at line 274 of file SeqFeatData.hpp.

SetSite() [1/2]

void CSeqFeatData::SetSite ( const TSite &  v )

inline

Definition at line 282 of file SeqFeatData.hpp.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CFeatureTableReader_Imp::x_SetupSeqFeat().

SetSite() [2/2]

TSite& CSeqFeatData::SetSite ( void  )

inline

Definition at line 282 of file SeqFeatData.hpp.

SetTxinit() [1/2]

void CSeqFeatData::SetTxinit ( TTxinit &  v )

inline

Definition at line 285 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC(), and CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeatData().

SetTxinit() [2/2]

TTxinit& CSeqFeatData::SetTxinit ( void  )

inline

Definition at line 285 of file SeqFeatData.hpp.

SetUser() [1/2]

void CSeqFeatData::SetUser ( TUser &  v )

inline

Definition at line 284 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data().

SetUser() [2/2]

TUser& CSeqFeatData::SetUser ( void  )

inline

Definition at line 284 of file SeqFeatData.hpp.

SetVariation() [1/2]

void CSeqFeatData::SetVariation ( TVariation &  v )

inline

Definition at line 292 of file SeqFeatData.hpp.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_data(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_ETC().

SetVariation() [2/2]

TVariation& CSeqFeatData::SetVariation ( void  )

inline

Definition at line 292 of file SeqFeatData.hpp.

ShouldRepresentAsGbqual() [1/2]

bool CSeqFeatData::ShouldRepresentAsGbqual ( CSeqFeatData::ESubtype  feat_subtype, const CGb_qual &  qual  )

static

Definition at line 4655 of file SeqFeatData.cpp.

References CGb_qual_Base::GetQual(), GetQualifierType(), and CGb_qual_Base::IsSetQual().

ShouldRepresentAsGbqual() [2/2]

bool CSeqFeatData::ShouldRepresentAsGbqual ( CSeqFeatData::ESubtype  feat_subtype, CSeqFeatData::EQualifier  qual_type  )

static

Definition at line 4555 of file SeqFeatData.cpp.

References eQual_allele, eQual_citation, eQual_codon, eQual_codon_start, eQual_db_xref, eQual_EC_number, eQual_evidence, eQual_exception, eQual_experiment, eQual_function, eQual_gdb_xref, eQual_gene, eQual_gene_synonym, eQual_inference, eQual_insertion_seq, eQual_label, eQual_locus_tag, eQual_map, eQual_note, eQual_number, eQual_old_locus_tag, eQual_operon, eQual_partial, eQual_product, eQual_protein_id, eQual_pseudo, eQual_pseudogene, eQual_ribosomal_slippage, eQual_rpt_unit, eQual_standard_name, eQual_trans_splicing, eQual_transl_table, eQual_translation, eQual_transposon, eQual_usedin, eSubtype_C_region, eSubtype_cdregion, eSubtype_D_segment, eSubtype_exon, eSubtype_gap, eSubtype_gene, eSubtype_J_segment, eSubtype_mat_peptide, eSubtype_misc_feature, eSubtype_N_region, eSubtype_operon, eSubtype_propeptide, eSubtype_repeat_region, eSubtype_S_region, eSubtype_sig_peptide, eSubtype_transit_peptide, eSubtype_V_region, eSubtype_V_segment, and eSubtype_variation.

SubtypeNameToValue()

static ESubtype CSeqFeatData::SubtypeNameToValue ( CTempString  sName )

static

Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.

Returns

eSubtype_bad on bad input

Referenced by BOOST_AUTO_TEST_CASE(), CMiscSeqTableColumn::CMiscSeqTableColumn(), CVarTrackFactory::CreateTracks(), CBulkEditFeatDlg::GetCommand(), CUpdateSeqPanel::GetData(), CFeature_field::GetFeatSubtype(), CMacroEditorContext::GetFeatureTypes(), GetSubtype(), CAggregateFeatureTrack::GetSubtypeList(), CFeatureTypePanel::ListPresentFeaturesFirst(), ParseFeatureBlock(), s_GetFeatureSubtypeFromString(), CFeatureFieldNamePanel::UpdateEditor(), CMacroFeatsOnSeqPanel::x_GetFeatureChoices(), CAdjustFeaturesForGaps::x_IsFeatureTypeSelected(), CAutoDefOptions::x_SetSuppressedFeatures(), CFeatureTableReader_Imp::x_SetupSeqFeat(), and XMLParseFeatureBlock().

SubtypeValueToName()

CTempString CSeqFeatData::SubtypeValueToName ( CSeqFeatData::ESubtype  eSubtype )

static

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum.

Returns

empty string on bad input

Definition at line 513 of file SeqFeatData.cpp.

References CTempString::find(), and kEmptyStr.

Referenced by CExportTableDlg::AddFeaturesToTable(), CImportFeatTable::AddSeqAnnotToSeqEntry(), BOOST_AUTO_TEST_CASE(), CConvertProtToImp::Convert(), CConvertRegionToImp::Convert(), CConvertCommentToImp::Convert(), CConvertGeneToImp::Convert(), CConvertRnaToImp::Convert(), CConvertSiteToImp::Convert(), CMacroEditorContext::GetAsnPathToFeature(), CMacroBioData_FeatIterBase::GetBestDescr(), CMacroBioData_FeatIntervalIter::GetBestDescr(), CConvertCDSToProt::GetDescription(), NMacroUtil::GetFeatSubtype(), CSequenceEditingEventHandler::GetFeatureLocation(), GetRegulatoryClass(), CBioseqEditor::MakeDefaultFeature(), NSearchFeatPanel::s_GetCustomLabel(), C5ColImportData::Serialize(), sGetFeatureGeneBiotypeWrapper(), CCrossRefFeatsDlg::TransferDataToWindow(), CSeq_featHandler::x_GetCustomLabel(), CAutoDefOptions::x_MakeSuppressedFeatures(), CMacroChoiceTypePanel::x_PopulateList(), CSequenceUpdater::x_ShouldImportFeature(), CConvertFeatureBase::x_SimpleConversion(), CSingleFeatValidator::x_ValidateBothStrands(), CGff3AnnotAssembler::xProcessFeatureDefault(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), and CFeatTableEdit::xPutErrorMissingTranscriptId().

x_InitFeatDataInfo()

void CSeqFeatData::x_InitFeatDataInfo ( void  ) const

private

Definition at line 250 of file SeqFeatData.cpp.

References CRNA_ref_Base::CanGetExt(), CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, CSeqFeatData_Base::e_Site, eSubtype_bad, eSubtype_imp, eSubtype_ncRNA, eSubtype_otherRNA, eSubtype_prot, eSubtype_site, eSubtype_tmRNA, CRNA_ref_Base::eType_other, CRNA_ref_Base::GetExt(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CRNA_ref_Base::C_Ext::GetName(), CSeqFeatData_Base::GetProt(), CSeqFeatData_Base::GetRna(), CSeqFeatData_Base::GetSite(), CRNA_ref_Base::GetType(), CRNA_ref_Base::C_Ext::IsName(), kEmptyStr, ncbi::grid::netcache::search::fields::key, kImportTable, kImportTableEnd, m_FeatDataInfo, CSeqFeatData::SFeatDataInfo::m_Key_full, CSeqFeatData::SFeatDataInfo::m_Key_gb, SImportEntry::m_Name, CSeqFeatData::SFeatDataInfo::m_Subtype, result, util::strcmp(), and CSeqFeatData_Base::Which().

Referenced by GetKey(), and GetSubtype().

Member Data Documentation

m_FeatDataInfo

SFeatDataInfo CSeqFeatData::m_FeatDataInfo

mutableprivate

Definition at line 542 of file SeqFeatData.hpp.

Referenced by GetKey(), GetSubtype(), InvalidateSubtype(), and x_InitFeatDataInfo().

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The documentation for this class was generated from the following files:

• include/objects/seqfeat/SeqFeatData.hpp
• src/objects/seqfeat/SeqFeatData.cpp