| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/valid/ |
| H A D | Comment_set.cpp | 71 CComment_rule::NormalizePrefix(search); in FindCommentRuleEx()
73 const CComment_rule& rule = **it; in FindCommentRuleEx()
75 CComment_rule::NormalizePrefix(this_prefix); in FindCommentRuleEx()
83 return CConstRef<CComment_rule>(); in FindCommentRuleEx()
162 string prefix_to_use = CComment_rule::MakePrefixFromRoot(prefix); in GetFieldNames()
170 const CComment_rule& rule = *ruler; in GetFieldNames()
185 string prefix = CComment_rule::GetStructuredCommentPrefix (user); in GetKeywords()
186 string prefix_to_use = CComment_rule::MakePrefixFromRoot(prefix); in GetKeywords()
194 const CComment_rule& rule = *ruler; in GetKeywords()
195 CComment_rule::TErrorList errors = rule.IsValid(user); in GetKeywords()
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| H A D | Comment_rule.cpp | 59 CComment_rule::~CComment_rule(void) in ~CComment_rule()
64 void CComment_rule::NormalizePrefix(string& prefix) in NormalizePrefix()
114 CComment_rule::NormalizePrefix(prefix); in GetStructuredCommentPrefix()
120 string CComment_rule::MakePrefixFromRoot(const string& root) in MakePrefixFromRoot()
123 CComment_rule::NormalizePrefix(prefix); in MakePrefixFromRoot()
129 string CComment_rule::MakeSuffixFromRoot(const string& root) in MakeSuffixFromRoot()
132 CComment_rule::NormalizePrefix(suffix); in MakeSuffixFromRoot()
154 CComment_rule::NormalizePrefix(compare); in KeywordForPrefix()
178 vector<string> CComment_rule::GetKeywordList() in GetKeywordList()
286 CComment_rule::TErrorList CComment_rule::IsValid(const CUser_object& user) const in IsValid()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/valid/ |
| H A D | Comment_set.cpp | 71 CComment_rule::NormalizePrefix(search); in FindCommentRuleEx()
73 const CComment_rule& rule = **it; in FindCommentRuleEx()
75 CComment_rule::NormalizePrefix(this_prefix); in FindCommentRuleEx()
83 return CConstRef<CComment_rule>(); in FindCommentRuleEx()
162 string prefix_to_use = CComment_rule::MakePrefixFromRoot(prefix); in GetFieldNames()
170 const CComment_rule& rule = *ruler; in GetFieldNames()
185 string prefix = CComment_rule::GetStructuredCommentPrefix (user); in GetKeywords()
186 string prefix_to_use = CComment_rule::MakePrefixFromRoot(prefix); in GetKeywords()
194 const CComment_rule& rule = *ruler; in GetKeywords()
195 CComment_rule::TErrorList errors = rule.IsValid(user); in GetKeywords()
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| H A D | Comment_rule.cpp | 59 CComment_rule::~CComment_rule(void) in ~CComment_rule()
64 void CComment_rule::NormalizePrefix(string& prefix) in NormalizePrefix()
114 CComment_rule::NormalizePrefix(prefix); in GetStructuredCommentPrefix()
120 string CComment_rule::MakePrefixFromRoot(const string& root) in MakePrefixFromRoot()
123 CComment_rule::NormalizePrefix(prefix); in MakePrefixFromRoot()
129 string CComment_rule::MakeSuffixFromRoot(const string& root) in MakeSuffixFromRoot()
132 CComment_rule::NormalizePrefix(suffix); in MakeSuffixFromRoot()
154 CComment_rule::NormalizePrefix(compare); in KeywordForPrefix()
178 vector<string> CComment_rule::GetKeywordList() in GetKeywordList()
286 CComment_rule::TErrorList CComment_rule::IsValid(const CUser_object& user) const in IsValid()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objects/valid/ |
| H A D | Comment_rule.hpp | 55 class NCBI_VALID_EXPORT CComment_rule : public CComment_rule_Base class
60 CComment_rule(void);
62 ~CComment_rule(void);
88 CComment_rule(const CComment_rule& value);
89 CComment_rule& operator=(const CComment_rule& value);
97 CComment_rule::CComment_rule(void) in CComment_rule() function in CComment_rule
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| H A D | Comment_set.hpp | 63 const CComment_rule& FindCommentRule (const string& prefix) const;
64 CConstRef<CComment_rule> FindCommentRuleEx (const string& prefix) const;
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objects/valid/ |
| H A D | Comment_rule.hpp | 55 class NCBI_VALID_EXPORT CComment_rule : public CComment_rule_Base class
60 CComment_rule(void);
62 ~CComment_rule(void);
88 CComment_rule(const CComment_rule& value);
89 CComment_rule& operator=(const CComment_rule& value);
97 CComment_rule::CComment_rule(void) in CComment_rule() function in CComment_rule
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| H A D | Comment_set.hpp | 63 const CComment_rule& FindCommentRule (const string& prefix) const;
64 CConstRef<CComment_rule> FindCommentRuleEx (const string& prefix) const;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
| H A D | seqdesc_per_bioseq.cpp | 183 static bool IsAppropriateRule(const CComment_rule& rule, const CUser_object& user) in IsAppropriateRule()
203 const CComment_rule* FindAppropriateRule(const CComment_set& rules, const CUser_object& user) in FindAppropriateRule()
205 const CComment_rule* ret = nullptr; in FindAppropriateRule()
208 CComment_rule::TErrorList errors = rule->IsValid(user); in FindAppropriateRule()
230 string prefix = CComment_rule::GetStructuredCommentPrefix(user);
234 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(prefix);
236 const CComment_rule& rule = *ruler;
237 CComment_rule::TErrorList errors = rule.IsValid(user);
239 … const CComment_rule* new_rule = FindAppropriateRule(*comment_rules, user);
241 … different prefix"].Add(*context.SeqdescObjRef(desc, &desc, const_cast<CComment_rule*>(new_rule)));
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| H A D | sequence_tests.cpp | 937 string prefix = CComment_rule::GetStructuredCommentPrefix(user);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | struc_comm_field.cpp | 422 if (!CComment_rule::IsStructuredComment(user)) { in IsStructuredCommentForThisField()
426 CComment_rule::NormalizePrefix(prefix); in IsStructuredCommentForThisField()
438 CComment_rule::NormalizePrefix(root); in MakeUserObject()
441 string pre = CComment_rule::MakePrefixFromRoot(root); in MakeUserObject()
446 string suf = CComment_rule::MakeSuffixFromRoot(root); in MakeUserObject()
464 string prefix = CComment_rule::GetStructuredCommentPrefix(obj); in IsValid()
476 const CComment_rule& rule = *ruler; in IsValid()
479 CComment_rule::TErrorList errors = rule.IsValid(obj); in IsValid()
490 CComment_rule::TErrorList errors = rule.IsValid(obj); in IsValid()
504 string prefix = CComment_rule::GetStructuredCommentPrefix(obj); in ReorderFields()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | struc_comm_field.cpp | 422 if (!CComment_rule::IsStructuredComment(user)) { in IsStructuredCommentForThisField()
426 CComment_rule::NormalizePrefix(prefix); in IsStructuredCommentForThisField()
438 CComment_rule::NormalizePrefix(root); in MakeUserObject()
441 string pre = CComment_rule::MakePrefixFromRoot(root); in MakeUserObject()
446 string suf = CComment_rule::MakeSuffixFromRoot(root); in MakeUserObject()
464 string prefix = CComment_rule::GetStructuredCommentPrefix(obj); in IsValid()
476 const CComment_rule& rule = *ruler; in IsValid()
479 CComment_rule::TErrorList errors = rule.IsValid(obj); in IsValid()
490 CComment_rule::TErrorList errors = rule.IsValid(obj); in IsValid()
504 string prefix = CComment_rule::GetStructuredCommentPrefix(obj); in ReorderFields()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | validerror_desc.cpp | 327 const CComment_rule& rule, in ValidateStructuredComment()
332 CComment_rule::TErrorList errors = rule.IsValid(usr); in ValidateStructuredComment()
343 void CValidError_desc::x_ReportStructuredCommentErrors(const CSeqdesc& desc, const CComment_rule::T… in x_ReportStructuredCommentErrors()
345 ITERATE(CComment_rule::TErrorList, it, errors) { in x_ReportStructuredCommentErrors()
361 CComment_rule::TErrorList errors = CComment_rule::CheckGeneralStructuredComment(usr); in ValidateStructuredCommentGeneric()
460 string prefix = CComment_rule::GetStructuredCommentPrefix(usr); in ValidateStructuredComment()
470 string report_prefix = CComment_rule::GetStructuredCommentPrefix(usr, false); in ValidateStructuredComment()
480 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(prefix); in ValidateStructuredComment()
482 const CComment_rule& rule = *ruler; in ValidateStructuredComment()
505 CComment_rule::NormalizePrefix(sfx); in ValidateStructuredComment()
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| H A D | validerror_bioseq.cpp | 8370 string prefix = CComment_rule::GetStructuredCommentPrefix(obj); in s_GetKeywordForStructuredComment()
8374 string keyword = CComment_rule::KeywordForPrefix(prefix); in s_GetKeywordForStructuredComment()
8387 if (CComment_rule::IsStructuredComment(obj)) { in CheckForMultipleStructuredComments()
8388 string prefix = CComment_rule::GetStructuredCommentPrefix(obj, false); in CheckForMultipleStructuredComments()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
| H A D | keywords_item.cpp | 304 if ( ! CComment_rule::IsStructuredComment (usr) ) continue; in x_GatherInfo()
305 string pfx = CComment_rule::GetStructuredCommentPrefix ( usr, true ); in x_GatherInfo()
309 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(pfx); in x_GatherInfo()
311 const CComment_rule& rule = *ruler; in x_GatherInfo()
312 CComment_rule::TErrorList errors = rule.IsValid(usr); in x_GatherInfo()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
| H A D | keywords_item.cpp | 304 if ( ! CComment_rule::IsStructuredComment (usr) ) continue; in x_GatherInfo()
305 string pfx = CComment_rule::GetStructuredCommentPrefix ( usr, true ); in x_GatherInfo()
309 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(pfx); in x_GatherInfo()
311 const CComment_rule& rule = *ruler; in x_GatherInfo()
312 CComment_rule::TErrorList errors = rule.IsValid(usr); in x_GatherInfo()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/validator/ |
| H A D | validerror_desc.hpp | 75 …tructuredComment(const CUser_object& usr, const CSeqdesc& desc, const CComment_rule& rule, bool re…
77 …void x_ReportStructuredCommentErrors(const CSeqdesc& desc, const CComment_rule::TErrorList& errors…
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/ |
| H A D | cleanup_user_object.cpp | 204 CComment_rule::NormalizePrefix(core); in s_CleanupStructuredComment()
205 …string new_val = is_prefix ? CComment_rule::MakePrefixFromRoot(core) : CComment_rule::MakeSuffixFr… in s_CleanupStructuredComment()
226 CConstRef<CComment_rule> ruler = rules->FindCommentRuleEx(kBarcode); in s_CleanupStructuredComment()
228 const CComment_rule& rule = *ruler; in s_CleanupStructuredComment()
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| H A D | newcleanupp.cpp | 8883 vector<string> controlled_keywords = CComment_rule::GetKeywordList(); in x_FixStructuredCommentKeywords()
8921 if ( ! CComment_rule::IsStructuredComment (usr) ) continue; in x_FixStructuredCommentKeywords()
8922 string prefix = CComment_rule::GetStructuredCommentPrefix (usr); in x_FixStructuredCommentKeywords()
8926 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(prefix); in x_FixStructuredCommentKeywords()
8928 const CComment_rule& rule = *ruler; in x_FixStructuredCommentKeywords()
8929 CComment_rule::TErrorList errors = rule.IsValid(usr); in x_FixStructuredCommentKeywords()
8931 string kywd = CComment_rule::KeywordForPrefix( prefix ); in x_FixStructuredCommentKeywords()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/ |
| H A D | cleanup_user_object.cpp | 204 CComment_rule::NormalizePrefix(core); in s_CleanupStructuredComment()
205 …string new_val = is_prefix ? CComment_rule::MakePrefixFromRoot(core) : CComment_rule::MakeSuffixFr… in s_CleanupStructuredComment()
226 CConstRef<CComment_rule> ruler = rules->FindCommentRuleEx(kBarcode); in s_CleanupStructuredComment()
228 const CComment_rule& rule = *ruler; in s_CleanupStructuredComment()
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| H A D | newcleanupp.cpp | 8824 vector<string> controlled_keywords = CComment_rule::GetKeywordList(); in x_FixStructuredCommentKeywords()
8861 if ( ! CComment_rule::IsStructuredComment (usr) ) continue; in x_FixStructuredCommentKeywords()
8862 string prefix = CComment_rule::GetStructuredCommentPrefix (usr); in x_FixStructuredCommentKeywords()
8866 CConstRef<CComment_rule> ruler = comment_rules->FindCommentRuleEx(prefix); in x_FixStructuredCommentKeywords()
8868 const CComment_rule& rule = *ruler; in x_FixStructuredCommentKeywords()
8869 CComment_rule::TErrorList errors = rule.IsValid(usr); in x_FixStructuredCommentKeywords()
8871 string kywd = CComment_rule::KeywordForPrefix( prefix ); in x_FixStructuredCommentKeywords()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/ |
| H A D | unit_test_field_handler.cpp | 189 string keyword = CComment_rule::KeywordForPrefix("MIGS:3.0-Data"); in BOOST_AUTO_TEST_CASE()
192 string prefix = CComment_rule::PrefixForKeyword("GSC:MIxS;MIMS:3.0"); in BOOST_AUTO_TEST_CASE()
195 vector<string> keywords = CComment_rule::GetKeywordList(); in BOOST_AUTO_TEST_CASE()
450 const CComment_rule& rule = rules->FindCommentRule(prefix); in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/edit/ |
| H A D | struc_comm_field.hpp | 46 class CComment_rule;
59 { CComment_rule::NormalizePrefix(m_Prefix); in CStructuredCommentField()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/edit/ |
| H A D | struc_comm_field.hpp | 46 class CComment_rule;
59 { CComment_rule::NormalizePrefix(m_Prefix); in CStructuredCommentField()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/biosample_util/ |
| H A D | biosample_util.cpp | 649 string prefix = CComment_rule::GetStructuredCommentPrefix(user); in s_IsReportableStructuredComment()
928 string prefix = CComment_rule::GetStructuredCommentPrefix(user); in GetBioseqDiffs()
971 … string this_prefix = CComment_rule::GetStructuredCommentPrefix((*it)->GetUser()); in GetBioseqDiffs()
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