#include <corelib/ncbistd.hpp>

Include dependency graph for objutil.hpp:

This graph shows which files directly or indirectly include this file:

Classes
struct	SDeltaSeqSummary

struct	SModelEvidance

Enumerations
enum	ETildeStyle { eTilde_tilde , eTilde_space , eTilde_newline , eTilde_comment , eTilde_note }

enum	EAccValFlag { eValidateAcc , eValidateAccDotVer }

enum	EDateToString { eDateToString_regular = 1 , eDateToString_cit_sub , eDateToString_patent }

enum	EResolveOrder { eResolve_NotFound , eResolve_RnaFirst , eResolve_ProtFirst }

Functions
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)

Variables
const char *	strLinkBaseNuc

const char *	strLinkBaseProt

const char *	strLinkBaseEntrezViewer

const char *	strLinkBaseTaxonomy

const char *	strLinkBaseTransTable

const char *	strLinkBasePubmed

const char *	strLinkBaseExpasy

const char *	strLinkBaseNucSearch

const char *	strLinkBaseGenomePrj

const char *	strLinkBaseLatLon

const char *	strLinkBaseGeneOntology

const char *	strLinkBaseGeneOntologyRef

const char *	strLinkBaseUSPTO

const char *	strLinkBaseUniProt

const char *	strDocLink

Enumeration Type Documentation

◆ EAccValFlag

enum EAccValFlag

Enumerator
eValidateAcc
eValidateAccDotVer

Definition at line 94 of file objutil.hpp.

◆ EDateToString

enum EDateToString

Enumerator
eDateToString_regular
eDateToString_cit_sub
eDateToString_patent

Definition at line 103 of file objutil.hpp.

◆ EResolveOrder

enum EResolveOrder

Enumerator
eResolve_NotFound
eResolve_RnaFirst
eResolve_ProtFirst

Definition at line 159 of file objutil.hpp.

◆ ETildeStyle

enum ETildeStyle

Enumerator
eTilde_tilde
eTilde_space
eTilde_newline
eTilde_comment
eTilde_note

Definition at line 47 of file objutil.hpp.

Function Documentation

◆ 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()

void CleanAndCompress	(	string &	dest,
		const CTempString &	instr
	)

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()

bool CommentHasSuspiciousHtml ( const string & str )

Definition at line 1879 of file objutil.cpp.

References ArraySize(), and str().

Referenced by CReferenceItem::x_GatherRemark(), and CFeatureItem::x_ImportQuals().

◆ CompressSpaces()

string& CompressSpaces	(	string &	str,
		const bool	trim_beginning = `true`,
		const bool	trim_end = `true`
	)

Definition at line 416 of file objutil.cpp.

References isgraph(), and str().

◆ ConvertQuotes() [1/2]

string ConvertQuotes ( const string & str )

Definition at line 246 of file objutil.cpp.

References ConvertQuotes(), and str().

◆ 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()

bool ConvertQuotesNotInHTMLTags ( string & str )

Definition at line 1774 of file objutil.cpp.

References str().

Referenced by CFlatStringQVal::Format(), CFlatOrgModQVal::Format(), CReferenceItem::x_CleanData(), and CDBSourceItem::x_GatherInfo().

◆ DateToString()

void DateToString	(	const CDate &	date,
		string &	str,
		EDateToString	format_choice = `eDateToString_regular`
	)

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()

void ExpandTildes	(	string &	s,
		ETildeStyle	style
	)

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
	)

Definition at line 1559 of file objutil.cpp.

References CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqportUtil::GetMapToIndex(), and kAANames.

Referenced by CFlatCodeBreakQVal::Format(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddFTableCdregionQuals(), and CRNAValidator::x_ValidateTrnaCodons().

◆ GetDeltaSeqSummary()

void GetDeltaSeqSummary	(	const CBioseq_Handle &	seq,
		SDeltaSeqSummary &	summary
	)

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()

bool GetModelEvidance	(	const CBioseq_Handle &	bsh,
		SModelEvidance &	me
	)

Definition at line 1534 of file objutil.cpp.

References CBioseq_Handle::GetInst_Mol(), GetNucleotideParent(), CSeq_inst::IsAa(), nuc, and s_GetModelEvidance().

Referenced by CFlatGatherer::x_IdComments().

◆ GetResolveOrder()

EResolveOrder GetResolveOrder	(	CScope &	scope,
		const CSeq_id_Handle &	mrna,
		const CSeq_id_Handle &	prot,
		CBioseq_Handle &	mrna_bsh,
		CBioseq_Handle &	prot_bsh
	)