Go to the source code of this file.
Go to the SVN repository for this file.
#define NCBI_USE_ERRCODE_X ObjMgr_SeqUtil #define SEQENTRY_HANDLE_ON_SEQENTRY_HANDLE_ITERATOR(Itr, Var) CSeq_entry_CI Itr(Var) #define FOR_EACH_SEQENTRY_HANDLE_ON_SEQENTRY_HANDLE(Itr, Var) for (SEQENTRY_HANDLE_ON_SEQENTRY_HANDLE_ITERATOR(Itr, Var); Itr; ++Itr) #define FOR_EACH_SEQID_ON_BIOSEQ_HANDLE(Itr, Var) ITERATE (CBioseq_Handle::TId, Itr, Var.GetId()) #define SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR(Itr, Var, Chs) CFeat_CI Itr(Var, CSeqFeatData::e_##Chs) #define FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE(Itr, Var, Chs) for (SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR(Itr, Var, Chs); Itr; ++Itr) #define SEQFEAT_ON_SCOPE_ITERATOR(Itr, Var, Loc, Chs) CFeat_CI Itr(Var, Loc, CSeqFeatData::e_##Chs) #define FOR_EACH_SEQFEAT_ON_SCOPE(Itr, Var, Loc, Chs) for (SEQFEAT_ON_SCOPE_ITERATOR(Itr, Var, Loc, Chs); Itr; ++Itr) #define SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR(Itr, Var, Sel) CFeat_CI Itr(Var, Sel) #define FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE(Itr, Var, Sel) for (SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR(Itr, Var, Sel); Itr; ++Itr) #define twochars(a, b) Uint2((a) << 8 | (b)) #define twocommas twochars(',',',') #define twospaces twochars(' ',' ') #define space_comma twochars(' ',',') #define space_bracket twochars(' ',')') #define bracket_space twochars('(',' ') #define space_semicolon twochars(' ',';') #define comma_space twochars(',',' ') #define semicolon_space twochars(';',' ') USING_SCOPE (objects) USING_SCOPE (sequence) USING_SCOPE (feature) void x_CleanAndCompress (string &dest, const CTempString &instr, bool isProt) static bool s_IsVirusOrPhage (const CTempString &taxname) static bool s_EndsWithStrain (const CTempString &taxname, const CTempString &strain) static string s_RemoveColonsAndWhiteSpace (string str) static string s_RemoveWhiteSpace (string str) static void s_AddVoucherAndIsolate (const CTempString &taxname, const CTempString &strain, const CTempString &specimen_voucher, const CTempString &isolate, CDefLineJoiner &joiner) static void x_FlyCG_PtoR (string &s) static CConstRef< CBioSource > x_GetSourceFeatViaCDS (const CBioseq_Handle &bsh) static string s_RemoveBracketedOrgFromEnd (string str, string taxname) static bool x_GetSegSeqInfoViaCDS (string &locus, string &product, const char *&completeness, const CBioseq_Handle &bsh) static void s_TrimMainTitle (string &str) static size_t s_TitleEndsInOrganism (string &title, CTempString taxname) ◆ bracket_space ◆ comma_space ◆ FOR_EACH_SEQENTRY_HANDLE_ON_SEQENTRY_HANDLE ◆ FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE ◆ FOR_EACH_SEQFEAT_ON_SCOPE ◆ FOR_EACH_SEQID_ON_BIOSEQ_HANDLE ◆ FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE ◆ NCBI_USE_ERRCODE_X ◆ SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR ◆ semicolon_space ◆ SEQENTRY_HANDLE_ON_SEQENTRY_HANDLE_ITERATOR ◆ SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR #define SEQFEAT_ON_BIOSEQ_HANDLE_ITERATOR ( Itr, Var, Chs ) CFeat_CI Itr(Var, CSeqFeatData::e_##Chs)Definition at line 178 of file create_defline.cpp.
◆ SEQFEAT_ON_SCOPE_ITERATOR ◆ space_bracket ◆ space_comma ◆ space_semicolon ◆ twochars ◆ twocommas ◆ twospaces ◆ EHidePart ◆ s_AddVoucherAndIsolate() ◆ s_EndsWithStrain()Definition at line 1472 of file create_defline.cpp.
References NStr::eNocase, NStr::eReverseSearch, CTempString::find(), NStr::Find(), ispunct(), isspace(), NPOS, and CTempString::size().
Referenced by s_AddVoucherAndIsolate(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().
◆ s_IsVirusOrPhage() ◆ s_RemoveBracketedOrgFromEnd() ◆ s_RemoveColonsAndWhiteSpace() ◆ s_RemoveWhiteSpace() ◆ s_TitleEndsInOrganism() ◆ s_TrimMainTitle() ◆ USING_SCOPE() [1/3] ◆ USING_SCOPE() [2/3] ◆ USING_SCOPE() [3/3] ◆ x_CleanAndCompress()Definition at line 219 of file create_defline.cpp.
References bracket_space, comma_space, CTempString::data(), in(), next(), out(), NStr::ReplaceInPlace(), semicolon_space, CTempString::size(), space_bracket, space_comma, space_semicolon, twocommas, and twospaces.
Referenced by CDeflineGenerator::GenerateDefline(), and s_RemoveBracketedOrgFromEnd().
◆ x_FlyCG_PtoR() ◆ x_GetSegSeqInfoViaCDS()Definition at line 2580 of file create_defline.cpp.
References eOverlap_Contained, CSeqFeatData::eSubtype_gene, fFGL_Content, FIELD_IS, FIELD_IS_SET, FOR_EACH_SEQFEAT_ON_SCOPE, FOR_EACH_SEQFEATXREF_ON_SEQFEAT, FOR_EACH_SYNONYM_ON_GENEREF, GET_FIELD, GetBestOverlappingFeat(), CBioseq_Handle::GetInst_Ext(), GetLabel(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetScope(), CSeq_ext_Base::GetSeg(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetPartial(), CConstRef< C, Locker >::NotEmpty(), and CSeq_loc::SetMix().
Referenced by CDeflineGenerator::x_SetTitleFromSegSeq().
◆ x_GetSourceFeatViaCDS()Definition at line 2046 of file create_defline.cpp.
References CSeq_loc::Assign(), eOverlap_SubsetRev, CSeqFeatData::eSubtype_biosrc, GetBestOverlappingFeat(), CSeqFeatData_Base::GetBiosrc(), GetCDSForProduct(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetScope(), CSeqFeatData_Base::IsBiosrc(), CSeq_feat_Base::IsSetData(), and SeqLocRevCmpl().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().
◆ s_proteinOrganellePrefix const char* s_proteinOrganellePrefix[] static Initial value:= {
"",
"",
"chloroplast",
"chromoplast",
"kinetoplast",
"mitochondrion",
"plastid",
"macronuclear",
"",
"plasmid",
"",
"",
"cyanelle",
"",
"",
"nucleomorph",
"apicoplast",
"leucoplast",
"protoplast",
"endogenous virus",
"hydrogenosome",
"",
"chromatophore"
}
Definition at line 2125 of file create_defline.cpp.
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().
◆ s_tpaPrefixList const char* s_tpaPrefixList[] static Initial value:= {
"MAG ",
"MAG:",
"MULTISPECIES:",
"TLS:",
"TPA:",
"TPA_exp:",
"TPA_inf:",
"TPA_reasm:",
"TPA_asm:",
"TPA_assembly:",
"TSA:",
"UNVERIFIED_ORG:",
"UNVERIFIED_ASMBLY:",
"UNVERIFIED_CONTAM:",
"UNVERIFIED:"
}
Definition at line 3433 of file create_defline.cpp.
Referenced by CDeflineGenerator::GenerateDefline().
◆ USING_NCBI_SCOPERetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4