NCBI C++ ToolKit
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Seq-id Management
+ 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_HandleCSeq_id_Handle::TMatches
 
typedef set< CSeq_id_HandleTSeq_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_HandleCSeq_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 stringSSeqIdRange::const_iterator::pointer
 
typedef stringSSeqIdRange::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_idCSeq_id_Info::GetSeqId (void) const
 
virtual CConstRef< CSeq_idCSeq_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_MapperCSeq_id_Info::GetMapper (void) const
 
CSeq_id_Which_TreeCSeq_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_InfoCSeq_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_idCSeq_id_Handle::GetSeqId (void) const
 
CConstRef< CSeq_idCSeq_id_Handle::GetSeqIdOrNull (void) const
 
CSeq_id_MapperCSeq_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_InfoCSeq_id_Handle::x_GetInfo (void) const
 
template<>
CConstRef< CSeq_idGet_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)
 
CNcbiOstreamoperator<< (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_MapperCSeq_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_idCSeq_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_TreeCSeq_id_Mapper::x_GetTree (CSeq_id::E_Choice type)
 
CSeq_id_Which_TreeCSeq_id_Mapper::x_GetTree (const CSeq_id &id)
 
CSeq_id_Which_TreeCSeq_id_Mapper::x_GetTree (const CSeq_id_Handle &idh)
 
 CSeq_id_Mapper::CSeq_id_Mapper (const CSeq_id_Mapper &)
 
CSeq_id_MapperCSeq_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_idCSeq_id::Set (const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)
 Reassign based on flat specifications; arguments interpreted as with constructors. More...
 
CSeq_idCSeq_id::Set (const CDbtag &tag, bool set_as_general=true)
 
CSeq_idCSeq_id::Set (E_Choice the_type, TIntId int_seq_id)
 
CSeq_idCSeq_id::Set (E_Choice the_type, const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr)
 
CSeq_idCSeq_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_idCSeq_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 CNcbiOstreamCSeq_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_idCSeq_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_iteratorSSeqIdRange::const_iterator::operator= (const const_iterator &it)
 
string SSeqIdRange::const_iterator::operator* (void) const
 
const stringSSeqIdRange::const_iterator::operator-> (void) const
 
string SSeqIdRange::const_iterator::operator[] (int n) const
 
CRef< CSeq_idSSeqIdRange::const_iterator::GetID (void) const
 
const_iteratorSSeqIdRange::const_iterator::operator++ (void)
 
const_iterator SSeqIdRange::const_iterator::operator++ (int)
 
const_iteratorSSeqIdRange::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_iteratorSSeqIdRange::const_iterator::operator+= (int n)
 
const_iteratorSSeqIdRange::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 stringSSeqIdRange::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_idGet_ConstRef_Seq_id (TId &id)
 Dummy convertor for container search functions. More...
 
template<class container >
CConstRef< CSeq_idGetSeq_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_idFindTextseq_id (const container &ids)
 Return text seq-id from id list if exists, return 0 otherwise. More...
 

Variables

atomic< Uint8CSeq_id_Info::m_LockCounter {0}
 
atomic< CSeq_id::E_ChoiceCSeq_id_Info::m_Seq_id_Type
 
CConstRef< CSeq_idCSeq_id_Info::m_Seq_id
 
CRef< CSeq_id_MapperCSeq_id_Info::m_Mapper
 
CConstRef< CSeq_id_Info, CSeq_id_InfoLockerCSeq_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 SSeqIdRangeSSeqIdRange::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

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

Definition at line 910 of file Seq_id.hpp.

◆ reference

Definition at line 911 of file Seq_id.hpp.

◆ TComposeOSLTFlags

Definition at line 823 of file Seq_id.hpp.

◆ TErrorFlags

Definition at line 113 of file Seq_id.hpp.

◆ TFlags

binary OR of EFlags

Definition at line 899 of file Seq_id.hpp.

◆ TLabelFlags

Definition at line 625 of file Seq_id.hpp.

◆ TMatches

Definition at line 241 of file seq_id_handle.hpp.

◆ TPacked [1/2]

Definition at line 71 of file seq_id_handle.hpp.

◆ TPacked [2/2]

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

Definition at line 104 of file Seq_id.hpp.

◆ 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

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]

Definition at line 72 of file seq_id_handle.hpp.

◆ TVariant [2/2]

Definition at line 161 of file seq_id_handle.hpp.

◆ value_type

Definition at line 908 of file Seq_id.hpp.

Enumeration Type Documentation

◆ 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

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

Enumerator
fRequireAccessions 

Definition at line 736 of file Seq_id.hpp.

◆ EAllowWeakMatch

Enumerator
eNoWeakMatch 
eAllowWeakMatch 

Definition at line 151 of file seq_id_handle.hpp.

◆ 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

Enumerator
eCountTotalBytes 
eDumpTotalBytes 
eDumpStatistics 
eDumpAllIds 

Definition at line 108 of file seq_id_mapper.hpp.

◆ 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

Enumerator
fNoError 
fEmptyId 
fInvalidChar 
fExceedsMaxLength 

Definition at line 107 of file Seq_id.hpp.

◆ EFastaAsTypeAndContent

Tag for method variants that would otherwise be ambiguous.

Enumerator
eFasta_AsTypeAndContent 

Definition at line 116 of file Seq_id.hpp.

◆ EFlags

Enumerator
fAllowUnderscores 

Allow prefixes to contain underscores.

Definition at line 896 of file Seq_id.hpp.

◆ 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

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

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

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

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

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

◆ 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(), 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(), PrintFastaUnaligned(), CBlastFormat::PrintOneResultSet(), PrintSAMUnaligned(), PrintTabularUnaligned(), 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.

References CSerialObject::Assign(), 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::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSerialObject::GetThisTypeInfo(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), CSeq_id_Base::Reset(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CSeq_id_Base::Which(), and x_Assign().

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(), CGff3LocationRecord::CGff3LocationRecord(), 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(), CPSGDataLoader_Impl::x_GetBioseqAndBlobInfo(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CPSGDataLoader_Impl::x_GetBioseqInfo(), CPSGDataLoader_Impl::x_GetIpgTaxId(), 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(), CPSGDataLoader_Impl::x_ProcessBlobReply(), 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

◆ BestRankScore()

int CSeq_id::BestRankScore ( void  ) const
inline

◆ 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.

References CanCmpAcc(), NStr::CompareNocase(), CSeq_id_Base::e_Ddbj, CSeq_id::e_DIFF, CSeq_id_Base::e_Embl, CSeq_id::e_error, 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::e_NO, 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::e_YES, CDbtag_Base::GetDb(), CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), CObject_id::Match(), CPatent_seq_id::Match(), CPDB_seq_id::Match(), CSeq_id::Match(), CTextseq_id::Match(), and CSeq_id_Base::Which().

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

◆ CompareOrdered() [2/3]

int CSeq_id_Handle::CompareOrdered ( const CSeq_id_Handle id) const

◆ 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

◆ 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_idsOSLT strings for the secondary ids
parse_flagsFlags 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.

References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::CanGetName(), 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_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id::fAllowLocalId, CSeq_id::fGpipeAddSecondary, CAliasBase< TPrim >::Get(), CTextseq_id_Base::GetAccession(), CId_pat_Base::C_Id::GetApp_number(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPatent_seq_id_Base::GetCit(), CId_pat_Base::GetCountry(), CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), GetId(), CId_pat_Base::GetId(), CObject_id_Base::GetId(), CSeq_id_Base::GetLocal(), CPDB_seq_id_Base::GetMol(), CTextseq_id_Base::GetName(), CId_pat_Base::C_Id::GetNumber(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CPatent_seq_id_Base::GetSeqid(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CObject_id_Base::IsId(), CId_pat_Base::C_Id::IsNumber(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), NStr::NumericToString(), string, suffix, NStr::ToUpper(), and CSeq_id_Base::Which().

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

◆ 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
tagInput dbtag.
set_as_generalWhether 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_idInput ID, preferably FASTA-style.
flagsHow 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_typeType of Seq_id to construct
acc_inPrimary string value – normally accession, overridden as country for patents, database for "general" IDs, molecule ID for PDB IDs.
name_inAdditional string value – normally name/locus, overridden as (application) number for patents, tag for "general" IDs, chain ID for PDB.
versionNumeric value – normally version number, overriden as sequence number for patents.
release_inHistorically 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 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_typeType of Seq-id (normally e_Gi)
int_seq_idNumeric 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_typeType of Seq_id to construct
the_contentFASTA-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

◆ 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

◆ 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)

◆ 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

◆ 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)

◆ 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

◆ 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().

Referenced by CSeqsRange::Add(), CCDDBlobCache::Add(), CHandleRangeMap::AddLocation(), CHandleRangeMap::AddRange(), CSAM_CIGAR_Formatter::AddRow(), SAlignment_Segment::AddRow(), CMasterSeqSegments::AddSegmentIds(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CBAMDataLoader_Impl::AddSrzDef(), CSeq_id_Descr::Assign(), CBedFeatureRecord::AssignLocation(), BioseqHandleFromLocation(), BOOST_AUTO_TEST_CASE(), CGencollIdMapper::CanMeetSpec(), CBAMBlobId::CBAMBlobId(), CBamFileInfo::CBamFileInfo(), CBioseq_SplitInfo::CBioseq_SplitInfo(), CCachedSequence::CCachedSequence(), CCmdChangeBioseqId::CCmdChangeBioseqId(), CCmdRemoveBioseqId::CCmdRemoveBioseqId(), CCSraDb_Impl::CCSraDb_Impl(), CCSraRefSeqIterator::CCSraRefSeqIterator(), CIdMapperScope::CIdMapperScope(), CIdRangeMap::CIdRangeMap(), IProjectViewFactory::CombineInputObjects(), IProjectViewFactory::CombineObjects(), CTableViewWithTextViewNav::CombineObjects(), CBioseq_Handle::ContainsSegment(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), Convert_Seq_align_Seq_id(), Convert_Seq_annot_Seq_id(), Convert_Seq_annot_Seq_loc_All(), Convert_Seq_annot_Seq_loc_TotalRange(), Convert_Seq_entry_Seq_id(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertInterval(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPoint(), CBlobSplitterImpl::CopySkeleton(), CSparseGraph::CreateCompoundID(), CGC_Assembly::CreateIndex(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSNPDb_Impl::CSNPDb_Impl(), CVDBGraphBlobId::CVDBGraphBlobId(), CVDBGraphDb_Impl::CVDBGraphDb_Impl(), CAdvancedAlignCleanup::DivideByQuerySubjectPairs(), DoImportFTable(), CMAViewManager::DoTransition(), CScope::Exists(), ExtractExtraIds(), FindCompartments(), FindLatestSequence(), sequpd::FindMatches(), CCSRABlobId::FromString(), CSNPBlobId::FromString(), fta_add_hist(), g_DoesNotReferencePrimary(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CFastaIdHandler::GenerateID(), CScore_OverlapBoth::Get(), CScore_OrdinalPos::Get(), CScore_BlastRatio::Get(), CIdResolver::GetAccessionVersion(), CCSRADataLoader_Impl::GetAccVerOnce(), CWGSDataLoader_Impl::GetAccVerOnce(), GetAlignmentForRna(), CLDS2_Database::GetAnnots(), GetBestCdsForMrna(), CMacroBioData_BioSourceIter::GetBestDescr(), CMacroBioData_PubdescIter::GetBestDescr(), CAlnWriter::GetBestId(), CGenbankIdResolve::GetBestId(), GetBestMrnaForCds(), CTotalRangeSynonymMapper::GetBestSynonym(), CDummySynonymMapper::GetBestSynonym(), CDefaultSynonymMapper::GetBestSynonym(), CTSE_Handle::GetBioseqHandle(), CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CScoreBuilder::GetBlastScoreProtToNucl(), CScoreBuilder::GetBlastScoreStd(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CSeqUtils::GetChrGI(), variation::GetFocusLocusIDs(), CGffIdGenerator::GetGffSourceId(), GetGIForSeqId(), CSeq_id_Handle::GetGiHandle(), GetId(), GetIdHandle(), CSeqTableLocColumns::GetIdHandle(), CScope::GetIds(), CHugeAsnDataLoader::GetIds(), CCSRADataLoader_Impl::GetIdsOnce(), CWGSDataLoader_Impl::GetIdsOnce(), CScope::GetLabel(), CMappedFeat::GetLocationId(), CSeq_feat_Handle::GetLocationId(), CSeq_id::GetMatchingIds(), CSeq_id::GetMatchingTextseqIds(), CTableDataBioTreeContainer::GetObjectValue(), CBioseqContext::GetPreferredSynonym(), CWGSResolver_DL::GetPrefixes(), CRemoveFeaturesDlg::GetProductId(), CMappedFeat::GetProductId(), CSeq_feat_Handle::GetProductId(), CAdvancedAlignCleanup::GetProsplignCompartments(), CMTTestThread::GetRandomId(), CSeqUtils::GetRangeCollection(), CMaskedRangeSet::GetRanges(), CSeqMap_CI::GetRefSeqid(), CGBDataLoader::GetSatSatkey(), CViewGraphic::GetSelection(), CAsnCacheStore::GetSeqIds(), CVDBGraphDb_Impl::GetSeqInfoAtRow(), GetSeqsStatus(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CScope::GetSequenceHash(), CSeq_loc_Mapper_Base::GetSequenceLength(), CScope::GetSequenceLength(), CScope::GetSequenceState(), CScope::GetSequenceType(), CIdMapperApp::GetSourceHandle(), CAdvancedAlignCleanup::GetSplignCompartments(), CScope::GetSynonyms(), CLDS2_Database::GetSynonyms(), CGencollIdMapper::GetSynonyms(), CScope::GetTaxId(), TaxClient::GetTaxIDForSeqId(), CGuiObjectInfoSeq_align::GetToolTip(), variation::GetUniquePrimaryTranscriptId(), GetWGSMasterSeq_id(), CSeq_loc_Mapper_Base::GetWidthById(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CGencollIdMapper::Guess(), CAsn2FastaApp::HandleSeqEntry(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CSNPClient::HaveValidSeq_id(), CIdMapperConfig::Initialize(), CMPCrossAlignView::InitView(), CWinMaskUtil::CIdSet_SeqId::insert(), CMaskedRangeSet::Insert(), CSeq_loc_I::InsertEmpty(), CSeq_loc_I::InsertInterval(), CSeq_loc_I::InsertPoint(), CSeq_loc_I::InsertWhole(), IsSameBioseq(), IsSequenceFetchable(), CBioseq_Handle::IsSynonym(), CSplitParser::Load(), CBamRefSeqInfo::LoadAlignChunk(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CCacheReader::LoadSeq_idAccVer(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CBamRefSeqInfo::LoadSeqChunk(), CBlobSplitterImpl::MakeID2Chunk(), MakeSubjectScores(), CMakeBadSpecificHostTable::MakeTable(), CIdMapper::Map(), CGencollIdMapperAdapter::Map(), CGencollIdMapper::Map(), CIdMapper::MapObject(), CAlignFilter::Match(), CSelectionEvent::MatchLocWithId(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), CCdsToMatPeptide::MergeConvert(), CMAViewManager::NeedAnchorPanel(), CProcessor::OffsetId(), SrcEditDialog::OneRowOk(), CAlignSort::SAlignExtractor::operator()(), CPsiBlastAlignmentProcessor::operator()(), variation::SFastLocSubtract::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), operator<<(), CSeqTableLocColumns::ParseDefaults(), CFastaReader::ParseDefLine(), CTabularFormatter_AllSeqIds::Print(), CTabularFormatter_SeqId::Print(), CTabularFormatter_Defline::Print(), CTabularFormatter_ProtRef::Print(), CTabularFormatter_AssemblyInfo::Print(), CTabularFormatter_PatchType::Print(), CProcessor_ExtAnnot::Process(), CSplitCacheApp::ProcessSeqId(), PsgIdToHandle(), CGlimmerReader::Read(), CSeqIdChunkFile::Read(), CCacheReader::ReadSeq_ids(), CSeq_entry::ReassignConflictingIds(), CCachedSequence::RegisterIds(), CScope::RemoveFromHistory(), CBioseq_Info::RemoveId(), CGBDocument::ReplaceGiSeqIds(), ReplaceWellknownSeqs(), CFastaIdsResolver::ResolveSeqId(), CMergeyApp::Run(), CFeatCompareJob_Align::Run(), CAgpFastaComparator::Run(), CTestCompartApplication::Run(), CAsnCacheTestApplication::Run(), CPrimeCacheApplication::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), CTestBMApp::Run(), RunNIterationsWithoutConverging(), s_CollectSeqIds(), s_Convert(), s_DumpSequences_wRange(), s_ExtractSeqidsAndRanges(), s_FindGaps(), s_FixIntervalProtToCds(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_IsVirtualLocation(), s_IsVirtualSeqInt(), s_Match_id(), s_ParseId< CSeq_id_Handle >(), s_ReadIdsFromFile(), s_Render_SeqAlign(), s_Seq_align_Seq_loc(), s_SeqAlignToXMLHit(), s_TestForOverlapEx(), CAlignCompare::SAlignment::SAlignment(), CConversionResultPanel::SetObjects(), CPhyTreeCalc::SetQuery(), CSeq_loc_I::SetSeq_id(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CGridTableSeqIds::SetValue(), sGenerateFields(), CLDS2_Seq_id_Hook::SkipObject(), CLDS2_AnnotType_Hook::SkipObject(), SortAndFetchSeqData(), CIdMapperConfig::SourceHandle(), StrippedAccVer(), sx_MakeUniqueId(), sx_ProcessId(), CIdMapperConfig::TargetHandle(), CMacroFunction_UpdateProteinSeqs::TheFunction(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_ApplyRNA::TheFunction(), CMacroFunction_ApplyGene::TheFunction(), CMacroFunction_ApplyOtherFeature::TheFunction(), UpdateOrgInformation(), CScore_OverlapBoth::UpdateState(), CAsnvalThreadState::ValidateAsync(), CFlatSeqLoc::x_Add(), CIdMapperGCAssembly::x_AddAccessionMapping(), CIdMapperGCAssembly::x_AddAliasMappings(), CSeq_loc_Mapper_Base::x_AddConversion(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddQualProteinId(), CFeatureItem::x_AddQualsRna(), CGencollIdMapper::x_AddSeqToMap(), CDBSourceItem::x_AddSPBlock(), CIdMapperGCAssembly::x_AddUnversionedMapping(), x_ApplyCmd(), CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly(), CBioseq_Info::x_CalcBioseqLength(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CSeq_id_Resolver::x_Create(), CSeq_id_Resolver__CCDS::x_Create(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CImportFeatTable::x_CreateCommand(), CBLASTSeqToolJob::x_CreateProjectItems(), CMergeAlignmentsJob::x_CreateProjectItems(), CComponentSearchJob::x_DoSearch(), CSGSegmentsSeqIDJob::x_Execute(), CPrimeCacheApplication::x_ExtractAndIndex(), CPrimeCacheApplication::x_ExtractDelta(), CGencollIdMapper::x_FindChromosomeSequence(), x_FindLatestSequence(), CImportFeatTable::x_FindLocalBioseq_Handle(), CGencollIdMapper::x_FindParentSequence(), CAlignFilter::x_FuncCall(), CDBSourceItem::x_GatherInfo(), CReportEntry::x_GetAdjustment(), CSeqMap::x_GetBioseqInfo(), x_GetCDDIds(), CCreateGeneModelTask::x_GetCommand(), CImportFeatTable::x_GetFixedId(), CAlnTableDS::x_GetNumSeqs(), CAlignFilter::x_GetRegionMap(), CCommonComponentScorer::x_GetSeqHistCompList(), CMacroBioData_SeqdescIter::x_GetSeqId(), CScope_Impl::x_GetSynonyms(), variation::CVariationUtil::CCdregionIndex::x_Index(), CSeq_align_Mapper_Base::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CIdMapperNumAssembly::x_InitializeMapping(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CWGSFileInfo::x_InitMasterDescr(), CGencollIdMapper::x_IsExactIdInAssembly(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CSeq_loc_Mapper_Base::x_IsSynonym(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), CSplign::x_LoadSequence(), CTreeAlignMerger::x_MakeMergeableGroups(), CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CPhyTreeFormatter::x_MarkLeavesBySeqId(), CPSGS_SNPProcessor::x_OnSeqIdResolveFinished(), CLDS2_Manager::x_ParseFile(), CGC_Assembly_Parser::x_ParseGCSequence(), x_ParseLocalCDDEntryId(), CSplitParser::x_ParseLocation(), CNgAlignApp::x_PrintNoHitList(), CGenBankLoadOptionPanel::x_ProccessText(), CPSGS_SNPProcessor::x_ProcessAnnotationRequest(), CProSplignJob::x_ProcessCompartment(), CId2ReaderBase::x_ProcessEmptyReply(), CId2ReaderBase::x_ProcessGetBlobId(), CId2ReaderBase::x_ProcessGetSeqId(), CId2ReaderBase::x_ProcessGetSeqIdSeqId(), CSplignApp::x_ProcessPair(), CPSGS_CDDProcessor::x_ProcessResolveRequest(), CAlignFilter::x_Query_Op(), CAltValidator::x_QueryAccessions(), CPrimeCacheApplication::x_Read_Ids(), CPSGDataLoader_Impl::x_ReadCDDChunk(), CSeqMap_CI::x_RefTSEMatch(), CID2SNPProcessor_Impl::x_ResolveBlobId(), CSeqMap::x_ResolveSegmentLength(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CAlignGroup::x_SeparateByTaxId(), CSeq_loc_CI_Impl::x_SetId(), CBioseqContext::x_SetLocation(), CMasterContext::x_SetNumParts(), CBioseq_Info::x_SetObject(), CMappingObjectLoader::x_ShowMappingDlg(), CSplitDataLoader::x_SplitAligns(), CSplitDataLoader::x_SplitSeq(), CBlastFormat::x_SplitSeqAlign(), CFeaturePanel::x_StartAssemblyJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), CAlnMultiDSBuilder::x_TestAlignments(), CSeq_annot_SNP_Info::x_UnmapAnnotObjects(), CSNPDb_Impl::x_Update(), CSeq_annot_SNP_Info::x_UpdateAnnotIndexContents(), CMappingObjectLoader::x_UpdateMap(), CProjectFileWriter::x_WriteGtf(), CFastaOstream::x_WriteSeqIds(), CGff3FlybaseWriter::xAssignAlignmentScores(), CGff3Writer::xAssignSourceSeqId(), CEditObjectFeaturePropagate::xInit(), CBsDiffApp::xLoadSeqEntry(), CWiggleWriter::xTableGetChromName(), CSrcChkApp::xTryProcessIdFile(), CAnnotWriterApp::xTryProcessInputId(), CGff3Writer::xWriteSequenceHeader(), CWiggleWriter::xWriteSingleGraphFixedStep(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), and CWiggleWriter::xWriteTableVariableStep().

◆ GetHandle() [2/4]

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

◆ 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

◆ GetID()

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

◆ GetInstance()

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

◆ 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)

◆ GetLabel() [3/6]

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

◆ GetLabel() [4/6]

string GetLabel ( const vector< CSeq_id_Handle > &  ids)

◆ 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
labelString to append to.
typeType of label (human-readable type-tagged content, by default).
flagsFlags 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(), CPSGS_OSGResolveBase::ProcessResolveReply(), 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_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
labelString to append to.
versionPointer to hold the returned version.
typeType 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, 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

◆ GetMatchingHandles() [1/4]

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

◆ GetMatchingHandles() [2/4]

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

◆ GetMatchingHandles() [3/4]

void CSeq_id_Handle::GetMatchingHandles ( TMatches matches) const

◆ GetMatchingHandles() [4/4]

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

◆ 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

◆ GetMatchingTextseqIds()

void CSeq_id::GetMatchingTextseqIds ( TSeqIdHandles matches) const

◆ GetPacked()

TPacked CSeq_id_Handle::GetPacked ( void  ) const
inline

◆ GetPackedSeqId()

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

◆ GetReverseMatchingHandles() [1/4]

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

◆ GetReverseMatchingHandles() [2/4]

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

◆ GetReverseMatchingHandles() [3/4]

void CSeq_id_Handle::GetReverseMatchingHandles ( TMatches matches) const

◆ GetReverseMatchingHandles() [4/4]

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

◆ 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.

Referenced by CLinkUtils::AddBlastProductLink(), CExplicit_Mapper_Sequence_Info::AddSeq(), CLinkUtils::AddSequenceLinks(), CSAM_CIGAR_Formatter::AdjustSeqIdType(), CSeq_id_Handle::AsString(), BestRank_SeqIdHandle(), BOOST_AUTO_TEST_CASE(), CReadDispatcher::CannotProcess(), CannotProcess(), variation::ChangeIdsInPlace(), CVisibleRange::Clamp(), CBarcodeTool::ClickLink(), CSeq_id_Info::CompareOrdered(), Convert_Seq_annot_Seq_id(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSparseGraph::CreateCompoundID(), CRevCompSequencesDlg::CreateControls(), CTextItemSeq_loc::CreateObject(), CGuiObjectInfoSeq_id::CreateObject(), CHgvsNaIrepReader::CreateSeqfeat(), CHgvsProtIrepReader::CreateSeqfeat(), CSixFramesTransTrackFactory::CreateTracks(), CSegmentGlyph::CSegmentGlyph(), CMAViewManager::DoTransition(), CAnnotCompareDS::DumpTextReport(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), FastaAARank_SeqIdHandle(), FastaNARank_SeqIdHandle(), FindLatestSequence(), CSNPDb_Impl::FindSeq(), Get_ConstRef_Seq_id(), GetAccession(), GetAccessionForGi(), GetAccessionForId(), GetAccVer(), CBAMDataLoader_Impl::GetAccVer(), CObjFingerprint::GetAlignSignature(), CFindRSites::GetAnnot(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CCDDClientPool::GetBlobBySeq_id(), CHugeAsnDataLoader::GetBlobId(), CCDDClientPool::GetBlobIdBySeq_id(), CRemoteBlastDbDataLoader::GetBlobs(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CBlobSplitterImpl::GetChunkData(), CBulkCDSAddPanel::GetCommand(), CFarPointerSeq::GetCommand(), CMixedStrands::GetCommand(), CRemoveSequencesDlg::GetCommand(), CObjFingerprint::GetComponentSignature(), CObjectCoords::GetCoordinates(), GetDeleteFeatureCommand(), CDesktopBioseqItem::GetDescription(), CDesktopBioseqsetItem::GetDescription(), GetDirectLabel(), CMappingRange::GetDstId(), CObjFingerprint::GetFeatSignature(), CWGSDataLoader_Impl::GetFileInfo(), CCSRABlobId::GetGeneralIdType(), GetGeneralOrLocal(), CCSRABlobId::GetGeneralSRAAccLabel(), CCSRABlobId::GetGeneralSRAAccReadId(), CObjFingerprint::GetGraphSignature(), CObjFingerprint::GetHistogramSignature(), GetId(), SGeneCdsmRnaFeats::GetID(), CHugeAsnDataLoader::GetIds(), CWriteUtil::GetIdType(), CSeq_featHandler::GetLabel(), GetLabel(), GetLocalGeneByLocus(), CBulkLocationPanel::GetLocForBioseq(), GetMiscTableFromSeqEntry(), CSequenceUpdater::GetNotImportedFeatsReport(), CTableDataBioTreeContainer::GetObjectValue(), GetProductToCDSMap(), CBioseq_Handle::GetRangeSeq_loc(), CObjFingerprint::GetRsiteSignature(), CSeq_id_Mapper::GetSeq_id(), CBioseq_Handle::GetSeqId(), CSeq_id_Handle_Wrapper::GetSeqId(), CSeq_id_Handle::GetSeqIdOrNull(), CVDBGraphDb_Impl::GetSeqInfo(), CObjFingerprint::GetSeqLocSignature(), CBlastDbDataLoader::GetSequenceLength(), CHugeAsnDataLoader::GetSequenceLength(), GetSequenceType(), CHugeAsnDataLoader::GetSequenceType(), CHugeAsnDataLoader::GetSequenceTypeFound(), CCommentItem::GetStringForTPA(), CTableDataGCAssembly::GetStringValue(), CLocalBlastDbAdapter::GetTaxId(), CHugeAsnDataLoader::GetTaxId(), CScope_Impl::GetTaxId(), CFeatGlyph::GetTooltip(), CGuiObjectInfoSeq_align::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CObjFingerprint::GetVcfVariantSignature(), GetWGSMasterSeq_id(), CAlignGroup::GroupBySequenceType(), HasNameAndAccession(), CSeq_id_Handle::IdentifyAccession(), CViewGraphic::InitView(), CVcfTableView::InitView(), CSeq_id_Handle::IsAccVer(), CSeq_id_Handle::IsAllowedSNPScaleLimit(), CSGUtils::IsChromosome(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CSGUtils::IsRefSeq(), CSGUtils::IsSegSet(), CValidError_bioseq::IsWp(), CId2ReaderBase::LoadBlobs(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), CId2ReaderBase::LoadSeq_idAccVer(), CId1Reader::LoadSeq_idBlob_ids(), CId2ReaderBase::LoadSeq_idBlob_ids(), CId1Reader::LoadSeq_idGi(), CId2ReaderBase::LoadSeq_idGi(), CPubseqReader::LoadSeq_idInfo(), CId2ReaderBase::LoadSeq_idLabel(), CId1Reader::LoadSeq_idSeq_ids(), CId2ReaderBase::LoadSeq_idSeq_ids(), CId2ReaderBase::LoadSeq_idTaxId(), CId2ReaderBase::LoadSequenceHash(), CId2ReaderBase::LoadSequenceLength(), CId2ReaderBase::LoadSequenceType(), CIdMapper::Map(), CIdMapper::MapObject(), CRevCompSequencesDlg::OnSelect(), CAlignSort::SAlignExtractor::operator()(), operator<<(), CTabularFormatter_SeqId::Print(), PrintBestSeqId(), CResolveRequest::Process(), CFeaturePropagator::Propagate(), CGlimmerReader::Read(), variation::CVariationUtil::RemapToAnnotatedTarget(), ReplaceWellknownSeqs(), ReportMailReportLine(), CFeatCompareJob_Align::Run(), CTestBMApp::Run(), s_AgpWrite(), s_ConvertId(), s_Fingerprint_Seq_id(), s_GetAccession(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_GetAnnotContent(), s_GetBestSynonym(), s_GetDescription(), s_GetIdBase(), CUpdateMultiSeq_Dlg::s_GetSeqIDLabel(), s_GetSeqLabel(), s_IdxSeqIdHandle(), s_IsIpgAccession(), s_Match_id(), s_RecordSeqId(), s_Render_SeqAlign(), s_ScoreForDBSource(), s_ScoreSeqIdHandle(), s_SeqAlignToXMLHit(), s_SeqMapForHandle(), Score_SeqIdHandle(), SeqLocMapperToPairwiseAligns(), CConversionResultPanel::SetObjects(), CSeqMap::SetSegmentRef(), sGenerateFields(), StrippedAccVer(), sx_GetReadId(), sx_MakeUniqueId(), sx_ProcessId(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CIdHandler::ToCanonical(), UpdateOrgInformation(), WorstRank_SeqIdHandle(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualsRna(), CMixedStrands::x_AddSequenceIds(), CDBSourceItem::x_AddSPBlock(), CFastaExportJob::x_CheckForDuplicates(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CImportFeatTable::x_CreateCommand(), CHgvsNaIrepReader::x_CreateConversionVarref(), CTreeBuilderJob::x_CreateProjectItems(), CHgvsNaIrepReader::x_CreateSimpleVariantFeat(), CHgvsProtIrepReader::x_CreateSimpleVariantFeat(), CComponentSearchJob::x_DoSearch(), CGenbankGatherer::x_DoSingleSection(), CDBSourceItem::x_FormatDBSourceID(), CDBSourceItem::x_GatherInfo(), CTableDataAlnSummary::x_GetAlnSummary(), CSGSegmentSmearJob::x_GetCacheKey(), x_GetCDDIds(), CCreateGeneModelTask::x_GetCommand(), CCommonComponentScorer::x_GetDeltaExtCompList(), CGridTableSeqIds::x_GetDescriptionLabel(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSparse(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CProjectFileWriter::x_GetGi(), x_GetId(), CGridTableSeqIds::x_GetLabel(), CUpdateSeqPanel::x_GetNameAndLength(), CBlastDbDataLoader::x_GetOid(), CScore_BlastRatio::x_GetPerfectScore(), CCommonComponentScorer::x_GetSeqHistCompList(), CPhyTreeFormatter::x_GetSeqIDString(), CPrimaryItem::x_GetStrForPrimary(), CCommonComponentScorer::x_GetUserCompList(), CFastaExportJob::x_GetWholeLoc(), variation::CHgvsParser::x_header(), CAnnot_Collector::x_Initialize(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CPhyTreeFormatter::x_InitTreeFeatures(), CAlignGlyph::x_IsSRA(), CBuffer_DataLoader::x_LoadData(), CTreeAlignMerger::x_MakeSeqAlign(), CReportEntry::x_NewCoordinate(), CGenBankLoadOptionPanel::x_ProccessText(), CProSplignJob::x_ProcessCompartment(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CAlignFilter::x_Query_Op(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), CSequenceSearchJob::x_SearchSequence(), CDeflineGenerator::x_SetFlags(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CAlnMultiDSBuilder::x_TestAlignments(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegType(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), CGff3Writer::xAssignFeatureMethod(), CEditObjectFeaturePropagate::xInit(), and CGff3Writer::xSplicedSegHasProteinProd().

◆ GetSeqIdOrNull()

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

◆ 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.

Referenced by CContigAssembly::Align(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CSparseGraph::CreateCompoundID(), variation::CVariationUtil::CreateFlankLocs(), CGBObjectLoader::Execute(), CFlatSeqIdQVal::Format(), CGBSeqFormatter::FormatFeature(), fta_seqid_same(), g_DoesNotReferencePrimary(), CFlatFileGenerator::Generate(), CSeqFastaReader::GenerateID(), CTextAlnReader::GenerateID(), GetAccessionForGi(), GetAccessionForId(), GetBlastSeqIdString(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CDesktopAlignItem::GetDescription(), CSNPTableModel::GetExtraValueAt(), CBioseq_set::GetLabel(), CVDBBlastUtil::GetOIDFromVDBSeqId(), CVDBBlastUtil::GetOidsFromSeqIds_WGS(), CAlignFormatUtil::GetSeqLinkoutInfo(), CCommentItem::GetStringForTPA(), CGencollIdMapper::Guess(), Make_SeqID_String(), CBamRefSequencesPanel::OnIdle(), CVcfRefSequencesPanel::OnIdle(), CProSplignText::Output(), CSeqFastaReader::PostProcessIDs(), CResolveRequest::Process(), CDemoContigAssemblyApp::Run(), CSeqDescrRetrievalJob::Run(), CAnnotMetaDataJob::Run(), CLocalFinderApp::Run(), CTestProtProd_EntrezNeighbors::RunTest(), s_AddTopLevelGenomicLinks(), s_CompareIdList(), s_CreateQueryMap(), s_DupIdsBioseq(), s_GenerateAccsList(), s_GetAlignTitle(), s_GetAnnotContent(), s_GetClipLoc(), s_GetQueryBioseq(), s_GetSeqLabel(), s_GetUngapLoc(), s_MakeFastaSubIds(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), CClippedScorer::ScoreAlignments(), CAliToSeq_align::Seq_idToString(), CSeqDBImpl::SeqidToOids(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CMultAlign::SetGenomic(), CConversionResultPanel::SetObjects(), CVDBBlastUtil::VDBIdType(), WriteBlastSeqidlistFile(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddQualProteinId(), CDBSourceItem::x_AddSPBlock(), CDescPlacementPanel::x_AddToStrings(), CGencollIdMapper::x_ApplyPatternToId(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CImportFeatTable::x_CheckCollidingIds(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CTreeBuilderJob::x_CreateProjectItems(), CElementaryMatching::x_CreateRemapData(), CGencollIdMapper::x_FindChromosomeSequence(), CBamUILoadManager::x_GetBamRefSeqs(), CGencollIdMapper::x_GetIdFromSeqAndSpec(), CPrimaryItem::x_GetStrForPrimary(), CClonePlacementGlyph::x_GetSupportTypeForNonPrototypeEnds(), CGencollIdMapper::x_Init(), CWriteDB_LMDB::x_InsertEntry(), CSplign::x_LoadSequence(), CGenbankFormatter::x_LocusHtmlPrefix(), CGencollIdMapper::x_MakeSpecForSeq(), CGencollIdMapper::x_NCBI34_Guess(), CGencollIdMapper::x_NCBI34_Map_IdFix(), CVcfLoadingJob::x_OnVCFVariantListReady(), CMultiAlnPrinter::x_PrintNexus(), CFastaDeflineReader::x_ProcessIDs(), CASN1InputSourceOMF::x_ReadOneSeq(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CAlignTabExportPage2::x_StartAlignNamesJob(), CFeaturePanel::x_StartAssemblyJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), CGff2Writer::xAssignFeatureAttributeProteinId(), and CEditObjectFeaturePropagate::xInit().

◆ 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 version.

◆ GetSNPScaleLimit_Name()

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

◆ GetSNPScaleLimit_Value()

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

◆ 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.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Other, 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::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), and CSeq_id_Base::Which().

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(), 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

◆ GetType()

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

◆ 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 
)

◆ HaveMatchingHandles() [3/4]

bool CSeq_id_Handle::HaveMatchingHandles ( EAllowWeakMatch  allow_weak_match) const

◆ HaveMatchingHandles() [4/4]

bool CSeq_id_Handle::HaveMatchingHandles ( void  ) const

◆ HaveReverseMatch() [1/4]

bool CSeq_id_Mapper::HaveReverseMatch ( const CSeq_id_Handle id)

◆ HaveReverseMatch() [2/4]

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

◆ HaveReverseMatch() [3/4]

bool CSeq_id_Handle::HaveReverseMatch ( EAllowWeakMatch  allow_weak_match) const

◆ HaveReverseMatch() [4/4]

bool CSeq_id_Handle::HaveReverseMatch ( void  ) const

◆ 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(), COSGConnectionPool::LoadConfig(), 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

◆ IsAccVer()

bool CSeq_id_Handle::IsAccVer ( void  ) const
inline

◆ 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

◆ IsBetter()

bool CSeq_id_Handle::IsBetter ( const CSeq_id_Handle h) const

◆ IsGi()

bool CSeq_id_Handle::IsGi ( void  ) const
inline

◆ 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

◆ IsSetVariant()

bool CSeq_id_Handle::IsSetVariant ( void  ) const
inline

◆ 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.

Referenced by CAlnGraphic::AlnGraphicDisplay(), BadMultipleSequenceLocation(), BOOST_AUTO_TEST_CASE(), CBuildAlnVecJob::Build(), CSeq_id::Compare(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CCdCore::CopyBioseqForSeqId(), CCreateProteinId::create_protein_ids(), CDisplaySeqalign::DisplaySeqalign(), CMAViewManager::DoTransition(), CAlignFormatUtil::ExtractQuerySeqAlign(), CSeqAlignFilter::FilterByAccessionType(), CSeqAlignFilter::FilterByTaxonomy(), CAlignFormatUtil::FilterSeqalignBySeqList(), FormatAsAsn(), CScore_Overlap::Get(), CCdCore::GetAllRowIndicesForSeqId(), GetBestMrnaForCds(), CCdCore::GetBioseqWithSeqid(), CSeqUtils::GetCdsMappingInfoFromRna(), CShowBlastDefline::GetFormattingInfo(), IBISInteraction::GetGi(), SGeneCdsmRnaFeats::GetID(), CClusterDBSource::GetNext(), CBioseq::GetNonLocalId(), CTableDataGCAssembly::GetObjectValue(), CCdCore::GetSeqEntryForRow(), CTableDataGCAssembly::GetStringValue(), CAlignFormatUtil::GetSubjectsNumber(), CAlignFormatUtil::GetTaxidForSeqid(), CAlignFormatUtil::HspListToHitList(), CAlignFormatUtil::HspListToHitMap(), CAlnGraphic::Init(), IsSameBioseq(), CAlignFormatUtil::LimitSeqalignByHsps(), MakeSubjectScores(), Sequence::MatchesSeqId(), operator<<(), PrintSAM(), PrintTabular(), CAlignFormatUtil::PruneSeqalign(), CAlignFormatUtil::PruneSeqalignAll(), remasterAlignannot(), RestoreModelReadingFrame(), s_AddSeqDataToPssm(), s_CanAdd(), s_CompareSeqId(), s_GetLabel(), s_GetRnaMappingLocs(), s_GetSeq_intervalLabel(), s_LocationSpansMultipleSeqs(), s_MergeAlignSet(), s_RestoreHspPos(), s_SeqAlignSetToXMLHits(), s_SetBlastXMlHitList(), s_TestFastaRoundTrip(), s_UpdateSubjectInSeqalign(), testResultAlignments(), CSearchResults::TrimSeqAlign(), CScore_Overlap::UpdateState(), CValidError_bioseq::ValidateIDSetAgainstDb(), CValidError_imp::ValidateSeqLocIds(), CAlnGraphic::x_BuildHtmlTable(), CFeatureGenerator::SImplementation::x_CheckMatch(), CIgBlast::x_ConvertResultType(), CImportFeatTable::x_DoImportCDS(), CPsiBlastInputData::x_ExtractAlignmentData(), CDisplaySeqalign::x_FillLocList(), CUpdateAlign::x_FindNotPresentIDs(), CSequenceEditingEventHandler::x_FindRelevantAlignRow(), CAlnGraphic::x_FormatGraphOverview(), CAlignmentTrack::x_GetAlignGlyphType(), CClonePlacementGlyph::x_GetCloneEnds(), CShowBlastDefline::x_InitDefline(), CShowBlastDefline::x_InitDeflineTable(), CTaxFormat::x_InitTaxInfoMap(), CBatchFeatJob::x_LoadFeatProducts(), CBlastFormat::x_PrintStructuredReport(), CBlastFormat::x_PrintXML2Report(), COligoSpecificityTemplate::x_SortHit(), and COligoSpecificityCheck::x_SortPrimerHit().

◆ 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

◆ operator+()

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

◆ 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

◆ operator+=()

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

◆ 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

◆ 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

◆ operator-=()

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

◆ operator->()

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

◆ 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 
)

◆ 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

◆ 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

◆ 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
idsDestination ID set. Existing contents will be preserved and appended to.
sInput string to parse.
allow_partial_failureIf 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

◆ 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

◆ Reset()

void CSeq_id_Handle::Reset ( void  )
inline

◆ 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.

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, CTempString::empty(), NStr::EqualNocase(), ERR_POST_X, NStr::eTrunc_Both, Info(), NCBI_THROW, CPDB_seq_id_Base::ResetChain(), CPDB_seq_id_Base::ResetChain_id(), CId_pat_Base::ResetDoc_type(), CPDB_seq_id_Base::ResetRel(), CSeq_id_Base::SelectionName(), CTextseq_id::Set(), CSeq_id::Set(), CId_pat_Base::C_Id::SetApp_number(), CPDB_seq_id_Base::SetChain(), CPDB_seq_id_Base::SetChain_id(), CPatent_seq_id_Base::SetCit(), CId_pat_Base::SetCountry(), CDbtag_Base::SetDb(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGpipe(), CId_pat_Base::SetId(), CSeq_id_Base::SetLocal(), CPDB_seq_id_Base::SetMol(), CSeq_id_Base::SetNamed_annot_track(), CId_pat_Base::C_Id::SetNumber(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CPatent_seq_id_Base::SetSeqid(), CObject_id::SetStrOrId(), CSeq_id_Base::SetSwissprot(), CDbtag_Base::SetTag(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CTempString::size(), NStr::StringToNonNegativeInt(), NStr::TruncateSpaces_Unsafe(), version, and ZERO_GI.

◆ 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 
)

◆ 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

◆ StrictAdjustScore()

int CSeq_id::StrictAdjustScore ( int  base_score) const
inline

◆ 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

◆ 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

◆ 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

◆ 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
ostrStream to write to
bioseqBioseq 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

◆ 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

◆ x_GetTree() [3/3]

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

◆ 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

◆ 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

◆ x_Match()

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

◆ 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

◆ x_WriteContentAsFasta()

void CSeq_id::x_WriteContentAsFasta ( ostream &  out) const
private

◆ ~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

◆ 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

◆ m_LockCounter

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

◆ 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

◆ m_Packed

TPacked CSeq_id_Handle::m_Packed
private

◆ m_Range

const SSeqIdRange* SSeqIdRange::const_iterator::m_Range
private

◆ m_Seq_id

CConstRef<CSeq_id> CSeq_id_Info::m_Seq_id
protected

◆ 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

◆ m_Variant

TVariant CSeq_id_Handle::m_Variant
private

◆ 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.

Modified on Wed Apr 17 13:10:40 2024 by modify_doxy.py rev. 669887