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NCBI C++ ToolKit: include/objmgr/util/objutil.hpp File Reference

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void  ExpandTildes (string &s, ETildeStyle style)   void  ConvertQuotes (string &str)   string  ConvertQuotes (const string &str)   void  JoinString (string &to, const string &prefix, const string &str, bool noRedundancy=true)   string  JoinString (const list< string > &l, const string &delim, bool noRedundancy=true)   bool  StripSpaces (string &str)   bool  TrimSpacesAndJunkFromEnds (string &str, bool allow_ellipsis=false)   void  TrimSpacesAndJunkFromEnds (string &result, const CTempString &str, bool allow_ellipsis=false)   void  TrimSpaces (string &str, size_t indent=0)   void  CleanAndCompress (string &dest, const CTempString &instr)   string &  CompressSpaces (string &str, const bool trim_beginning=true, const bool trim_end=true)   bool  RemovePeriodFromEnd (string &str, bool keep_ellipsis=true)   void  AddPeriod (string &str)   bool  IsValidAccession (const string &accn, EAccValFlag flag=eValidateAcc)   void  DateToString (const CDate &date, string &str, EDateToString format_choice=eDateToString_regular)   void  GetDeltaSeqSummary (const CBioseq_Handle &seq, SDeltaSeqSummary &summary)   const string &  GetTechString (int tech)   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)   template<typename T > void  NcbiId (CNcbiOstream &os, const T &id, bool html=false)   bool  ConvertQuotesNotInHTMLTags (string &str)   void  TryToSanitizeHtml (std::string &str)   void  TryToSanitizeHtml (std::string &result, const CTempString &str)   void  TryToSanitizeHtmlList (std::list< std::string > &strs)   bool  CommentHasSuspiciousHtml (const string &str)   ◆ EAccValFlag Enumerator eValidateAcc  eValidateAccDotVer 

Definition at line 94 of file objutil.hpp.

◆ EDateToString Enumerator eDateToString_regular  eDateToString_cit_sub  eDateToString_patent 

Definition at line 103 of file objutil.hpp.

◆ EResolveOrder Enumerator eResolve_NotFound  eResolve_RnaFirst  eResolve_ProtFirst 

Definition at line 159 of file objutil.hpp.

◆ ETildeStyle Enumerator eTilde_tilde  eTilde_space  eTilde_newline  eTilde_comment  eTilde_note 

Definition at line 47 of file objutil.hpp.

◆ 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() ◆ IsValidAccession() ◆ JoinString() [1/2] ◆ JoinString() [2/2] ◆ NcbiId() ◆ RemovePeriodFromEnd() ◆ StripSpaces() ◆ TrimSpaces() void TrimSpaces ( string &  str, size_t  indent = 0  ) ◆ 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]

Referenced by CGenbankFormatter::FormatAccession(), CGenbankFormatter::FormatComment(), CGenbankFormatter::FormatDBSource(), CGenbankFormatter::FormatDefline(), CGenbankFormatter::FormatGenomeProject(), CGenbankFormatter::FormatLocus(), CGenbankFormatter::FormatOrigin(), CGenbankFormatter::FormatPrimary(), CHTMLFormatterEx::FormatTaxid(), CGenbankFormatter::FormatTSA(), CGenbankFormatter::FormatVersion(), CGenbankFormatter::FormatWGS(), CGenbankFormatter::x_Authors(), CGenbankFormatter::x_Consortium(), CGenbankFormatter::x_FormatOrganismLine(), CGenbankFormatter::x_FormatSourceLine(), CGenomeProjectItem::x_GatherInfo(), CGenbankFormatter::x_Journal(), CGenbankFormatter::x_Reference(), CGenbankFormatter::x_Remark(), CGenbankFormatter::x_SmartWrapQuals(), and CGenbankFormatter::x_Title().

◆ TryToSanitizeHtmlList() void TryToSanitizeHtmlList ( std::list< std::string > &  strs ) ◆ strDocLink ◆ strLinkBaseEntrezViewer const char* strLinkBaseEntrezViewer extern ◆ strLinkBaseExpasy const char* strLinkBaseExpasy extern ◆ strLinkBaseGeneOntology const char* strLinkBaseGeneOntology extern ◆ strLinkBaseGeneOntologyRef const char* strLinkBaseGeneOntologyRef extern ◆ strLinkBaseGenomePrj const char* strLinkBaseGenomePrj extern ◆ strLinkBaseLatLon ◆ strLinkBaseNuc const char* strLinkBaseNuc extern ◆ strLinkBaseNucSearch ◆ strLinkBaseProt const char* strLinkBaseProt extern ◆ strLinkBasePubmed const char* strLinkBasePubmed extern ◆ strLinkBaseTaxonomy ◆ strLinkBaseTransTable const char* strLinkBaseTransTable extern ◆ strLinkBaseUniProt const char* strLinkBaseUniProt extern ◆ strLinkBaseUSPTO const char* strLinkBaseUSPTO extern

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