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◆ THIS_FILE #define THIS_FILE "utilfeat.cpp"Definition at line 60 of file utilfeat.cpp.
◆ CheckDelGbblockSource() ◆ CheckDelGbblockSourceFromDescrs()Definition at line 331 of file utilfeat.cpp.
References NStr::EqualNocase(), fta_StringCpy(), CGB_block_Base::GetSource(), len, MemFree(), names, CGB_block_Base::ResetSource(), ShrinkSpaces(), StringChr, StringEquN(), StringEquNI(), StringLen(), StringMatchIcase(), StringSave, t, and valid_organelle.
Referenced by CheckDelGbblockSource().
◆ CpTheQualValue()Definition at line 120 of file utilfeat.cpp.
References ERR_FEATURE_UnknownQualSpelling, FtaErrPost, NStr::Sanitize(), SEV_ERROR, and val.
Referenced by EndAdded(), ErrByteStorePtr(), GetProtRefAnnot(), GetProtRefDescr(), GetProtRefSeqId(), GetRnaRef(), InternalStopCodon(), SpProcFeatBlk(), and SrchGene().
◆ DeleteQual() ◆ GetGenomeInfo()Definition at line 225 of file utilfeat.cpp.
References CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_extrachrom, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_macronuclear, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_plasmid, CBioSource_Base::eGenome_plastid, i, ParFlat_GImod, CBioSource_Base::SetGenome(), and StringMatchIcase().
Referenced by FakeEmblBioSources(), FakeGenBankBioSources(), and XMLFakeBioSources().
◆ GetQualValueAa() Uint1 GetQualValueAa ( string_view qval, bool checkseq ) ◆ GetTaxnameName() ◆ GetTaxnameNameFromDescrs()Definition at line 256 of file utilfeat.cpp.
References COrgMod_Base::eSubtype_acronym, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_old_name, CSubSource_Base::eSubtype_other, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, COrg_ref_Base::GetCommon(), COrgName_Base::GetMod(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetCommon(), COrgName_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), mod(), names, and StringIStr().
Referenced by GetTaxnameName().
◆ GetTheQualValue()Definition at line 147 of file utilfeat.cpp.
References ERR_FEATURE_UnknownQualSpelling, FtaErrPost, SEV_ERROR, tata_save(), and val.
Referenced by FixAnnot(), fta_parse_rrna_feat(), GetProtRefAnnot(), GetRnaRef(), ParseSourceFeat(), ProcFeatBlk(), and SrchGene().
◆ location_to_string()Definition at line 473 of file utilfeat.cpp.
References CSeq_loc::GetLabel(), and MakeLocStrCompatible().
Referenced by check_end_internal(), check_short_CDS(), CkCdRegion(), CkEndStop(), CkProteinTransl(), ErrByteStorePtr(), fta_check_codon_quals(), fta_check_exception(), GetProtRefAnnot(), GetProtRefSeqId(), IfOnlyStopCodon(), InternalStopCodon(), location_to_string_or_unknown(), and SrchCdRegion().
◆ MakeLocStrCompatible() void MakeLocStrCompatible ( string & str ) ◆ MaybeCutGbblockSource() void MaybeCutGbblockSource ( TEntryList & seq_entries ) ◆ SeqLocHaveFuzz() ◆ USING_SCOPE() ◆ ParFlat_GImod const char* ParFlat_GImod[] Initial value:= {
"Mitochondr",
"Chloroplast",
"Kinetoplas",
"Cyanelle",
"Chromoplast",
"Plastid",
"Macronuclear",
"Extrachrom",
"Plasmid",
"Leucoplast",
"Apicoplast",
nullptr
}
Definition at line 65 of file utilfeat.cpp.
Referenced by GetGenomeInfo().
◆ valid_organelle const char* valid_organelle[] Initial value:= {
"apicoplast",
"chloroplast",
"chromatophore",
"chromoplast",
"cyanelle",
"hydrogenosome",
"kinetoplast",
"leucoplast",
"mitochondrion",
"nucleomorph",
"plastid",
"proplastid",
nullptr
}
Definition at line 80 of file utilfeat.cpp.
Referenced by CheckDelGbblockSourceFromDescrs().
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