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#define twochars(a, b) Uint2((a) << 8 | (b)) #define twocommas twochars(',',',') #define twospaces twochars(' ',' ') #define twosemicolons 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(';',' ') SAFE_CONST_STATIC_STRING (kLegalPathChars, "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_-.") bool IsPartOfUrl (const string &sentence, size_t pos) static bool s_RunOfStars (string &s, SIZE_TYPE start, SIZE_TYPE length) void ExpandTildes (string &s, ETildeStyle style) void ConvertQuotes (string &str) string ConvertQuotes (const string &str) bool StripSpaces (string &str) bool RemovePeriodFromEnd (string &str, bool keep_ellipsis) void AddPeriod (string &str) void TrimSpaces (string &str, size_t indent) string & CompressSpaces (string &str, const bool trim_beginning, const bool trim_end) bool TrimSpacesAndJunkFromEnds (string &str, bool allow_ellipsis) void TrimSpacesAndJunkFromEnds (string &result, const CTempString &str, bool allow_ellipsis) void CleanAndCompress (string &dest, const CTempString &instr) static bool s_IsWholeWord (const string &str, size_t pos) void JoinString (string &to, const string &prefix, const string &str, bool noRedundancy) string JoinString (const list< string > &l, const string &delim, bool noRedundancy) static bool s_IsValidDotVersion (const string &accn) bool IsValidAccession (const string &accn, EAccValFlag flag) void DateToString (const CDate &date, string &str, EDateToString format_choice) void GetDeltaSeqSummary (const CBioseq_Handle &seq, SDeltaSeqSummary &summary) SAFE_CONST_STATIC_STRING (kTS_concept_trans, "conceptual translation") SAFE_CONST_STATIC_STRING (kTS_concept_trans_a, "conceptual translation supplied by author") SAFE_CONST_STATIC_STRING (kTS_both, "conceptual translation with partial peptide sequencing") SAFE_CONST_STATIC_STRING (kTS_seq_pept, "direct peptide sequencing") SAFE_CONST_STATIC_STRING (kTS_seq_pept_homol, "sequenced peptide, ordered by homology") SAFE_CONST_STATIC_STRING (kTS_seq_pept_overlap, "sequenced peptide, ordered by overlap") const string & GetTechString (int tech) bool s_IsModelEvidanceUop (const CUser_object &uo) const CUser_object * s_FindModelEvidanceUop (const CUser_object &uo) bool s_GetModelEvidance (const CBioseq_Handle &bsh, SModelEvidance &me) bool GetModelEvidance (const CBioseq_Handle &bsh, SModelEvidance &me) const char * GetAAName (unsigned char aa, bool is_ascii) EResolveOrder GetResolveOrder (CScope &scope, const CSeq_id_Handle &mrna, const CSeq_id_Handle &prot, CBioseq_Handle &mrna_bsh, CBioseq_Handle &prot_bsh) bool ConvertQuotesNotInHTMLTags (string &str) void TryToSanitizeHtml (string &str) void TryToSanitizeHtml (std::string &result, const CTempString &str) void TryToSanitizeHtmlList (std::list< std::string > &strs) bool CommentHasSuspiciousHtml (const string &str) ◆ bracket_space ◆ comma_space ◆ semicolon_space ◆ space_bracket ◆ space_comma ◆ space_semicolon ◆ twochars ◆ twocommas ◆ twosemicolons ◆ twospaces ◆ AddPeriod() void AddPeriod ( string & str )Definition at line 377 of file objutil.cpp.
References str().
Referenced by CCommentItem::AddPeriod(), CFlatOrgModQVal::Format(), CFlatSubSourceQVal::Format(), CCommentItem::GetStringForHTGS(), CCommentItem::GetStringForUnordered(), s_NoteFinalize(), CCommentItem::x_GatherDescInfo(), CDeflineItem::x_GatherInfo(), CReferenceItem::x_GatherRemark(), CFlatGatherer::x_GBBSourceComment(), CFlatGatherer::x_HTGSComments(), CCommentItem::x_SetCommentWithURLlinks(), and CSourceItem::x_SetSource().
◆ CleanAndCompress()Definition at line 823 of file objutil.cpp.
References bracket_space, comma_space, CTempString::data(), in(), next(), out(), semicolon_space, CTempString::size(), space_bracket, space_comma, space_semicolon, twocommas, twosemicolons, and twospaces.
Referenced by CFlatStringQVal::CFlatStringQVal(), CFormatQual::CFormatQual(), CFlatOrgModQVal::Format(), CFlatSubSourceQVal::Format(), CReferenceItem::FormatAffil(), s_FormatPatent(), s_GetGOText(), CGenbankFormatter::x_Authors(), CDeflineItem::x_GatherInfo(), and CFlatItemFormatter::x_GetKeywords().
◆ CommentHasSuspiciousHtml() ◆ CompressSpaces() ◆ ConvertQuotes() [1/2] ◆ ConvertQuotes() [2/2] void ConvertQuotes ( string & str )Definition at line 240 of file objutil.cpp.
References str().
Referenced by ConvertQuotes(), CFlatSubSourceQVal::Format(), CReferenceItem::FormatAffil(), CCommentItem::GetStringForHTGS(), CCommentItem::GetStringForUnordered(), s_FormatThesis(), s_ParseParentQual(), CFeatureItem::x_AddQualSeqfeatNote(), CReferenceItem::x_CleanData(), CCommentItem::x_GatherDescInfo(), CDeflineItem::x_GatherInfo(), and CCommentItem::x_SetCommentWithURLlinks().
◆ ConvertQuotesNotInHTMLTags() ◆ DateToString()Definition at line 1238 of file objutil.cpp.
References eDateToString_cit_sub, eDateToString_patent, format, CDate::GetDate(), str(), and NStr::ToUpper().
Referenced by CEmblFormatter::FormatDate(), s_FormatCitSub(), s_FormatPatent(), s_GetDate(), CDBSourceItem::x_AddPDBBlock(), and CLocusItem::x_SetDate().
◆ ExpandTildes()Definition at line 152 of file objutil.cpp.
References eTilde_comment, eTilde_newline, eTilde_note, eTilde_space, eTilde_tilde, isdigit(), IsPartOfUrl(), next(), NPOS, result, and s_RunOfStars().
Referenced by CCommentItem::CCommentItem(), CFlatStringQVal::Format(), CFlatOrgModQVal::Format(), CFlatSubSourceQVal::Format(), s_GetStrForStructuredComment(), s_NoteFinalize(), s_ParseParentQual(), CReferenceItem::x_CleanData(), CFlatItemFormatter::x_GetKeywords(), CCommentItem::x_SetComment(), and CCommentItem::x_SetCommentWithURLlinks().
◆ GetAAName() const char* GetAAName ( unsigned char aa, bool is_ascii ) ◆ GetDeltaSeqSummary()Definition at line 1257 of file objutil.cpp.
References CSeq_literal_Base::CanGetFuzz(), CSeq_literal_Base::CanGetLength(), CSeq_literal_Base::CanGetSeq_data(), CSeq_data_Base::e_Gap, CDelta_seq_Base::e_Literal, CDelta_seq_Base::e_Loc, CInt_fuzz_Base::eLim_unk, CSeq_inst_Base::eRepr_delta, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_literal_Base::GetFuzz(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Repr(), GetLength(), CSeq_literal_Base::GetLength(), CInt_fuzz_Base::GetLim(), CBioseq_Handle::GetScope(), CSeq_literal_Base::GetSeq_data(), CSeq_ext_Base::IsDelta(), CInt_fuzz_Base::IsLim(), CSeq_loc_Base::IsNull(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Repr(), len, next(), SDeltaSeqSummary::num_faked_gaps, SDeltaSeqSummary::num_gaps, SDeltaSeqSummary::num_segs, SDeltaSeqSummary::residues, SDeltaSeqSummary::text, text(), unk, and CSeq_data_Base::Which().
Referenced by CCommentItem::GetStringForHTGS(), and CCommentItem::GetStringForUnordered().
◆ GetModelEvidance() ◆ GetResolveOrder()Definition at line 1571 of file objutil.cpp.
References CScope::AddDefaults(), eResolve_NotFound, eResolve_ProtFirst, eResolve_RnaFirst, CScope::GetBioseqHandle(), CSeq_entry_Handle::GetBioseqHandle(), CObjectManager::GetInstance(), CBioseq_Handle::GetTopLevelEntry(), and prot.
Referenced by CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), and CFlatGatherer::x_GatherFeaturesOnWholeLocation().
◆ GetTechString() ◆ IsPartOfUrl() ◆ IsValidAccession() ◆ JoinString() [1/2] ◆ JoinString() [2/2] ◆ RemovePeriodFromEnd() ◆ s_FindModelEvidanceUop() ◆ s_GetModelEvidance()Definition at line 1441 of file objutil.cpp.
References SModelEvidance::assembly, data, CSeqdesc_Base::e_User, SModelEvidance::estEv, CTextseq_id_Base::GetAccession(), CScope::GetAccVer(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetFields(), CSeq_id_Handle::GetGiHandle(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::GetInts(), CUser_field_Base::GetLabel(), CUser_field_Base::GetNum(), CBioseq_Handle::GetScope(), CSeq_id_Handle::GetSeqIdOrNull(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), SModelEvidance::gi, GI_FROM, CUser_field::HasField(), CUser_object::HasField(), NStr::IntToString(), CUser_field_Base::C_Data::IsFields(), CUser_field_Base::C_Data::IsInt(), CUser_field_Base::C_Data::IsInts(), CTextseq_id_Base::IsSetAccession(), CUser_field_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CUser_field_Base::IsSetNum(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), ITERATE, label, SModelEvidance::method, SModelEvidance::mrnaEv, SModelEvidance::name, CConstRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::Reset(), result, s_FindModelEvidanceUop(), SModelEvidance::span, and ZERO_GI.
Referenced by GetModelEvidance().
◆ s_IsModelEvidanceUop() ◆ s_IsValidDotVersion() ◆ s_IsWholeWord() ◆ s_RunOfStars() ◆ SAFE_CONST_STATIC_STRING() [1/7] SAFE_CONST_STATIC_STRING ( kLegalPathChars , "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_-." ) ◆ SAFE_CONST_STATIC_STRING() [2/7] SAFE_CONST_STATIC_STRING ( kTS_both , "conceptual translation with partial peptide sequencing" ) ◆ SAFE_CONST_STATIC_STRING() [3/7] SAFE_CONST_STATIC_STRING ( kTS_concept_trans , "conceptual translation" ) ◆ SAFE_CONST_STATIC_STRING() [4/7] SAFE_CONST_STATIC_STRING ( kTS_concept_trans_a , "conceptual translation supplied by author" ) ◆ SAFE_CONST_STATIC_STRING() [5/7] SAFE_CONST_STATIC_STRING ( kTS_seq_pept , "direct peptide sequencing" ) ◆ SAFE_CONST_STATIC_STRING() [6/7] SAFE_CONST_STATIC_STRING ( kTS_seq_pept_homol , "sequenced peptide, ordered by homology" ) ◆ SAFE_CONST_STATIC_STRING() [7/7] SAFE_CONST_STATIC_STRING ( kTS_seq_pept_overlap , "sequenced peptide, ordered by overlap" ) ◆ StripSpaces() ◆ TrimSpaces() void TrimSpaces ( string & str, size_t indent ) ◆ TrimSpacesAndJunkFromEnds() [1/2] ◆ TrimSpacesAndJunkFromEnds() [2/2]Definition at line 475 of file objutil.cpp.
References _ASSERT, int, isalnum(), and str().
Referenced by CCommentItem::CCommentItem(), CFlatXrefQVal::Format(), s_FormatJournal(), s_NoteFinalize(), CFeatureItem::x_AddQualProtComment(), CFeatureItem::x_AddQualProtDesc(), CFeatureItem::x_AddQualProtNote(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsProt(), CCommentItem::x_GatherDescInfo(), and CGenbankFormatter::x_SmartWrapQuals().
◆ TryToSanitizeHtml() [1/2] ◆ TryToSanitizeHtml() [2/2] void TryToSanitizeHtml ( string & str ) ◆ TryToSanitizeHtmlList() void TryToSanitizeHtmlList ( std::list< std::string > & strs ) ◆ kAANames Initial value:= {
"---", "Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
"Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr", "Val",
"Trp", "OTHER", "Tyr", "Glx", "Sec", "TERM", "Pyl", "Xle"
}
Definition at line 1552 of file objutil.cpp.
Referenced by GetAAName().
◆ strDocLink ◆ strLinkBaseEntrezViewer const char* strLinkBaseEntrezViewer ◆ strLinkBaseExpasy const char* strLinkBaseExpasy ◆ strLinkBaseGeneOntology const char* strLinkBaseGeneOntology ◆ strLinkBaseGeneOntologyRef const char* strLinkBaseGeneOntologyRef Initial value:=
"http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:"
Definition at line 1660 of file objutil.cpp.
Referenced by s_GetGOText().
◆ strLinkBaseGenomePrj const char* strLinkBaseGenomePrj ◆ strLinkBaseLatLon const char* strLinkBaseLatLon Initial value:=
"https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html"
Definition at line 1656 of file objutil.cpp.
◆ strLinkBaseNuc const char* strLinkBaseNuc ◆ strLinkBaseNucSearch const char* strLinkBaseNucSearch Initial value:=
"https://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&term="
Definition at line 1652 of file objutil.cpp.
◆ strLinkBaseProt const char* strLinkBaseProt ◆ strLinkBasePubmed const char* strLinkBasePubmed ◆ strLinkBaseTaxonomy const char* strLinkBaseTaxonomy Initial value:=
"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?"
Definition at line 1644 of file objutil.cpp.
◆ strLinkBaseTransTable const char* strLinkBaseTransTable ◆ strLinkBaseUniProt const char* strLinkBaseUniProt ◆ strLinkBaseUSPTO const char* strLinkBaseUSPTORetroSearch is an open source project built by @garambo | Open a GitHub Issue
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