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NCBI C++ ToolKit: Regular Expressions

Type definitions used for code clarity.

Compilation options.

Definition at line 84 of file regexp.hpp.

Flags for compile regular expressions.

PCRE compiler flags used in the constructor and in Set(). If fCompile_ignore_case is set, matches are case insensitive. If fCompile_dotall is set, a dot meta-character in the pattern matches all characters, including newlines. Without it, newlines are excluded. If fCompile_newline is set then ^ matches the start of a line and $ matches the end of a line. If not set, ^ matches only the start of the entire string and $ matches only the end of the entire string. If fCompile_ungreedy inverts the "greediness" of the quantifiers so that they are not greedy by default, but become greedy if followed by "?". It is not compatible with Perl.

The settings can be changed from within the pattern by a sequence of Perl option letters enclosed between "(?" and ")". The option letters are: i for PCRE_CASELESS m for PCRE_MULTILINE s for PCRE_DOTALL x for PCRE_EXTENDED U for PCRE_UNGREEDY

Definition at line 109 of file regexp.hpp.

Definition at line 118 of file regexp.hpp.

Definition at line 555 of file regexp.hpp.

Error types that tester can generate.

file open error

file/template line number mismatch

file/template lines do not match

variable not found

variable definition error

unknown operation

operation definition error

'test' operation return FALSE

Definition at line 357 of file regexp_template_tester.hpp.

Skip empty lines in the source.

Skip empty lines in the template.

Definition at line 204 of file regexp_template_tester.hpp.

Flags for match string against a precompiled pattern.

Setting fMatch_not_begin causes ^ not to match before the first character of a line. Without setting fCompile_newline, ^ won't match anything if fMatch_not_begin is set. Setting fMatch_not_end causes $ not to match immediately before a new line. Without setting fCompile_newline, $ won't match anything if fMatch_not_end is set.

^ won't match string begin.

$ won't match string end.

Definition at line 134 of file regexp.hpp.

Definition at line 141 of file regexp.hpp.

Range processing type.

Defines which part of the specified range should be processed.

Process substrings inside range.

Process substrings outside range.

Definition at line 447 of file regexp.hpp.

Constructor.

Set and compile the PCRE pattern specified by argument according to compile options. Also allocate memory for compiled PCRE.

Parameters

pattern Perl regular expression to compile. flags Regular expression compilation flags.

See also

ECompile

Definition at line 111 of file regexp.cpp.

References flags, and CRegexp::Set().

Get matching pattern and subpatterns.

Return a string corresponding to the match to pattern or subpattern. Set noreturn to true when GetSub() or GetResults() will be used to retrieve pattern and subpatterns. Calling GetMatch() causes the entire search to be performed again. If you want to retrieve a different pattern/subpattern from an already performed search, it is more efficient to use GetSub() or GetResults(). If you need to get numeric offset of the found pattern or subpattern, that use GetResults() method. Doo not use functions like strstr(), or string's find() method and etc, because in general they give you wrong results. This is very dependent from used regular expression.

Parameters

str String to search. offset Starting offset in str. idx (Sub) match to return. Use idx = 0 for complete pattern. Use idx > 0 for subpatterns. flags Flags to match. noreturn Return empty string if noreturn is true.

Returns

Return (sub) match with number idx or empty string when no match found or if noreturn is true.

See also

EMatch, GetSub, GetResult

Definition at line 242 of file regexp.cpp.

References flags, CRegexp::GetSub(), offset, str(), and CRegexp::x_Match().

Referenced by BrBookURLToCCddBookRef(), BrFcgiBookTermToEutilsTerm(), CapitalizeAfterApostrophe(), CPepXML::ConvertScanID(), DoesPatternMatchHighlightedResidues(), CRegexpUtil::Exists(), CRegexpUtil::Extract(), extract_date_iso8601(), CFindPattern::Find(), FixAffiliationShortWordsInElement(), FixOrdinalNumbers(), NMItemData::GetResolveFuncForPubQual(), CSpectrumSet::LoadMultDTA(), PortalBookURLToCCddBookRef(), CRegexpUtil::Replace(), CRegexpUtil::ReplaceRange(), NSearchFeatPanel::SplitPosOrRange(), transform_range(), CMsvcConfigure::WriteBuildVer(), CConvertAuthorToConsortiumWhereConstraint::x_ApplyToCAuth(), COrfSearchJob::x_DoSearch(), CSequenceSearchJob::x_GetMatches(), and CFeatureSearchJob::x_Match().

Get result string.

See also

operator string

Definition at line 597 of file regexp.hpp.

References CRegexpUtil::m_Content, CRegexpUtil::m_IsDivided, and CRegexpUtil::x_Join().

Referenced by CapitalizeSAfterNumber(), CPhyObjectLoader::Execute(), FindReplaceString_CountryFixes(), FixAbbreviationsInElement(), FixAffiliationShortWordsInElement(), CFixProductNames::FixCaps(), FixCountryCapitalization(), FixKnownAbbreviationsInElement(), FixShortWordsInElement(), FixupMouseStrain(), InsertMissingSpacesAfterCommas(), InsertMissingSpacesAfterNo(), CFindASN1Dlg::ReplaceValue(), CMacroFunction_EditStringQual::s_EditText(), s_RegexpReplace(), and CMacroFunction_FixSpelling::s_SpellingFixes().

Get location of pattern/subpattern for the last GetMatch().

Parameters

idx Index of pattern/subpattern to obtaining. Use idx = 0 for pattern, idx > 0 for sub patterns.

Returns

Return array where index 0 is location of first character in pattern/sub pattern and index 1 is 1 beyond last character in pattern/sub pattern. Throws if called with idx >= NumFound().

See also

GetMatch(), NumFound()

Definition at line 584 of file regexp.hpp.

References CRegexp::m_NumFound, and CRegexp::m_Results.

Referenced by CapitalizeAfterApostrophe(), CFindPattern::Find(), FixAffiliationShortWordsInElement(), FixOrdinalNumbers(), CNcbiApplogApp::GetRawAppName(), CRegexpUtil::Replace(), CNcbiApplogApp::Run(), and CSequenceSearchJob::x_GetMatches().

Get pattern/subpattern from previous GetMatch().

Should only be called after GetMatch() has been called with the same string. GetMatch() internally stores locations on string where pattern and subpatterns were found.

Parameters

str String to search. idx (Sub) match to return.

Returns

Return the substring at location of pattern match (idx 0) or subpattern match (idx > 0). Return empty string when no match.

See also

GetMatch(), GetResult()

Definition at line 200 of file regexp.cpp.

References CRegexp::m_NumFound, CRegexp::m_Results, PCRE2_SIZE, PCRE2_UNSET, and str().

Referenced by BrBookURLToCCddBookRef(), BrFcgiBookTermToEutilsTerm(), extract_date_iso8601(), CRegexp::GetMatch(), NMItemData::GetResolveFuncForPubQual(), CRegexp::GetSub(), PortalBookURLToCCddBookRef(), CReadBlastApp::ReadBlast(), s_ChrName(), CTabularFormatter::SetFormat(), sParseVersion(), NSearchFeatPanel::SplitPosOrRange(), transform_ambiguous_date(), transform_range(), CRegexpTemplateTester::x_CompareLines(), and CSeq_id_Resolver__LRG::x_Create().

Check existence substring which match a specified pattern.

Using IsMatch() reset all results from previous GetMatch() call. The subsequent NumFound() always returns 1 for successful IsMatch().

Parameters

str String to search. flags Flags to match.

Returns

Return TRUE if a string corresponding to the match to pattern.

See also

EMatch, GetMatch, NumFound

Definition at line 253 of file regexp.cpp.

References flags, CRegexp::m_NumFound, str(), and CRegexp::x_Match().

Referenced by CSeq_id_Resolver::CanCreate(), CProjectsLstFileFilter::CheckProject(), CPepXML::ConvertScanID(), extract_date_iso8601(), NSearchFeatPanel::GatherFeatures(), CAssemblyInfo::IsSameAssembly(), CMaskRegexp::Match(), CFilterColumnsDlg::OnRangeTextctrlTextUpdated(), CReadBlastApp::ReadBlast(), CNcbiApplogApp::Redirect(), CNcbiApplogApp::Run(), s_ChrName(), s_IsAllDigits(), CTabularFormatter::SetFormat(), sParseVersion(), NSearchFeatPanel::SplitPosOrRange(), CRegexpTemplateFilter::TestAttribute(), transform_ambiguous_date(), transform_range(), CRegexpValidator::Validate(), CRemoveDescDlg::x_ApplyToSeq_entry(), CRegexpTemplateTester::x_CompareLines(), CFeatureCheckPanel::x_InitTree(), CPSGS_AnnotProcessor::x_IsNameValid(), CFeatureSearchJob::x_IsSNP(), CRegexpTemplateTester::x_Op_Test(), and CGenBankLoadOptionPanel::x_ProccessText().

Get number of patterns + subpatterns.

Returns

Return the number of patterns + subpatterns found as a result of the most recent GetMatch() call (check on >= 0).

See also

GetMatch, IsMatch

Definition at line 577 of file regexp.hpp.

References CRegexp::m_NumFound.

Referenced by BrBookURLToCCddBookRef(), CapitalizeAfterApostrophe(), DoesPatternMatchHighlightedResidues(), CRegexpUtil::Exists(), FixAffiliationShortWordsInElement(), FixOrdinalNumbers(), PortalBookURLToCCddBookRef(), CRegexpUtil::Replace(), CRegexpUtil::ReplaceRange(), NSearchFeatPanel::SplitPosOrRange(), CConvertAuthorToConsortiumWhereConstraint::x_ApplyToCAuth(), CRegexpTemplateTester::x_CompareLines(), and CSequenceSearchJob::x_GetMatches().

Replace occurrences of a substring within a string by pattern.

Parameters

search Regular expression to match a substring value that is replaced. replace Replace "search" substring with this value. The matched subpatterns (if any) can be found and inserted into replace string using variables $1, $2, $3, and so forth. The variable can be enclosed in the curly brackets {}, that will be deleted on substitution. compile_flags Regular expression compilation flags. match_flags Flags to match. max_replace Replace no more than "max_replace" occurrences of substring "search". If "max_replace" is zero (default), then replace all occurrences with "replace".

Returns

Return the count of replacements.

See also

CRegexp, ReplaceRange()

Definition at line 349 of file regexp.cpp.

References CTempString::assign(), count, CTempString::data(), CTempString::empty(), CRegexp::GetMatch(), CRegexp::GetResults(), int, kMax_Int, CTempString::length(), CRegexpUtil::m_Content, n, NPOS, CRegexp::NumFound(), result, rapidjson::value, and CRegexpUtil::x_Join().

Referenced by CapitalizeSAfterNumber(), CPhyObjectLoader::Execute(), FindReplaceString_CountryFixes(), FixAbbreviationsInElement(), FixAffiliationShortWordsInElement(), CFixProductNames::FixCaps(), FixCountryCapitalization(), FixKnownAbbreviationsInElement(), FixShortWordsInElement(), FixupMouseStrain(), InsertMissingSpacesAfterCommas(), InsertMissingSpacesAfterNo(), CRegexpUtil::ReplaceRange(), CFindASN1Dlg::ReplaceValue(), CMacroFunction_EditStringQual::s_EditText(), s_RegexpReplace(), and CMacroFunction_FixSpelling::s_SpellingFixes().

Replace all occurrences of a substring within a string by pattern.

Use range specified by SetRange() method. Work like SED command s/.

Parameters

search Regular expression to match a substring value that is replaced. replace Replace "search" substring with this value. The matched subpatterns (if any) can be found and inserted into replace string using variables $1, $2, $3, and so forth. The variable can be enclosed in the curly brackets {}, that will be deleted on substitution. compile_flags Regular expression compilation flags. match_flags Flags to match. process_within Define which part of the range should be processed. max_replace Replace no more than "max_replace" occurrences of substring "search" in the every substring. If "max_replace" is zero (default), then replace all occurrences with "replace".

Returns

Return the count of replacements.

See also

ERange, SetRange(), ClearRange()

Definition at line 450 of file regexp.cpp.

References CRegexpUtil::eInside, CTempString::empty(), CRegexpUtil::eOutside, CRegexp::fMatch_default, CRegexp::GetMatch(), i, CRegexpUtil::m_ContentList, CRegexpUtil::m_RangeEnd, CRegexpUtil::m_RangeStart, NON_CONST_ITERATE, CRegexp::NumFound(), CRegexpUtil::Replace(), and CRegexpUtil::x_Divide().

Set and compile PCRE.

Set and compile the PCRE pattern specified by argument according to compile options. Also deallocate/allocate memory for compiled PCRE.

Parameters

pattern Perl regular expression to compile. flags Regular expression compilation flags.

See also

ECompile

Definition at line 138 of file regexp.cpp.

References ArraySize(), CTempString::data(), flags, CTempStringEx::HasZeroAtEnd(), CRegexp::m_MatchData, CRegexp::m_PReg, NCBI_THROW, NULL, pcre2_code, pcre2_code_free(), pcre2_compile(), pcre2_get_error_message(), pcre2_match_data, pcre2_match_data_create_from_pattern(), pcre2_match_data_free(), PCRE2_SPTR, PCRE2_UCHAR, s_GetRealCompileFlags(), and CTempString::size().

Referenced by CRegexp::CRegexp(), and CRemoveDescDlg::x_ApplyToSeq_entry().

Set new range for range-dependent functions.

The matched string will be split up by "delimiter". And then in range-dependent functions every part (substring) is checked to fall into the range, specified by start and end addresses.

The addresses works similar to the Unix utility SED, except that regular expressions is Perl-compatible:

• empty address in the range correspond to any substring.
• command with one address correspond to any substring that matches the address.
• command with two addresses correspond to inclusive range from the start address to through the next pattern space that matches the end address.

Specified range have effect only for range-dependent functions. Otherwise range is ignored.

Parameters

addr_start Regular expression which assign a starting address of range. addr_end Regular expression which assign an ending address of range. Should be empty if the start address is empty. delimiter Split a source string by "delimiter.

See also

ClearRange, ReplaceRange()

Definition at line 337 of file regexp.cpp.

References delimiter, CRegexpUtil::m_Delimiter, CRegexpUtil::m_RangeEnd, CRegexpUtil::m_RangeStart, and CRegexpUtil::x_Divide().

Referenced by CRegexpUtil::ClearRange().

Main compare method, compare streams.

Can be used recursively to process includes. Return TRUE if 'stop' command found.

Definition at line 199 of file regexp_template_tester.cpp.

References CRegexpTemplateTester::eFile, ERROR_TEMPLATE, CRegexpTemplateTester::eStop, CRegexpTemplateTester::eTemplate, CRegexpTemplateTester::eTemplateEOF, len, CRegexpTemplateTester::m_CommentStart, CRegexpTemplateTester::m_FileLine, CRegexpTemplateTester::m_FileLineNum, CRegexpTemplateTester::m_OpStart, CRegexpTemplateTester::m_ReprocessFileLine, CRegexpTemplateTester::m_TemplateLine, NStr::StartsWith(), str(), NStr::TruncateSpaces_Unsafe(), CRegexpTemplateTester::x_CompareLines(), CRegexpTemplateTester::x_GetLine(), CRegexpTemplateTester::x_Op_Echo(), CRegexpTemplateTester::x_Op_Include(), CRegexpTemplateTester::x_Op_Set(), CRegexpTemplateTester::x_Op_Skip(), and CRegexpTemplateTester::x_Op_Test().

Referenced by CRegexpTemplateTester::Compare(), and CRegexpTemplateTester::x_Op_Include().

Get line from the stream 'is'.

Definition at line 263 of file regexp_template_tester.cpp.

References _TROUBLE, CRegexpTemplateTester::eFile, CRegexpTemplateTester::eTemplate, CRegexpTemplateTester::fSkipEmptySourceLines, CRegexpTemplateTester::fSkipEmptyTemplateLines, CRegexpTemplateTester::m_EOLs, CRegexpTemplateTester::m_FileLine, CRegexpTemplateTester::m_FileLineNum, CRegexpTemplateTester::m_Flags, CRegexpTemplateTester::m_TemplateLine, CRegexpTemplateTester::m_TemplateLineNum, NcbiGetline(), NULL, and str().

Referenced by CRegexpTemplateTester::Compare(), CRegexpTemplateTester::x_Compare(), and CRegexpTemplateTester::x_Op_Skip().

Definition at line 219 of file regexp.cpp.

References f, flags, kRegexpMaxSubPatterns, CRegexp::m_JITStatus, CRegexp::m_MatchData, CRegexp::m_NumFound, CRegexp::m_PReg, CRegexp::m_Results, match_data, NULL, offset, pcre2_code, pcre2_get_ovector_pointer(), pcre2_jit_match(), pcre2_match(), pcre2_match_data, PCRE2_UCHAR, s_GetRealMatchFlags(), and str().

Referenced by CRegexp::GetMatch(), and CRegexp::IsMatch().

Definition at line 541 of file regexp_template_tester.cpp.

References _ASSERT, CDirEntry::ConcatPath(), ERROR_TEMPLATE, i, len, CRegexpTemplateTester::m_TemplateLineNum, CRegexpTemplateTester::m_TemplateName, SKIP_SPACES, CDirEntry::SplitPath(), str(), and CRegexpTemplateTester::x_Compare().

Referenced by CRegexpTemplateTester::x_Compare().

Definition at line 443 of file regexp_template_tester.cpp.

References _ASSERT, ERROR_TEMPLATE, i, len, CRegexpTemplateTester::m_Vars, n, NULL, SKIP_SPACES, str(), CRegexpTemplateTester::x_ParseVarName(), and CRegexpTemplateTester::x_SubstituteVars().

Referenced by CRegexpTemplateTester::x_Compare().

Definition at line 577 of file regexp_template_tester.cpp.

References _ASSERT, CRegexpTemplateTester::eFile, CTempString::empty(), eNumber, ERROR_TEMPLATE, i, len, CRegexpTemplateTester::m_FileLine, CRegexpTemplateTester::m_ReprocessFileLine, NULL, NStr::NumericToString(), NStr::PrintableString(), AutoPtr< X, Del >::reset(), SKIP_SPACES, NStr::StartsWith(), str(), CTempString::substr(), CRegexpTemplateTester::x_GetLine(), and CRegexpTemplateTester::x_SubstituteVars().

Referenced by CRegexpTemplateTester::x_Compare().

Definition at line 477 of file regexp_template_tester.cpp.

References _ASSERT, ncbi::grid::netcache::search::eEqual, eMatch, ERROR_TEMPLATE, NStr::Find(), i, CRegexp::IsMatch(), len, NPOS, NULL, NStr::PrintableString(), SKIP_SPACES, str(), and CRegexpTemplateTester::x_SubstituteVars().

Referenced by CRegexpTemplateTester::x_Compare().

Replace all variables in the string with corresponding values.

Also used for preparing inline variables for consecutive regexp matching.

Definition at line 365 of file regexp_template_tester.cpp.

References CTempString::empty(), ERROR_TEMPLATE, CTempString::find(), NStr::Find(), CRegexpTemplateTester::GetVar(), last(), CTempString::length(), CRegexpTemplateTester::m_VarEnd, CRegexpTemplateTester::m_VarStart, n, NPOS, NULL, out(), str(), CTempString::substr(), CRegexpTemplateTester::x_ParseVar(), and CRegexpTemplateTester::x_ParseVarName().

Referenced by CRegexpTemplateTester::x_CompareLines(), CRegexpTemplateTester::x_Op_Echo(), CRegexpTemplateTester::x_Op_Set(), CRegexpTemplateTester::x_Op_Skip(), and CRegexpTemplateTester::x_Op_Test().

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