Search Toolkit Book for CSeq_id
#include <objects/seqloc/Seq_id.hpp>
Inheritance diagram for CSeq_id:
Collaboration diagram for CSeq_id:
Public Types | |
| enum | EParseFlags { fParse_PartialOK = 0x01 , fParse_RawText = 0x02 , fParse_RawGI = 0x04 , fParse_AnyRaw = fParse_RawText | fParse_RawGI , fParse_ValidLocal = 0x08 , fParse_AnyLocal = 0x18 , fParse_NoFASTA = 0x20 , fParse_FallbackOK = 0x40 , fParse_Cautiously = 0x80 , fParse_NoThrow = 0x100 , fParse_NoWarn = 0x200 , fParse_Default = fParse_RawText | fParse_ValidLocal } |
| enum | EErrorFlags { fNoError = 0 , fEmptyId = 1 , fInvalidChar = 1 << 1 , fExceedsMaxLength = 1 << 2 } |
| enum | EFastaAsTypeAndContent { eFasta_AsTypeAndContent } |
| Tag for method variants that would otherwise be ambiguous. More... | |
| enum | EAccessionInfo { eSeqId_not_set = e_not_set , eSeqId_local = e_Local , eSeqId_gibbsq = e_Gibbsq , eSeqId_gibbmt = e_Gibbmt , eSeqId_giim = e_Giim , eSeqId_genbank = e_Genbank , eSeqId_embl = e_Embl , eSeqId_pir = e_Pir , eSeqId_swissprot = e_Swissprot , eSeqId_patent = e_Patent , eSeqId_other = e_Other , eSeqId_refseq = eSeqId_other , eSeqId_general = e_General , eSeqId_gi = e_Gi , eSeqId_ddbj = e_Ddbj , eSeqId_prf = e_Prf , eSeqId_pdb = e_Pdb , eSeqId_tpg = e_Tpg , eSeqId_tpe = e_Tpe , eSeqId_tpd = e_Tpd , eSeqId_gpipe = e_Gpipe , eSeqId_named_annot_track = e_Named_annot_track , eAcc_type_mask = 0xff , fAcc_nuc = 0x80000000 , fAcc_prot = 0x40000000 , fAcc_seq = 0 , fAcc_predicted = 0x20000000 , fAcc_specials = 0x10000000 , fAcc_master = 0x08000000 , fAcc_ncbo = 0x04000000 , fAcc_fallback = 0x02000000 , fAcc_vdb_only = 0x01000000 , eAcc_flag_mask = 0xff000000 , eAcc_other = 0 << 8 , eAcc_est = 1 << 8 , eAcc_dirsub = 2 << 8 , eAcc_div_patent = 3 << 8 , eAcc_mrna = 4 << 8 , eAcc_ncrna = 5 << 8 , eAcc_gsdb_ds = 6 << 8 , eAcc_gsdb = 7 << 8 , eAcc_backbone = 8 << 8 , eAcc_tsa = 9 << 8 , eAcc_segset = 10 << 8 , eAcc_gss = 11 << 8 , eAcc_unique = 12 << 8 , eAcc_ambig = 112 << 8 , eAcc_ambig_g = 113 << 8 , eAcc_ambig_e = 114 << 8 , eAcc_ambig_ge = 115 << 8 , eAcc_ambig_d = 116 << 8 , eAcc_ambig_gd = 117 << 8 , eAcc_ambig_ed = 118 << 8 , eAcc_ambig_ged = 119 << 8 , eAcc_unreserved = 127 << 8 , fAcc_genomic = 128 << 8 , eAcc_genome = 128 << 8 , eAcc_htgs = 129 << 8 , eAcc_con = 130 << 8 , eAcc_wgs = 131 << 8 , eAcc_chromosome = 133 << 8 , eAcc_genomic_rgn = 134 << 8 , eAcc_wgs_intermed = 135 << 8 , eAcc_sts = 136 << 8 , eAcc_mga = 137 << 8 , eAcc_optical_map = 138 << 8 , eAcc_targeted = 139 << 8 , eAcc_division_mask = 0xff00 , eAcc_wgs_master = eAcc_wgs | fAcc_master , eAcc_wgs_intermed_master = eAcc_wgs_intermed | fAcc_master , eAcc_tsa_master = eAcc_tsa | fAcc_master , eAcc_targeted_master = eAcc_targeted | fAcc_master , eAcc_wgs_vdb_only = eAcc_wgs | fAcc_vdb_only , eAcc_wgs_intermed_vdb_only = eAcc_wgs_intermed | fAcc_vdb_only , eAcc_tsa_vdb_only = eAcc_tsa | fAcc_vdb_only , eAcc_targeted_vdb_only = eAcc_targeted | fAcc_vdb_only , eAcc_wgs_vdb_master = eAcc_wgs | fAcc_master | fAcc_vdb_only , eAcc_wgs_intermed_vdb_master = eAcc_wgs_intermed | fAcc_master | fAcc_vdb_only , eAcc_tsa_vdb_master = eAcc_tsa | fAcc_master | fAcc_vdb_only , eAcc_targeted_vdb_master = eAcc_targeted | fAcc_master | fAcc_vdb_only , eAcc_unknown = eSeqId_not_set | eAcc_other | fAcc_seq , eAcc_ambiguous_nuc = eSeqId_not_set | eAcc_ambig | fAcc_nuc , eAcc_maybe_gb = eSeqId_not_set | eAcc_ambig_g | fAcc_nuc , eAcc_maybe_embl = eSeqId_not_set | eAcc_ambig_e | fAcc_nuc , eAcc_maybe_ddbj = eSeqId_not_set | eAcc_ambig_d | fAcc_nuc , eAcc_gb_embl = eSeqId_not_set | eAcc_ambig_ge | fAcc_nuc , eAcc_gb_ddbj = eSeqId_not_set | eAcc_ambig_gd | fAcc_nuc , eAcc_embl_ddbj = eSeqId_not_set | eAcc_ambig_ed | fAcc_nuc , eAcc_gb_embl_ddbj = eSeqId_not_set | eAcc_ambig_ged | fAcc_nuc , eAcc_unreserved_nuc = eSeqId_not_set | eAcc_unreserved | fAcc_nuc , eAcc_unreserved_prot = eSeqId_not_set | eAcc_unreserved | fAcc_prot , eAcc_local = eSeqId_local | eAcc_other | fAcc_seq , eAcc_gibbsq = eSeqId_gibbsq | eAcc_other | fAcc_seq , eAcc_gibbmt = eSeqId_gibbmt | eAcc_other | fAcc_seq , eAcc_giim = eSeqId_giim | eAcc_other | fAcc_seq , eAcc_gb_other = eSeqId_genbank | eAcc_other | fAcc_seq , eAcc_gb_prot = eSeqId_genbank | eAcc_other | fAcc_prot , eAcc_gb_other_nuc = eSeqId_genbank | eAcc_other | fAcc_nuc , eAcc_gb_est = eSeqId_genbank | eAcc_est | fAcc_nuc , eAcc_gb_dirsub = eSeqId_genbank | eAcc_dirsub | fAcc_nuc , eAcc_gb_patent = eSeqId_genbank | eAcc_div_patent | fAcc_seq , eAcc_gb_patent_prot = eSeqId_genbank | eAcc_div_patent | fAcc_prot , eAcc_gb_cdna = eSeqId_genbank | eAcc_mrna | fAcc_nuc , eAcc_gsdb_dirsub = eSeqId_genbank | eAcc_gsdb_ds | fAcc_nuc , eAcc_gb_gsdb = eSeqId_genbank | eAcc_gsdb | fAcc_nuc , eAcc_gb_backbone = eSeqId_genbank | eAcc_backbone | fAcc_nuc , eAcc_gb_tsa_nuc = eSeqId_genbank | eAcc_tsa | fAcc_nuc , eAcc_gb_tsa_prot = eSeqId_genbank | eAcc_tsa | fAcc_prot , eAcc_gb_tsam_nuc = eSeqId_genbank | eAcc_tsa_master | fAcc_nuc , eAcc_gb_tsam_prot = eSeqId_genbank | eAcc_tsa_master | fAcc_prot , eAcc_gb_tsav_nuc = eSeqId_genbank | eAcc_tsa_vdb_only | fAcc_nuc , eAcc_gb_tsav_prot = eSeqId_genbank | eAcc_tsa_vdb_only | fAcc_prot , eAcc_gb_tsavm_nuc = eSeqId_genbank | eAcc_tsa_vdb_master | fAcc_nuc , eAcc_gb_tsavm_prot = eSeqId_genbank | eAcc_tsa_vdb_master | fAcc_prot , eAcc_gb_segset = eSeqId_genbank | eAcc_segset | fAcc_seq , eAcc_gb_gss = eSeqId_genbank | eAcc_gss | fAcc_nuc , eAcc_gb_genome = eSeqId_genbank | eAcc_genome | fAcc_nuc , eAcc_gb_htgs = eSeqId_genbank | eAcc_htgs | fAcc_nuc , eAcc_gb_con = eSeqId_genbank | eAcc_con | fAcc_nuc , eAcc_gb_wgs_nuc = eSeqId_genbank | eAcc_wgs | fAcc_nuc , eAcc_gb_wgs_prot = eSeqId_genbank | eAcc_wgs | fAcc_prot , eAcc_gb_wgsm_nuc = eSeqId_genbank | eAcc_wgs_master | fAcc_nuc , eAcc_gb_wgsm_prot = eSeqId_genbank | eAcc_wgs_master | fAcc_prot , eAcc_gb_wgsv_nuc = eSeqId_genbank | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_gb_wgsv_prot = eSeqId_genbank | eAcc_wgs_vdb_only | fAcc_prot , eAcc_gb_wgsvm_nuc = eSeqId_genbank | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_gb_wgsvm_prot = eSeqId_genbank | eAcc_wgs_vdb_master | fAcc_prot , eAcc_gb_chromosome = eSeqId_genbank | eAcc_chromosome | fAcc_nuc , eAcc_gb_sts = eSeqId_genbank | eAcc_sts | fAcc_nuc , eAcc_gb_mga = eSeqId_genbank | eAcc_mga | fAcc_nuc , eAcc_gb_optical_map = eSeqId_genbank | eAcc_optical_map | fAcc_nuc , eAcc_gb_targeted_nuc = eSeqId_genbank | eAcc_targeted | fAcc_nuc , eAcc_embl_other = eSeqId_embl | eAcc_other | fAcc_seq , eAcc_embl_prot = eSeqId_embl | eAcc_other | fAcc_prot , eAcc_embl_other_nuc = eSeqId_embl | eAcc_other | fAcc_nuc , eAcc_embl_est = eSeqId_embl | eAcc_est | fAcc_nuc , eAcc_embl_dirsub = eSeqId_embl | eAcc_dirsub | fAcc_nuc , eAcc_embl_patent = eSeqId_embl | eAcc_div_patent | fAcc_nuc , eAcc_embl_tsa_nuc = eSeqId_embl | eAcc_tsa | fAcc_nuc , eAcc_embl_tsa_prot = eSeqId_embl | eAcc_tsa | fAcc_prot , eAcc_embl_tsam_nuc = eSeqId_embl | eAcc_tsa_master | fAcc_nuc , eAcc_embl_tsam_prot = eSeqId_embl | eAcc_tsa_master | fAcc_prot , eAcc_embl_tsav_nuc = eSeqId_embl | eAcc_tsa_vdb_only | fAcc_nuc , eAcc_embl_tsav_prot = eSeqId_embl | eAcc_tsa_vdb_only | fAcc_prot , eAcc_embl_tsavm_nuc = eSeqId_embl | eAcc_tsa_vdb_master | fAcc_nuc , eAcc_embl_tsavm_prot = eSeqId_embl | eAcc_tsa_vdb_master | fAcc_prot , eAcc_embl_gss = eSeqId_embl | eAcc_gss | fAcc_nuc , eAcc_embl_genome = eSeqId_embl | eAcc_genome | fAcc_nuc , eAcc_embl_htgs = eSeqId_embl | eAcc_htgs | fAcc_nuc , eAcc_embl_con = eSeqId_embl | eAcc_con | fAcc_nuc , eAcc_embl_wgs_nuc = eSeqId_embl | eAcc_wgs | fAcc_nuc , eAcc_embl_wgs_prot = eSeqId_embl | eAcc_wgs | fAcc_prot , eAcc_embl_wgsm_nuc = eSeqId_embl | eAcc_wgs_master | fAcc_nuc , eAcc_embl_wgsm_prot = eSeqId_embl | eAcc_wgs_master | fAcc_prot , eAcc_embl_wgsv_nuc = eSeqId_embl | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_embl_wgsv_prot = eSeqId_embl | eAcc_wgs_vdb_only | fAcc_prot , eAcc_embl_wgsvm_nuc = eSeqId_embl | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_embl_wgsvm_prot = eSeqId_embl | eAcc_wgs_vdb_master | fAcc_prot , eAcc_embl_mga = eSeqId_embl | eAcc_mga | fAcc_nuc , eAcc_pir = eSeqId_pir | eAcc_other | fAcc_prot , eAcc_swissprot = eSeqId_swissprot | eAcc_other | fAcc_prot , eAcc_patent = eSeqId_patent | eAcc_div_patent | fAcc_seq , eAcc_refseq_prot = eSeqId_refseq | eAcc_other | fAcc_prot , eAcc_refseq_mrna = eSeqId_refseq | eAcc_mrna | fAcc_nuc , eAcc_refseq_ncrna = eSeqId_refseq | eAcc_ncrna | fAcc_nuc , eAcc_refseq_unique_prot = eSeqId_refseq | eAcc_unique | fAcc_prot , eAcc_refseq_unreserved = eSeqId_refseq | eAcc_unreserved | fAcc_seq , eAcc_refseq_genome = eSeqId_refseq | eAcc_genome | fAcc_nuc , eAcc_refseq_contig = eSeqId_refseq | eAcc_con | fAcc_nuc , eAcc_refseq_wgs_nuc = eSeqId_refseq | eAcc_wgs | fAcc_nuc , eAcc_refseq_wgs_prot = eSeqId_refseq | eAcc_wgs | fAcc_prot , eAcc_refseq_wgsm_nuc = eSeqId_refseq | eAcc_wgs_master | fAcc_nuc , eAcc_refseq_wgsm_prot = eSeqId_refseq | eAcc_wgs_master | fAcc_prot , eAcc_refseq_wgsv_nuc = eSeqId_refseq | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_refseq_wgsv_prot = eSeqId_refseq | eAcc_wgs_vdb_only | fAcc_prot , eAcc_refseq_wgsvm_nuc = eSeqId_refseq | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_refseq_wgsvm_prot = eSeqId_refseq | eAcc_wgs_vdb_master | fAcc_prot , eAcc_refseq_chromosome = eSeqId_refseq | eAcc_chromosome | fAcc_nuc , eAcc_refseq_genomic = eSeqId_refseq | eAcc_genomic_rgn | fAcc_nuc , eAcc_refseq_wgs_intermed = eSeqId_refseq | eAcc_wgs_intermed | fAcc_nuc , eAcc_refseq_wgsm_intermed , eAcc_refseq_wgsv_intermed , eAcc_refseq_wgsvm_intermed , eAcc_refseq_prot_predicted = eAcc_refseq_prot | fAcc_predicted , eAcc_refseq_mrna_predicted = eAcc_refseq_mrna | fAcc_predicted , eAcc_refseq_ncrna_predicted = eAcc_refseq_ncrna | fAcc_predicted , eAcc_refseq_chromosome_ncbo = eAcc_refseq_chromosome | fAcc_ncbo , eAcc_refseq_contig_ncbo = eAcc_refseq_contig | fAcc_ncbo , eAcc_general = eSeqId_general | eAcc_other | fAcc_seq , eAcc_general_nuc = eSeqId_general | eAcc_other | fAcc_nuc , eAcc_general_prot = eSeqId_general | eAcc_other | fAcc_prot , eAcc_gi = eSeqId_gi | eAcc_other | fAcc_seq , eAcc_ddbj_other = eSeqId_ddbj | eAcc_other | fAcc_seq , eAcc_ddbj_prot = eSeqId_ddbj | eAcc_other | fAcc_prot , eAcc_ddbj_other_nuc = eSeqId_ddbj | eAcc_other | fAcc_nuc , eAcc_ddbj_est = eSeqId_ddbj | eAcc_est | fAcc_nuc , eAcc_ddbj_dirsub = eSeqId_ddbj | eAcc_dirsub | fAcc_nuc , eAcc_ddbj_patent = eSeqId_ddbj | eAcc_div_patent | fAcc_nuc , eAcc_ddbj_patent_prot = eSeqId_ddbj | eAcc_div_patent | fAcc_prot , eAcc_ddbj_mrna = eSeqId_ddbj | eAcc_mrna | fAcc_nuc , eAcc_ddbj_tsa_nuc = eSeqId_ddbj | eAcc_tsa | fAcc_nuc , eAcc_ddbj_tsa_prot = eSeqId_ddbj | eAcc_tsa | fAcc_prot , eAcc_ddbj_tsam_nuc = eSeqId_ddbj | eAcc_tsa_master | fAcc_nuc , eAcc_ddbj_tsam_prot = eSeqId_ddbj | eAcc_tsa_master | fAcc_prot , eAcc_ddbj_tsav_nuc = eSeqId_ddbj | eAcc_tsa_vdb_only | fAcc_nuc , eAcc_ddbj_tsav_prot = eSeqId_ddbj | eAcc_tsa_vdb_only | fAcc_prot , eAcc_ddbj_tsavm_nuc = eSeqId_ddbj | eAcc_tsa_vdb_master | fAcc_nuc , eAcc_ddbj_tsavm_prot = eSeqId_ddbj | eAcc_tsa_vdb_master | fAcc_prot , eAcc_ddbj_gss = eSeqId_ddbj | eAcc_gss | fAcc_nuc , eAcc_ddbj_genome = eSeqId_ddbj | eAcc_genome | fAcc_nuc , eAcc_ddbj_htgs = eSeqId_ddbj | eAcc_htgs | fAcc_nuc , eAcc_ddbj_con = eSeqId_ddbj | eAcc_con | fAcc_nuc , eAcc_ddbj_wgs_nuc = eSeqId_ddbj | eAcc_wgs | fAcc_nuc , eAcc_ddbj_wgs_prot = eSeqId_ddbj | eAcc_wgs | fAcc_prot , eAcc_ddbj_wgsm_nuc = eSeqId_ddbj | eAcc_wgs_master | fAcc_nuc , eAcc_ddbj_wgsm_prot = eSeqId_ddbj | eAcc_wgs_master | fAcc_prot , eAcc_ddbj_wgsv_nuc = eSeqId_ddbj | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_ddbj_wgsv_prot = eSeqId_ddbj | eAcc_wgs_vdb_only | fAcc_prot , eAcc_ddbj_wgsvm_nuc = eSeqId_ddbj | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_ddbj_wgsvm_prot = eSeqId_ddbj | eAcc_wgs_vdb_master | fAcc_prot , eAcc_ddbj_mga = eSeqId_ddbj | eAcc_mga | fAcc_nuc , eAcc_ddbj_targeted_nuc = eSeqId_ddbj | eAcc_targeted | fAcc_nuc , eAcc_ddbj_targetedm_nuc = eSeqId_ddbj | eAcc_targeted_master | fAcc_nuc , eAcc_ddbj_targetedv_nuc = eSeqId_ddbj | eAcc_targeted_vdb_only | fAcc_nuc , eAcc_ddbj_targetedvm_nuc = eSeqId_ddbj | eAcc_targeted_vdb_master | fAcc_nuc , eAcc_prf = eSeqId_prf | eAcc_other | fAcc_prot , eAcc_pdb = eSeqId_pdb | eAcc_other | fAcc_seq , eAcc_gb_tpa_other = eSeqId_tpg | eAcc_other | fAcc_seq , eAcc_gb_tpa_nuc = eSeqId_tpg | eAcc_other | fAcc_nuc , eAcc_gb_tpa_prot = eSeqId_tpg | eAcc_other | fAcc_prot , eAcc_gb_tpa_segset = eSeqId_tpg | eAcc_segset | fAcc_nuc , eAcc_gb_tpa_con = eSeqId_tpg | eAcc_con | fAcc_nuc , eAcc_gb_tpa_wgs_nuc = eSeqId_tpg | eAcc_wgs | fAcc_nuc , eAcc_gb_tpa_wgs_prot = eSeqId_tpg | eAcc_wgs | fAcc_prot , eAcc_gb_tpa_wgsm_nuc = eSeqId_tpg | eAcc_wgs_master | fAcc_nuc , eAcc_gb_tpa_wgsm_prot = eSeqId_tpg | eAcc_wgs_master | fAcc_prot , eAcc_gb_tpa_wgsv_nuc = eSeqId_tpg | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_gb_tpa_wgsv_prot = eSeqId_tpg | eAcc_wgs_vdb_only | fAcc_prot , eAcc_gb_tpa_wgsvm_nuc = eSeqId_tpg | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_gb_tpa_wgsvm_prot = eSeqId_tpg | eAcc_wgs_vdb_master | fAcc_prot , eAcc_gb_tpa_chromosome = eSeqId_tpg | eAcc_chromosome | fAcc_nuc , eAcc_embl_tpa_other = eSeqId_tpe | eAcc_other | fAcc_seq , eAcc_embl_tpa_nuc = eSeqId_tpe | eAcc_other | fAcc_nuc , eAcc_embl_tpa_prot = eSeqId_tpe | eAcc_other | fAcc_prot , eAcc_embl_tpa_tsa_nuc = eSeqId_tpe | eAcc_tsa | fAcc_nuc , eAcc_embl_tpa_tsa_prot = eSeqId_tpe | eAcc_tsa | fAcc_prot , eAcc_embl_tpa_tsam_nuc = eSeqId_tpe | eAcc_tsa_master | fAcc_nuc , eAcc_embl_tpa_tsam_prot = eSeqId_tpe | eAcc_tsa_master | fAcc_prot , eAcc_embl_tpa_tsav_nuc = eSeqId_tpe | eAcc_tsa_vdb_only | fAcc_nuc , eAcc_embl_tpa_tsav_prot = eSeqId_tpe | eAcc_tsa_vdb_only | fAcc_prot , eAcc_embl_tpa_tsavm_nuc = eSeqId_tpe | eAcc_tsa_vdb_master | fAcc_nuc , eAcc_embl_tpa_tsavm_prot = eSeqId_tpe | eAcc_tsa_vdb_master | fAcc_prot , eAcc_embl_tpa_wgs_nuc = eSeqId_tpe | eAcc_wgs | fAcc_nuc , eAcc_embl_tpa_wgs_prot = eSeqId_tpe | eAcc_wgs | fAcc_prot , eAcc_embl_tpa_wgsm_nuc = eSeqId_tpe | eAcc_wgs_master | fAcc_nuc , eAcc_embl_tpa_wgsm_prot = eSeqId_tpe | eAcc_wgs_master | fAcc_prot , eAcc_embl_tpa_wgsv_nuc = eSeqId_tpe | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_embl_tpa_wgsv_prot = eSeqId_tpe | eAcc_wgs_vdb_only | fAcc_prot , eAcc_embl_tpa_wgsvm_nuc = eSeqId_tpe | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_embl_tpa_wgsvm_prot = eSeqId_tpe | eAcc_wgs_vdb_master | fAcc_prot , eAcc_ddbj_tpa_other = eSeqId_tpd | eAcc_other | fAcc_seq , eAcc_ddbj_tpa_nuc = eSeqId_tpd | eAcc_other | fAcc_nuc , eAcc_ddbj_tpa_prot = eSeqId_tpd | eAcc_other | fAcc_prot , eAcc_ddbj_tpa_tsa_nuc = eSeqId_tpd | eAcc_tsa | fAcc_nuc , eAcc_ddbj_tpa_tsa_prot = eSeqId_tpd | eAcc_tsa | fAcc_prot , eAcc_ddbj_tpa_tsam_nuc = eSeqId_tpd | eAcc_tsa_master | fAcc_nuc , eAcc_ddbj_tpa_tsam_prot = eSeqId_tpd | eAcc_tsa_master | fAcc_prot , eAcc_ddbj_tpa_tsav_nuc = eSeqId_tpd | eAcc_tsa_vdb_only | fAcc_nuc , eAcc_ddbj_tpa_tsav_prot = eSeqId_tpd | eAcc_tsa_vdb_only | fAcc_prot , eAcc_ddbj_tpa_tsavm_nuc = eSeqId_tpd | eAcc_tsa_vdb_master | fAcc_nuc , eAcc_ddbj_tpa_tsavm_prot = eSeqId_tpd | eAcc_tsa_vdb_master | fAcc_prot , eAcc_ddbj_tpa_con = eSeqId_tpd | eAcc_con | fAcc_nuc , eAcc_ddbj_tpa_wgs_nuc = eSeqId_tpd | eAcc_wgs | fAcc_nuc , eAcc_ddbj_tpa_wgs_prot = eSeqId_tpd | eAcc_wgs | fAcc_prot , eAcc_ddbj_tpa_wgsm_nuc = eSeqId_tpd | eAcc_wgs_master | fAcc_nuc , eAcc_ddbj_tpa_wgsm_prot = eSeqId_tpd | eAcc_wgs_master | fAcc_prot , eAcc_ddbj_tpa_wgsv_nuc = eSeqId_tpd | eAcc_wgs_vdb_only | fAcc_nuc , eAcc_ddbj_tpa_wgsv_prot = eSeqId_tpd | eAcc_wgs_vdb_only | fAcc_prot , eAcc_ddbj_tpa_wgsvm_nuc = eSeqId_tpd | eAcc_wgs_vdb_master | fAcc_nuc , eAcc_ddbj_tpa_wgsvm_prot = eSeqId_tpd | eAcc_wgs_vdb_master | fAcc_prot , eAcc_ddbj_tpa_chromosome = eSeqId_tpd | eAcc_chromosome | fAcc_nuc , eAcc_ddbj_tpa_targeted_nuc = eSeqId_tpd | eAcc_targeted | fAcc_nuc , eAcc_ddbj_tpa_targetedm_nuc = eSeqId_tpd | eAcc_targeted_master | fAcc_nuc , eAcc_ddbj_tpa_targetedv_nuc = eSeqId_tpd | eAcc_targeted_vdb_only | fAcc_nuc , eAcc_ddbj_tpa_targetedvm_nuc = eSeqId_tpd | eAcc_targeted_vdb_master | fAcc_nuc , eAcc_gpipe_other_nuc = eSeqId_gpipe | eAcc_other | fAcc_nuc , eAcc_gpipe_prot = eSeqId_gpipe | eAcc_other | fAcc_prot , eAcc_gpipe_scaffold = eSeqId_gpipe | eAcc_con | fAcc_nuc , eAcc_gpipe_mrna = eSeqId_gpipe | eAcc_mrna | fAcc_nuc , eAcc_gpipe_chromosome = eSeqId_gpipe | eAcc_chromosome | fAcc_nuc , eAcc_gpipe_genomic = eSeqId_gpipe | eAcc_genomic_rgn | fAcc_nuc , eAcc_gpipe_ncrna = eSeqId_gpipe | eAcc_ncrna | fAcc_nuc , eAcc_gpipe_unreserved = eSeqId_gpipe | eAcc_unreserved | fAcc_seq , eAcc_named_annot_track = eSeqId_named_annot_track | eAcc_other | fAcc_seq } |
| For IdentifyAccession (below) More... | |
| enum | ELoadFlags { fFullyLoadSpecials = 1 , fAlwaysLoad = 2 } |
| enum | EAssessment { eInvalid , eLocalOnly , ePlausible , eUnreserved , eIdentifiable , eTagged } |
| enum | E_SIC { e_error = 0 , e_DIFF , e_NO , e_YES } |
| Compare return values. More... | |
| enum | ELabelType { eType , eContent , eBoth , eFasta , eFastaContent , eDefault = eBoth } |
| return the label for a given string More... | |
| enum | ELabelFlags { fLabel_Version = 0x10 , fLabel_GeneralDbIsContent = 0x20 , fLabel_Trimmed = 0x40 , fLabel_UpperCase = 0x80 , fLabel_Default = fLabel_Version } |
| enum | EStringFormat { eFormat_FastA , eFormat_ForceGI , eFormat_BestWithoutVersion , eFormat_BestWithVersion } |
| Get a string representation of the sequence IDs of a given bioseq. More... | |
| enum | EMaxScore { kMaxScore = 99999 } |
| Numerical quality ranking; lower is better. More... | |
| enum | EAdjustScoreFlags { fRequireAccessions = 1 << 0 } |
| enum | EComposeOSLTFlags { fAllowLocalId = (1 << 0) , fGpipeAddSecondary = (1 << 1) } |
| Flags specifying special treatment for certain types of Seq-ids in ComposeOSLT(). More... | |
| enum | ESNPScaleLimit { eSNPScaleLimit_Default , eSNPScaleLimit_Unit , eSNPScaleLimit_Contig , eSNPScaleLimit_Supercontig , eSNPScaleLimit_Chromosome } |
| SNP annotation scale limits. More... | |
| typedef int | TParseFlags |
| using | TErrorFlags = int |
| typedef int | TLoadFlags |
| binary OR of ELoadFlags More... | |
| typedef int | TLabelFlags |
| typedef set< CSeq_id_Handle > | TSeqIdHandles |
| typedef int | TComposeOSLTFlags |
| Public Types inherited from CSeq_id_Base | |
| enum | E_Choice { e_not_set = 0 , e_Local , e_Gibbsq , e_Gibbmt , e_Giim , e_Genbank , e_Embl , e_Pir , e_Swissprot , e_Patent , e_Other , e_General , e_Gi , e_Ddbj , e_Prf , e_Pdb , e_Tpg , e_Tpe , e_Tpd , e_Gpipe , e_Named_annot_track } |
| Choice variants. More... | |
| enum | E_ChoiceStopper { e_MaxChoice = 21 } |
| Maximum+1 value of the choice variant enumerator. More... | |
| typedef CObject_id | TLocal |
| typedef int | TGibbsq |
| typedef int | TGibbmt |
| typedef CGiimport_id | TGiim |
| typedef CTextseq_id | TGenbank |
| typedef CTextseq_id | TEmbl |
| typedef CTextseq_id | TPir |
| typedef CTextseq_id | TSwissprot |
| typedef CPatent_seq_id | TPatent |
| typedef CTextseq_id | TOther |
| typedef CDbtag | TGeneral |
| typedef NCBI_NS_NCBI::TGi | TGi |
| typedef CTextseq_id | TDdbj |
| typedef CTextseq_id | TPrf |
| typedef CPDB_seq_id | TPdb |
| typedef CTextseq_id | TTpg |
| typedef CTextseq_id | TTpe |
| typedef CTextseq_id | TTpd |
| typedef CTextseq_id | TGpipe |
| typedef CTextseq_id | TNamed_annot_track |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is std::atomic<> More... | |
| typedef TCounter::value_type | TCount |
| Alias for value type of counter. More... | |
| Public Types inherited from CSerializable | |
| enum | EOutputType { eAsFasta , eAsAsnText , eAsAsnBinary , eAsXML , eAsString } |
Public Member Functions | |
| CSeq_id (void) | |
| See also CSeq_id related functions in "util/sequence.hpp": More... | |
| CSeq_id (const CTempString &the_id, TParseFlags flags=fParse_AnyRaw, EPDBMolFormat pdbfmt=ePDB_AsIs) | |
| Construct a Seq-id from a flat string. More... | |
| CSeq_id (const CDbtag &tag, bool set_as_general=true, TParseFlags flags=0) | |
| Construct a seq-id from a dbtag. More... | |
| CSeq_id (const CDbtag &tag, TParseFlags flags) | |
| CSeq_id (E_Choice the_type, TIntId int_seq_id, TParseFlags flags=0) | |
| Construct a numeric Seq-id. More... | |
| CSeq_id (E_Choice the_type, TGi gi, TParseFlags flags=0) | |
| CSeq_id (E_Choice the_type, const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr, TParseFlags flags=0, EPDBMolFormat pdbfmt=ePDB_AsIs) | |
| Construct a Seq-id from a flat representation. More... | |
| CSeq_id (E_Choice the_type, const CTempString &acc_in, TParseFlags flags, EPDBMolFormat pdbfmt=ePDB_AsIs) | |
| CSeq_id (EFastaAsTypeAndContent, E_Choice the_type, const CTempString &the_content, TParseFlags flags=0) | |
| Construct a Seq-id from a FASTA string with the leading (type) component already parsed out. More... | |
| CSeq_id & | Set (const CTempString &the_id, TParseFlags flags=fParse_AnyRaw, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| Reassign based on flat specifications; arguments interpreted as with constructors. More... | |
| CSeq_id & | Set (const CDbtag &tag, bool set_as_general=true, TParseFlags flags=0) |
| CSeq_id & | Set (const CDbtag &tag, TParseFlags flags) |
| CSeq_id & | Set (E_Choice the_type, TIntId int_seq_id, TParseFlags flags=0) |
| CSeq_id & | Set (E_Choice the_type, const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr, TParseFlags flags=0, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| CSeq_id & | Set (E_Choice the_type, const CTempString &acc_in, TParseFlags flags, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| CSeq_id & | Set (EFastaAsTypeAndContent, E_Choice the_type, const CTempString &the_content, TParseFlags flags=0) |
| virtual | ~CSeq_id (void) |
| Destructor. More... | |
| EAccessionInfo | IdentifyAccession (TParseFlags flags=fParse_AnyRaw|fParse_AnyLocal) const |
| bool | Match (const CSeq_id &sid2) const |
| Match() - TRUE if SeqIds are equivalent. More... | |
| E_SIC | Compare (const CSeq_id &sid2) const |
| Compare() - more general. More... | |
| int | CompareOrdered (const CSeq_id &sid2) const |
| bool | operator< (const CSeq_id &sid2) const |
| const CTextseq_id * | GetTextseq_Id (void) const |
| Return embedded CTextseq_id, if any. More... | |
| virtual void | WriteAsFasta (ostream &out) const |
| Implement serializable interface. More... | |
| void | WriteAsFasta (ostream &out, EPDBMolFormat pdbfmt) const |
| CProxy | DumpAsFasta (void) const |
| const string | AsFastaString (EPDBMolFormat pdbfmt=ePDB_AsIs) const |
| void | GetLabel (string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default, EPDBMolFormat pdbfmt=ePDB_AsIs) const |
| Append a label for this Seq-id to the supplied string. More... | |
| void | GetLabel (string *label, int *version, ELabelType type=eDefault, EPDBMolFormat pdbfmt=ePDB_AsIs) const |
| Append a label for this Seq-id to the supplied string, splitting out the version to a separate output parameter. More... | |
| string | GetSeqIdString (bool with_version=false, EPDBMolFormat pdbfmt=ePDB_AsIs) const |
| Return seqid string with optional version for text seqid type. More... | |
| string | GetSeqIdString (int *version, EPDBMolFormat pdbfmt=ePDB_AsIs) const |
| Return seqid string for text seqid type with separate integer version. More... | |
| DECLARE_SAFE_FLAGS_TYPE (EAdjustScoreFlags, TAdjustScoreFlags) | |
| int | AdjustScore (int base_score, TAdjustScoreFlags flags=TAdjustScoreFlags()) const |
| int | StrictAdjustScore (int base_score) const |
| int | BaseTextScore (void) const |
| int | BaseBestRankScore (void) const |
| int | BaseWorstRankScore (void) const |
| int | BaseFastaAAScore (void) const |
| int | BaseFastaNAScore (void) const |
| int | BaseBlastScore (void) const |
| int | TextScore (void) const |
| int | BestRankScore (void) const |
| int | WorstRankScore (void) const |
| int | FastaAAScore (void) const |
| int | FastaNAScore (void) const |
| int | BlastScore (void) const |
| int | StrictTextScore (void) const |
| int | StrictBestRankScore (void) const |
| int | StrictFastaAAScore (void) const |
| int | StrictFastaNAScore (void) const |
| int | StrictBlastScore (void) const |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Optimized implementation of CSerialObject::Assign, which is not so efficient. More... | |
| void | GetMatchingIds (TSeqIdHandles &matches) const |
| Collect partially matching seq-ids: no-version, no-name etc. More... | |
| void | GetMatchingTextseqIds (TSeqIdHandles &matches) const |
| Collect partially matching textseq-ids. More... | |
| string | 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... | |
| bool | IsAllowedSNPScaleLimit (ESNPScaleLimit scale_limit) const |
| Public Member Functions inherited from CSeq_id_Base | |
| CSeq_id_Base (void) | |
| virtual | ~CSeq_id_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| virtual void | ResetSelection (void) |
| Reset the selection (set it to e_not_set). More... | |
| E_Choice | Which (void) const |
| Which variant is currently selected. More... | |
| void | CheckSelected (E_Choice index) const |
| Verify selection, throw exception if it differs from the expected. More... | |
| void | ThrowInvalidSelection (E_Choice index) const |
| Throw 'InvalidSelection' exception. More... | |
| void | Select (E_Choice index, EResetVariant reset=eDoResetVariant) |
| Select the requested variant if needed. More... | |
| void | Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) |
| Select the requested variant if needed, allocating CObject variants from memory pool. More... | |
| bool | IsLocal (void) const |
| Check if variant Local is selected. More... | |
| const TLocal & | GetLocal (void) const |
| Get the variant data. More... | |
| TLocal & | SetLocal (void) |
| Select the variant. More... | |
| void | SetLocal (TLocal &value) |
| Select the variant and set its data. More... | |
| bool | IsGibbsq (void) const |
| Check if variant Gibbsq is selected. More... | |
| TGibbsq | GetGibbsq (void) const |
| Get the variant data. More... | |
| TGibbsq & | SetGibbsq (void) |
| Select the variant. More... | |
| void | SetGibbsq (TGibbsq value) |
| Select the variant and set its data. More... | |
| bool | IsGibbmt (void) const |
| Check if variant Gibbmt is selected. More... | |
| TGibbmt | GetGibbmt (void) const |
| Get the variant data. More... | |
| TGibbmt & | SetGibbmt (void) |
| Select the variant. More... | |
| void | SetGibbmt (TGibbmt value) |
| Select the variant and set its data. More... | |
| bool | IsGiim (void) const |
| Check if variant Giim is selected. More... | |
| const TGiim & | GetGiim (void) const |
| Get the variant data. More... | |
| TGiim & | SetGiim (void) |
| Select the variant. More... | |
| void | SetGiim (TGiim &value) |
| Select the variant and set its data. More... | |
| bool | IsGenbank (void) const |
| Check if variant Genbank is selected. More... | |
| const TGenbank & | GetGenbank (void) const |
| Get the variant data. More... | |
| TGenbank & | SetGenbank (void) |
| Select the variant. More... | |
| void | SetGenbank (TGenbank &value) |
| Select the variant and set its data. More... | |
| bool | IsEmbl (void) const |
| Check if variant Embl is selected. More... | |
| const TEmbl & | GetEmbl (void) const |
| Get the variant data. More... | |
| TEmbl & | SetEmbl (void) |
| Select the variant. More... | |
| void | SetEmbl (TEmbl &value) |
| Select the variant and set its data. More... | |
| bool | IsPir (void) const |
| Check if variant Pir is selected. More... | |
| const TPir & | GetPir (void) const |
| Get the variant data. More... | |
| TPir & | SetPir (void) |
| Select the variant. More... | |
| void | SetPir (TPir &value) |
| Select the variant and set its data. More... | |
| bool | IsSwissprot (void) const |
| Check if variant Swissprot is selected. More... | |
| const TSwissprot & | GetSwissprot (void) const |
| Get the variant data. More... | |
| TSwissprot & | SetSwissprot (void) |
| Select the variant. More... | |
| void | SetSwissprot (TSwissprot &value) |
| Select the variant and set its data. More... | |
| bool | IsPatent (void) const |
| Check if variant Patent is selected. More... | |
| const TPatent & | GetPatent (void) const |
| Get the variant data. More... | |
| TPatent & | SetPatent (void) |
| Select the variant. More... | |
| void | SetPatent (TPatent &value) |
| Select the variant and set its data. More... | |
| bool | IsOther (void) const |
| Check if variant Other is selected. More... | |
| const TOther & | GetOther (void) const |
| Get the variant data. More... | |
| TOther & | SetOther (void) |
| Select the variant. More... | |
| void | SetOther (TOther &value) |
| Select the variant and set its data. More... | |
| bool | IsGeneral (void) const |
| Check if variant General is selected. More... | |
| const TGeneral & | GetGeneral (void) const |
| Get the variant data. More... | |
| TGeneral & | SetGeneral (void) |
| Select the variant. More... | |
| void | SetGeneral (TGeneral &value) |
| Select the variant and set its data. More... | |
| bool | IsGi (void) const |
| Check if variant Gi is selected. More... | |
| TGi | GetGi (void) const |
| Get the variant data. More... | |
| TGi & | SetGi (void) |
| Select the variant. More... | |
| void | SetGi (TGi value) |
| Select the variant and set its data. More... | |
| bool | IsDdbj (void) const |
| Check if variant Ddbj is selected. More... | |
| const TDdbj & | GetDdbj (void) const |
| Get the variant data. More... | |
| TDdbj & | SetDdbj (void) |
| Select the variant. More... | |
| void | SetDdbj (TDdbj &value) |
| Select the variant and set its data. More... | |
| bool | IsPrf (void) const |
| Check if variant Prf is selected. More... | |
| const TPrf & | GetPrf (void) const |
| Get the variant data. More... | |
| TPrf & | SetPrf (void) |
| Select the variant. More... | |
| void | SetPrf (TPrf &value) |
| Select the variant and set its data. More... | |
| bool | IsPdb (void) const |
| Check if variant Pdb is selected. More... | |
| const TPdb & | GetPdb (void) const |
| Get the variant data. More... | |
| TPdb & | SetPdb (void) |
| Select the variant. More... | |
| void | SetPdb (TPdb &value) |
| Select the variant and set its data. More... | |
| bool | IsTpg (void) const |
| Check if variant Tpg is selected. More... | |
| const TTpg & | GetTpg (void) const |
| Get the variant data. More... | |
| TTpg & | SetTpg (void) |
| Select the variant. More... | |
| void | SetTpg (TTpg &value) |
| Select the variant and set its data. More... | |
| bool | IsTpe (void) const |
| Check if variant Tpe is selected. More... | |
| const TTpe & | GetTpe (void) const |
| Get the variant data. More... | |
| TTpe & | SetTpe (void) |
| Select the variant. More... | |
| void | SetTpe (TTpe &value) |
| Select the variant and set its data. More... | |
| bool | IsTpd (void) const |
| Check if variant Tpd is selected. More... | |
| const TTpd & | GetTpd (void) const |
| Get the variant data. More... | |
| TTpd & | SetTpd (void) |
| Select the variant. More... | |
| void | SetTpd (TTpd &value) |
| Select the variant and set its data. More... | |
| bool | IsGpipe (void) const |
| Check if variant Gpipe is selected. More... | |
| const TGpipe & | GetGpipe (void) const |
| Get the variant data. More... | |
| TGpipe & | SetGpipe (void) |
| Select the variant. More... | |
| void | SetGpipe (TGpipe &value) |
| Select the variant and set its data. More... | |
| bool | IsNamed_annot_track (void) const |
| Check if variant Named_annot_track is selected. More... | |
| const TNamed_annot_track & | GetNamed_annot_track (void) const |
| Get the variant data. More... | |
| TNamed_annot_track & | SetNamed_annot_track (void) |
| Select the variant. More... | |
| void | SetNamed_annot_track (TNamed_annot_track &value) |
| Select the variant and set its data. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More... | |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) noexcept |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const noexcept |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const noexcept |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const noexcept |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const noexcept |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const noexcept |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
| Public Member Functions inherited from CSerializable | |
| virtual | ~CSerializable () |
| CProxy | Dump (EOutputType output_type) const |
Static Public Member Functions | |
| static E_Choice | WhichInverseSeqId (const CTempString &SeqIdCode) |
| Converts a string to a choice, no need to require a member. More... | |
| static const char * | WhichFastaTag (E_Choice choice) |
| Converts a choice to a FASTA tag, with no trailing vertical bar. More... | |
| static E_Choice | GetAccType (EAccessionInfo info) |
| static EAccessionInfo | 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... | |
| static void | LoadAccessionGuide (const string &filename, TLoadFlags flags=0) |
| static void | LoadAccessionGuide (ILineReader &in, const CTime &t=CCurrentTime(), TLoadFlags flags=0) |
| static bool | RefreshAccessionGuide (TLoadFlags flags=fFullyLoadSpecials) |
| Bails (returning false) if the file hasn't changed; otherwise, loads it and returns true (or throws an exception if loading somehow fails). More... | |
| static EAssessment | AssessAccession (const CTempString &accession) |
| static string | GetStringDescr (const CBioseq &bioseq, EStringFormat fmt, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| static CNcbiOstream & | WriteAsFasta (CNcbiOstream &ostr, const CBioseq &bioseq, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| Write a bioseq's IDs in FASTA format. More... | |
| static bool | 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 | 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 | ParseIDs (CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| Parse a string representing one or more Seq-ids, appending the results to IDS. More... | |
| static bool | IsValid (const CBioseq::TId &ids, TParseFlags flags=fParse_Default) |
| static bool | IsValid (const CSeq_id &id, TParseFlags flags=fParse_Default) |
| static SIZE_TYPE | ParseFastaIds (CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false, EPDBMolFormat pdbfmt=ePDB_AsIs) |
| Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS. More... | |
| static int | Score (const CRef< CSeq_id > &id) |
| Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp> More... | |
| static int | ConstScore (const CConstRef< CSeq_id > &id) |
| static int | BestRank (const CRef< CSeq_id > &id) |
| static int | WorstRank (const CRef< CSeq_id > &id) |
| static int | FastaAARank (const CRef< CSeq_id > &id) |
| static int | FastaNARank (const CRef< CSeq_id > &id) |
| static int | BlastRank (const CRef< CSeq_id > &id) |
| static int | StrictScore (const CRef< CSeq_id > &id) |
| static int | StrictBestRank (const CRef< CSeq_id > &id) |
| static int | StrictFastaAARank (const CRef< CSeq_id > &id) |
| static int | StrictFastaNARank (const CRef< CSeq_id > &id) |
| static int | StrictBlastRank (const CRef< CSeq_id > &id) |
| static bool | 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 | AvoidGi (void) |
| Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI). More... | |
| static const char * | GetSNPScaleLimit_Name (ESNPScaleLimit value) |
| static ESNPScaleLimit | GetSNPScaleLimit_Value (const string &name) |
| Static Public Member Functions inherited from CSeq_id_Base | |
| static string | SelectionName (E_Choice index) |
| Retrieve selection name (for diagnostic purposes). More... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
Static Public Attributes | |
| static const size_t | kMaxLocalIDLength = 50 |
| ID length restrictions. More... | |
| static const size_t | kMaxGeneralDBLength = 20 |
| static const size_t | kMaxGeneralTagLength = 50 |
| static const size_t | kMaxAccessionLength = 30 |
| Static Public Attributes inherited from CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
Private Types | |
| enum | ETypeVariant { eTV_plain , eTV_tr , eTV_pgp } |
| typedef CSeq_id_Base | Tparent |
Private Member Functions | |
| void | x_Reject (const CDiagCompileInfo &info, int subcode, TParseFlags flags, const CTempString &msg) |
| E_Choice | x_Init (list< CTempString > &fasta_pieces, E_Choice type, ETypeVariant tv, TParseFlags flags, EPDBMolFormat pdbfmt) |
| CSeq_id (const CSeq_id &) | |
| CSeq_id & | operator= (const CSeq_id &) |
| void | x_WriteContentAsFasta (ostream &out, EPDBMolFormat pdbfmt) const |
Static Private Member Functions | |
| static ETypeVariant | x_IdentifyTypeVariant (E_Choice type, const CTempString &str) |
| static EAccessionInfo | x_IdentifyAccession (const CTempString &main_acc, TParseFlags flags, bool has_version) |
Additional Inherited Members | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Protected Member Functions inherited from CSerializable | |
| virtual void | WriteAsFasta (CNcbiOstream &out) const |
| virtual void | WriteAsAsnText (CNcbiOstream &out) const |
| virtual void | WriteAsAsnBinary (CNcbiOstream &out) const |
| virtual void | WriteAsXML (CNcbiOstream &out) const |
| virtual void | WriteAsString (CNcbiOstream &out) const |
Detailed Description
Definition at line 70 of file Seq_id.hpp.
The documentation for this class was generated from the following files:
- include/objects/seqloc/Seq_id.hpp
- src/objects/seqloc/Seq_id.cpp
