Collaboration diagram for Seq-id Management:

Classes
class	CSeq_id_Info

class	CSeq_id_InfoLocker

class	CSeq_id_Handle

struct	CSeq_id_Handle::PLessOrdered
	Predicate for sorting CSeq_id_Handles in a defined order. More...

class	CSeq_id_Mapper

class	CSeq_id

struct	SSeqIdRange
	SSeqIdRange –. More...

class	SSeqIdRange::const_iterator

class	CSeqIdException
	CSeqIdException –. More...

Macros
#define	NCBI_ACC(type, div, mol) eSeqId_##type \| eAcc_##div \| fAcc_##mol

Typedefs
typedef TIntId	CSeq_id_Info::TPacked

typedef Uint8	CSeq_id_Info::TVariant

typedef CSeq_id_Info::TPacked	CSeq_id_Handle::TPacked

typedef CSeq_id_Info::TVariant	CSeq_id_Handle::TVariant

typedef set< CSeq_id_Handle >	CSeq_id_Handle::TMatches

typedef set< CSeq_id_Handle >	TSeq_id_HandleSet
	CSeq_id_Mapper:: More...

typedef vector< CRef< CSeq_id_Which_Tree > >	CSeq_id_Mapper::TTrees

typedef CSeq_id_Base	CSeq_id::Tparent

typedef int	CSeq_id::TParseFlags

using	CSeq_id::TErrorFlags = int

typedef int	CSeq_id::TLabelFlags

typedef set< CSeq_id_Handle >	CSeq_id::TSeqIdHandles

typedef int	CSeq_id::TComposeOSLTFlags

typedef int	SSeqIdRange::TFlags
	binary OR of EFlags More...

typedef random_access_iterator_tag	SSeqIdRange::const_iterator::iterator_category

typedef string	SSeqIdRange::const_iterator::value_type

typedef ptrdiff_t	SSeqIdRange::const_iterator::difference_type

typedef const string *	SSeqIdRange::const_iterator::pointer

typedef string &	SSeqIdRange::const_iterator::reference

Enumerations
enum	EAllowWeakMatch { eNoWeakMatch , eAllowWeakMatch }

enum	CSeq_id_Mapper::EDumpDetails { CSeq_id_Mapper::eCountTotalBytes , CSeq_id_Mapper::eDumpTotalBytes , CSeq_id_Mapper::eDumpStatistics , CSeq_id_Mapper::eDumpAllIds }

enum	CSeq_id::EParseFlags { CSeq_id::fParse_PartialOK = 0x01 , CSeq_id::fParse_RawText = 0x02 , CSeq_id::fParse_RawGI = 0x04 , CSeq_id::fParse_AnyRaw = fParse_RawText \| fParse_RawGI , CSeq_id::fParse_ValidLocal = 0x08 , CSeq_id::fParse_AnyLocal = 0x18 , CSeq_id::fParse_NoFASTA = 0x20 , CSeq_id::fParse_FallbackOK = 0x40 , CSeq_id::fParse_Default = fParse_RawText \| fParse_ValidLocal }

enum	CSeq_id::EErrorFlags { CSeq_id::fNoError = 0 , CSeq_id::fEmptyId = 1 , CSeq_id::fInvalidChar = 1 << 1 , CSeq_id::fExceedsMaxLength = 1 << 2 }

enum	CSeq_id::EFastaAsTypeAndContent { CSeq_id::eFasta_AsTypeAndContent }
	Tag for method variants that would otherwise be ambiguous. More...

enum	CSeq_id::EAccessionInfo { CSeq_id::eSeqId_not_set = e_not_set , CSeq_id::eSeqId_local = e_Local , CSeq_id::eSeqId_gibbsq = e_Gibbsq , CSeq_id::eSeqId_gibbmt = e_Gibbmt , CSeq_id::eSeqId_giim = e_Giim , CSeq_id::eSeqId_genbank = e_Genbank , CSeq_id::eSeqId_embl = e_Embl , CSeq_id::eSeqId_pir = e_Pir , CSeq_id::eSeqId_swissprot = e_Swissprot , CSeq_id::eSeqId_patent = e_Patent , CSeq_id::eSeqId_other = e_Other , CSeq_id::eSeqId_refseq = eSeqId_other , CSeq_id::eSeqId_general = e_General , CSeq_id::eSeqId_gi = e_Gi , CSeq_id::eSeqId_ddbj = e_Ddbj , CSeq_id::eSeqId_prf = e_Prf , CSeq_id::eSeqId_pdb = e_Pdb , CSeq_id::eSeqId_tpg = e_Tpg , CSeq_id::eSeqId_tpe = e_Tpe , CSeq_id::eSeqId_tpd = e_Tpd , CSeq_id::eSeqId_gpipe = e_Gpipe , CSeq_id::eSeqId_named_annot_track = e_Named_annot_track , CSeq_id::eAcc_type_mask = 0xff , CSeq_id::fAcc_nuc = 0x80000000 , CSeq_id::fAcc_prot = 0x40000000 , CSeq_id::fAcc_seq = 0 , CSeq_id::fAcc_predicted = 0x20000000 , CSeq_id::fAcc_specials = 0x10000000 , CSeq_id::fAcc_master = 0x08000000 , CSeq_id::fAcc_ncbo = 0x04000000 , CSeq_id::fAcc_fallback = 0x02000000 , CSeq_id::fAcc_vdb_only = 0x01000000 , CSeq_id::eAcc_flag_mask = 0xff000000 , CSeq_id::eAcc_other = 0 << 8 , CSeq_id::eAcc_est = 1 << 8 , CSeq_id::eAcc_dirsub = 2 << 8 , CSeq_id::eAcc_div_patent = 3 << 8 , CSeq_id::eAcc_mrna = 4 << 8 , CSeq_id::eAcc_ncrna = 5 << 8 , CSeq_id::eAcc_gsdb_ds = 6 << 8 , CSeq_id::eAcc_gsdb = 7 << 8 , CSeq_id::eAcc_backbone = 8 << 8 , CSeq_id::eAcc_tsa = 9 << 8 , CSeq_id::eAcc_segset = 10 << 8 , CSeq_id::eAcc_gss = 11 << 8 , CSeq_id::eAcc_unique = 12 << 8 , CSeq_id::eAcc_ambig = 112 << 8 , CSeq_id::eAcc_ambig_g = 113 << 8 , CSeq_id::eAcc_ambig_e = 114 << 8 , CSeq_id::eAcc_ambig_ge = 115 << 8 , CSeq_id::eAcc_ambig_d = 116 << 8 , CSeq_id::eAcc_ambig_gd = 117 << 8 , CSeq_id::eAcc_ambig_ed = 118 << 8 , CSeq_id::eAcc_ambig_ged = 119 << 8 , CSeq_id::eAcc_unreserved = 127 << 8 , CSeq_id::fAcc_genomic = 128 << 8 , CSeq_id::eAcc_genome = 128 << 8 , CSeq_id::eAcc_htgs = 129 << 8 , CSeq_id::eAcc_con = 130 << 8 , CSeq_id::eAcc_wgs = 131 << 8 , CSeq_id::eAcc_chromosome = 133 << 8 , CSeq_id::eAcc_genomic_rgn = 134 << 8 , CSeq_id::eAcc_wgs_intermed = 135 << 8 , CSeq_id::eAcc_sts = 136 << 8 , CSeq_id::eAcc_mga = 137 << 8 , CSeq_id::eAcc_optical_map = 138 << 8 , CSeq_id::eAcc_targeted = 139 << 8 , CSeq_id::eAcc_division_mask = 0xff00 , CSeq_id::eAcc_wgs_master = eAcc_wgs \| fAcc_master , CSeq_id::eAcc_wgs_intermed_master = eAcc_wgs_intermed \| fAcc_master , CSeq_id::eAcc_tsa_master = eAcc_tsa \| fAcc_master , CSeq_id::eAcc_targeted_master = eAcc_targeted \| fAcc_master , CSeq_id::eAcc_wgs_vdb_only = eAcc_wgs \| fAcc_vdb_only , CSeq_id::eAcc_wgs_intermed_vdb_only = eAcc_wgs_intermed \| fAcc_vdb_only , CSeq_id::eAcc_tsa_vdb_only = eAcc_tsa \| fAcc_vdb_only , CSeq_id::eAcc_targeted_vdb_only = eAcc_targeted \| fAcc_vdb_only , CSeq_id::eAcc_wgs_vdb_master = eAcc_wgs \| fAcc_master \| fAcc_vdb_only , CSeq_id::eAcc_wgs_intermed_vdb_master = eAcc_wgs_intermed \| fAcc_master \| fAcc_vdb_only , CSeq_id::eAcc_tsa_vdb_master = eAcc_tsa \| fAcc_master \| fAcc_vdb_only , CSeq_id::eAcc_targeted_vdb_master = eAcc_targeted \| fAcc_master \| fAcc_vdb_only , CSeq_id::eAcc_unknown = eSeqId_not_set \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_ambiguous_nuc = eSeqId_not_set \| eAcc_ambig \| fAcc_nuc , CSeq_id::eAcc_maybe_gb = eSeqId_not_set \| eAcc_ambig_g \| fAcc_nuc , CSeq_id::eAcc_maybe_embl = eSeqId_not_set \| eAcc_ambig_e \| fAcc_nuc , CSeq_id::eAcc_maybe_ddbj = eSeqId_not_set \| eAcc_ambig_d \| fAcc_nuc , CSeq_id::eAcc_gb_embl = eSeqId_not_set \| eAcc_ambig_ge \| fAcc_nuc , CSeq_id::eAcc_gb_ddbj = eSeqId_not_set \| eAcc_ambig_gd \| fAcc_nuc , CSeq_id::eAcc_embl_ddbj = eSeqId_not_set \| eAcc_ambig_ed \| fAcc_nuc , CSeq_id::eAcc_gb_embl_ddbj = eSeqId_not_set \| eAcc_ambig_ged \| fAcc_nuc , CSeq_id::eAcc_unreserved_nuc = eSeqId_not_set \| eAcc_unreserved \| fAcc_nuc , CSeq_id::eAcc_unreserved_prot = eSeqId_not_set \| eAcc_unreserved \| fAcc_prot , CSeq_id::eAcc_local = eSeqId_local \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gibbsq = eSeqId_gibbsq \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gibbmt = eSeqId_gibbmt \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_giim = eSeqId_giim \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gb_other = eSeqId_genbank \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gb_prot = eSeqId_genbank \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_gb_other_nuc = eSeqId_genbank \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_gb_est = eSeqId_genbank \| eAcc_est \| fAcc_nuc , CSeq_id::eAcc_gb_dirsub = eSeqId_genbank \| eAcc_dirsub \| fAcc_nuc , CSeq_id::eAcc_gb_patent = eSeqId_genbank \| eAcc_div_patent \| fAcc_seq , CSeq_id::eAcc_gb_patent_prot = eSeqId_genbank \| eAcc_div_patent \| fAcc_prot , CSeq_id::eAcc_gb_cdna = eSeqId_genbank \| eAcc_mrna \| fAcc_nuc , CSeq_id::eAcc_gsdb_dirsub = eSeqId_genbank \| eAcc_gsdb_ds \| fAcc_nuc , CSeq_id::eAcc_gb_gsdb = eSeqId_genbank \| eAcc_gsdb \| fAcc_nuc , CSeq_id::eAcc_gb_backbone = eSeqId_genbank \| eAcc_backbone \| fAcc_nuc , CSeq_id::eAcc_gb_tsa_nuc = eSeqId_genbank \| eAcc_tsa \| fAcc_nuc , CSeq_id::eAcc_gb_tsa_prot = eSeqId_genbank \| eAcc_tsa \| fAcc_prot , CSeq_id::eAcc_gb_tsam_nuc = eSeqId_genbank \| eAcc_tsa_master \| fAcc_nuc , CSeq_id::eAcc_gb_tsam_prot = eSeqId_genbank \| eAcc_tsa_master \| fAcc_prot , CSeq_id::eAcc_gb_tsav_nuc = eSeqId_genbank \| eAcc_tsa_vdb_only \| fAcc_nuc , CSeq_id::eAcc_gb_tsav_prot = eSeqId_genbank \| eAcc_tsa_vdb_only \| fAcc_prot , CSeq_id::eAcc_gb_tsavm_nuc = eSeqId_genbank \| eAcc_tsa_vdb_master \| fAcc_nuc , CSeq_id::eAcc_gb_tsavm_prot = eSeqId_genbank \| eAcc_tsa_vdb_master \| fAcc_prot , CSeq_id::eAcc_gb_segset = eSeqId_genbank \| eAcc_segset \| fAcc_seq , CSeq_id::eAcc_gb_gss = eSeqId_genbank \| eAcc_gss \| fAcc_nuc , CSeq_id::eAcc_gb_genome = eSeqId_genbank \| eAcc_genome \| fAcc_nuc , CSeq_id::eAcc_gb_htgs = eSeqId_genbank \| eAcc_htgs \| fAcc_nuc , CSeq_id::eAcc_gb_con = eSeqId_genbank \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_gb_wgs_nuc = eSeqId_genbank \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_gb_wgs_prot = eSeqId_genbank \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_gb_wgsm_nuc = eSeqId_genbank \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_gb_wgsm_prot = eSeqId_genbank \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_gb_wgsv_nuc = eSeqId_genbank \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_gb_wgsv_prot = eSeqId_genbank \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_gb_wgsvm_nuc = eSeqId_genbank \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_gb_wgsvm_prot = eSeqId_genbank \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_gb_chromosome = eSeqId_genbank \| eAcc_chromosome \| fAcc_nuc , CSeq_id::eAcc_gb_sts = eSeqId_genbank \| eAcc_sts \| fAcc_nuc , CSeq_id::eAcc_gb_mga = eSeqId_genbank \| eAcc_mga \| fAcc_nuc , CSeq_id::eAcc_gb_optical_map = eSeqId_genbank \| eAcc_optical_map \| fAcc_nuc , CSeq_id::eAcc_gb_targeted_nuc = eSeqId_genbank \| eAcc_targeted \| fAcc_nuc , CSeq_id::eAcc_embl_other = eSeqId_embl \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_embl_prot = eSeqId_embl \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_embl_other_nuc = eSeqId_embl \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_embl_est = eSeqId_embl \| eAcc_est \| fAcc_nuc , CSeq_id::eAcc_embl_dirsub = eSeqId_embl \| eAcc_dirsub \| fAcc_nuc , CSeq_id::eAcc_embl_patent = eSeqId_embl \| eAcc_div_patent \| fAcc_nuc , CSeq_id::eAcc_embl_tsa_nuc = eSeqId_embl \| eAcc_tsa \| fAcc_nuc , CSeq_id::eAcc_embl_tsa_prot = eSeqId_embl \| eAcc_tsa \| fAcc_prot , CSeq_id::eAcc_embl_tsam_nuc = eSeqId_embl \| eAcc_tsa_master \| fAcc_nuc , CSeq_id::eAcc_embl_tsam_prot = eSeqId_embl \| eAcc_tsa_master \| fAcc_prot , CSeq_id::eAcc_embl_tsav_nuc = eSeqId_embl \| eAcc_tsa_vdb_only \| fAcc_nuc , CSeq_id::eAcc_embl_tsav_prot = eSeqId_embl \| eAcc_tsa_vdb_only \| fAcc_prot , CSeq_id::eAcc_embl_tsavm_nuc = eSeqId_embl \| eAcc_tsa_vdb_master \| fAcc_nuc , CSeq_id::eAcc_embl_tsavm_prot = eSeqId_embl \| eAcc_tsa_vdb_master \| fAcc_prot , CSeq_id::eAcc_embl_gss = eSeqId_embl \| eAcc_gss \| fAcc_nuc , CSeq_id::eAcc_embl_genome = eSeqId_embl \| eAcc_genome \| fAcc_nuc , CSeq_id::eAcc_embl_htgs = eSeqId_embl \| eAcc_htgs \| fAcc_nuc , CSeq_id::eAcc_embl_con = eSeqId_embl \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_embl_wgs_nuc = eSeqId_embl \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_embl_wgs_prot = eSeqId_embl \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_embl_wgsm_nuc = eSeqId_embl \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_embl_wgsm_prot = eSeqId_embl \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_embl_wgsv_nuc = eSeqId_embl \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_embl_wgsv_prot = eSeqId_embl \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_embl_wgsvm_nuc = eSeqId_embl \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_embl_wgsvm_prot = eSeqId_embl \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_embl_mga = eSeqId_embl \| eAcc_mga \| fAcc_nuc , CSeq_id::eAcc_pir = eSeqId_pir \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_swissprot = eSeqId_swissprot \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_patent = eSeqId_patent \| eAcc_div_patent \| fAcc_seq , CSeq_id::eAcc_refseq_prot = eSeqId_refseq \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_refseq_mrna = eSeqId_refseq \| eAcc_mrna \| fAcc_nuc , CSeq_id::eAcc_refseq_ncrna = eSeqId_refseq \| eAcc_ncrna \| fAcc_nuc , CSeq_id::eAcc_refseq_unique_prot = eSeqId_refseq \| eAcc_unique \| fAcc_prot , CSeq_id::eAcc_refseq_unreserved = eSeqId_refseq \| eAcc_unreserved \| fAcc_seq , CSeq_id::eAcc_refseq_genome = eSeqId_refseq \| eAcc_genome \| fAcc_nuc , CSeq_id::eAcc_refseq_contig = eSeqId_refseq \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_refseq_wgs_nuc = eSeqId_refseq \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_refseq_wgs_prot = eSeqId_refseq \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_refseq_wgsm_nuc = eSeqId_refseq \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_refseq_wgsm_prot = eSeqId_refseq \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_refseq_wgsv_nuc = eSeqId_refseq \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_refseq_wgsv_prot = eSeqId_refseq \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_refseq_wgsvm_nuc = eSeqId_refseq \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_refseq_wgsvm_prot = eSeqId_refseq \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_refseq_chromosome = eSeqId_refseq \| eAcc_chromosome \| fAcc_nuc , CSeq_id::eAcc_refseq_genomic = eSeqId_refseq \| eAcc_genomic_rgn \| fAcc_nuc , CSeq_id::eAcc_refseq_wgs_intermed = eSeqId_refseq \| eAcc_wgs_intermed \| fAcc_nuc , CSeq_id::eAcc_refseq_wgsm_intermed , CSeq_id::eAcc_refseq_wgsv_intermed , CSeq_id::eAcc_refseq_wgsvm_intermed , CSeq_id::eAcc_refseq_prot_predicted = eAcc_refseq_prot \| fAcc_predicted , CSeq_id::eAcc_refseq_mrna_predicted = eAcc_refseq_mrna \| fAcc_predicted , CSeq_id::eAcc_refseq_ncrna_predicted = eAcc_refseq_ncrna \| fAcc_predicted , CSeq_id::eAcc_refseq_chromosome_ncbo = eAcc_refseq_chromosome \| fAcc_ncbo , CSeq_id::eAcc_refseq_contig_ncbo = eAcc_refseq_contig \| fAcc_ncbo , CSeq_id::eAcc_general = eSeqId_general \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_general_nuc = eSeqId_general \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_general_prot = eSeqId_general \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_gi = eSeqId_gi \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_ddbj_other = eSeqId_ddbj \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_ddbj_prot = eSeqId_ddbj \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_ddbj_other_nuc = eSeqId_ddbj \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_ddbj_est = eSeqId_ddbj \| eAcc_est \| fAcc_nuc , CSeq_id::eAcc_ddbj_dirsub = eSeqId_ddbj \| eAcc_dirsub \| fAcc_nuc , CSeq_id::eAcc_ddbj_patent = eSeqId_ddbj \| eAcc_div_patent \| fAcc_nuc , CSeq_id::eAcc_ddbj_mrna = eSeqId_ddbj \| eAcc_mrna \| fAcc_nuc , CSeq_id::eAcc_ddbj_tsa_nuc = eSeqId_ddbj \| eAcc_tsa \| fAcc_nuc , CSeq_id::eAcc_ddbj_tsa_prot = eSeqId_ddbj \| eAcc_tsa \| fAcc_prot , CSeq_id::eAcc_ddbj_tsam_nuc = eSeqId_ddbj \| eAcc_tsa_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tsam_prot = eSeqId_ddbj \| eAcc_tsa_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tsav_nuc = eSeqId_ddbj \| eAcc_tsa_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_tsav_prot = eSeqId_ddbj \| eAcc_tsa_vdb_only \| fAcc_prot , CSeq_id::eAcc_ddbj_tsavm_nuc = eSeqId_ddbj \| eAcc_tsa_vdb_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tsavm_prot = eSeqId_ddbj \| eAcc_tsa_vdb_master \| fAcc_prot , CSeq_id::eAcc_ddbj_gss = eSeqId_ddbj \| eAcc_gss \| fAcc_nuc , CSeq_id::eAcc_ddbj_genome = eSeqId_ddbj \| eAcc_genome \| fAcc_nuc , CSeq_id::eAcc_ddbj_htgs = eSeqId_ddbj \| eAcc_htgs \| fAcc_nuc , CSeq_id::eAcc_ddbj_con = eSeqId_ddbj \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_ddbj_wgs_nuc = eSeqId_ddbj \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_ddbj_wgs_prot = eSeqId_ddbj \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_ddbj_wgsm_nuc = eSeqId_ddbj \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_wgsm_prot = eSeqId_ddbj \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_ddbj_wgsv_nuc = eSeqId_ddbj \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_wgsv_prot = eSeqId_ddbj \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_ddbj_wgsvm_nuc = eSeqId_ddbj \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_wgsvm_prot = eSeqId_ddbj \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_ddbj_mga = eSeqId_ddbj \| eAcc_mga \| fAcc_nuc , CSeq_id::eAcc_ddbj_targeted_nuc = eSeqId_ddbj \| eAcc_targeted \| fAcc_nuc , CSeq_id::eAcc_ddbj_targetedm_nuc = eSeqId_ddbj \| eAcc_targeted_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_targetedv_nuc = eSeqId_ddbj \| eAcc_targeted_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_targetedvm_nuc = eSeqId_ddbj \| eAcc_targeted_vdb_master \| fAcc_nuc , CSeq_id::eAcc_prf = eSeqId_prf \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_pdb = eSeqId_pdb \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gb_tpa_other = eSeqId_tpg \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_gb_tpa_nuc = eSeqId_tpg \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_prot = eSeqId_tpg \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_gb_tpa_segset = eSeqId_tpg \| eAcc_segset \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_con = eSeqId_tpg \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_wgs_nuc = eSeqId_tpg \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_wgs_prot = eSeqId_tpg \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_gb_tpa_wgsm_nuc = eSeqId_tpg \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_wgsm_prot = eSeqId_tpg \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_gb_tpa_wgsv_nuc = eSeqId_tpg \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_wgsv_prot = eSeqId_tpg \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_gb_tpa_wgsvm_nuc = eSeqId_tpg \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_gb_tpa_wgsvm_prot = eSeqId_tpg \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_gb_tpa_chromosome = eSeqId_tpg \| eAcc_chromosome \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_other = eSeqId_tpe \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_embl_tpa_nuc = eSeqId_tpe \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_prot = eSeqId_tpe \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_embl_tpa_tsa_nuc = eSeqId_tpe \| eAcc_tsa \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_tsa_prot = eSeqId_tpe \| eAcc_tsa \| fAcc_prot , CSeq_id::eAcc_embl_tpa_tsam_nuc = eSeqId_tpe \| eAcc_tsa_master \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_tsam_prot = eSeqId_tpe \| eAcc_tsa_master \| fAcc_prot , CSeq_id::eAcc_embl_tpa_tsav_nuc = eSeqId_tpe \| eAcc_tsa_vdb_only \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_tsav_prot = eSeqId_tpe \| eAcc_tsa_vdb_only \| fAcc_prot , CSeq_id::eAcc_embl_tpa_tsavm_nuc = eSeqId_tpe \| eAcc_tsa_vdb_master \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_tsavm_prot = eSeqId_tpe \| eAcc_tsa_vdb_master \| fAcc_prot , CSeq_id::eAcc_embl_tpa_wgs_nuc = eSeqId_tpe \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_wgs_prot = eSeqId_tpe \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_embl_tpa_wgsm_nuc = eSeqId_tpe \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_wgsm_prot = eSeqId_tpe \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_embl_tpa_wgsv_nuc = eSeqId_tpe \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_wgsv_prot = eSeqId_tpe \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_embl_tpa_wgsvm_nuc = eSeqId_tpe \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_embl_tpa_wgsvm_prot = eSeqId_tpe \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_other = eSeqId_tpd \| eAcc_other \| fAcc_seq , CSeq_id::eAcc_ddbj_tpa_nuc = eSeqId_tpd \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_prot = eSeqId_tpd \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_tsa_nuc = eSeqId_tpd \| eAcc_tsa \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_tsa_prot = eSeqId_tpd \| eAcc_tsa \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_tsam_nuc = eSeqId_tpd \| eAcc_tsa_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_tsam_prot = eSeqId_tpd \| eAcc_tsa_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_tsav_nuc = eSeqId_tpd \| eAcc_tsa_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_tsav_prot = eSeqId_tpd \| eAcc_tsa_vdb_only \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_tsavm_nuc = eSeqId_tpd \| eAcc_tsa_vdb_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_tsavm_prot = eSeqId_tpd \| eAcc_tsa_vdb_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_con = eSeqId_tpd \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_wgs_nuc = eSeqId_tpd \| eAcc_wgs \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_wgs_prot = eSeqId_tpd \| eAcc_wgs \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_wgsm_nuc = eSeqId_tpd \| eAcc_wgs_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_wgsm_prot = eSeqId_tpd \| eAcc_wgs_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_wgsv_nuc = eSeqId_tpd \| eAcc_wgs_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_wgsv_prot = eSeqId_tpd \| eAcc_wgs_vdb_only \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_wgsvm_nuc = eSeqId_tpd \| eAcc_wgs_vdb_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_wgsvm_prot = eSeqId_tpd \| eAcc_wgs_vdb_master \| fAcc_prot , CSeq_id::eAcc_ddbj_tpa_chromosome = eSeqId_tpd \| eAcc_chromosome \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_targeted_nuc = eSeqId_tpd \| eAcc_targeted \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_targetedm_nuc = eSeqId_tpd \| eAcc_targeted_master \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_targetedv_nuc = eSeqId_tpd \| eAcc_targeted_vdb_only \| fAcc_nuc , CSeq_id::eAcc_ddbj_tpa_targetedvm_nuc = eSeqId_tpd \| eAcc_targeted_vdb_master \| fAcc_nuc , CSeq_id::eAcc_gpipe_other_nuc = eSeqId_gpipe \| eAcc_other \| fAcc_nuc , CSeq_id::eAcc_gpipe_prot = eSeqId_gpipe \| eAcc_other \| fAcc_prot , CSeq_id::eAcc_gpipe_scaffold = eSeqId_gpipe \| eAcc_con \| fAcc_nuc , CSeq_id::eAcc_gpipe_mrna = eSeqId_gpipe \| eAcc_mrna \| fAcc_nuc , CSeq_id::eAcc_gpipe_chromosome = eSeqId_gpipe \| eAcc_chromosome \| fAcc_nuc , CSeq_id::eAcc_gpipe_genomic = eSeqId_gpipe \| eAcc_genomic_rgn \| fAcc_nuc , CSeq_id::eAcc_gpipe_ncrna = eSeqId_gpipe \| eAcc_ncrna \| fAcc_nuc , CSeq_id::eAcc_gpipe_unreserved = eSeqId_gpipe \| eAcc_unreserved \| fAcc_seq , CSeq_id::eAcc_named_annot_track = eSeqId_named_annot_track \| eAcc_other \| fAcc_seq }
	For IdentifyAccession (below) More...

enum	CSeq_id::E_SIC { CSeq_id::e_error = 0 , CSeq_id::e_DIFF , CSeq_id::e_NO , CSeq_id::e_YES }
	Compare return values. More...

enum	CSeq_id::ELabelType { CSeq_id::eType , CSeq_id::eContent , CSeq_id::eBoth , CSeq_id::eFasta , CSeq_id::eFastaContent , CSeq_id::eDefault = eBoth }
	return the label for a given string More...

enum	CSeq_id::ELabelFlags { CSeq_id::fLabel_Version = 0x10 , CSeq_id::fLabel_GeneralDbIsContent = 0x20 , CSeq_id::fLabel_Trimmed = 0x40 , CSeq_id::fLabel_UpperCase = 0x80 , CSeq_id::fLabel_Default = fLabel_Version }

enum	CSeq_id::EStringFormat { CSeq_id::eFormat_FastA , CSeq_id::eFormat_ForceGI , CSeq_id::eFormat_BestWithoutVersion , CSeq_id::eFormat_BestWithVersion }
	Get a string representation of the sequence IDs of a given bioseq. More...

enum	CSeq_id::EMaxScore { CSeq_id::kMaxScore = 99999 }
	Numerical quality ranking; lower is better. More...

enum	CSeq_id::EAdjustScoreFlags { CSeq_id::fRequireAccessions = 1 << 0 }

enum	CSeq_id::EComposeOSLTFlags { CSeq_id::fAllowLocalId = (1 << 0) , CSeq_id::fGpipeAddSecondary = (1 << 1) }
	Flags specifying special treatment for certain types of Seq-ids in ComposeOSLT(). More...

enum	CSeq_id::ESNPScaleLimit { CSeq_id::eSNPScaleLimit_Default , CSeq_id::eSNPScaleLimit_Unit , CSeq_id::eSNPScaleLimit_Contig , CSeq_id::eSNPScaleLimit_Supercontig , CSeq_id::eSNPScaleLimit_Chromosome }
	SNP annotation scale limits. More...

enum	CSeq_id::ETypeVariant { CSeq_id::eTV_plain , CSeq_id::eTV_tr , CSeq_id::eTV_pgp }

enum	SSeqIdRange::EFlags { SSeqIdRange::fAllowUnderscores = 0x1 }

enum	CSeqIdException::EErrCode { CSeqIdException::eUnknownType , CSeqIdException::eFormat }
	Error types that CSeq_id can generate. More...

Functions
	CSeq_id_Info::CSeq_id_Info (CSeq_id::E_Choice type, CSeq_id_Mapper *mapper)

	CSeq_id_Info::CSeq_id_Info (const CConstRef< CSeq_id > &seq_id, CSeq_id_Mapper *mapper)

	CSeq_id_Info::~CSeq_id_Info (void)

CConstRef< CSeq_id >	CSeq_id_Info::GetSeqId (void) const

virtual CConstRef< CSeq_id >	CSeq_id_Info::GetPackedSeqId (TPacked packed, TVariant variant) const

void	CSeq_id_Info::AddLock (void) const

void	CSeq_id_Info::RemoveLock (void) const

bool	CSeq_id_Info::IsLocked (void) const

CSeq_id::E_Choice	CSeq_id_Info::GetType (void) const

CSeq_id_Mapper &	CSeq_id_Info::GetMapper (void) const

CSeq_id_Which_Tree &	CSeq_id_Info::GetTree (void) const

virtual int	CSeq_id_Info::CompareOrdered (const CSeq_id_Info &other, const CSeq_id_Handle &h_this, const CSeq_id_Handle &h_other) const

void	CSeq_id_Info::x_RemoveLastLock (void) const

	CSeq_id_Info::CSeq_id_Info (const CSeq_id_Info &)

const CSeq_id_Info &	CSeq_id_Info::operator= (const CSeq_id_Info &)

void	CSeq_id_InfoLocker::Lock (const CSeq_id_Info *info) const

void	CSeq_id_InfoLocker::Relock (const CSeq_id_Info *info) const

void	CSeq_id_InfoLocker::Unlock (const CSeq_id_Info *info) const

	CSeq_id_Handle::CSeq_id_Handle (void)

	CSeq_id_Handle::CSeq_id_Handle (const CSeq_id_Info *info, TPacked packed=0, TVariant variant=0)

	CSeq_id_Handle::CSeq_id_Handle (ENull)

static CSeq_id_Handle	CSeq_id_Handle::GetHandle (const CSeq_id &id)
	Normal way of getting a handle, works for any seq-id. More...

static CSeq_id_Handle	CSeq_id_Handle::GetHandle (const string &str_id)
	Construct CSeq_id from string representation and return handle for it. More...

static CSeq_id_Handle	CSeq_id_Handle::GetHandle (TGi gi)
	Faster way to create a handle for a gi. More...

static CSeq_id_Handle	CSeq_id_Handle::GetGiHandle (TGi gi)
	Faster way to create a handle for a gi. More...

bool	CSeq_id_Handle::operator== (const CSeq_id_Handle &handle) const

bool	CSeq_id_Handle::operator!= (const CSeq_id_Handle &handle) const

bool	CSeq_id_Handle::operator< (const CSeq_id_Handle &handle) const

bool	CSeq_id_Handle::operator== (const CSeq_id &id) const

int	CSeq_id_Handle::CompareOrdered (const CSeq_id_Handle &id) const
	Compare ids in a defined order (see CSeq_id::CompareOrdered()) More...

bool	CSeq_id_Handle::PLessOrdered::operator() (const CSeq_id_Handle &id1, const CSeq_id_Handle &id2) const

	CSeq_id_Handle::DECLARE_OPERATOR_BOOL_REF (m_Info)
	Check if the handle is a valid or an empty one. More...

void	CSeq_id_Handle::Reset (void)
	Reset the handle (remove seq-id reference) More...

bool	CSeq_id_Handle::HaveMatchingHandles (void) const

bool	CSeq_id_Handle::HaveReverseMatch (void) const

bool	CSeq_id_Handle::HaveMatchingHandles (EAllowWeakMatch allow_weak_match) const

bool	CSeq_id_Handle::HaveReverseMatch (EAllowWeakMatch allow_weak_match) const

void	CSeq_id_Handle::GetMatchingHandles (TMatches &matches) const

void	CSeq_id_Handle::GetReverseMatchingHandles (TMatches &matches) const

void	CSeq_id_Handle::GetMatchingHandles (TMatches &matches, EAllowWeakMatch allow_weak_match) const

void	CSeq_id_Handle::GetReverseMatchingHandles (TMatches &matches, EAllowWeakMatch allow_weak_match) const

bool	CSeq_id_Handle::MatchesTo (const CSeq_id_Handle &h) const
	True if *this matches to h. More...

bool	CSeq_id_Handle::IsBetter (const CSeq_id_Handle &h) const
	True if "this" is a better bioseq than "h". More...

string	CSeq_id_Handle::AsString (void) const

CSeq_id::E_Choice	CSeq_id_Handle::Which (void) const

bool	CSeq_id_Handle::IsPacked (void) const

TPacked	CSeq_id_Handle::GetPacked (void) const

bool	CSeq_id_Handle::IsSetVariant (void) const

TVariant	CSeq_id_Handle::GetVariant (void) const

bool	CSeq_id_Handle::IsGi (void) const

TGi	CSeq_id_Handle::GetGi (void) const

bool	CSeq_id_Handle::IsAccVer (void) const

unsigned	CSeq_id_Handle::GetHash (void) const

CSeq_id::EAccessionInfo	CSeq_id_Handle::IdentifyAccession (void) const

CConstRef< CSeq_id >	CSeq_id_Handle::GetSeqId (void) const

CConstRef< CSeq_id >	CSeq_id_Handle::GetSeqIdOrNull (void) const

CSeq_id_Mapper &	CSeq_id_Handle::GetMapper (void) const

void	CSeq_id_Handle::Swap (CSeq_id_Handle &idh)

bool	CSeq_id_Handle::IsAllowedSNPScaleLimit (CSeq_id::ESNPScaleLimit scale_limit) const

const CSeq_id_Info *	CSeq_id_Handle::x_GetInfo (void) const

template<>
CConstRef< CSeq_id >	Get_ConstRef_Seq_id (const CSeq_id_Handle &idh)
	Get CConstRef<CSeq_id> from a seq-id handle (for container searching template functions) More...

string	GetDirectLabel (const CSeq_id &id)
	Return best label for a sequence from single Seq-id, or set of Seq-ids. More...

string	GetDirectLabel (const CSeq_id_Handle &id)

string	GetLabel (const CSeq_id &id)

string	GetLabel (const CSeq_id_Handle &id)

string	GetLabel (const vector< CSeq_id_Handle > &ids)

string	GetLabel (const vector< CRef< CSeq_id > > &ids)

CNcbiOstream &	operator<< (CNcbiOstream &out, const CSeq_id_Handle &idh)

BEGIN_STD_SCOPE void	swap (NCBI_NS_NCBI::objects::CSeq_id_Handle &idh1, NCBI_NS_NCBI::objects::CSeq_id_Handle &idh2)

static CRef< CSeq_id_Mapper >	CSeq_id_Mapper::GetInstance (void)

virtual	CSeq_id_Mapper::~CSeq_id_Mapper (void)

CSeq_id_Handle	CSeq_id_Mapper::GetGiHandle (TGi gi)
	Get seq-id handle. More...

CSeq_id_Handle	CSeq_id_Mapper::GetHandle (const CSeq_id &id, bool do_not_create=false)

bool	CSeq_id_Mapper::HaveMatchingHandles (const CSeq_id_Handle &id)
	Get the list of matching handles, do not create new handles. More...

void	CSeq_id_Mapper::GetMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)

bool	CSeq_id_Mapper::HaveReverseMatch (const CSeq_id_Handle &id)

void	CSeq_id_Mapper::GetReverseMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)

bool	CSeq_id_Mapper::HaveMatchingHandles (const CSeq_id_Handle &id, EAllowWeakMatch allow_weak_match)

void	CSeq_id_Mapper::GetMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set, EAllowWeakMatch allow_weak_match)

bool	CSeq_id_Mapper::HaveReverseMatch (const CSeq_id_Handle &id, EAllowWeakMatch allow_weak_match)

void	CSeq_id_Mapper::GetReverseMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set, EAllowWeakMatch allow_weak_match)

void	CSeq_id_Mapper::GetMatchingHandlesStr (string sid, TSeq_id_HandleSet &h_set)
	Get the list of string-matching handles, do not create new handles. More...

static CConstRef< CSeq_id >	CSeq_id_Mapper::GetSeq_id (const CSeq_id_Handle &handle)
	Get seq-id for the given handle. More...

size_t	CSeq_id_Mapper::Dump (CNcbiOstream &out, EDumpDetails details=eDumpTotalBytes) const

	CSeq_id_Mapper::CSeq_id_Mapper (void)

bool	CSeq_id_Mapper::x_Match (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)

bool	CSeq_id_Mapper::x_IsBetter (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)

CSeq_id_Which_Tree &	CSeq_id_Mapper::x_GetTree (CSeq_id::E_Choice type)

CSeq_id_Which_Tree &	CSeq_id_Mapper::x_GetTree (const CSeq_id &id)

CSeq_id_Which_Tree &	CSeq_id_Mapper::x_GetTree (const CSeq_id_Handle &idh)

	CSeq_id_Mapper::CSeq_id_Mapper (const CSeq_id_Mapper &)

CSeq_id_Mapper &	CSeq_id_Mapper::operator= (const CSeq_id_Mapper &)

	CSeq_id::CSeq_id (void)
	See also CSeq_id related functions in "util/sequence.hpp": More...

	CSeq_id::CSeq_id (const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)
	Construct a Seq-id from a flat string. More...

	CSeq_id::CSeq_id (const CDbtag &tag, bool set_as_general=true)
	Construct a seq-id from a dbtag. More...

	CSeq_id::CSeq_id (E_Choice the_type, TIntId int_seq_id)
	Construct a numeric Seq-id. More...

	CSeq_id::CSeq_id (E_Choice the_type, TGi gi)

	CSeq_id::CSeq_id (E_Choice the_type, const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr)
	Construct a Seq-id from a flat representation. More...

	CSeq_id::CSeq_id (EFastaAsTypeAndContent, E_Choice the_type, const CTempString &the_content)
	Construct a Seq-id from a FASTA string with the leading (type) component already parsed out. More...

CSeq_id &	CSeq_id::Set (const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)
	Reassign based on flat specifications; arguments interpreted as with constructors. More...

CSeq_id &	CSeq_id::Set (const CDbtag &tag, bool set_as_general=true)

CSeq_id &	CSeq_id::Set (E_Choice the_type, TIntId int_seq_id)

CSeq_id &	CSeq_id::Set (E_Choice the_type, const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr)

CSeq_id &	CSeq_id::Set (EFastaAsTypeAndContent, E_Choice the_type, const CTempString &the_content)

virtual	CSeq_id::~CSeq_id (void)
	Destructor. More...

static E_Choice	CSeq_id::WhichInverseSeqId (const CTempString &SeqIdCode)
	Converts a string to a choice, no need to require a member. More...

static const char *	CSeq_id::WhichFastaTag (E_Choice choice)
	Converts a choice to a FASTA tag, with no trailing vertical bar. More...

static E_Choice	CSeq_id::GetAccType (EAccessionInfo info)

static EAccessionInfo	CSeq_id::IdentifyAccession (const CTempString &accession, TParseFlags flags=fParse_AnyRaw)
	Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on properties. More...

EAccessionInfo	CSeq_id::IdentifyAccession (TParseFlags flags=fParse_AnyRaw\|fParse_AnyLocal) const

static void	CSeq_id::LoadAccessionGuide (const string &filename)

static void	CSeq_id::LoadAccessionGuide (ILineReader &in)

bool	CSeq_id::Match (const CSeq_id &sid2) const
	Match() - TRUE if SeqIds are equivalent. More...

E_SIC	CSeq_id::Compare (const CSeq_id &sid2) const
	Compare() - more general. More...

int	CSeq_id::CompareOrdered (const CSeq_id &sid2) const

bool	CSeq_id::operator< (const CSeq_id &sid2) const

const CTextseq_id *	CSeq_id::GetTextseq_Id (void) const
	Return embedded CTextseq_id, if any. More...

virtual void	CSeq_id::WriteAsFasta (ostream &out) const
	Implement serializable interface. More...

CProxy	CSeq_id::DumpAsFasta (void) const

const string	CSeq_id::AsFastaString (void) const

void	CSeq_id::GetLabel (string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const
	Append a label for this Seq-id to the supplied string. More...

void	CSeq_id::GetLabel (string label, int version, ELabelType type=eDefault) const
	Append a label for this Seq-id to the supplied string, splitting out the version to a separate output parameter. More...

string	CSeq_id::GetSeqIdString (bool with_version=false) const
	Return seqid string with optional version for text seqid type. More...

string	CSeq_id::GetSeqIdString (int *version) const
	Return seqid string for text seqid type with separate integer version. More...

static string	CSeq_id::GetStringDescr (const CBioseq &bioseq, EStringFormat fmt)

static CNcbiOstream &	CSeq_id::WriteAsFasta (CNcbiOstream &ostr, const CBioseq &bioseq)
	Write a bioseq's IDs in FASTA format. More...

static bool	CSeq_id::IsValidLocalID (const CTempString &s)
	Perform rudimentary validation on potential local IDs, whose contents should be pure ASCII and limited to letters, digits, and certain punctuation characters (-_. More...

static TErrorFlags	CSeq_id::CheckLocalID (const CTempString &s)
	Perform rudimentary validation on potential local IDs, whose contents should not exceed fifty characters and are limited to ASCII characters excluding >[]\|"". More...

static SIZE_TYPE	CSeq_id::ParseIDs (CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)
	Parse a string representing one or more Seq-ids, appending the results to IDS. More...

static bool	CSeq_id::IsValid (const CBioseq::TId &ids, TParseFlags flags=fParse_Default)

static bool	CSeq_id::IsValid (const CSeq_id &id, TParseFlags flags=fParse_Default)

static SIZE_TYPE	CSeq_id::ParseFastaIds (CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)
	Parse an entire set of \|-delimited FASTA-style IDs, appending the results to IDS. More...

	CSeq_id::DECLARE_SAFE_FLAGS_TYPE (EAdjustScoreFlags, TAdjustScoreFlags)

int	CSeq_id::AdjustScore (int base_score, TAdjustScoreFlags flags=TAdjustScoreFlags()) const

int	CSeq_id::StrictAdjustScore (int base_score) const

int	CSeq_id::BaseTextScore (void) const

int	CSeq_id::BaseBestRankScore (void) const

int	CSeq_id::BaseWorstRankScore (void) const

int	CSeq_id::BaseFastaAAScore (void) const

int	CSeq_id::BaseFastaNAScore (void) const

int	CSeq_id::BaseBlastScore (void) const

int	CSeq_id::TextScore (void) const

int	CSeq_id::BestRankScore (void) const

int	CSeq_id::WorstRankScore (void) const

int	CSeq_id::FastaAAScore (void) const

int	CSeq_id::FastaNAScore (void) const

int	CSeq_id::BlastScore (void) const

int	CSeq_id::StrictTextScore (void) const

int	CSeq_id::StrictBestRankScore (void) const

int	CSeq_id::StrictFastaAAScore (void) const

int	CSeq_id::StrictFastaNAScore (void) const

int	CSeq_id::StrictBlastScore (void) const

static int	CSeq_id::Score (const CRef< CSeq_id > &id)
	Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp> More...

static int	CSeq_id::BestRank (const CRef< CSeq_id > &id)

static int	CSeq_id::WorstRank (const CRef< CSeq_id > &id)

static int	CSeq_id::FastaAARank (const CRef< CSeq_id > &id)

static int	CSeq_id::FastaNARank (const CRef< CSeq_id > &id)

static int	CSeq_id::BlastRank (const CRef< CSeq_id > &id)

static int	CSeq_id::StrictScore (const CRef< CSeq_id > &id)

static int	CSeq_id::StrictBestRank (const CRef< CSeq_id > &id)

static int	CSeq_id::StrictFastaAARank (const CRef< CSeq_id > &id)

static int	CSeq_id::StrictFastaNARank (const CRef< CSeq_id > &id)

static int	CSeq_id::StrictBlastRank (const CRef< CSeq_id > &id)

virtual void	CSeq_id::Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Optimized implementation of CSerialObject::Assign, which is not so efficient. More...

void	CSeq_id::GetMatchingIds (TSeqIdHandles &matches) const
	Collect partially matching seq-ids: no-version, no-name etc. More...

void	CSeq_id::GetMatchingTextseqIds (TSeqIdHandles &matches) const
	Collect partially matching textseq-ids. More...

static bool	CSeq_id::PreferAccessionOverGi (void)
	Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SEQ_ID_PREFER_ACCESSION_OVER_GI). More...

static bool	CSeq_id::AvoidGi (void)
	Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI). More...

string	CSeq_id::ComposeOSLT (list< string > *secondary_ids=nullptr, TComposeOSLTFlags parse_flags=0) const
	JIRA ID-5188 : Compose OSLT string for the primary id, as well as OSLT strings for the secondary ids, if any. More...

static const char *	CSeq_id::GetSNPScaleLimit_Name (ESNPScaleLimit value)

static ESNPScaleLimit	CSeq_id::GetSNPScaleLimit_Value (const string &name)

bool	CSeq_id::IsAllowedSNPScaleLimit (ESNPScaleLimit scale_limit) const

static ETypeVariant	CSeq_id::x_IdentifyTypeVariant (E_Choice type, const CTempString &str)

E_Choice	CSeq_id::x_Init (list< CTempString > &fasta_pieces, E_Choice type, ETypeVariant tv)

	CSeq_id::CSeq_id (const CSeq_id &)

CSeq_id &	CSeq_id::operator= (const CSeq_id &)

static EAccessionInfo	CSeq_id::x_IdentifyAccession (const CTempString &main_acc, TParseFlags flags, bool has_version)

void	CSeq_id::x_WriteContentAsFasta (ostream &out) const

	SSeqIdRange::SSeqIdRange (const CTempString &s, TFlags flags=0)

	SSeqIdRange::const_iterator::const_iterator (const SSeqIdRange &range)

	SSeqIdRange::const_iterator::const_iterator (const SSeqIdRange &range, int number)

	SSeqIdRange::const_iterator::const_iterator (const const_iterator &it)

const_iterator &	SSeqIdRange::const_iterator::operator= (const const_iterator &it)

string	SSeqIdRange::const_iterator::operator* (void) const

const string *	SSeqIdRange::const_iterator::operator-> (void) const

string	SSeqIdRange::const_iterator::operator[] (int n) const

CRef< CSeq_id >	SSeqIdRange::const_iterator::GetID (void) const

const_iterator &	SSeqIdRange::const_iterator::operator++ (void)

const_iterator	SSeqIdRange::const_iterator::operator++ (int)

const_iterator &	SSeqIdRange::const_iterator::operator-- (void)

const_iterator	SSeqIdRange::const_iterator::operator-- (int)

const_iterator	SSeqIdRange::const_iterator::operator+ (int n) const

const_iterator	SSeqIdRange::const_iterator::operator- (int n) const

const_iterator &	SSeqIdRange::const_iterator::operator+= (int n)

const_iterator &	SSeqIdRange::const_iterator::operator-= (int n)

bool	SSeqIdRange::const_iterator::operator== (const const_iterator &it) const

bool	SSeqIdRange::const_iterator::operator!= (const const_iterator &it) const

bool	SSeqIdRange::const_iterator::operator< (const const_iterator &it) const

bool	SSeqIdRange::const_iterator::operator> (const const_iterator &it) const

bool	SSeqIdRange::const_iterator::operator<= (const const_iterator &it) const

bool	SSeqIdRange::const_iterator::operator>= (const const_iterator &it) const

int	SSeqIdRange::const_iterator::operator- (const const_iterator &it) const

const string &	SSeqIdRange::const_iterator::x_SetAccession (void) const

const_iterator	SSeqIdRange::begin (void) const

const_iterator	SSeqIdRange::end (void) const

size_t	SSeqIdRange::size (void) const

virtual const char *	CSeqIdException::GetErrCodeString (void) const override
	Translate from the error code value to its string representation. More...

	CSeqIdException::NCBI_EXCEPTION_DEFAULT (CSeqIdException, CException)

template<class TId >
CConstRef< CSeq_id >	Get_ConstRef_Seq_id (TId &id)
	Dummy convertor for container search functions. More...

template<class container >
CConstRef< CSeq_id >	GetSeq_idByType (const container &ids, CSeq_id::E_Choice choice)
	Search the container of CRef<CSeq_id> for the id of given type. More...

template<class container >
TGi	FindGi (const container &ids)
	Return gi from id list if exists, return 0 otherwise. More...

template<class container >
CConstRef< CSeq_id >	FindTextseq_id (const container &ids)
	Return text seq-id from id list if exists, return 0 otherwise. More...

Variables
atomic< Uint8 >	CSeq_id_Info::m_LockCounter {0}

atomic< CSeq_id::E_Choice >	CSeq_id_Info::m_Seq_id_Type

CConstRef< CSeq_id >	CSeq_id_Info::m_Seq_id

CRef< CSeq_id_Mapper >	CSeq_id_Info::m_Mapper

CConstRef< CSeq_id_Info, CSeq_id_InfoLocker >	CSeq_id_Handle::m_Info

TPacked	CSeq_id_Handle::m_Packed

TVariant	CSeq_id_Handle::m_Variant

TTrees	CSeq_id_Mapper::m_Trees

CMutex	CSeq_id_Mapper::m_IdMapMutex

static const size_t	CSeq_id::kMaxLocalIDLength = 50
	ID length restrictions. More...

static const size_t	CSeq_id::kMaxGeneralDBLength = 20

static const size_t	CSeq_id::kMaxGeneralTagLength = 50

static const size_t	CSeq_id::kMaxAccessionLength = 30

const SSeqIdRange *	SSeqIdRange::const_iterator::m_Range

int	SSeqIdRange::const_iterator::m_Number

string	SSeqIdRange::const_iterator::m_Accession

string	SSeqIdRange::prefix

int	SSeqIdRange::start

int	SSeqIdRange::stop

int	SSeqIdRange::digits

CSeq_id::EAccessionInfo	SSeqIdRange::acc_info

Friends
class	CSeq_id_Info::CSeq_id_Which_Tree

class	CSeq_id_Handle::CSeq_id_Mapper

class	CSeq_id_Handle::CSeq_id_Which_Tree

class	CSeq_id_Mapper::CSeq_id_Handle

class	CSeq_id_Mapper::CSeq_id_Info

Detailed Description

Macro Definition Documentation

◆ NCBI_ACC

#define NCBI_ACC	(	type,
		div,
		mol
	)	eSeqId_##type \| eAcc_##div \| fAcc_##mol

Definition at line 317 of file Seq_id.hpp.

Typedef Documentation

◆ difference_type

typedef ptrdiff_t SSeqIdRange::const_iterator::difference_type

Definition at line 909 of file Seq_id.hpp.

◆ iterator_category

typedef random_access_iterator_tag SSeqIdRange::const_iterator::iterator_category

Definition at line 907 of file Seq_id.hpp.

◆ pointer

typedef const string* SSeqIdRange::const_iterator::pointer

Definition at line 910 of file Seq_id.hpp.

◆ reference

typedef string& SSeqIdRange::const_iterator::reference

Definition at line 911 of file Seq_id.hpp.

◆ TComposeOSLTFlags

typedef int CSeq_id::TComposeOSLTFlags

Definition at line 823 of file Seq_id.hpp.

◆ TErrorFlags

using CSeq_id::TErrorFlags = int

Definition at line 113 of file Seq_id.hpp.

◆ TFlags

typedef int SSeqIdRange::TFlags

binary OR of EFlags

Definition at line 899 of file Seq_id.hpp.

◆ TLabelFlags

typedef int CSeq_id::TLabelFlags

Definition at line 625 of file Seq_id.hpp.

◆ TMatches

typedef set<CSeq_id_Handle> CSeq_id_Handle::TMatches

Definition at line 241 of file seq_id_handle.hpp.

◆ TPacked [1/2]

typedef TIntId CSeq_id_Info::TPacked

Definition at line 71 of file seq_id_handle.hpp.

◆ TPacked [2/2]

typedef CSeq_id_Info::TPacked CSeq_id_Handle::TPacked

Definition at line 160 of file seq_id_handle.hpp.

◆ Tparent

typedef CSeq_id_Base CSeq_id::Tparent

private

Definition at line 72 of file Seq_id.hpp.

◆ TParseFlags

typedef int CSeq_id::TParseFlags

Definition at line 104 of file Seq_id.hpp.

◆ TSeq_id_HandleSet

typedef set<CSeq_id_Handle> TSeq_id_HandleSet

CSeq_id_Mapper::

Allows fast convertions between CSeq_id and CSeq_id_Handle, including searching for multiple matches for a given seq-id.

Definition at line 69 of file seq_id_mapper.hpp.

◆ TSeqIdHandles

typedef set<CSeq_id_Handle> CSeq_id::TSeqIdHandles

Definition at line 801 of file Seq_id.hpp.

◆ TTrees

typedef vector<CRef<CSeq_id_Which_Tree> > CSeq_id_Mapper::TTrees

private

Definition at line 141 of file seq_id_mapper.hpp.

◆ TVariant [1/2]

typedef Uint8 CSeq_id_Info::TVariant

Definition at line 72 of file seq_id_handle.hpp.

◆ TVariant [2/2]

typedef CSeq_id_Info::TVariant CSeq_id_Handle::TVariant

Definition at line 161 of file seq_id_handle.hpp.

◆ value_type

typedef string SSeqIdRange::const_iterator::value_type

Definition at line 908 of file Seq_id.hpp.

Enumeration Type Documentation

◆ E_SIC

enum CSeq_id::E_SIC

Compare return values.

Enumerator
e_error
e_DIFF	some problem
e_NO	different SeqId types-can't compare
e_YES	SeqIds compared, but are different. SeqIds compared, are equivalent

Definition at line 579 of file Seq_id.hpp.

◆ EAccessionInfo

enum CSeq_id::EAccessionInfo

For IdentifyAccession (below)

Enumerator
eSeqId_not_set
eSeqId_local
eSeqId_gibbsq
eSeqId_gibbmt
eSeqId_giim
eSeqId_genbank
eSeqId_embl
eSeqId_pir
eSeqId_swissprot
eSeqId_patent
eSeqId_other
eSeqId_refseq
eSeqId_general
eSeqId_gi
eSeqId_ddbj
eSeqId_prf
eSeqId_pdb
eSeqId_tpg
eSeqId_tpe
eSeqId_tpd
eSeqId_gpipe
eSeqId_named_annot_track
eAcc_type_mask
fAcc_nuc
fAcc_prot
fAcc_seq
fAcc_predicted
fAcc_specials
fAcc_master
fAcc_ncbo
fAcc_fallback
fAcc_vdb_only
eAcc_flag_mask
eAcc_other
eAcc_est
eAcc_dirsub
eAcc_div_patent
eAcc_mrna
eAcc_ncrna
eAcc_gsdb_ds
eAcc_gsdb
eAcc_backbone
eAcc_tsa
eAcc_segset
eAcc_gss
eAcc_unique
eAcc_ambig
eAcc_ambig_g
eAcc_ambig_e
eAcc_ambig_ge
eAcc_ambig_d
eAcc_ambig_gd
eAcc_ambig_ed
eAcc_ambig_ged
eAcc_unreserved
fAcc_genomic
eAcc_genome
eAcc_htgs
eAcc_con
eAcc_wgs
eAcc_chromosome
eAcc_genomic_rgn
eAcc_wgs_intermed
eAcc_sts
eAcc_mga
eAcc_optical_map
eAcc_targeted
eAcc_division_mask
eAcc_wgs_master
eAcc_wgs_intermed_master
eAcc_tsa_master
eAcc_targeted_master
eAcc_wgs_vdb_only
eAcc_wgs_intermed_vdb_only
eAcc_tsa_vdb_only
eAcc_targeted_vdb_only
eAcc_wgs_vdb_master
eAcc_wgs_intermed_vdb_master
eAcc_tsa_vdb_master
eAcc_targeted_vdb_master
eAcc_unknown
eAcc_ambiguous_nuc
eAcc_maybe_gb
eAcc_maybe_embl
eAcc_maybe_ddbj
eAcc_gb_embl
eAcc_gb_ddbj
eAcc_embl_ddbj
eAcc_gb_embl_ddbj
eAcc_unreserved_nuc
eAcc_unreserved_prot
eAcc_local
eAcc_gibbsq
eAcc_gibbmt
eAcc_giim
eAcc_gb_other
eAcc_gb_prot
eAcc_gb_other_nuc
eAcc_gb_est
eAcc_gb_dirsub
eAcc_gb_patent
eAcc_gb_patent_prot
eAcc_gb_cdna
eAcc_gsdb_dirsub
eAcc_gb_gsdb
eAcc_gb_backbone
eAcc_gb_tsa_nuc
eAcc_gb_tsa_prot
eAcc_gb_tsam_nuc
eAcc_gb_tsam_prot
eAcc_gb_tsav_nuc
eAcc_gb_tsav_prot
eAcc_gb_tsavm_nuc
eAcc_gb_tsavm_prot
eAcc_gb_segset
eAcc_gb_gss
eAcc_gb_genome
eAcc_gb_htgs
eAcc_gb_con
eAcc_gb_wgs_nuc
eAcc_gb_wgs_prot
eAcc_gb_wgsm_nuc
eAcc_gb_wgsm_prot
eAcc_gb_wgsv_nuc
eAcc_gb_wgsv_prot
eAcc_gb_wgsvm_nuc
eAcc_gb_wgsvm_prot
eAcc_gb_chromosome
eAcc_gb_sts
eAcc_gb_mga
eAcc_gb_optical_map
eAcc_gb_targeted_nuc
eAcc_embl_other
eAcc_embl_prot
eAcc_embl_other_nuc
eAcc_embl_est
eAcc_embl_dirsub
eAcc_embl_patent
eAcc_embl_tsa_nuc
eAcc_embl_tsa_prot
eAcc_embl_tsam_nuc
eAcc_embl_tsam_prot
eAcc_embl_tsav_nuc
eAcc_embl_tsav_prot
eAcc_embl_tsavm_nuc
eAcc_embl_tsavm_prot
eAcc_embl_gss
eAcc_embl_genome
eAcc_embl_htgs
eAcc_embl_con
eAcc_embl_wgs_nuc
eAcc_embl_wgs_prot
eAcc_embl_wgsm_nuc
eAcc_embl_wgsm_prot
eAcc_embl_wgsv_nuc
eAcc_embl_wgsv_prot
eAcc_embl_wgsvm_nuc
eAcc_embl_wgsvm_prot
eAcc_embl_mga
eAcc_pir
eAcc_swissprot
eAcc_patent
eAcc_refseq_prot
eAcc_refseq_mrna
eAcc_refseq_ncrna
eAcc_refseq_unique_prot
eAcc_refseq_unreserved
eAcc_refseq_genome
eAcc_refseq_contig
eAcc_refseq_wgs_nuc
eAcc_refseq_wgs_prot
eAcc_refseq_wgsm_nuc
eAcc_refseq_wgsm_prot
eAcc_refseq_wgsv_nuc
eAcc_refseq_wgsv_prot
eAcc_refseq_wgsvm_nuc
eAcc_refseq_wgsvm_prot
eAcc_refseq_chromosome
eAcc_refseq_genomic
eAcc_refseq_wgs_intermed
eAcc_refseq_wgsm_intermed
eAcc_refseq_wgsv_intermed
eAcc_refseq_wgsvm_intermed
eAcc_refseq_prot_predicted
eAcc_refseq_mrna_predicted
eAcc_refseq_ncrna_predicted
eAcc_refseq_chromosome_ncbo
eAcc_refseq_contig_ncbo
eAcc_general
eAcc_general_nuc
eAcc_general_prot
eAcc_gi
eAcc_ddbj_other
eAcc_ddbj_prot
eAcc_ddbj_other_nuc
eAcc_ddbj_est
eAcc_ddbj_dirsub
eAcc_ddbj_patent
eAcc_ddbj_mrna
eAcc_ddbj_tsa_nuc
eAcc_ddbj_tsa_prot
eAcc_ddbj_tsam_nuc
eAcc_ddbj_tsam_prot
eAcc_ddbj_tsav_nuc
eAcc_ddbj_tsav_prot
eAcc_ddbj_tsavm_nuc
eAcc_ddbj_tsavm_prot
eAcc_ddbj_gss
eAcc_ddbj_genome
eAcc_ddbj_htgs
eAcc_ddbj_con
eAcc_ddbj_wgs_nuc
eAcc_ddbj_wgs_prot
eAcc_ddbj_wgsm_nuc
eAcc_ddbj_wgsm_prot
eAcc_ddbj_wgsv_nuc
eAcc_ddbj_wgsv_prot
eAcc_ddbj_wgsvm_nuc
eAcc_ddbj_wgsvm_prot
eAcc_ddbj_mga
eAcc_ddbj_targeted_nuc
eAcc_ddbj_targetedm_nuc
eAcc_ddbj_targetedv_nuc
eAcc_ddbj_targetedvm_nuc
eAcc_prf
eAcc_pdb
eAcc_gb_tpa_other
eAcc_gb_tpa_nuc
eAcc_gb_tpa_prot
eAcc_gb_tpa_segset
eAcc_gb_tpa_con
eAcc_gb_tpa_wgs_nuc
eAcc_gb_tpa_wgs_prot
eAcc_gb_tpa_wgsm_nuc
eAcc_gb_tpa_wgsm_prot
eAcc_gb_tpa_wgsv_nuc
eAcc_gb_tpa_wgsv_prot
eAcc_gb_tpa_wgsvm_nuc
eAcc_gb_tpa_wgsvm_prot
eAcc_gb_tpa_chromosome
eAcc_embl_tpa_other
eAcc_embl_tpa_nuc
eAcc_embl_tpa_prot
eAcc_embl_tpa_tsa_nuc
eAcc_embl_tpa_tsa_prot
eAcc_embl_tpa_tsam_nuc
eAcc_embl_tpa_tsam_prot
eAcc_embl_tpa_tsav_nuc
eAcc_embl_tpa_tsav_prot
eAcc_embl_tpa_tsavm_nuc
eAcc_embl_tpa_tsavm_prot
eAcc_embl_tpa_wgs_nuc
eAcc_embl_tpa_wgs_prot
eAcc_embl_tpa_wgsm_nuc
eAcc_embl_tpa_wgsm_prot
eAcc_embl_tpa_wgsv_nuc
eAcc_embl_tpa_wgsv_prot
eAcc_embl_tpa_wgsvm_nuc
eAcc_embl_tpa_wgsvm_prot
eAcc_ddbj_tpa_other
eAcc_ddbj_tpa_nuc
eAcc_ddbj_tpa_prot
eAcc_ddbj_tpa_tsa_nuc
eAcc_ddbj_tpa_tsa_prot
eAcc_ddbj_tpa_tsam_nuc
eAcc_ddbj_tpa_tsam_prot
eAcc_ddbj_tpa_tsav_nuc
eAcc_ddbj_tpa_tsav_prot
eAcc_ddbj_tpa_tsavm_nuc
eAcc_ddbj_tpa_tsavm_prot
eAcc_ddbj_tpa_con
eAcc_ddbj_tpa_wgs_nuc
eAcc_ddbj_tpa_wgs_prot
eAcc_ddbj_tpa_wgsm_nuc
eAcc_ddbj_tpa_wgsm_prot
eAcc_ddbj_tpa_wgsv_nuc
eAcc_ddbj_tpa_wgsv_prot
eAcc_ddbj_tpa_wgsvm_nuc
eAcc_ddbj_tpa_wgsvm_prot
eAcc_ddbj_tpa_chromosome
eAcc_ddbj_tpa_targeted_nuc
eAcc_ddbj_tpa_targetedm_nuc
eAcc_ddbj_tpa_targetedv_nuc
eAcc_ddbj_tpa_targetedvm_nuc
eAcc_gpipe_other_nuc
eAcc_gpipe_prot
eAcc_gpipe_scaffold
eAcc_gpipe_mrna
eAcc_gpipe_chromosome
eAcc_gpipe_genomic
eAcc_gpipe_ncrna
eAcc_gpipe_unreserved
eAcc_named_annot_track

Definition at line 220 of file Seq_id.hpp.

◆ EAdjustScoreFlags

enum CSeq_id::EAdjustScoreFlags

Enumerator
fRequireAccessions

Definition at line 736 of file Seq_id.hpp.

◆ EAllowWeakMatch

enum EAllowWeakMatch

Enumerator
eNoWeakMatch
eAllowWeakMatch

Definition at line 151 of file seq_id_handle.hpp.

◆ EComposeOSLTFlags

enum CSeq_id::EComposeOSLTFlags

Flags specifying special treatment for certain types of Seq-ids in ComposeOSLT().

See also: ComposeOSLT

Enumerator
fAllowLocalId
fGpipeAddSecondary	Add "ACC.VER(=1)" for a 2ndary id.

Definition at line 819 of file Seq_id.hpp.

◆ EDumpDetails

enum CSeq_id_Mapper::EDumpDetails

Enumerator
eCountTotalBytes
eDumpTotalBytes
eDumpStatistics
eDumpAllIds

Definition at line 108 of file seq_id_mapper.hpp.

◆ EErrCode

enum CSeqIdException::EErrCode

Error types that CSeq_id can generate.

Enumerator
eUnknownType	Unrecognized Seq-id type.
eFormat	Contents not parsable as expected.

Definition at line 1004 of file Seq_id.hpp.

◆ EErrorFlags

enum CSeq_id::EErrorFlags

Enumerator
fNoError
fEmptyId
fInvalidChar
fExceedsMaxLength

Definition at line 107 of file Seq_id.hpp.

◆ EFastaAsTypeAndContent

enum CSeq_id::EFastaAsTypeAndContent

Tag for method variants that would otherwise be ambiguous.

Enumerator
eFasta_AsTypeAndContent

Definition at line 116 of file Seq_id.hpp.

◆ EFlags

enum SSeqIdRange::EFlags

Enumerator
fAllowUnderscores	Allow prefixes to contain underscores.

Definition at line 896 of file Seq_id.hpp.

◆ ELabelFlags

enum CSeq_id::ELabelFlags

Enumerator
fLabel_Version	Show the version.
fLabel_GeneralDbIsContent	For type general, use the database name as the tag and the (text or numeric) key as the content.
fLabel_Trimmed	Trim trailing FASTA delimeters.
fLabel_UpperCase	Upper case label, with special encoding for PDB chain-ids.
fLabel_Default	default options - always show the version

Definition at line 614 of file Seq_id.hpp.

◆ ELabelType

enum CSeq_id::ELabelType

return the label for a given string

Enumerator
eType	FASTA-style type, or database in GeneralDbIsContent mode.
eContent	Untagged human-readable accession or the like.
eBoth	Type and content, delimited by a vertical bar.
eFasta	Tagged ID in NCBI's traditional FASTA style.
eFastaContent	Like eFasta, but without any tag.
eDefault	default is to show type + content

Definition at line 603 of file Seq_id.hpp.

◆ EMaxScore

enum CSeq_id::EMaxScore

Numerical quality ranking; lower is better.

(Text)Score, aka WorstRank, corresponds to the C Toolkit's SeqIdFindWorst, which favors textual accessions, whereas BestRank corresponds to the C Toolkit's SeqIdFindBest and favors GIs. In addition, there is a pair of methods corresponding to the C Toolkit's GetOrderBySeqId, used when generating FASTA deflines.

All rankings give a slight bonus to accessions that carry versions.

Enumerator
kMaxScore

Definition at line 732 of file Seq_id.hpp.

◆ EParseFlags

enum CSeq_id::EParseFlags

Enumerator
fParse_PartialOK	Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions, either from unsupported syntax or because it is only possible to accept a single ID anyway (in the string-based constructor and corresponding Set() variant).
fParse_RawText	Try to ID raw non-numeric accessions.
fParse_RawGI	Treat raw numbers as GIs, not local IDs.
fParse_AnyRaw
fParse_ValidLocal	Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validation. Also, accept PDB accessions with chains but no delimiters.
fParse_AnyLocal	Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style IDs (or ID sets).
fParse_NoFASTA	Don't bother checking for a tag.
fParse_FallbackOK	For IdentifyAccession, don't warn about falling back to a different specific type because broad identification is sufficient. (Automatically on when calling IdentifyAccession internally.)
fParse_Default	By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local accessions. (The string-based constructor and Set method have a stricter default: fParse_AnyRaw.)

Definition at line 75 of file Seq_id.hpp.

◆ ESNPScaleLimit

enum CSeq_id::ESNPScaleLimit

SNP annotation scale limits.

Enumerator
eSNPScaleLimit_Default
eSNPScaleLimit_Unit
eSNPScaleLimit_Contig
eSNPScaleLimit_Supercontig
eSNPScaleLimit_Chromosome

Definition at line 847 of file Seq_id.hpp.

◆ EStringFormat

enum CSeq_id::EStringFormat

Get a string representation of the sequence IDs of a given bioseq.

This function produces strings in a number of possible formats.

Enumerator
eFormat_FastA
eFormat_ForceGI
eFormat_BestWithoutVersion
eFormat_BestWithVersion

Definition at line 661 of file Seq_id.hpp.

◆ ETypeVariant

enum CSeq_id::ETypeVariant

private

Enumerator
eTV_plain
eTV_tr
eTV_pgp

Definition at line 860 of file Seq_id.hpp.

Function Documentation

◆ AddLock()

void CSeq_id_Info::AddLock ( void ) const

inline

Definition at line 87 of file seq_id_handle.hpp.

References CSeq_id_Info::m_LockCounter.

◆ AdjustScore()

int CSeq_id::AdjustScore	(	int	base_score,
		TAdjustScoreFlags	flags = `TAdjustScoreFlags()`
	)		const

Definition at line 3195 of file Seq_id.cpp.

References flags, CSeq_id::fRequireAccessions, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsGeneral(), and kMax_Int.

Referenced by CSeq_id::BestRankScore(), CSeq_id::BlastScore(), CSeq_id::FastaAAScore(), CSeq_id::FastaNAScore(), PSGRank(), CSeq_id::StrictAdjustScore(), and CSeq_id::TextScore().

◆ AsFastaString()

const string CSeq_id::AsFastaString ( void ) const

Definition at line 2266 of file Seq_id.cpp.

References str(), and CSeq_id::WriteAsFasta().

Referenced by CGapAnalysis::AddBioseqGaps(), AddChromosomeNoLocation(), CGBProjectHelper::AddProjectItemsFromRID(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CTaxIdSet::AddTaxId(), BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::BuildUserUrl(), CAlnMapPrinter::CAlnMapPrinter(), CAlnMix::ChooseSeqId(), CBlastBioseqMaker::CreateBioseqFromId(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), CVcfTrackDataFactory::CreateTrackData(), CAlignResultsSet::DropQuery(), CRawWiggleRecord::Dump(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqId(), CFtableFormatter::FormatFeatHeader(), CFlatFileGenerator::Generate(), CScore_FrameShifts::Get(), CScore_SequenceLength::Get(), CScore_SymmetricOverlap::Get(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), CScore_GeneID::Get(), CScore_RibosomalSlippage::Get(), CScore_SegPct::Get(), CScore_Entropy::Get(), CObjFingerprint::GetAlignSignature(), CAlnVec::GetBioseqHandle(), GetBlastSeqIdString(), CObjFingerprint::GetComponentSignature(), CObjFingerprint::GetFeatSignature(), CObjFingerprint::GetGraphSignature(), CObjFingerprint::GetHistogramSignature(), GetIdStartStopStrandStr(), CSeq_id::GetLabel(), CGuiObjectInfoSeq_align::GetLinks(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CObjFingerprint::GetRsiteSignature(), CShowBlastDefline::GetSeqIdListString(), IRepeatRegion::GetSeqIdString(), CObjFingerprint::GetSeqLocSignature(), CAlnMixSeq::GetSeqString(), CWriteUtil::GetStringId(), CObjFingerprint::GetVcfVariantSignature(), CAlignFormatUtil::HspListToHitMap(), IdRefLess(), CBlastBioseqMaker::IsProtein(), CSeqUtils::isTopLevel(), CMergeTreeThread::Main(), MakeEmptyResults(), MakeKey(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CAnnotObjectType_Less::operator()(), CAlignSort::SAlignExtractor::operator()(), hash_seqid::operator()(), CSeqIdBioseqHandleComp< TSeqIdPtr >::operator()(), CFastaReader::ParseDefLine(), CFastaReader::PostWarning(), CTabularFormatter_Indels::Print(), CTabularFormatter_StartCodonChanges::Print(), PrintBestSeqId(), CReadBlastApp::processFeature(), CAlignResultsSet::QueryExists(), CFeature_table_reader::ReadSequinFeatureTables(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), RemasterWithStructure(), CSeedTopApp::Run(), CVectorScreen::Run(), CWalkAsnCacheApplication::Run(), CBlastDemoApplication::Run(), CTestBlastp_All::RunTest(), s_BlastXMLAddIteration(), s_CompareProtProdToTrans(), s_DeflineCompare(), s_GetBestIDForURL(), s_GetCountIdentityMismatch(), s_GetLabel(), s_GetSequenceId(), s_GetSplicedSegIdentityMismatch(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_SeqAlignToXMLHit(), s_SetBlastXMLSearch(), s_TestFastaRoundTrip(), s_ValidateExon(), SeqDB_SimplifySeqid(), CSeqDBImpl::SeqidToOids(), CSeqDBVol::SeqidToOids(), CIgBlastTabularInfo::SetAirrFormatData(), CPhyTreeCalc::SetQuery(), CHookBioseq__Seq_id::SkipClassMember(), CUnorderedSplitter::SplitId(), CSeqDBIsam::StringToOids(), SeqSwapper::swapSequences(), sx_MakeUniqueId(), TestOneOtherAcc(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CValidError_bioseq::ValidateIDSetAgainstDb(), CVdbFastaExtractor::Write(), WriteBlastSeqidlistFile(), CAlnWriter::WriteSparseAlign(), CWriteDB_IsamIndex::x_AddLocal(), CWriteDB_IsamIndex::x_AddPatent(), CWriteDB_IsamIndex::x_AddPdb(), CWriteDB_IsamIndex::x_AddStringIds(), CHugeFileDemoApp::x_AddUserObjects(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CSourceModParser::CBadModError::x_CalculateErrorString(), CSourceModParser::CUnkModError::x_CalculateErrorString(), CFeatureGenerator::SImplementation::x_CheckInconsistentDbxrefs(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CDeflineProcess::x_FastaSeqIdWrite(), CShowBlastDefline::x_FillDeflineAndId(), CIgBlast::x_FillJDomain(), CUnorderedSplitter::x_FixAlignment(), CSeqVectorProcess::x_FsaSeqIdWrite(), CSeqMap_CI::x_GetBioseq(), CBlastDbDataLoader::x_GetOid(), CColumnarVCFLoaderManager::x_GetRefSeqs(), CPsiBlastInputData::x_GetSubjectSequence(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CWriteDB_LMDB::x_InsertEntry(), CAlignGlyph::x_IsSRA(), CAppHitFilter::x_LoadConstraints(), CSplign::x_LoadSequence(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CRNAValidator::x_ReportRNATranslationProblems(), CBuildDatabase::x_ResolveFromSource(), CBlastFormat::x_ReverseQuery(), CFeatureItem::x_SeqIdWriteForTable(), CBlastDBExtractor::x_SetGi2SeqIdMap(), CBlastTabularInfo::x_SetQueryCovSubject(), CBlastTabularInfo::x_SetQueryCovUniqSubject(), CVariationNormalization_base< T >::x_Shift(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CSequenceDataTester::x_TestSingleSequence_Remote(), CTitleProcess::x_TitleSeqIdWrite(), CValidError_bioseq::x_TranscriptIDsMatch(), CVectorTrimPanel::x_TrimSelected(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().

◆ Assign()

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

virtual

Optimized implementation of CSerialObject::Assign, which is not so efficient.

Reimplemented from CSerialObject.

Definition at line 318 of file Seq_id.cpp.

Referenced by CAlnMixSequences::Add(), CBioseq_Info::AddId(), CCleanup::AddProtein(), AddSentinelRNASeq(), AddSpanningSentinelFeat(), CVDBBlastUtil::AddSubjectsToScope(), AdjustMappedStop(), CTable2AsnContext::ApplyAccession(), CNWFormatter::AsDenseSeg(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CSeq_loc::Assign(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CContigAssembly::BandedGlobalAlignment(), Blast_FindWindowMaskerLoc(), BOOST_AUTO_TEST_CASE(), CSeqAnnotFromFasta::BuildMasterSlaveSeqAlign(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CCompareSeqRegions::CCompareSeqRegions(), CGtfLocationRecord::CGtfLocationRecord(), CLocMapper_Default::CLocMapper_Default(), CFixForTransSplicing::CombineFeatures(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyGiSeqId(), CopyPdbSeqId(), CpSeqId(), CBlastBioseqMaker::CreateBioseqFromId(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CreateSparseAlign(), CRemoveSeqId::CRemoveSeqId(), CValidError_feat::DoesCDSHaveShortIntrons(), CCmdAddCDS::Execute(), CDense_seg::ExtractRows(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), sequpd::FixCollidingIDs_Bioseq(), FixMixLoc(), fta_get_acc_minmax_strand(), CFlatFileGenerator::Generate(), get_bioseq(), GetAccAndVersion(), CCDDClientPool::GetBlobBySeq_id(), CCDDClientPool::GetBlobBySeq_ids(), CSeqUtils::GetCdsMappingInfoFromRna(), CApplyRNAITSDlg::GetCommand(), CFarPointerSeq::GetCommand(), CFuseFeaturesDlg::GetCommand(), CLocationListCtrl::GetIdFromForm(), CBioseq::GetLabel(), GetLastCodonLoc(), CFeatureGenePanel::GetLocationForGene(), GetLowHighFromSeqLoc(), CSeqUtils::GetMappingInfoFromLocation(), CTableDataBioTreeContainer::GetObjectValue(), CCleanup::GetProteinLocationFromNucleotideLocation(), CSelectionEvent::GetRangeSelectionAsLocs(), CProjectTreeView::GetSearchLoc(), GetSeqLocFromString(), CSeq_align::GetSeqRange(), CFeatGlyph::GetTooltip(), GetWGSMasterSeq_id(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CNSeq::Init(), CAlignCollapser::InitContig(), InitSplicedsegFromPairwiseAln(), IsInScope(), CFastaObjectLoader::LoadFromStream(), MakeCompartment(), MakeEmptyResults(), MakeMaskingBioseq(), CAliToSeq_align::MakeSeq_align(), CAlignModel::MakeSeqAlign(), CGtfLocationMerger::MergeLocationForGene(), CBioseqEditor::OnCreateBiosourceFeat(), CBioseqEditor::OnCreateFeature(), SCigarAlignment::operator()(), CGtfLocationRecord::operator=(), PatchTargetSequence(), CBlastFormat::PrintPhiResult(), CHgvsReader::ReadSeqAnnot(), RenameGeneratedBioseqs(), CTableDataVcfJob::Run(), CLocalFinderApp::Run(), CXcompareAnnotsApplication::Run(), CTestBMApp::Run(), s_AddCDS(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_AssignSeq_id(), s_CodonVariation(), s_ConvertWholeToInt(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_CreateMappingInfo(), s_DoNWalign(), s_FixCollidingIDs_Annot(), s_GetCDSLoc(), s_GetQuerySequence(), s_Load_Seq_point(), s_MakeSliceMapper(), s_RemapFeatureSeqIds(), s_ReplaceGIs(), s_ReplaceLocalId(), CWeightedIdentityScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CProSplign::CImplementation::SeekStartStop(), CSeqDBImpl::SeqidToOids(), CAutoDefExonListClause::SeqLocIntersect(), CSeq_loc::SetId(), CCDSTranslationPanel::SetProtein(), SimpleSeqLocFromBioseq(), SModelData::SModelData(), CFeatGapInfo::Split(), CFeatureGenerator::SImplementation::StitchSmallHoles(), BlockModel::toSeqAlign(), MarkupTrustedGenes::transform_align(), ProjectCDS::transform_align(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), TranslateCDSCommand(), CFeatGapInfo::Trim(), CScore_Overlap::UpdateState(), CValidError_bioseq::ValidateIDSetAgainstDb(), CAlnWriter::WriteAlignSplicedSeg(), CGC_Assembly_Parser::x_AddBioseq(), CIdMapperGCAssembly::x_AddUnversionedMapping(), CSeq_loc_Mapper::x_AddVirtualBioseq(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CProSplignJob::x_CreateProjectItems(), CBamLoadingJob::x_CreateProjectItems(), CVcfLoadingJob::x_CreateSeqIdProjectItem(), CVcfFeatureJob::x_Execute(), CSequenceUpdater::x_FixIDInNewEntry(), CCommonComponentScorer::x_GetCompList(), CCommonComponentScorer::x_GetDeltaExtCompList(), CAutoDef::x_GetFeatureClauses(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), CEditingBtnsPanel::x_GetSelectedLocations(), CCommonComponentScorer::x_GetSeqHistCompList(), CCdregionValidator::x_GetShortIntrons(), CCommonComponentScorer::x_GetUserCompList(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CBioseqIndex::x_InitFeats(), CSplign::x_LoadSequence(), CTreeAlignMerger::x_MakeSeqAlign(), CSequenceUpdater::x_PrepareNewEntry(), CGenBankLoadOptionPanel::x_ProccessText(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CGencollIdMapper::x_RecursiveSeqFix(), CGencollIdMapper::x_RemoveHiddenAccessions(), CSequenceUpdater::x_RemoveNewIDInFeature(), CGFFReader::x_ResolveNewID(), CSplign::x_RunOnCompartment(), CSequenceSearchJob::x_SearchSequence(), CFeatureGenerator::SImplementation::x_SetComment(), CBioseqContext::x_SetId(), CCDSTranslationPanel::x_SetLocationForProtein(), CGencollIdMapper::x_StripPseudoSeq(), CFeatTrim::x_TrimLocation(), CVectorTrimPanel::x_TrimSelected(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CRNAValidator::x_ValidateTrnaType(), CFeatureTableReader::xAddProteinToSeqEntry(), and xgbint_ver().

◆ AsString()

string CSeq_id_Handle::AsString ( void ) const

Definition at line 220 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, and CSeq_id::WriteAsFasta().

Referenced by CAlnSeqId::AsString(), BOOST_AUTO_TEST_CASE(), CCSRAFileInfo::CCSRAFileInfo(), CAlignCompare::SAlignment::CompareGroup(), CBlobSplitterImpl::CopySkeleton(), CFeatureGenerator::CreateMicroIntrons(), CLDS2_ObjectParser::EndBlob(), CFeatTableEdit::GenerateLocusTags(), GetAccVer(), CLDS2_Database::GetAnnotBlobs(), CSplitCacheApp::GetBioseqHandle(), CLDS2_Database::GetBioseqId(), CAsnCache_DataLoader::GetBlobById(), CHugeAsnDataLoader::GetBlobId(), CAgpFastaComparator::CTmpSeqVecStorage::GetFileName(), CFeatGlyph::GetHTMLActiveAreas(), GetLabel(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), CGBDataLoader_Native::GetNamedAnnotAccessions(), CPSGDataLoader_Impl::GetRecordsOnce(), CWGSDataLoader_Impl::GetRecordsOnce(), CIdMapperApp::GetTargetString(), idAlpha(), CPubseqReader::LoadSeq_idInfo(), CReadDispatcher::LogStat(), CIdMapper::MapErrorString(), CTreeAlignMerger::Merge_Dist(), SBlobInserter::operator()(), PConvertToString< CSeq_id_Handle >::operator()(), CFastaReader::ParseDefLine(), PatchTargetSequence(), CSplitCacheApp::ProcessBlob(), CSplitCacheApp::ProcessSeqId(), ReplaceWellknownSeqs(), CGBDataLoader_Native::ResolveConflict(), CAgpFastaComparator::Run(), CPrimeCacheApplication::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), s_IdxGetBestIdString(), CCacheWriter::SaveSeq_idAccVer(), CBAMBlobId::ToString(), CScope_Impl::x_AddSynonym(), CSeq_id_Resolver__LRG::x_Create(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CAsnSubCacheCreateApplication::x_FetchMissingBlobs(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CScore_BlastRatio::x_GetPerfectScore(), CGBDataLoader_Native::x_GetRecords(), variation::CHgvsParser::x_header(), CBioseqIndex::x_InitFeats(), CLDS2_Database::x_InitGetBioseqsSql(), CSeq_loc_Mapper_Base::x_MapNextRange(), CPrimeCacheApplication::x_Process_Fasta(), CPrimeCacheApplication::x_Process_Ids(), CAlignFilter::x_Query_Op(), CScope_Impl::x_ReportNewDataConflict(), CHugeFileDemoApp::x_TestRW1848(), and CFeatTableEdit::xGenerateMissingGeneForFeats().

◆ AvoidGi()

bool CSeq_id::AvoidGi ( void )

static

Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI).

Definition at line 3410 of file Seq_id.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), GetGiForAccession(), GetGiForId(), CSeq_id::PreferAccessionOverGi(), and x_GetId().

◆ BaseBestRankScore()

int CSeq_id::BaseBestRankScore ( void ) const

◆ BaseBlastScore()

int CSeq_id::BaseBlastScore ( void ) const

◆ BaseFastaAAScore()

int CSeq_id::BaseFastaAAScore ( void ) const

◆ BaseFastaNAScore()

int CSeq_id::BaseFastaNAScore ( void ) const

◆ BaseTextScore()

int CSeq_id::BaseTextScore ( void ) const

◆ BaseWorstRankScore()

int CSeq_id::BaseWorstRankScore ( void ) const

inline

Definition at line 748 of file Seq_id.hpp.

References CSeq_id::BaseTextScore().

◆ begin()

const_iterator SSeqIdRange::begin ( void ) const

inline

Definition at line 977 of file Seq_id.hpp.

Referenced by CDescrModApply::x_SetGBblockIds(), and CModAdder::x_SetHist().

◆ BestRank()

static int CSeq_id::BestRank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 774 of file Seq_id.hpp.

References kMax_Int.

Referenced by CSourceModParser::ApplyAllMods(), BestRank_SeqIdHandle(), BOOST_AUTO_TEST_CASE(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), ChangeSeqId(), CAlnMix::ChooseSeqId(), Convert_Bioseq_Seq_id(), Convert_Seq_entry_Seq_id(), Convert_Seq_entry_Seq_loc(), Convert_SeqSubmit_Seq_id(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CSeqFastaReader::GenerateID(), CAlnReader::GenerateID(), CTextAlnReader::GenerateID(), GetBestBioseqLabel(), CSequenceUpdater::GetRevCompReport(), GetSequenceLengthAndId(), CFastaReader::ParseDefLine(), CFastaReader::PostProcessIDs(), CSeqFastaReader::PostProcessIDs(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertSubjects2TSeqLocVector(), s_ExtractQueryIdsFromBioseqSet(), s_FixBioseqDeltas(), s_UseFastaReaderDeflines(), SeqDB_SimplifyAccession(), CBlastDB_FastaFormatter::Write(), CBlastFormat::x_CreateSubjectBioseq(), CImportFeatTable::x_DoImportCDS(), CRemoteBlast::x_ExtractQueryIds(), CBlastFastaInputSource::x_FastaToSeqLoc(), CAutoDef::x_GetFeatureClauses(), CFeatModApply::x_GetWholeSeqLoc(), CBlastKmerResults::x_InitScoreVec(), CCompareWithBiosample::x_LoadData(), and CSequenceUpdater::x_RemoveNewIDInFeature().

◆ BestRankScore()

int CSeq_id::BestRankScore ( void ) const

inline

Definition at line 754 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::BaseBestRankScore().

Referenced by CDefaultSynonymMapper::GetBestSynonym(), and s_GetBestSynonym().

◆ BlastRank()

static int CSeq_id::BlastRank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 782 of file Seq_id.hpp.

References kMax_Int.

Referenced by PrintSAMHeader(), s_CreateSeqAlign(), s_DeflineBlastRankAA(), and s_LimitDeflines().

◆ BlastScore()

int CSeq_id::BlastScore ( void ) const

inline

Definition at line 758 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::BaseBlastScore().

◆ CheckLocalID()

CSeq_id::TErrorFlags CSeq_id::CheckLocalID ( const CTempString & s )

static

Perform rudimentary validation on potential local IDs, whose contents should not exceed fifty characters and are limited to ASCII characters excluding >[]|"".

Definition at line 2583 of file Seq_id.cpp.

References CTempString::begin(), CTempString::end(), CSeq_id::fEmptyId, CSeq_id::fExceedsMaxLength, CSeq_id::fInvalidChar, CSeq_id::fNoError, NStr::IsBlank(), CSeq_id::kMaxLocalIDLength, and CTempString::length().

Referenced by CSeq_id::IsValidLocalID(), CFastaIdValidate::IsValidLocalString(), and CSeqIdValidate::operator()().

◆ Compare()

CSeq_id::E_SIC CSeq_id::Compare ( const CSeq_id & sid2 ) const

Compare() - more general.

Definition at line 411 of file Seq_id.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdregionFeatBC(), CheckForeignLoc(), fta_seqid_same(), GetAlignColl(), GetLocalGeneByLocus(), GetLowHighFromSeqLoc(), CRemoteBlast::GetMasks(), CRemoteBlast::GetSeqAlignSets(), CSeq_align::GetSeqRange(), CPacked_seqint::GetStrand(), CSeq_loc_mix::GetStrand(), CSeq_id::Match(), OkToAdjustLoc(), CNewCleanup_imp::RnaFeatBC(), s_IdsMatch(), s_MatchSeqIds(), s_SplitAlignVectorBySubjects(), s_TestFastaRoundTrip(), CStructuredCommentsReader::SeqIdMatchesCommentId(), and CBlastDbDataLoader::x_GetOid().

◆ CompareOrdered() [1/3]

int CSeq_id::CompareOrdered ( const CSeq_id & sid2 ) const

Definition at line 486 of file Seq_id.cpp.

References CDbtag::Compare(), CObject_id::Compare(), CPatent_seq_id::Compare(), CPDB_seq_id::Compare(), CTextseq_id::Compare(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id::GetTextseq_Id(), and CSeq_id_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), Compare(), seqsubmit_split::SIdCompare::compare_seq(), CSeq_id_Info::CompareOrdered(), SAlignSortByQueryId::operator()(), SCompareOrdered< TSeqIdPtr >::operator()(), CSeq_id::operator<(), CSourceModParser::SMod::operator<(), s_LocSortCompare(), s_SeqIdCompare(), s_SeqIdMatch(), CSeq_loc::x_CompareSingleId(), and CMultiAligner::x_SetDomainHits().

◆ CompareOrdered() [2/3]

int CSeq_id_Handle::CompareOrdered ( const CSeq_id_Handle & id ) const

Compare ids in a defined order (see CSeq_id::CompareOrdered())

Definition at line 197 of file seq_id_handle.cpp.

References CSeq_id_Info::CompareOrdered(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Info, and CSeq_id_Handle::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and CSeq_id_Handle::PLessOrdered::operator()().

◆ CompareOrdered() [3/3]

int CSeq_id_Info::CompareOrdered	(	const CSeq_id_Info &	other,
		const CSeq_id_Handle &	h_this,
		const CSeq_id_Handle &	h_other
	)		const

virtual

Reimplemented in CSeq_id_General_Str_Info, CSeq_id_General_Id_Info, and CSeq_id_Textseq_Info.

Definition at line 95 of file seq_id_handle.cpp.

References CSeq_id::CompareOrdered(), and CSeq_id_Handle::GetSeqId().

Referenced by CSeq_id_Handle::CompareOrdered(), CSeq_id_Textseq_Info::CompareOrdered(), CSeq_id_General_Id_Info::CompareOrdered(), and CSeq_id_General_Str_Info::CompareOrdered().

◆ ComposeOSLT()

string CSeq_id::ComposeOSLT	(	list< string > *	secondary_ids = `nullptr`,
		TComposeOSLTFlags	parse_flags = `0`
	)		const

JIRA ID-5188 : Compose OSLT string for the primary id, as well as OSLT strings for the secondary ids, if any.

NB: given a single Seq-id, it is not always possible to determine whether it should be treated as primary or secondary if it were part of a list of Seq-ids in a Bioseq. In that case, this function returns it as primary, and the final judgement needs to be made by the caller.

Parameters

secondary_ids	OSLT strings for the secondary ids
parse_flags	Flags specifying special treatment for certain types of Seq-ids.

Returns: OSLT string for the primary id

Definition at line 3416 of file Seq_id.cpp.

Referenced by CSeq_id::GetLabel(), and CPSGS_ResolveBase::x_ComposeOSLT().

◆ const_iterator() [1/3]

SSeqIdRange::const_iterator::const_iterator ( const const_iterator & it )

inline

Definition at line 921 of file Seq_id.hpp.

◆ const_iterator() [2/3]

SSeqIdRange::const_iterator::const_iterator ( const SSeqIdRange & range )

inline

Definition at line 913 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::operator+(), and SSeqIdRange::const_iterator::operator-().

◆ const_iterator() [3/3]

SSeqIdRange::const_iterator::const_iterator	(	const SSeqIdRange &	range,
		int	number
	)

inline

Definition at line 917 of file Seq_id.hpp.

References _ASSERT, number, and compile_time_bits::range().

◆ CSeq_id() [1/8]

CSeq_id::CSeq_id	(	const CDbtag &	tag,
		bool	set_as_general = `true`
	)

explicit

Construct a seq-id from a dbtag.

Parameters

tag	Input dbtag.
set_as_general	Whether to store tags from unrecognized databases as is in Seq-ids of type general rather than rejecting them altogether.

Definition at line 2379 of file Seq_id.cpp.

References CSeq_id::Set().

◆ CSeq_id() [2/8]

CSeq_id::CSeq_id ( const CSeq_id & )

private

◆ CSeq_id() [3/8]

CSeq_id::CSeq_id	(	const CTempString &	the_id,
		TParseFlags	flags = `fParse_AnyRaw`
	)

explicit

Construct a Seq-id from a flat string.

Parameters

the_id	Input ID, preferably FASTA-style.
flags	How to interpret anything other than a single FASTA-style ID.

Definition at line 2452 of file Seq_id.cpp.

References flags, and CSeq_id::Set().

◆ CSeq_id() [4/8]

CSeq_id::CSeq_id	(	E_Choice	the_type,
		const CTempString &	acc_in,
		const CTempString &	name_in = `kEmptyStr`,
		int	version = `0`,
		const CTempString &	release_in = `kEmptyStr`
	)

Construct a Seq-id from a flat representation.

Parameters

the_type	Type of Seq_id to construct
acc_in	Primary string value – normally accession, overridden as country for patents, database for "general" IDs, molecule ID for PDB IDs.
name_in	Additional string value – normally name/locus, overridden as (application) number for patents, tag for "general" IDs, chain ID for PDB.
version	Numeric value – normally version number, overriden as sequence number for patents.
release_in	Historically used to convey release identifiers; for patents, may be set to "pgp" (case-insensitive) to indicate a Pre-Grant Patent [application].

Definition at line 2887 of file Seq_id.cpp.

References CSeq_id::Set(), and dtl::version.

◆ CSeq_id() [5/8]

CSeq_id::CSeq_id	(	E_Choice	the_type,
		TGi	gi
	)

Definition at line 2844 of file Seq_id.cpp.

References GI_TO, and CSeq_id::Set().

◆ CSeq_id() [6/8]

CSeq_id::CSeq_id	(	E_Choice	the_type,
		TIntId	int_seq_id
	)

Construct a numeric Seq-id.

Parameters

the_type	Type of Seq-id (normally e_Gi)
int_seq_id	Numeric value.

Definition at line 2838 of file Seq_id.cpp.

References CSeq_id::Set().

◆ CSeq_id() [7/8]

CSeq_id::CSeq_id	(	EFastaAsTypeAndContent	f,
		E_Choice	the_type,
		const CTempString &	the_content
	)

Construct a Seq-id from a FASTA string with the leading (type) component already parsed out.

Parameters

the_type	Type of Seq_id to construct
the_content	FASTA-style content, with embedded vertical bars as appropriate.

Definition at line 2554 of file Seq_id.cpp.

References f, and CSeq_id::Set().

◆ CSeq_id() [8/8]

CSeq_id::CSeq_id ( void )

See also CSeq_id related functions in "util/sequence.hpp":

TSeqPos GetLength(const CSeq_id&, CScope*); bool IsSameBioseq(const CSeq_id&, const CSeq_id&, CScope*); Default constructor

Definition at line 139 of file Seq_id.cpp.

Referenced by CSeq_id::ParseIDs().

◆ CSeq_id_Handle() [1/3]

CSeq_id_Handle::CSeq_id_Handle	(	const CSeq_id_Info *	info,
		TPacked	packed = `0`,
		TVariant	variant = `0`
	)

inlineexplicit

Definition at line 168 of file seq_id_handle.hpp.

References _ASSERT, and info.

◆ CSeq_id_Handle() [2/3]

CSeq_id_Handle::CSeq_id_Handle ( ENull )

inline

Definition at line 173 of file seq_id_handle.hpp.

◆ CSeq_id_Handle() [3/3]

CSeq_id_Handle::CSeq_id_Handle ( void )

inline

Definition at line 164 of file seq_id_handle.hpp.

◆ CSeq_id_Info() [1/3]

CSeq_id_Info::CSeq_id_Info	(	const CConstRef< CSeq_id > &	seq_id,
		CSeq_id_Mapper *	mapper
	)

Definition at line 60 of file seq_id_handle.cpp.

References _ASSERT.

◆ CSeq_id_Info() [2/3]

CSeq_id_Info::CSeq_id_Info ( const CSeq_id_Info & )

private

◆ CSeq_id_Info() [3/3]

CSeq_id_Info::CSeq_id_Info	(	CSeq_id::E_Choice	type,
		CSeq_id_Mapper *	mapper
	)

Definition at line 51 of file seq_id_handle.cpp.

References _ASSERT.

◆ CSeq_id_Mapper() [1/2]

CSeq_id_Mapper::CSeq_id_Mapper ( const CSeq_id_Mapper & )

private

◆ CSeq_id_Mapper() [2/2]

CSeq_id_Mapper::CSeq_id_Mapper ( void )

private

Definition at line 81 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::Initialize(), and CSeq_id_Mapper::m_Trees.

◆ DECLARE_OPERATOR_BOOL_REF()

CSeq_id_Handle::DECLARE_OPERATOR_BOOL_REF ( m_Info )

Check if the handle is a valid or an empty one.

◆ DECLARE_SAFE_FLAGS_TYPE()

CSeq_id::DECLARE_SAFE_FLAGS_TYPE	(	EAdjustScoreFlags	,
		TAdjustScoreFlags
	)

◆ Dump()

size_t CSeq_id_Mapper::Dump	(	CNcbiOstream &	out,
		EDumpDetails	details = `eDumpTotalBytes`
	)		const

Definition at line 314 of file seq_id_mapper.cpp.

References CSeq_id_Mapper::eDumpTotalBytes, i, CSeq_id_Mapper::m_Trees, and out().

Referenced by CDemoApp::Run().

◆ DumpAsFasta()

CProxy CSeq_id::DumpAsFasta ( void ) const

inline

Definition at line 599 of file Seq_id.hpp.

References CSerializable::Dump(), and CSerializable::eAsFasta.

◆ end()

const_iterator SSeqIdRange::end ( void ) const

inline

Definition at line 979 of file Seq_id.hpp.

References SSeqIdRange::stop.

Referenced by CDescrModApply::x_SetGBblockIds(), and CModAdder::x_SetHist().

◆ FastaAARank()

static int CSeq_id::FastaAARank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 778 of file Seq_id.hpp.

References kMax_Int.

Referenced by FastaAARank_SeqIdHandle(), CSeq_id::GetStringDescr(), PdbBadRank(), s_DeflineCompareAA(), s_GetDeflineIdString(), CSeq_id::WriteAsFasta(), and CFastaOstream::x_GetBestId().

◆ FastaAAScore()

int CSeq_id::FastaAAScore ( void ) const

inline

Definition at line 756 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::BaseFastaAAScore().

◆ FastaNARank()

static int CSeq_id::FastaNARank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 780 of file Seq_id.hpp.

References kMax_Int.

Referenced by FastaNARank_SeqIdHandle(), CSeq_id::GetStringDescr(), s_DeflineCompareNA(), s_GetDeflineIdString(), CSeq_id::WriteAsFasta(), and CFastaOstream::x_GetBestId().

◆ FastaNAScore()

int CSeq_id::FastaNAScore ( void ) const

inline

Definition at line 757 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::BaseFastaNAScore().

◆ FindGi()

template<class container >

TGi FindGi ( const container & ids )

Return gi from id list if exists, return 0 otherwise.

Definition at line 1041 of file Seq_id.hpp.

References CSeq_id_Base::e_Gi, GetSeq_idByType(), and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::BuildUserUrl(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CAlignFormatUtil::GetDbType(), CAlignFormatUtil::GetLinkoutUrl(), CAlignFormatUtil::GetSeqLinkoutInfo(), s_GetFullLinkoutUrl(), s_GetSeqIdListString(), s_ModifySeqAlnWithFilteredSeqIDs(), CAsn2FlatApp::x_AddSNPAnnots(), CDisplaySeqalign::x_DisplayBl2SeqLink(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), CDisplaySeqalign::x_GetFeatureInfo(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), and CDisplaySeqalign::x_PrepareRowData().

◆ FindTextseq_id()

template<class container >

CConstRef<CSeq_id> FindTextseq_id ( const container & ids )

Return text seq-id from id list if exists, return 0 otherwise.

Definition at line 1050 of file Seq_id.hpp.

References Get_ConstRef_Seq_id(), CSeq_id::GetTextseq_Id(), and ITERATE.

◆ Get_ConstRef_Seq_id() [1/2]

template<>

CConstRef<CSeq_id> Get_ConstRef_Seq_id ( const CSeq_id_Handle & idh )

inline

Get CConstRef<CSeq_id> from a seq-id handle (for container searching template functions)

Definition at line 356 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetSeqId().

◆ Get_ConstRef_Seq_id() [2/2]

template<class TId >

CConstRef<CSeq_id> Get_ConstRef_Seq_id ( TId & id )

Dummy convertor for container search functions.

Definition at line 1019 of file Seq_id.hpp.

Referenced by FindTextseq_id(), and GetSeq_idByType().

◆ GetAccType()

static E_Choice CSeq_id::GetAccType ( EAccessionInfo info )

inlinestatic

Definition at line 562 of file Seq_id.hpp.

References CSeq_id::eAcc_type_mask, and info.

Referenced by fta_fix_seq_id(), SSeqIdRange::const_iterator::GetID(), GetNucAccOwner(), GetProtAccOwner(), CSeq_id::IdentifyAccession(), CSeq_id::IsAllowedSNPScaleLimit(), CSeq_id::Set(), ValidSeqType(), and CGenBankLoadOptionPanel::x_ProccessText().

◆ GetDirectLabel() [1/2]

string GetDirectLabel ( const CSeq_id & id )

Return best label for a sequence from single Seq-id, or set of Seq-ids.

Return empty string if the label cannot be determined. GetDirectLabel() will return non-empty string only if the Seq-id is very likely enough to get good label without loading full set of sequence Seq-ids.

Definition at line 253 of file seq_id_handle.cpp.

References CTextseq_id_Base::GetAccession(), CDbtag_Base::GetDb(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), and CObject_id_Base::IsStr().

Referenced by GetDirectLabel(), CScope_Impl::GetLabel(), and CScope_Impl::GetLabels().

◆ GetDirectLabel() [2/2]

string GetDirectLabel ( const CSeq_id_Handle & id )

Definition at line 278 of file seq_id_handle.cpp.

References GetDirectLabel(), CSeq_id_Handle::GetSeqId(), and CSeq_id_Handle::IsGi().

◆ GetErrCodeString()

const char * CSeqIdException::GetErrCodeString ( void ) const

overridevirtual

Translate from the error code value to its string representation.

Reimplemented from CException.

Definition at line 128 of file Seq_id.cpp.

References CSeqIdException::eFormat, CSeqIdException::eUnknownType, CException::GetErrCode(), and CException::GetErrCodeString().

◆ GetGi()

TGi CSeq_id_Handle::GetGi ( void ) const

inline

Definition at line 283 of file seq_id_handle.hpp.

References CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Packed, and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id_Handle::CompareOrdered(), CRemoveFeatChecker::Do(), CAddFeatChecker::Do(), CSeqUtils::GetAccessionPlacementsMsec(), CLDS2_Database::GetAnnotBlobs(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CLDS2_Database::GetBioseqId(), CBlobSplitterImpl::GetChunkData(), CWGSDataLoader_Impl::GetFileInfo(), CBAMDataLoader_Impl::GetGi(), GetGiForAccession(), GetGiForId(), CTestMapperSeqInfo::GetSequenceLength(), CTestMapperSeqInfo::GetSequenceType(), CLocalBlastDbAdapter::GetTaxId(), CId1Reader::LoadGiBlob_ids(), CPubseqReader::LoadGiHash(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idInfo(), CHgvsReader::ReadSeqAnnot(), CGiCache::RecordKnown(), ReplaceWellknownSeqs(), s_GetBestSynonym(), s_GetFeatureKeyLinkLocation(), s_GetGi(), sx_MakeUniqueId(), CTreeBuilderJob::x_CreateProjectItems(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CAlignGroup::x_GetTaxId(), CNAUtils::x_Init(), CSFTranslationJob::x_InitGeneticCode(), CLDS2_Database::x_InitGetBioseqsSql(), x_LocalCDDEntryIdToBioId(), x_MakeLocalCDDEntryId(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), and CAssemblyListPanel::x_UpdateSearchTerm().

◆ GetGiHandle() [1/2]

static CSeq_id_Handle CSeq_id_Handle::GetGiHandle ( TGi gi )

inlinestatic

◆ GetGiHandle() [2/2]

CSeq_id_Handle CSeq_id_Mapper::GetGiHandle ( TGi gi )

Get seq-id handle.

Create new handle if not found and do_not_create is false. Get only the exactly equal seq-id handle.

Definition at line 114 of file seq_id_mapper.cpp.

References _ASSERT, CSeq_id_Base::e_Gi, and CSeq_id_Mapper::m_Trees.

Referenced by CSeq_id_Handle::GetHandle().

◆ GetHandle() [1/4]

CSeq_id_Handle CSeq_id_Handle::GetHandle ( const CSeq_id & id )

static

Normal way of getting a handle, works for any seq-id.

Definition at line 113 of file seq_id_handle.cpp.

References CSeq_id_Mapper::GetHandle(), and CSeq_id_Mapper::GetInstance().

◆ GetHandle() [2/4]

CSeq_id_Handle CSeq_id_Mapper::GetHandle	(	const CSeq_id &	id,
		bool	do_not_create = `false`
	)

Definition at line 121 of file seq_id_mapper.cpp.

References CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Handle::GetHandle(), and CSeq_id_Handle::operator==().

◆ GetHandle() [3/4]

CSeq_id_Handle CSeq_id_Handle::GetHandle ( const string & str_id )

static

Construct CSeq_id from string representation and return handle for it.

Definition at line 119 of file seq_id_handle.cpp.

References CSeq_id_Mapper::GetHandle(), and CSeq_id_Mapper::GetInstance().

◆ GetHandle() [4/4]

CSeq_id_Handle CSeq_id_Handle::GetHandle ( TGi gi )

static

Faster way to create a handle for a gi.

Definition at line 107 of file seq_id_handle.cpp.

References CSeq_id_Mapper::GetGiHandle(), and CSeq_id_Mapper::GetInstance().

◆ GetHash()

unsigned CSeq_id_Handle::GetHash ( void ) const

Definition at line 236 of file seq_id_handle.cpp.

References CConstRef< C, Locker >::GetPointerOrNull(), INT_ID_TO, CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

◆ GetID()

CRef< CSeq_id > SSeqIdRange::const_iterator::GetID ( void ) const

Definition at line 3641 of file Seq_id.cpp.

References SSeqIdRange::acc_info, SSeqIdRange::digits, CSeq_id_Base::e_not_set, CSeq_id::eAcc_unknown, CSeq_id::eAcc_unreserved_nuc, CSeq_id::eAcc_unreserved_prot, flags, CSeq_id::fParse_AnyRaw, CSeq_id::fParse_FallbackOK, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), SSeqIdRange::const_iterator::m_Range, SSeqIdRange::prefix, and SSeqIdRange::size().

◆ GetInstance()

CRef< TInstance > TInstance::GetInstance ( void )

static

Definition at line 53 of file seq_id_mapper.cpp.

References _ASSERT, CRef< C, Locker >::Release(), CRef< C, Locker >::Reset(), and s_Instance.

Referenced by CSeq_id_Handle::GetHandle(), and CDemoApp::Run().

◆ GetLabel() [1/6]

string GetLabel ( const CSeq_id & id )

Definition at line 288 of file seq_id_handle.cpp.

References CTextseq_id_Base::GetAccession(), CDbtag_Base::GetDb(), CTextseq_id_Base::GetName(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), and NStr::ToUpper().

Referenced by CheckOneFeatureType(), CProjectTreeViewFactory::CreateInstanceByFingerprint(), CwxGLTestViewFactory::CreateInstanceByFingerprint(), CClockViewFactory::CreateInstanceByFingerprint(), CDiagConsoleViewFactory::CreateInstanceByFingerprint(), CEventViewFactory::CreateInstanceByFingerprint(), CTaskViewFactory::CreateInstanceByFingerprint(), CSelectionViewFactory::CreateInstanceByFingerprint(), CFeatTableDS::SFeatureRow::FillIn(), CFixedSeq_ids::FindLabel(), CHTMLFormatterEx::FormatLocation(), CDiscrepancyContext::GetAminoacidName(), CDesktopFeatItem::GetDescription(), CValidErrorFormat::GetFeatureContentLabel(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CGroupMapWidget::CGroupItem::GetFullDescr(), CSeq_featHandler::GetLabel(), CUserFeatHandler::GetLabel(), CDataLoader::GetLabel(), CDataSource::GetLabel(), CBAMDataLoader_Impl::GetLabel(), GetLabel(), CScope_Impl::GetLabel(), CCSRADataLoader_Impl::GetLabelOnce(), CDataSource::GetLabels(), CScope_Impl::GetLabels(), CPSGDataLoader_Impl::GetLabelsOnce(), GetRNAProductString(), GetSeqFeatLabel(), CTableDataFTable::GetStringValue(), GetTitle(), CAlignSmearGlyph::GetTooltip(), CGuiObjectInfoImpFeature::GetToolTip(), CGuiObjectInfoRegionFeature::GetToolTip(), CGuiObjectInfoSiteFeature::GetToolTip(), CGuiObjectInfoVariation::GetToolTip(), CCompareSeqRegions::NextComparisonGroup(), CMacroAddConstraint::OnAccept(), CMacroEditor::OnAcceptClick(), CDiscrepancyDlg::OnRefresh(), SFeats_OpLess::operator()(), SCompareFeats_OpLess::operator()(), SFeatureByName::operator()(), CDemoApp::Run(), s_AreFeatureLabelsSame(), s_GetFeatDesc(), CCompareFeats::s_GetFeatLabel(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetProductFlagFromCDSProductNames(), s_ReportDuplicateIds(), CCompareSeqRegions::SelectMatches(), SeqLocToBioseq(), CwxLabelEditDlg::SetParams(), CReportEditingDialog::Show(), CMiscFeatValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CLinkUtils::x_AddDbxrefFeatureLinks(), CFeatureItem::x_AddFTableRnaQuals(), CGeneModelFeatJob::x_CreateGeneModels(), CSortedProteins::x_GatherProteinNames(), CDisplaySeqalign::x_GetFeatureInfo(), CGuiObjectInfoSeq_feat::x_GetFeatureToolTip(), CGuiObjectInfoSeq_feat::x_GetGroupToolTip(), CAutoDefFeatureClause::x_GetProductName(), CCompareSeqRegions::x_GetPutativeMatches(), x_GetSegSeqInfoViaCDS(), CAlignedFeatureGraph::x_GetTooltip(), CXcompareAnnotsApplication::x_ProcessComparison(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CEditingBtnsPanel::x_ResetRemovedTab(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CHugeAsnReader::x_ThrowDuplicateId(), CIdentifiersPanel::x_UpdateXrefDescriptions(), CGeneValidator::x_ValidateOperon(), and CVcfWriter::x_WriteFeatureGenotypeData().

◆ GetLabel() [2/6]

string GetLabel ( const CSeq_id_Handle & id )

Definition at line 319 of file seq_id_handle.cpp.

References CSeq_id_Handle::AsString(), GetLabel(), CSeq_id_Handle::GetSeqId(), and CSeq_id_Handle::IsGi().

◆ GetLabel() [3/6]

string GetLabel ( const vector< CRef< CSeq_id > > & ids )

Definition at line 370 of file seq_id_handle.cpp.

References ERR_POST, CTextseq_id_Base::GetAccession(), GetLabel(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsGi(), CTextseq_id_Base::IsSetVersion(), ITERATE, CSeq_id::kMaxScore, and ZERO_GI.

◆ GetLabel() [4/6]

string GetLabel ( const vector< CSeq_id_Handle > & ids )

Definition at line 332 of file seq_id_handle.cpp.

References ERR_POST, CTextseq_id_Base::GetAccession(), GetLabel(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetTextseq_Id(), CSeq_id_Handle::IsGi(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), ITERATE, CSeq_id::kMaxScore, and ZERO_GI.

◆ GetLabel() [5/6]

void CSeq_id::GetLabel	(	string *	label,
		ELabelType	type = `eDefault`,
		TLabelFlags	flags = `fLabel_Default`
	)		const

Append a label for this Seq-id to the supplied string.

Parameters

label	String to append to.
type	Type of label (human-readable type-tagged content, by default).
flags	Flags fine-tuning behavior for human-readable output (ignored in eFasta and eFastaContent mode).

See also: ELabelType, ELabelFlags

Definition at line 2040 of file Seq_id.cpp.

References CSeq_id::AsFastaString(), CSeq_id::ComposeOSLT(), CSeq_id::eBoth, CSeq_id::eContent, CSeq_id::eFasta, CSeq_id::eFastaContent, CSeq_id::eType, CSeq_id::fAllowLocalId, CSeq_id::fLabel_Trimmed, CSeq_id::fLabel_UpperCase, CSeq_id::fLabel_Version, flags, CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetVersion(), label, NULL, NStr::ToUpper(), x_GetLabel_Content(), x_GetLabel_Type(), and CSeq_id::x_WriteContentAsFasta().

Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), CExportTableDlg::AddDblinkToTable(), CExportTableDlg::AddDeflinesToTable(), CExportTableDlg::AddFeaturesToTable(), CGBProjectHelper::AddProjectItemsFromRID(), CExportTableDlg::AddPubsToTable(), CExportTableDlg::AddRnaToTable(), CExportTableDlg::AddSourceToTable(), CTrimN::apply(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), CDiscrepancyContext::BuildSeqSummary(), CheckDuplicates(), CBarcodeTool::ClickLink(), CPSG_BioId::CPSG_BioId(), CRevCompSequencesDlg::CreateControls(), CCDSTranslationPanel::CreateControls(), CBlastDBExtractor::ExtractAccession(), CSelectTargetDlg::FindBioseq(), CFlatSeqIdQVal::Format(), fta_check_feat_overlap(), GetBarcodeId(), CGenbankIdResolve::GetBestId(), CAddFluComments::GetBestLabel(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CWGSClient::GetBioseqInfo(), CBulkCDSAddPanel::GetCommand(), CMixedStrands::GetCommand(), CRemoveSequencesDlg::GetCommand(), CObjectCoords::GetCoordinates(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CDesktopBioseqItem::GetDescription(), CDesktopBioseqsetItem::GetDescription(), GetGeneralOrLocal(), CSeq_featHandler::GetLabel(), CAlignFormatUtil::GetLinkoutUrl(), CLocationListCtrl::GetListIdStrForSeqId(), CBamAlignIterator::GetMatchAlign(), GetNewProtId(), CSequenceUpdater::GetNotImportedFeatsReport(), CSequenceUpdater::GetRevCompReport(), CShowBlastDefline::GetSeqIdListString(), CSeq_id::GetSeqIdString(), CSeq_id::GetStringDescr(), CTableDataGCAssembly::GetStringValue(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CGuiObjectInfoSeq_align::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CSeqIdField::GetVal(), CLocalIDField::GetVals(), CEditingActionDescLocalId::GetValue(), CEditingActionSeqid::GetValue(), CEditingActionFileId::GetValue(), CAlignGroup::GroupBySequenceType(), CSeqTextPanel::InitObject(), CVcfTableView::InitView(), CTextPanel::InitWidget(), CLocalIDField::IsEmpty(), CAttribTableColumnIdPanel::IsInputValid(), CNGAlignParams::LogDump(), CAssemblyTrackingPanel::OnPopulateBtnClick(), CRevCompSequencesDlg::OnSelect(), CSeqVectorCache::PrefetchSequence(), CTabularFormatter_SeqId::Print(), CBlastFormat::PrintReport(), CFeaturePropagator::Propagate(), RelaxedMatch(), ReportMailReportLine(), s_AddOtherRelatedInfoLinks(), s_AgpWrite(), s_CompareSeqAlignByEvalue(), s_CompareSeqAlignByScoreAndName(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_DescribeSegment(), s_ExtendEntriesFromAlignments(), s_GetAccession(), s_GetAlignmentTooltip(), s_GetDescription(), CCompareSeqRegions::s_GetGeneId(), s_GetIdBase(), s_GetSeqIdListString(), NSearchFeatPanel::s_GetSeqLabel(), s_GetSeqLabel(), s_GetSequenceRegionId(), s_IdLabel(), s_MatchSeqIds(), s_Render_SeqAlign(), s_SetCloneInfo(), SeqDB_SimplifySeqid(), CAgpwriteProcess::SeqEntryProcess(), CIgBlastTabularInfo::SetAirrFormatData(), sGenerateFields(), pub_report::CSkipSeqIdHook::SkipClassMember(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), CCreateSeqHistForTpa::ValidateAlignments(), CValidError_bioseq::ValidateSegRef(), CConversionApp::Write(), CUCSCRegionWriter::WriteAnnot(), CVcfWriter::WriteAnnot(), CFeatureItem::x_AddQualsRna(), CMixedStrands::x_AddSequenceIds(), CAsn2FlatApp::x_AddSNPAnnots(), CFeaturePropagator::x_CdsMapCodeBreaks(), CImportFeatTable::x_DoImportCDS(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), CSGSegmentSmearJob::x_GetCacheKey(), CCreateGeneModelTask::x_GetCommand(), CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign(), CGridTableSeqIds::x_GetLabel(), CUpdateSeqPanel::x_GetNameAndLength(), CEditObjectSeq_feat::x_HandleCdsProduct(), CDisplaySeqalign::x_InitAlignParams(), CDisplaySeqalign::x_InitDefLinesHeader(), CFeatureTableReader_Imp::x_InitId(), CReportEntry::x_NewCoordinate(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CFeaturePropagator::x_PropagatetRNA(), CCdregionValidator::x_ReportTranslationProblems(), CBlastDBExtractor::x_SetGi2AccMap(), CBioseqContext::x_SetId(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphValues(), CVcfWriter::x_WriteFeature(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CFeatTableEdit::xConvertToGeneralIds(), CSrcWriter::xGatherLocalId(), CWiggleWriter::xTableGetChromName(), CBedGraphWriter::xWriteAnnotSeqTable(), CBedGraphWriter::xWriteSingleFeature(), and CWiggleWriter::xWriteSingleGraphFixedStep().

◆ GetLabel() [6/6]

void CSeq_id::GetLabel	(	string *	label,
		int *	version,
		ELabelType	type = `eDefault`
	)		const

Append a label for this Seq-id to the supplied string, splitting out the version to a separate output parameter.

Note: In eFasta and eFastaContent mode, this method includes the version (if any) in the label and does not touch *version.

Parameters

label	String to append to.
version	Pointer to hold the returned version.
type	Type of label (human-readable type-tagged content, by default).

See also: ELabelType

Definition at line 2106 of file Seq_id.cpp.

References CSeq_id::AsFastaString(), CSeq_id::eBoth, CSeq_id::eContent, CSeq_id::eFasta, CSeq_id::eFastaContent, CSeq_id::eType, label, dtl::version, x_GetLabel_Content(), x_GetLabel_Type(), and CSeq_id::x_WriteContentAsFasta().

◆ GetMapper() [1/2]

CSeq_id_Mapper& CSeq_id_Info::GetMapper ( void ) const

inline

Definition at line 106 of file seq_id_handle.hpp.

References CSeq_id_Info::m_Mapper.

Referenced by CSeq_id_Handle::GetMapper(), and CSeq_id_Info::GetTree().

◆ GetMapper() [2/2]

CSeq_id_Mapper& CSeq_id_Handle::GetMapper ( void ) const

inline

Definition at line 323 of file seq_id_handle.hpp.

References CSeq_id_Info::GetMapper(), and CSeq_id_Handle::m_Info.

Referenced by CSeq_id_Handle::GetMatchingHandles(), CSeq_id_Handle::GetReverseMatchingHandles(), CSeq_id_Handle::HaveMatchingHandles(), CSeq_id_Handle::HaveReverseMatch(), CSeq_id_Handle::IsBetter(), CSeq_id_Handle::MatchesTo(), and CSeq_id_Handle::operator==().

◆ GetMatchingHandles() [1/4]

void CSeq_id_Mapper::GetMatchingHandles	(	const CSeq_id_Handle &	id,
		TSeq_id_HandleSet &	h_set
	)

Definition at line 134 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::FindMatch(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Mapper::GetMatchingHandles(), and CSeq_id_Handle::GetMatchingHandles().

◆ GetMatchingHandles() [2/4]

void CSeq_id_Mapper::GetMatchingHandles	(	const CSeq_id_Handle &	id,
		TSeq_id_HandleSet &	h_set,
		EAllowWeakMatch	allow_weak_match
	)

Definition at line 186 of file seq_id_mapper.cpp.

References CSeq_id_Base::e_Gi, eNoWeakMatch, CSeq_id_Mapper::GetMatchingHandles(), i, CSeq_id_Mapper::m_Trees, and CSeq_id_Mapper::x_GetTree().

◆ GetMatchingHandles() [3/4]

void CSeq_id_Handle::GetMatchingHandles ( TMatches & matches ) const

Definition at line 150 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::GetMatchingHandles().

Referenced by CDataSource::GetLoadedBlob_ids(), CDataSource_ScopeInfo::x_GetSeqMatch(), and CDataSource::x_GetSeqMatch().

◆ GetMatchingHandles() [4/4]

void CSeq_id_Handle::GetMatchingHandles	(	TMatches &	matches,
		EAllowWeakMatch	allow_weak_match
	)		const

Definition at line 162 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::GetMatchingHandles().

◆ GetMatchingHandlesStr()

void CSeq_id_Mapper::GetMatchingHandlesStr	(	string	sid,
		TSeq_id_HandleSet &	h_set
	)

Get the list of string-matching handles, do not create new handles.

Definition at line 274 of file seq_id_mapper.cpp.

References ITERATE, CSeq_id_Mapper::m_Trees, and NCBI_THROW.

◆ GetMatchingIds()

void CSeq_id::GetMatchingIds ( TSeqIdHandles & matches ) const

Collect partially matching seq-ids: no-version, no-name etc.

The original id is not added to the set.

Definition at line 3335 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::GetGeneral(), CSeq_id_Handle::GetHandle(), CSeq_id_Base::GetLocal(), CSeq_id::GetMatchingTextseqIds(), CSeq_id_Base::GetPdb(), set< Key, Compare >::insert(), match(), and CSeq_id_Base::Which().

Referenced by CSeq_loc_Mapper_Base::CollectSynonyms().

◆ GetMatchingTextseqIds()

void CSeq_id::GetMatchingTextseqIds ( TSeqIdHandles & matches ) const

Collect partially matching textseq-ids.

See also: GetMatchingIds

Definition at line 3268 of file Seq_id.cpp.

References A, CSeq_id_Handle::GetHandle(), CSeq_id::GetTextseq_Id(), set< Key, Compare >::insert(), kEmptyStr, match(), N, orig, r(), CTextseq_id_Base::Reset(), CTextseq_id_Base::ResetRelease(), CTextseq_id_Base::ResetVersion(), s_GetTextseq_id(), CTextseq_id_Base::SetAccession(), CTextseq_id_Base::SetName(), CTextseq_id_Base::SetRelease(), CTextseq_id_Base::SetVersion(), and CSeq_id_Base::Which().

Referenced by CSeq_id::GetMatchingIds().

◆ GetPacked()

TPacked CSeq_id_Handle::GetPacked ( void ) const

inline

Definition at line 267 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Packed.

Referenced by CSeq_id_Textseq_Info::CompareOrdered(), CSeq_id_General_Id_Info::CompareOrdered(), and operator<<().

◆ GetPackedSeqId()

CConstRef< CSeq_id > CSeq_id_Info::GetPackedSeqId	(	TPacked	packed,
		TVariant	variant
	)		const

virtual

Reimplemented in CSeq_id_Gi_Info, CSeq_id_PDB_Info, CSeq_id_General_PlainInfo, CSeq_id_General_Str_Info, CSeq_id_General_Id_Info, CSeq_id_Local_Info, CSeq_id_Textseq_Info, and CSeq_id_Textseq_PlainInfo.

Definition at line 82 of file seq_id_handle.cpp.

References NCBI_THROW.

Referenced by CSeq_id_Handle::GetSeqId().

◆ GetReverseMatchingHandles() [1/4]

void CSeq_id_Mapper::GetReverseMatchingHandles	(	const CSeq_id_Handle &	id,
		TSeq_id_HandleSet &	h_set
	)

Definition at line 147 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::FindReverseMatch(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Mapper::GetReverseMatchingHandles(), and CSeq_id_Handle::GetReverseMatchingHandles().

◆ GetReverseMatchingHandles() [2/4]

void CSeq_id_Mapper::GetReverseMatchingHandles	(	const CSeq_id_Handle &	id,
		TSeq_id_HandleSet &	h_set,
		EAllowWeakMatch	allow_weak_match
	)

Definition at line 246 of file seq_id_mapper.cpp.

References CSeq_id_Base::e_Gi, eNoWeakMatch, CSeq_id_Mapper::GetReverseMatchingHandles(), i, CSeq_id_Mapper::m_Trees, and CSeq_id_Mapper::x_GetTree().

◆ GetReverseMatchingHandles() [3/4]

void CSeq_id_Handle::GetReverseMatchingHandles ( TMatches & matches ) const

Definition at line 156 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::GetReverseMatchingHandles().

Referenced by CMTTestThread::Main().

◆ GetReverseMatchingHandles() [4/4]

void CSeq_id_Handle::GetReverseMatchingHandles	(	TMatches &	matches,
		EAllowWeakMatch	allow_weak_match
	)		const

Definition at line 169 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::GetReverseMatchingHandles().

◆ GetSeq_id()

CConstRef< CSeq_id > CSeq_id_Mapper::GetSeq_id ( const CSeq_id_Handle & handle )

inlinestatic

Get seq-id for the given handle.

Definition at line 156 of file seq_id_mapper.hpp.

References CSeq_id_Handle::GetSeqId().

◆ GetSeq_idByType()

template<class container >

CConstRef<CSeq_id> GetSeq_idByType	(	const container &	ids,
		CSeq_id::E_Choice	choice
	)

Search the container of CRef<CSeq_id> for the id of given type.

Return the id of requested type, or null CRef.

Definition at line 1028 of file Seq_id.hpp.

References Get_ConstRef_Seq_id(), ITERATE, and CSeq_id_Base::Which().

Referenced by CAlignFormatUtil::BuildUserUrl(), FindGi(), CAlignFormatUtil::GetTaxidForSeqid(), s_GetBestIDForURL(), and s_GetSRASeqMetadata().

◆ GetSeqId() [1/2]

CConstRef<CSeq_id> CSeq_id_Info::GetSeqId ( void ) const

inline

Definition at line 80 of file seq_id_handle.hpp.

References CSeq_id_Info::m_Seq_id.

Referenced by CSeq_id_Handle::GetSeqId().

◆ GetSeqId() [2/2]

CConstRef<CSeq_id> CSeq_id_Handle::GetSeqId ( void ) const

inline

Definition at line 304 of file seq_id_handle.hpp.

References CSeq_id_Info::GetPackedSeqId(), CSeq_id_Info::GetSeqId(), CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, and CSeq_id_Handle::m_Variant.

◆ GetSeqIdOrNull()

CConstRef<CSeq_id> CSeq_id_Handle::GetSeqIdOrNull ( void ) const

inline

Definition at line 315 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetSeqId(), and CSeq_id_Handle::m_Info.

Referenced by CBioseq_Handle::GetInitialSeqIdOrNull(), CGuiObjectInfoSeq_align::GetToolTip(), CRepeatMaskerReader::ParseRecord(), s_FindGi(), s_FindLocalId(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_GetModelEvidance(), s_ReplaceGIs(), sGenerateFields(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CVectorScreen::x_FindAccession(), CVectorScreen::x_FindLocalId(), CVectorScreen::x_FindTypeGeneral(), and CFeaturePanel::x_StartAssemblyJob().

◆ GetSeqIdString() [1/2]

string CSeq_id::GetSeqIdString ( bool with_version = false ) const

Return seqid string with optional version for text seqid type.

Definition at line 2145 of file Seq_id.cpp.

References CSeq_id::eContent, CSeq_id::fLabel_Version, flags, CSeq_id::GetLabel(), and label.

◆ GetSeqIdString() [2/2]

string CSeq_id::GetSeqIdString ( int * version ) const

Return seqid string for text seqid type with separate integer version.

Definition at line 2156 of file Seq_id.cpp.

References CSeq_id::eContent, CSeq_id::GetLabel(), label, and dtl::version.

◆ GetSNPScaleLimit_Name()

const char * CSeq_id::GetSNPScaleLimit_Name ( ESNPScaleLimit value )

static

Definition at line 3549 of file Seq_id.cpp.

References CSeq_id::eSNPScaleLimit_Chromosome, CSeq_id::eSNPScaleLimit_Contig, CSeq_id::eSNPScaleLimit_Supercontig, CSeq_id::eSNPScaleLimit_Unit, and rapidjson::value.

Referenced by CId2ReaderBase::LoadSeq_idBlob_ids(), CReaderRequestResult::s_KeyBlobIds(), and CId2ReaderBase::x_SetContextData().

◆ GetSNPScaleLimit_Value()

CSeq_id::ESNPScaleLimit CSeq_id::GetSNPScaleLimit_Value ( const string & name )

static

Definition at line 3561 of file Seq_id.cpp.

References CSeq_id::eSNPScaleLimit_Chromosome, CSeq_id::eSNPScaleLimit_Contig, CSeq_id::eSNPScaleLimit_Default, CSeq_id::eSNPScaleLimit_Supercontig, and CSeq_id::eSNPScaleLimit_Unit.

Referenced by CDemoApp::Run(), and CPSGS_SNPProcessor::x_LoadConfig().

◆ GetStringDescr()

string CSeq_id::GetStringDescr	(	const CBioseq &	bioseq,
		EStringFormat	fmt
	)

static

◆ GetTextseq_Id()

const CTextseq_id * CSeq_id::GetTextseq_Id ( void ) const

Return embedded CTextseq_id, if any.

Definition at line 169 of file Seq_id.cpp.

Referenced by CSeq_id::AdjustScore(), AllowOrphanedProtein(), CSeq_id_Descr::Assign(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CSeq_id_Textseq_Tree::Dump(), CSeq_id_Textseq_Tree::FindMatch(), CSNPDb_Impl::FindSeq(), FindTextseq_id(), FTASeqLocCheck(), GetAccession(), GetAccessionAndDatabaseSource(), GetAccVer(), CBAMDataLoader_Impl::GetAccVer(), CWholeFileAnnotation::GetAndUseAnnot(), CDefaultSynonymMapper::GetBestSynonym(), GetGiForAccession(), GetLabel(), CBioseq::GetLabel(), CSeq_id::GetLabel(), CSeq_id::GetMatchingTextseqIds(), CSeq_id_Textseq_PlainInfo::GetPackedSeqId(), CSeq_id_Textseq_Info::GetPackedSeqId(), GetWGSMasterSeq_id(), HasNameAndAccession(), CSeq_id::IdentifyAccession(), IsAccessionNoVersion(), CSeq_id::IsAllowedSNPScaleLimit(), CSNPClient::IsValidSeqId(), CSeq_id_Textseq_PlainInfo::ParseCaseVariant(), s_CheckQuals_cdregion(), s_GetBestSynonym(), s_GetModelEvidance(), s_GetNameForBioseq(), s_IsIpgAccession(), s_Match_id(), s_Matches(), s_PSGRank(), s_ValidateAcc(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_imp::Setup(), StrippedAccVer(), CValidError_imp::ValidateBioSource(), CWriteDB_IsamIndex::x_AddStringIds(), CGencollIdMapper::x_ApplyPatternToId(), CFeatureGenerator::SImplementation::x_CheckMatch(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CComponentSearchJob::x_DoSearch(), CGencollIdMapper::x_FixImperfectId(), x_GetId(), CScope_Impl::x_GetSynonyms(), CSeq_id_Textseq_Tree::x_GetVersion(), CWriteDB_LMDB::x_InsertEntry(), CFlatSeqLoc::x_IsAccessionVersion(), CFlatGatherer::x_MergeEqualBioSources(), CBuildDatabase::x_ResolveRemoteId(), CPSGS_ResolveBase::x_ResolveSeqId(), CPSGS_ResolveBase::x_ResolveViaComposeOSLTInCache(), CSingleFeatValidator::x_ValidateSeqFeatProduct(), and CFastaOstream::x_WriteAsFasta().

◆ GetTree()

CSeq_id_Which_Tree & CSeq_id_Info::GetTree ( void ) const

Definition at line 76 of file seq_id_handle.cpp.

References CSeq_id_Info::GetMapper(), CSeq_id_Info::GetType(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Mapper::x_GetTree(), and CSeq_id_Info::x_RemoveLastLock().

◆ GetType()

CSeq_id::E_Choice CSeq_id_Info::GetType ( void ) const

inline

Definition at line 102 of file seq_id_handle.hpp.

References CSeq_id_Info::m_Seq_id_Type.

Referenced by CSeq_id_Textseq_Info::GetPackedSeqId(), CSeq_id_Info::GetTree(), CSeq_id_Handle::IsGi(), and CSeq_id_Handle::Which().

◆ GetVariant()

TVariant CSeq_id_Handle::GetVariant ( void ) const

inline

Definition at line 275 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Variant.

◆ HaveMatchingHandles() [1/4]

bool CSeq_id_Mapper::HaveMatchingHandles ( const CSeq_id_Handle & id )

Get the list of matching handles, do not create new handles.

Definition at line 128 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::HaveMatch(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Mapper::HaveMatchingHandles(), and CSeq_id_Handle::HaveMatchingHandles().

◆ HaveMatchingHandles() [2/4]

bool CSeq_id_Mapper::HaveMatchingHandles	(	const CSeq_id_Handle &	id,
		EAllowWeakMatch	allow_weak_match
	)

Definition at line 154 of file seq_id_mapper.cpp.

References CSeq_id_Base::e_Gi, eNoWeakMatch, CSeq_id_Mapper::HaveMatchingHandles(), i, CSeq_id_Mapper::m_Trees, and CSeq_id_Mapper::x_GetTree().

◆ HaveMatchingHandles() [3/4]

bool CSeq_id_Handle::HaveMatchingHandles ( EAllowWeakMatch allow_weak_match ) const

Definition at line 138 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::HaveMatchingHandles().

◆ HaveMatchingHandles() [4/4]

bool CSeq_id_Handle::HaveMatchingHandles ( void ) const

Definition at line 126 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::HaveMatchingHandles().

Referenced by GetAccession(), CDataSource::GetLoadedBlob_ids(), CDataSource_ScopeInfo::x_GetSeqMatch(), and CDataSource::x_GetSeqMatch().

◆ HaveReverseMatch() [1/4]

bool CSeq_id_Mapper::HaveReverseMatch ( const CSeq_id_Handle & id )

Definition at line 141 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::HaveReverseMatch(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Mapper::HaveReverseMatch(), and CSeq_id_Handle::HaveReverseMatch().

◆ HaveReverseMatch() [2/4]

bool CSeq_id_Mapper::HaveReverseMatch	(	const CSeq_id_Handle &	id,
		EAllowWeakMatch	allow_weak_match
	)

Definition at line 214 of file seq_id_mapper.cpp.

References CSeq_id_Base::e_Gi, eNoWeakMatch, CSeq_id_Mapper::HaveReverseMatch(), i, CSeq_id_Mapper::m_Trees, and CSeq_id_Mapper::x_GetTree().

◆ HaveReverseMatch() [3/4]

bool CSeq_id_Handle::HaveReverseMatch ( EAllowWeakMatch allow_weak_match ) const

Definition at line 144 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::HaveReverseMatch().

◆ HaveReverseMatch() [4/4]

bool CSeq_id_Handle::HaveReverseMatch ( void ) const

Definition at line 132 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::HaveReverseMatch().

◆ IdentifyAccession() [1/3]

CSeq_id::EAccessionInfo CSeq_id::IdentifyAccession	(	const CTempString &	accession,
		TParseFlags	flags = `fParse_AnyRaw`
	)

static

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on properties.

Definition at line 1634 of file Seq_id.cpp.

References CTempString::data(), CSeq_id::eAcc_unknown, CTempString::find(), CTempString::find_first_not_of(), flags, i, kDigits, NPOS, CTempString::size(), NStr::ToUpper(), toupper(), and CSeq_id::x_IdentifyAccession().

Referenced by CLinkUtils::AddSequenceLinks(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CSixFramesTransTrackFactory::CreateTracks(), CAutoColValidatoraccession::DoValidate(), fta_fix_seq_id(), CWGSDataLoader_Impl::GetFileInfoByAcc(), SSeqIdRange::const_iterator::GetID(), GetNameCategory(), GetNucAccOwner(), GetProtAccOwner(), GetSequenceType(), GetTitle(), CVDBBlastUtil::GetVDBSeqIdFromOID(), GetWGSMasterSeq_id(), CAlignGroup::GroupBySequenceType(), CSeq_id::IdentifyAccession(), CSeq_id_Handle::IdentifyAccession(), IdentifyLocalId(), CSeq_id::IsAllowedSNPScaleLimit(), CSGUtils::IsChromosome(), CGuiSeqInfoSeq_id::IsDNA(), CGencollSvc::isGenCollSequence(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CGuiSeqInfoSeq_id::IsProtein(), CSeqUtils::isQuasiLocal(), CSeqUtils::isTopLevel(), CValidError_bioseq::IsTSAAccession(), IsValidAccession(), CSNPClient::IsValidSeqId(), CValidError_bioseq::IsWGSAccession(), IsWGSAccession(), CValidError_bioseq::IsWp(), CAgpValidateReader::OnGapOrComponent(), CAgpValidateReader::OnObjectChange(), OverrideLenIfAccession(), CWGSResolver_Ids::ParseWGSPrefix(), CReadBlastApp::processFeature(), CAlignFormatUtil::RemoveSeqsOfAccessionTypeFromSeqInUse(), CWGSClient::ResolveAcc(), s_GetDescription(), s_GetSeqLabel(), s_ModifySeqAlnWithFilteredSeqIDs(), s_RenderAccList(), CSeq_id::Set(), CGffAlignmentRecord::SetMatchType(), ValidateAccessionFormat(), CValidError_bioseq::ValidateSeqId(), ValidSeqType(), CVDBBlastUtil::VDBIdType(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), x_GetCDDIds(), CTableColumnTypeGuesser::x_GuessType(), x_IsWgsSecondary(), CGenBankLoadOptionPanel::x_ProccessText(), COligoSpecificityCheck::x_SavePrimerInfo(), CDeflineGenerator::x_SetFlags(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CUCSCRegionReader::xParseFeatureUCSCFormat(), and CGff3Writer::xSplicedSegHasProteinProd().

◆ IdentifyAccession() [2/3]

CSeq_id::EAccessionInfo CSeq_id::IdentifyAccession ( TParseFlags flags = fParse_AnyRaw | fParse_AnyLocal ) const

◆ IdentifyAccession() [3/3]

CSeq_id::EAccessionInfo CSeq_id_Handle::IdentifyAccession ( void ) const

inline

Definition at line 299 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetSeqId(), and CSeq_id::IdentifyAccession().

Referenced by CAlnSeqId::GetSequenceType(), variation::CVariationUtil::RemapToAnnotatedTarget(), s_IsIpgAccession(), s_LocIdType(), and variation::CHgvsParser::x_header().

◆ IsAccVer()

bool CSeq_id_Handle::IsAccVer ( void ) const

inline

Definition at line 287 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetSeqId(), and CSeq_id_Handle::IsGi().

Referenced by CScope_Impl::GetAccVer(), and CPSGDataLoader_Impl::GetAccVersOnce().

◆ IsAllowedSNPScaleLimit() [1/2]

bool CSeq_id_Handle::IsAllowedSNPScaleLimit ( CSeq_id::ESNPScaleLimit scale_limit ) const

Definition at line 246 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetSeqId().

◆ IsAllowedSNPScaleLimit() [2/2]

bool CSeq_id::IsAllowedSNPScaleLimit ( ESNPScaleLimit scale_limit ) const

Definition at line 3571 of file Seq_id.cpp.

References CSeq_id_Base::e_Other, CSeq_id::eAcc_chromosome, CSeq_id::eAcc_con, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_wgs_intermed, CSeq_id::eSNPScaleLimit_Chromosome, CSeq_id::eSNPScaleLimit_Contig, CSeq_id::eSNPScaleLimit_Default, CSeq_id::eSNPScaleLimit_Supercontig, CSeq_id::eSNPScaleLimit_Unit, CSeq_id::GetAccType(), CSeq_id::GetTextseq_Id(), CSeq_id::IdentifyAccession(), and CSeq_id_Base::IsGi().

◆ IsBetter()

bool CSeq_id_Handle::IsBetter ( const CSeq_id_Handle & h ) const

True if "this" is a better bioseq than "h".

Definition at line 176 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::x_IsBetter().

Referenced by CBlobSplitterImpl::CopySkeleton(), s_GetIdBase(), CDataSource_ScopeInfo::x_GetSeqMatch(), and CDataSource::x_GetSeqMatch().

◆ IsGi()

bool CSeq_id_Handle::IsGi ( void ) const

inline

Definition at line 279 of file seq_id_handle.hpp.

References CSeq_id_Base::e_Gi, CSeq_id_Info::GetType(), CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::CompareOrdered(), CBlobSplitterImpl::CopySkeleton(), CBAMDataLoader_Impl::GetAccVer(), CLDS2_Database::GetAnnotBlobs(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CLDS2_Database::GetBioseqId(), CBlobSplitterImpl::GetChunkData(), GetDirectLabel(), CWGSDataLoader_Impl::GetFileInfo(), CBAMDataLoader_Impl::GetGi(), CSeq_id_Handle::GetGi(), GetGiForAccession(), GetGiForId(), sequpd::GetGoodSeqIdHandle(), GetId(), GetLabel(), CTestMapperSeqInfo::GetSequenceLength(), CTestMapperSeqInfo::GetSequenceType(), CLocalBlastDbAdapter::GetTaxId(), CSeq_id_Handle::IsAccVer(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idInfo(), CCacheReader::LoadSequenceHash(), operator<<(), CSeq_id_Handle::operator==(), ReplaceWellknownSeqs(), s_GetBestSynonym(), s_GetFeatureKeyLinkLocation(), sx_ProcessId(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CPhyTreeFormatter::x_GetSeqIDString(), CSeq_id_Mapper::x_GetTree(), CLDS2_Database::x_InitGetBioseqsSql(), x_MakeLocalCDDEntryId(), and CFeaturePanel::x_StartAssemblyJob().

◆ IsLocked()

bool CSeq_id_Info::IsLocked ( void ) const

inline

Definition at line 97 of file seq_id_handle.hpp.

References CSeq_id_Info::m_LockCounter.

◆ IsPacked()

bool CSeq_id_Handle::IsPacked ( void ) const

inline

Definition at line 263 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Packed.

Referenced by CSeq_id_Textseq_Info::CompareOrdered(), and CSeq_id_General_Id_Info::CompareOrdered().

◆ IsSetVariant()

bool CSeq_id_Handle::IsSetVariant ( void ) const

inline

Definition at line 271 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Variant.

Referenced by CSeq_id_Textseq_Info::CompareOrdered(), and CSeq_id_General_Id_Info::CompareOrdered().

◆ IsValid() [1/2]

bool CSeq_id::IsValid	(	const CBioseq::TId &	ids,
		TParseFlags	flags = `fParse_Default`
	)

static

Definition at line 3223 of file Seq_id.cpp.

◆ IsValid() [2/2]

bool CSeq_id::IsValid	(	const CSeq_id &	id,
		TParseFlags	flags = `fParse_Default`
	)

static

Definition at line 3228 of file Seq_id.cpp.

◆ IsValidLocalID()

bool CSeq_id::IsValidLocalID ( const CTempString & s )

static

Perform rudimentary validation on potential local IDs, whose contents should be pure ASCII and limited to letters, digits, and certain punctuation characters (-_.

:*# as of August 2010).

Definition at line 2576 of file Seq_id.cpp.

References CSeq_id::CheckLocalID(), and CSeq_id::fNoError.

Referenced by BOOST_AUTO_TEST_CASE(), CheckForBadLocalIdChars(), CFastaReader::IsValidLocalID(), and CSeq_id::Set().

◆ LoadAccessionGuide() [1/2]

void CSeq_id::LoadAccessionGuide ( const string & filename )

static

Definition at line 1882 of file Seq_id.cpp.

References s_Guide.

Referenced by CTestBMApp::Init().

◆ LoadAccessionGuide() [2/2]

void CSeq_id::LoadAccessionGuide ( ILineReader & in )

static

Definition at line 1887 of file Seq_id.cpp.

References in(), and s_Guide.

◆ Lock()

void CSeq_id_InfoLocker::Lock ( const CSeq_id_Info * info ) const

inline

Definition at line 134 of file seq_id_handle.hpp.

References info, and CObjectCounterLocker::Lock().

Referenced by CSeq_id_InfoLocker::Relock().

◆ Match()

bool CSeq_id::Match ( const CSeq_id & sid2 ) const

inline

Match() - TRUE if SeqIds are equivalent.

Definition at line 1065 of file Seq_id.hpp.

References CSeq_id::Compare(), and CSeq_id::e_YES.

◆ MatchesTo()

bool CSeq_id_Handle::MatchesTo ( const CSeq_id_Handle & h ) const

True if *this matches to h.

This mean that *this is either the same as h, or more generic version of h.

Definition at line 182 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetMapper(), and CSeq_id_Mapper::x_Match().

Referenced by BOOST_AUTO_TEST_CASE(), GetAlignmentForRna(), and s_Match_id().

◆ NCBI_EXCEPTION_DEFAULT()

CSeqIdException::NCBI_EXCEPTION_DEFAULT	(	CSeqIdException	,
		CException
	)

◆ operator!=() [1/2]

bool SSeqIdRange::const_iterator::operator!= ( const const_iterator & it ) const

inline

Definition at line 956 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator!=() [2/2]

bool CSeq_id_Handle::operator!= ( const CSeq_id_Handle & handle ) const

inline

Definition at line 197 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

Referenced by CAlnSeqId::operator!=().

◆ operator()()

bool CSeq_id_Handle::PLessOrdered::operator()	(	const CSeq_id_Handle &	id1,
		const CSeq_id_Handle &	id2
	)		const

inline

Definition at line 216 of file seq_id_handle.hpp.

References CSeq_id_Handle::CompareOrdered().

◆ operator*()

string SSeqIdRange::const_iterator::operator* ( void ) const

inline

Definition at line 928 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, and SSeqIdRange::const_iterator::x_SetAccession().

◆ operator+()

const_iterator SSeqIdRange::const_iterator::operator+ ( int n ) const

inline

Definition at line 945 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::const_iterator(), SSeqIdRange::const_iterator::m_Number, SSeqIdRange::const_iterator::m_Range, and n.

◆ operator++() [1/2]

const_iterator SSeqIdRange::const_iterator::operator++ ( int )

inline

Definition at line 939 of file Seq_id.hpp.

References orig.

◆ operator++() [2/2]

const_iterator& SSeqIdRange::const_iterator::operator++ ( void )

inline

Definition at line 937 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, and SSeqIdRange::const_iterator::m_Number.

◆ operator+=()

const_iterator& SSeqIdRange::const_iterator::operator+= ( int n )

inline

Definition at line 949 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, SSeqIdRange::const_iterator::m_Number, and n.

◆ operator-() [1/2]

int SSeqIdRange::const_iterator::operator- ( const const_iterator & it ) const

inline

Definition at line 966 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator-() [2/2]

const_iterator SSeqIdRange::const_iterator::operator- ( int n ) const

inline

Definition at line 947 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::const_iterator(), SSeqIdRange::const_iterator::m_Number, SSeqIdRange::const_iterator::m_Range, and n.

◆ operator--() [1/2]

const_iterator SSeqIdRange::const_iterator::operator-- ( int )

inline

Definition at line 943 of file Seq_id.hpp.

References orig.

◆ operator--() [2/2]

const_iterator& SSeqIdRange::const_iterator::operator-- ( void )

inline

Definition at line 941 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, and SSeqIdRange::const_iterator::m_Number.

◆ operator-=()

const_iterator& SSeqIdRange::const_iterator::operator-= ( int n )

inline

Definition at line 951 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, SSeqIdRange::const_iterator::m_Number, and n.

◆ operator->()

const string* SSeqIdRange::const_iterator::operator-> ( void ) const

inline

Definition at line 930 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Accession, and SSeqIdRange::const_iterator::x_SetAccession().

◆ operator<() [1/3]

bool SSeqIdRange::const_iterator::operator< ( const const_iterator & it ) const

inline

Definition at line 958 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator<() [2/3]

bool CSeq_id::operator< ( const CSeq_id & sid2 ) const

inline

Definition at line 589 of file Seq_id.hpp.

References CSeq_id::CompareOrdered().

◆ operator<() [3/3]

bool CSeq_id_Handle::operator< ( const CSeq_id_Handle & handle ) const

inline

Definition at line 201 of file seq_id_handle.hpp.

References INT_ID_TO, CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

◆ operator<<()

CNcbiOstream& operator<<	(	CNcbiOstream &	out,
		const CSeq_id_Handle &	idh
	)

Definition at line 407 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetPacked(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), out(), and CSeq_id::WriteAsFasta().

◆ operator<=()

bool SSeqIdRange::const_iterator::operator<= ( const const_iterator & it ) const

inline

Definition at line 962 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator=() [1/4]

const_iterator& SSeqIdRange::const_iterator::operator= ( const const_iterator & it )

inline

Definition at line 925 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number, and SSeqIdRange::const_iterator::m_Range.

◆ operator=() [2/4]

CSeq_id& CSeq_id::operator= ( const CSeq_id & )

private

◆ operator=() [3/4]

const CSeq_id_Info& CSeq_id_Info::operator= ( const CSeq_id_Info & )

private

◆ operator=() [4/4]

CSeq_id_Mapper& CSeq_id_Mapper::operator= ( const CSeq_id_Mapper & )

private

◆ operator==() [1/3]

bool SSeqIdRange::const_iterator::operator== ( const const_iterator & it ) const

inline

Definition at line 954 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator==() [2/3]

bool CSeq_id_Handle::operator== ( const CSeq_id & id ) const

Definition at line 188 of file seq_id_handle.cpp.

References CSeq_id_Mapper::GetHandle(), CSeq_id_Handle::GetMapper(), CSeq_id_Handle::IsGi(), and CSeq_id_Handle::m_Packed.

◆ operator==() [3/3]

bool CSeq_id_Handle::operator== ( const CSeq_id_Handle & handle ) const

inline

Definition at line 193 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

Referenced by CAlnSeqId::operator==().

◆ operator>()

bool SSeqIdRange::const_iterator::operator> ( const const_iterator & it ) const

inline

Definition at line 960 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator>=()

bool SSeqIdRange::const_iterator::operator>= ( const const_iterator & it ) const

inline

Definition at line 964 of file Seq_id.hpp.

References SSeqIdRange::const_iterator::m_Number.

◆ operator[]()

string SSeqIdRange::const_iterator::operator[] ( int n ) const

inline

Definition at line 932 of file Seq_id.hpp.

References n.

◆ ParseFastaIds()

SIZE_TYPE CSeq_id::ParseFastaIds	(	CBioseq::TId &	ids,
		const CTempString &	s,
		bool	allow_partial_failure = `false`
	)

static

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

Parameters

ids	Destination ID set. Existing contents will be preserved and appended to.
s	Input string to parse.
allow_partial_failure	If s contains invalid IDs, warn about them and try to process the remainder of the string, rather than throwing any exceptions.

Returns: The number of IDs successfully parsed.

Definition at line 2603 of file Seq_id.cpp.

References flags, CSeq_id::fParse_AnyLocal, CSeq_id::fParse_PartialOK, CSeq_id::fParse_RawText, and CSeq_id::ParseIDs().

Referenced by BOOST_AUTO_TEST_CASE(), ExtractAccession(), CVDBBlastUtil::GetVDBSeqIdFromOID(), CAgpValidateReader::OnObjectChange(), CGlimmerReader::Read(), CFastaIdsResolver::ResolveSeqId(), CSplignApp::Run(), s_MakeDefline(), s_TestFastaRoundTrip(), SeqDB_SimplifyAccession(), CAliToSeq_align::StringToSeq_id(), CIdMapperConfig::TargetHandle(), CImportFeatTable::x_CheckConsistentProteinIds(), CImportFeatTable::x_DoImportCDS(), CWriteDB_Impl::x_GetFastaReaderDeflines(), and CAgpConverter::x_InitializeCopyOfTemplate().

◆ ParseIDs()

SIZE_TYPE CSeq_id::ParseIDs	(	CBioseq::TId &	ids,
		const CTempString &	s,
		TParseFlags	flags = `fParse_Default`
	)

static

Parse a string representing one or more Seq-ids, appending the results to IDS.

Multiple IDs must appear in FASTA style.

Parameters

ids	Destination ID set. Existing contents will be preserved and appended to.
s	Input string to parse.
flags	How to interpret anything other than well-formed FASTA IDs.

Returns: The number of IDs successfully parsed.

Definition at line 2613 of file Seq_id.cpp.

References _ASSERT, count, CSeq_id::CSeq_id(), CSeq_id_Base::e_General, CSeq_id_Base::e_not_set, CTempString::empty(), ERR_POST_X, NStr::eTrunc_Both, CSeq_id::eTV_plain, flags, CSeq_id::fParse_NoFASTA, CSeq_id::fParse_PartialOK, l(), NCBI_THROW, s_HasFastaTag(), NStr::Split(), NStr::TruncateSpaces_Unsafe(), Warning(), CSeq_id::WhichInverseSeqId(), and CSeq_id::x_IdentifyTypeVariant().

Referenced by BOOST_AUTO_TEST_CASE(), CFast5colReader::FindAnnots(), GetProtRefSeqId(), CSeqUtils::MapStringId(), CSeq_id::ParseFastaIds(), s_ConfigureDeflineTitle(), s_GetRefSeq_id(), s_RejoinDeflineTitle(), sx_GetRefSeq_id(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CAsn2FlatApp::x_GenerateHugeMode(), CFast5colReader::x_IndexFile(), CFeatureTableReader_Imp::x_InitId(), CCSraDb_Impl::x_MakeRefSeq_ids(), CAlnReader::x_ParseAndValidateSeqIds(), CFastaDeflineReader::x_ProcessIDs(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

◆ PreferAccessionOverGi()

bool CSeq_id::PreferAccessionOverGi ( void )

static

Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SEQ_ID_PREFER_ACCESSION_OVER_GI).

Definition at line 3404 of file Seq_id.cpp.

References CSeq_id::AvoidGi().

Referenced by CSeq_id::BaseBestRankScore(), CSeq_id::BaseBlastScore(), CSeq_id::BaseFastaAAScore(), CSeq_id::BaseFastaNAScore(), CSeq_id::BaseTextScore(), BOOST_AUTO_TEST_CASE(), GetId(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), and CDeltaBlastTestFixture::x_CountNumberUniqueIds().

◆ Relock()

void CSeq_id_InfoLocker::Relock ( const CSeq_id_Info * info ) const

inline

Definition at line 139 of file seq_id_handle.hpp.

References info, and CSeq_id_InfoLocker::Lock().

◆ RemoveLock()

void CSeq_id_Info::RemoveLock ( void ) const

inline

Definition at line 91 of file seq_id_handle.hpp.

References CSeq_id_Info::m_LockCounter, and CSeq_id_Info::x_RemoveLastLock().

◆ Reset()

void CSeq_id_Handle::Reset ( void )

inline

Reset the handle (remove seq-id reference)

Definition at line 227 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, CSeq_id_Handle::m_Variant, and CConstRef< C, Locker >::Reset().

Referenced by CIdMapper::AddMapping(), CSNPBlobId::FromSatString(), CCSRABlobId::FromString(), CSNPBlobId::FromString(), GetId(), SAnnotObject_Key::Reset(), CBioseq_Handle::Reset(), SAnnotObject_Key::SetMultiple(), CTSE_Info::SetSeq_entry(), and x_GetCDDIds().

◆ Score()

static int CSeq_id::Score ( const CRef< CSeq_id > & id )

inlinestatic

◆ Set() [1/5]

CSeq_id & CSeq_id::Set	(	const CDbtag &	tag,
		bool	set_as_general = `true`
	)

◆ Set() [2/5]

CSeq_id & CSeq_id::Set	(	const CTempString &	the_id,
		TParseFlags	flags = `fParse_AnyRaw`
	)

Reassign based on flat specifications; arguments interpreted as with constructors.

(Returns a reference to self.)

Definition at line 2457 of file Seq_id.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Prf, CTempString::empty(), ERR_POST_X, NStr::eTrunc_Both, CTempString::find(), flags, CSeq_id::fParse_AnyLocal, CSeq_id::fParse_AnyRaw, CSeq_id::fParse_FallbackOK, CSeq_id::fParse_NoFASTA, CSeq_id::fParse_PartialOK, CSeq_id::fParse_ValidLocal, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), CSeq_id::IsValidLocalID(), ITERATE, kEmptyStr, NCBI_THROW, NPOS, s_CheckForFastaTag(), s_SplitVersion(), CTempString::size(), NStr::Split(), CTempString::substr(), NStr::ToUpper(), NStr::TruncateSpaces_Unsafe(), Warning(), CSeq_id::x_IdentifyTypeVariant(), and CSeq_id::x_Init().

Referenced by CSeq_id::CSeq_id(), CLocationListCtrl::GetIdFromForm(), CIdMapperConfig::Initialize(), IPSGS_Processor::ParseInputSeqId(), PrintFastaUnaligned(), PrintSAMUnaligned(), PrintTabularUnaligned(), s_MakeFastaSubIds(), CHangScorer::ScoreAlignments(), CSeq_id::Set(), CIdMapperGCAssembly::x_AddAliasMappings(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CURLTooltipHandler::x_DisplayUnalignedRegion(), CGencollIdMapper::x_FixImperfectId(), CShortReadFastaInputSource::x_GetNextSeqId(), CSeq_id::x_Init(), CPSGS_GetProcessor::x_OnSeqIdResolveFinished(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CAltValidator::x_QueryAccessions(), CUpdateSeq_Input::x_ReadAccession(), and CAssemblyListPanel::x_UpdateSearchTerm().

◆ Set() [3/5]

CSeq_id & CSeq_id::Set	(	E_Choice	the_type,
		const CTempString &	acc_in,
		const CTempString &	name_in = `kEmptyStr`,
		int	version = `0`,
		const CTempString &	release_in = `kEmptyStr`
	)

Definition at line 2898 of file Seq_id.cpp.

◆ Set() [4/5]

CSeq_id & CSeq_id::Set	(	E_Choice	the_type,
		TIntId	int_seq_id
	)

◆ Set() [5/5]

CSeq_id & CSeq_id::Set	(	EFastaAsTypeAndContent	f,
		E_Choice	the_type,
		const CTempString &	the_content
	)

Definition at line 2560 of file Seq_id.cpp.

References CSeq_id::eTV_plain, NStr::Split(), CSeq_id::WhichInverseSeqId(), CSeq_id::x_IdentifyTypeVariant(), and CSeq_id::x_Init().

◆ size()

size_t SSeqIdRange::size ( void ) const

inline

Definition at line 983 of file Seq_id.hpp.

References SSeqIdRange::start, and SSeqIdRange::stop.

Referenced by SSeqIdRange::const_iterator::GetID().

◆ SSeqIdRange()

SSeqIdRange::SSeqIdRange	(	const CTempString &	s,
		TFlags	flags = `0`
	)

explicit

Definition at line 3598 of file Seq_id.cpp.

References SSeqIdRange::digits, SSeqIdRange::fAllowUnderscores, flags, isalpha(), isdigit(), n, NCBI_THROW, SSeqIdRange::prefix, CTempString::size(), SSeqIdRange::start, and SSeqIdRange::stop.

◆ StrictAdjustScore()

int CSeq_id::StrictAdjustScore ( int base_score ) const

inline

Definition at line 744 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::fRequireAccessions.

Referenced by CSeq_id::StrictBestRankScore(), CSeq_id::StrictBlastScore(), CSeq_id::StrictFastaAAScore(), CSeq_id::StrictFastaNAScore(), and CSeq_id::StrictTextScore().

◆ StrictBestRank()

static int CSeq_id::StrictBestRank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 787 of file Seq_id.hpp.

References kMax_Int.

◆ StrictBestRankScore()

int CSeq_id::StrictBestRankScore ( void ) const

inline

Definition at line 762 of file Seq_id.hpp.

References CSeq_id::BaseBestRankScore(), and CSeq_id::StrictAdjustScore().

◆ StrictBlastRank()

static int CSeq_id::StrictBlastRank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 793 of file Seq_id.hpp.

References kMax_Int.

◆ StrictBlastScore()

int CSeq_id::StrictBlastScore ( void ) const

inline

Definition at line 768 of file Seq_id.hpp.

References CSeq_id::BaseBlastScore(), and CSeq_id::StrictAdjustScore().

◆ StrictFastaAARank()

static int CSeq_id::StrictFastaAARank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 789 of file Seq_id.hpp.

References kMax_Int.

◆ StrictFastaAAScore()

int CSeq_id::StrictFastaAAScore ( void ) const

inline

Definition at line 764 of file Seq_id.hpp.

References CSeq_id::BaseFastaAAScore(), and CSeq_id::StrictAdjustScore().

◆ StrictFastaNARank()

static int CSeq_id::StrictFastaNARank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 791 of file Seq_id.hpp.

References kMax_Int.

◆ StrictFastaNAScore()

int CSeq_id::StrictFastaNAScore ( void ) const

inline

Definition at line 766 of file Seq_id.hpp.

References CSeq_id::BaseFastaNAScore(), and CSeq_id::StrictAdjustScore().

◆ StrictScore()

static int CSeq_id::StrictScore ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 785 of file Seq_id.hpp.

References kMax_Int.

◆ StrictTextScore()

int CSeq_id::StrictTextScore ( void ) const

inline

Definition at line 760 of file Seq_id.hpp.

References CSeq_id::BaseTextScore(), and CSeq_id::StrictAdjustScore().

◆ Swap()

void CSeq_id_Handle::Swap ( CSeq_id_Handle & idh )

inline

Definition at line 328 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, CSeq_id_Handle::m_Variant, swap(), and CConstRef< C, Locker >::Swap().

Referenced by sequpd::GetGoodSeqIdHandle().

◆ swap()

BEGIN_STD_SCOPE void swap	(	NCBI_NS_NCBI::objects::CSeq_id_Handle &	idh1,
		NCBI_NS_NCBI::objects::CSeq_id_Handle &	idh2
	)

inline

Definition at line 393 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::Swap().

◆ TextScore()

int CSeq_id::TextScore ( void ) const

inline

Definition at line 753 of file Seq_id.hpp.

References CSeq_id::AdjustScore(), and CSeq_id::BaseTextScore().

Referenced by CSeq_id::WorstRankScore().

◆ Unlock()

void CSeq_id_InfoLocker::Unlock ( const CSeq_id_Info * info ) const

inline

Definition at line 143 of file seq_id_handle.hpp.

References info, and CObjectCounterLocker::Unlock().

◆ Which()

CSeq_id::E_Choice CSeq_id_Handle::Which ( void ) const

inline

Definition at line 259 of file seq_id_handle.hpp.

References CSeq_id_Info::GetType(), and CSeq_id_Handle::m_Info.

Referenced by CLinkUtils::AddBlastProductLink(), CReadDispatcher::CannotProcess(), CannotProcess(), CSeq_id_Handle::CompareOrdered(), GetDescrType(), CWGSDataLoader_Impl::GetFileInfo(), CCSRABlobId::GetGeneralIdType(), GetId(), CCSRADataLoader_Impl::GetRecordsOnce(), CScope_Impl::GetTaxId(), GetWGSMasterSeq_id(), CValidError_bioseq::IsWp(), CId1Reader::LoadGiBlob_ids(), CPubseqReader::LoadGiHash(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CPubseqReader::LoadSeq_idAccVer(), CId1Reader::LoadSeq_idBlob_ids(), CId1Reader::LoadSeq_idSeq_ids(), CPubseqReader::LoadSeq_idSeq_ids(), CPubseqReader::LoadSequenceHash(), CSortableSeq_id::operator<(), s_LocIdType(), s_Match_id(), sx_GetReadId(), CSequenceUpdater::x_ChangeIDInFeature(), CGenbankGatherer::x_DoSingleSection(), CDBSourceItem::x_GatherInfo(), CUpdateSeq_Input::x_ReadAccession(), and CDeflineGenerator::x_SetFlags().

◆ WhichFastaTag()

const char * CSeq_id::WhichFastaTag ( E_Choice choice )

static

Converts a choice to a FASTA tag, with no trailing vertical bar.

Definition at line 609 of file Seq_id.cpp.

References ArraySize(), kEmptyCStr, and s_TextId.

◆ WhichInverseSeqId()

CSeq_id::E_Choice CSeq_id::WhichInverseSeqId ( const CTempString & SeqIdCode )

static

Converts a string to a choice, no need to require a member.

Definition at line 599 of file Seq_id.cpp.

References CSeq_id_Base::e_not_set.

Referenced by CSeq_id::ParseIDs(), s_CheckForFastaTag(), s_ParseFastaIdString(), s_SeqDB_EndOfFastaID(), CSeq_id::Set(), and CSeq_id::x_Init().

◆ WorstRank()

static int CSeq_id::WorstRank ( const CRef< CSeq_id > & id )

inlinestatic

Definition at line 776 of file Seq_id.hpp.

References CSeq_id::Score().

Referenced by BOOST_AUTO_TEST_CASE(), ChangeSeqId(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CBlastDBExtractor::ExtractAccession(), CBlastDBExtractor::ExtractSeqId(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CBioseq::GetLabel(), CAlignFormatUtil::GetLinkoutUrl(), CAlignFormatUtil::GetSeqLinkoutInfo(), s_AddOtherRelatedInfoLinks(), s_GetBestIDForURL(), s_GetFullLinkoutUrl(), s_ModifySeqAlnWithFilteredSeqIDs(), s_SetCloneInfo(), CIgBlastTabularInfo::SetAirrFormatData(), WorstRank_SeqIdHandle(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CShowBlastDefline::x_FillDeflineAndId(), CDisplaySeqalign::x_FillSeqid(), CAlnGraphic::x_GetAlnInfo(), CDisplaySeqalign::x_GetDumpgnlLink(), CDisplaySeqalign::x_InitAlignParams(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CDisplaySeqalign::x_PrintDefLine(), COligoSpecificityCheck::x_SavePrimerInfo(), CBlastDBExtractor::x_SetGi2AccMap(), and CBlastDBExtractor::x_SetGi2SeqIdMap().

◆ WorstRankScore()

int CSeq_id::WorstRankScore ( void ) const

inline

Definition at line 755 of file Seq_id.hpp.

References CSeq_id::TextScore().

◆ WriteAsFasta() [1/2]

CNcbiOstream & CSeq_id::WriteAsFasta	(	CNcbiOstream &	ostr,
		const CBioseq &	bioseq
	)

static

Write a bioseq's IDs in FASTA format.

Parameters

ostr	Stream to write to
bioseq	Bioseq to get IDs from

Returns: The stream that was passed in, after all writes occurred

Definition at line 2347 of file Seq_id.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_id::FastaAARank(), CSeq_id::FastaNARank(), FindBestChoice(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), CSeq_id_Base::IsGi(), ITERATE, CRef< C, Locker >::NotEmpty(), and CSeq_id::WriteAsFasta().

◆ WriteAsFasta() [2/2]

void CSeq_id::WriteAsFasta ( ostream & out ) const

virtual

Implement serializable interface.

Definition at line 2164 of file Seq_id.cpp.

References CSeq_id_Base::e_MaxChoice, CSeq_id_Base::e_not_set, GetId(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::IsPatent(), CSeq_id_Base::IsSwissprot(), out(), s_TextId, CSeq_id_Base::Which(), and CSeq_id::x_WriteContentAsFasta().

Referenced by CSeq_id::AsFastaString(), CSeq_id_Handle::AsString(), CSeq_id::GetStringDescr(), operator<<(), s_WriteGnlAndAcc(), CSeq_id::WriteAsFasta(), CDeflineProcess::x_FastaSeqIdWrite(), CSeqVectorProcess::x_FsaSeqIdWrite(), CTitleProcess::x_TitleSeqIdWrite(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), and CFastaOstream::x_WriteAsFasta().

◆ x_GetInfo()

const CSeq_id_Info* CSeq_id_Handle::x_GetInfo ( void ) const

inline

Definition at line 338 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info.

◆ x_GetTree() [1/3]

CSeq_id_Which_Tree & CSeq_id_Mapper::x_GetTree ( const CSeq_id & id )

inlineprivate

Definition at line 171 of file seq_id_mapper.hpp.

References CSeq_id_Base::Which(), and CSeq_id_Mapper::x_GetTree().

◆ x_GetTree() [2/3]

CSeq_id_Which_Tree & CSeq_id_Mapper::x_GetTree ( const CSeq_id_Handle & idh )

inlineprivate

Definition at line 97 of file seq_id_mapper.cpp.

References _ASSERT, CSeq_id_Base::e_Gi, CSeq_id_Base::e_not_set, CSeq_id_Info::GetTree(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Info, CSeq_id_Mapper::m_Trees, and type.

◆ x_GetTree() [3/3]

CSeq_id_Which_Tree & CSeq_id_Mapper::x_GetTree ( CSeq_id::E_Choice type )

inlineprivate

Definition at line 163 of file seq_id_mapper.hpp.

References _ASSERT, CSeq_id_Mapper::m_Trees, and type.

Referenced by CSeq_id_Mapper::GetHandle(), CSeq_id_Mapper::GetMatchingHandles(), CSeq_id_Mapper::GetReverseMatchingHandles(), CSeq_id_Info::GetTree(), CSeq_id_Mapper::HaveMatchingHandles(), CSeq_id_Mapper::HaveReverseMatch(), CSeq_id_Mapper::x_GetTree(), CSeq_id_Mapper::x_IsBetter(), and CSeq_id_Mapper::x_Match().

◆ x_IdentifyAccession()

CSeq_id::EAccessionInfo CSeq_id::x_IdentifyAccession	(	const CTempString &	main_acc,
		TParseFlags	flags,
		bool	has_version
	)

staticprivate

◆ x_IdentifyTypeVariant()

CSeq_id::ETypeVariant CSeq_id::x_IdentifyTypeVariant	(	CSeq_id::E_Choice	type,
		const CTempString &	str
	)

inlinestaticprivate

Definition at line 2439 of file Seq_id.cpp.

References CSeq_id_Base::e_Patent, CSeq_id_Base::e_Swissprot, NStr::EqualNocase(), CSeq_id::eTV_pgp, CSeq_id::eTV_plain, CSeq_id::eTV_tr, and str().

Referenced by CSeq_id::ParseIDs(), and CSeq_id::Set().

◆ x_Init()

CSeq_id::E_Choice CSeq_id::x_Init	(	list< CTempString > &	fasta_pieces,
		E_Choice	type,
		ETypeVariant	tv
	)

private

◆ x_IsBetter()

bool CSeq_id_Mapper::x_IsBetter	(	const CSeq_id_Handle &	h1,
		const CSeq_id_Handle &	h2
	)

private

Definition at line 301 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::IsBetterVersion(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Handle::IsBetter().

◆ x_Match()

bool CSeq_id_Mapper::x_Match	(	const CSeq_id_Handle &	h1,
		const CSeq_id_Handle &	h2
	)

private

Definition at line 288 of file seq_id_mapper.cpp.

References CSeq_id_Which_Tree::Match(), and CSeq_id_Mapper::x_GetTree().

Referenced by CSeq_id_Handle::MatchesTo().

◆ x_RemoveLastLock()

void CSeq_id_Info::x_RemoveLastLock ( void ) const

protected

Definition at line 89 of file seq_id_handle.cpp.

References CSeq_id_Which_Tree::DropInfo(), and CSeq_id_Info::GetTree().

Referenced by CSeq_id_Info::RemoveLock().

◆ x_SetAccession()

const string & SSeqIdRange::const_iterator::x_SetAccession ( void ) const

private

Definition at line 3675 of file Seq_id.cpp.

Referenced by SSeqIdRange::const_iterator::operator*(), and SSeqIdRange::const_iterator::operator->().

◆ x_WriteContentAsFasta()

void CSeq_id::x_WriteContentAsFasta ( ostream & out ) const

private

Definition at line 2186 of file Seq_id.cpp.

Referenced by CSeq_id::GetLabel(), and CSeq_id::WriteAsFasta().

◆ ~CSeq_id()

CSeq_id::~CSeq_id ( void )

virtual

Destructor.

Definition at line 145 of file Seq_id.cpp.

◆ ~CSeq_id_Info()

CSeq_id_Info::~CSeq_id_Info ( void )

Definition at line 70 of file seq_id_handle.cpp.

References _ASSERT, and CSeq_id_Info::m_LockCounter.

◆ ~CSeq_id_Mapper()

CSeq_id_Mapper::~CSeq_id_Mapper ( void )

virtual

Definition at line 87 of file seq_id_mapper.cpp.

References _ASSERT, ITERATE, CSeq_id_Mapper::m_Trees, and s_ResetInstance().

Variable Documentation

◆ acc_info

CSeq_id::EAccessionInfo SSeqIdRange::acc_info

mutable

Definition at line 990 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::GetID().

◆ digits

int SSeqIdRange::digits

Definition at line 989 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::GetID(), and SSeqIdRange::SSeqIdRange().

◆ kMaxAccessionLength

const size_t CSeq_id::kMaxAccessionLength = 30

static

Definition at line 844 of file Seq_id.hpp.

◆ kMaxGeneralDBLength

const size_t CSeq_id::kMaxGeneralDBLength = 20

static

Definition at line 842 of file Seq_id.hpp.

Referenced by CValidError_bioseq::ValidateSeqId().

◆ kMaxGeneralTagLength

const size_t CSeq_id::kMaxGeneralTagLength = 50

static

Definition at line 843 of file Seq_id.hpp.

Referenced by CValidError_bioseq::ValidateSeqId().

◆ kMaxLocalIDLength

const size_t CSeq_id::kMaxLocalIDLength = 50

static

ID length restrictions.

Definition at line 841 of file Seq_id.hpp.

Referenced by CSeq_id::CheckLocalID(), and CValidError_bioseq::ValidateSeqId().

◆ m_Accession

string SSeqIdRange::const_iterator::m_Accession

mutableprivate

Definition at line 974 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::operator*(), SSeqIdRange::const_iterator::operator++(), SSeqIdRange::const_iterator::operator+=(), SSeqIdRange::const_iterator::operator--(), SSeqIdRange::const_iterator::operator-=(), and SSeqIdRange::const_iterator::operator->().

◆ m_IdMapMutex

CMutex CSeq_id_Mapper::m_IdMapMutex

mutableprivate

Definition at line 144 of file seq_id_mapper.hpp.

◆ m_Info

CConstRef<CSeq_id_Info, CSeq_id_InfoLocker> CSeq_id_Handle::m_Info

private

Definition at line 347 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::CompareOrdered(), CSeq_id_Handle::GetHash(), CSeq_id_Handle::GetMapper(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::GetSeqIdOrNull(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::operator!=(), CSeq_id_Handle::operator<(), CSeq_id_Handle::operator==(), CSeq_id_Handle::Reset(), CSeq_id_Handle::Swap(), CSeq_id_Handle::Which(), CSeq_id_Handle::x_GetInfo(), and CSeq_id_Mapper::x_GetTree().

◆ m_LockCounter

atomic<Uint8> CSeq_id_Info::m_LockCounter {0}

mutableprotected

Definition at line 119 of file seq_id_handle.hpp.

Referenced by CSeq_id_Info::AddLock(), CSeq_id_Info::IsLocked(), CSeq_id_Info::RemoveLock(), and CSeq_id_Info::~CSeq_id_Info().

◆ m_Mapper

CRef<CSeq_id_Mapper> CSeq_id_Info::m_Mapper

mutableprotected

Definition at line 122 of file seq_id_handle.hpp.

Referenced by CSeq_id_Info::GetMapper().

◆ m_Number

int SSeqIdRange::const_iterator::m_Number

private

Definition at line 973 of file Seq_id.hpp.

◆ m_Packed

TPacked CSeq_id_Handle::m_Packed

private

Definition at line 348 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::GetHash(), CSeq_id_Handle::GetPacked(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::IsPacked(), CSeq_id_Handle::operator!=(), CSeq_id_Handle::operator<(), CSeq_id_Handle::operator==(), CSeq_id_Handle::Reset(), and CSeq_id_Handle::Swap().

◆ m_Range

const SSeqIdRange* SSeqIdRange::const_iterator::m_Range

private

Definition at line 972 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::GetID(), SSeqIdRange::const_iterator::operator+(), SSeqIdRange::const_iterator::operator-(), and SSeqIdRange::const_iterator::operator=().

◆ m_Seq_id

CConstRef<CSeq_id> CSeq_id_Info::m_Seq_id

protected

Definition at line 121 of file seq_id_handle.hpp.

◆ m_Seq_id_Type

atomic<CSeq_id::E_Choice> CSeq_id_Info::m_Seq_id_Type

protected

Definition at line 120 of file seq_id_handle.hpp.

Referenced by CSeq_id_Info::GetType().

◆ m_Trees

TTrees CSeq_id_Mapper::m_Trees

private

Definition at line 143 of file seq_id_mapper.hpp.

Referenced by CSeq_id_Mapper::CSeq_id_Mapper(), CSeq_id_Mapper::Dump(), CSeq_id_Mapper::GetGiHandle(), CSeq_id_Mapper::GetMatchingHandles(), CSeq_id_Mapper::GetMatchingHandlesStr(), CSeq_id_Mapper::GetReverseMatchingHandles(), CSeq_id_Mapper::HaveMatchingHandles(), CSeq_id_Mapper::HaveReverseMatch(), CSeq_id_Mapper::x_GetTree(), and CSeq_id_Mapper::~CSeq_id_Mapper().

◆ m_Variant

TVariant CSeq_id_Handle::m_Variant

private

Definition at line 349 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::GetVariant(), CSeq_id_Handle::IsSetVariant(), CSeq_id_Handle::Reset(), and CSeq_id_Handle::Swap().

◆ prefix

string SSeqIdRange::prefix

Definition at line 986 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::GetID(), and SSeqIdRange::SSeqIdRange().

◆ start

int SSeqIdRange::start

Definition at line 987 of file Seq_id.hpp.

Referenced by SSeqIdRange::size(), and SSeqIdRange::SSeqIdRange().

◆ stop

int SSeqIdRange::stop

Definition at line 988 of file Seq_id.hpp.

Referenced by SSeqIdRange::end(), SSeqIdRange::size(), and SSeqIdRange::SSeqIdRange().

Friends

◆ CSeq_id_Handle

friend class CSeq_id_Handle

friend

Definition at line 120 of file seq_id_mapper.hpp.

◆ CSeq_id_Info

friend class CSeq_id_Info

friend

Definition at line 121 of file seq_id_mapper.hpp.

◆ CSeq_id_Mapper

friend class CSeq_id_Mapper

friend

Definition at line 343 of file seq_id_handle.hpp.

◆ CSeq_id_Which_Tree [1/2]

friend class CSeq_id_Which_Tree

friend

Definition at line 115 of file seq_id_handle.hpp.

◆ CSeq_id_Which_Tree [2/2]

friend class CSeq_id_Which_Tree

friend

Definition at line 344 of file seq_id_handle.hpp.

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Friends

Detailed Description

Macro Definition Documentation

◆ NCBI_ACC

Typedef Documentation

◆ difference_type

◆ iterator_category

◆ pointer

◆ reference

◆ TComposeOSLTFlags

◆ TErrorFlags

◆ TFlags

◆ TLabelFlags

◆ TMatches

◆ TPacked [1/2]

◆ TPacked [2/2]

◆ Tparent

◆ TParseFlags

◆ TSeq_id_HandleSet

◆ TSeqIdHandles

◆ TTrees

◆ TVariant [1/2]

◆ TVariant [2/2]

◆ value_type

Enumeration Type Documentation

◆ E_SIC

◆ EAccessionInfo

◆ EAdjustScoreFlags

◆ EAllowWeakMatch

◆ EComposeOSLTFlags

◆ EDumpDetails

◆ EErrCode

◆ EErrorFlags

◆ EFastaAsTypeAndContent

◆ EFlags

◆ ELabelFlags

◆ ELabelType

◆ EMaxScore

◆ EParseFlags

◆ ESNPScaleLimit

◆ EStringFormat

◆ ETypeVariant

Function Documentation

◆ AddLock()

◆ AdjustScore()

◆ AsFastaString()

◆ Assign()

◆ AsString()

◆ AvoidGi()

◆ BaseBestRankScore()

◆ BaseBlastScore()

◆ BaseFastaAAScore()

◆ BaseFastaNAScore()

◆ BaseTextScore()

◆ BaseWorstRankScore()

◆ begin()

◆ BestRank()

◆ BestRankScore()

◆ BlastRank()

◆ BlastScore()

◆ CheckLocalID()

◆ Compare()

◆ CompareOrdered() [1/3]

◆ CompareOrdered() [2/3]

◆ CompareOrdered() [3/3]

◆ ComposeOSLT()

◆ const_iterator() [1/3]

◆ const_iterator() [2/3]

◆ const_iterator() [3/3]

◆ CSeq_id() [1/8]

◆ CSeq_id() [2/8]

◆ CSeq_id() [3/8]

◆ CSeq_id() [4/8]

◆ CSeq_id() [5/8]