#include <corelib/ncbiobj.hpp>#include <corelib/ncbistd.hpp>#include <util/compile_time.hpp>#include "testnames.inc"
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Classes | |
| class | CReportObj |
| class | CAutofixReport |
| class | CReportItem |
| class | CReportItemFactory |
| class | CDiscrepancyCase |
| class | CDiscrepancyProduct |
| class | CDiscrepancySet |
| class | CDiscrepancyGroup |
Macros | |
| #define | NEW_DISCREPANCY_API |
Typedefs | |
| using | TTestNamesSet = ct::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames > |
| template<eTestTypes _type> | |
| using | TTypeTag = std::integral_constant< eTestTypes, _type > |
| typedef vector< CRef< CReportObj > > | TReportObjectList |
| typedef vector< CRef< CReportItem > > | TReportItemList |
| typedef map< eTestNames, CRef< CDiscrepancyCase > > | TDiscrepancyCaseMap |
| typedef unsigned short | TGroup |
| typedef std::function< CRef< objects::CSeq_feat >) > | GetFeatureFunc |
Enumerations | |
| enum class | eTestTypes { SEQUENCE , FEAT , STRING , SEQ_SET , DESC , BIOSRC , AUTHORS , SUBMIT , PUBDESC , max_num_types } |
| enum | EGroup { eAll = 0 , eDisc = 1 , eOncaller = 2 , eSubmitter = 4 , eSmart = 8 , eBig = 16 , eTSA = 32 , eFatal = 64 , eAutofix = 128 } |
Functions | |
| eTestNames | GetDiscrepancyCaseName (string_view) |
| string_view | GetDiscrepancyCaseName (eTestNames name) |
| string_view | GetDiscrepancyDescr (eTestNames name) |
| TGroup | GetDiscrepancyGroup (eTestNames name) |
| TTestNamesSet | GetDiscrepancyTests (TGroup group) |
| vector< string_view > | GetDiscrepancyAliases (eTestNames name) |
| NCBI_DISCREPANCY_EXPORT string_view | GetDiscrepancyDescr (string_view name) |
| NCBI_DISCREPANCY_EXPORT TGroup | GetDiscrepancyGroup (string_view name) |
| NCBI_DISCREPANCY_EXPORT vector< string > | GetDiscrepancyNames (TGroup group=EGroup::eAll) |
| bool | IsShortrRNA (const objects::CSeq_feat &f, objects::CScope *scope) |
| string | FixProductName (const objects::CSuspect_rule *rule, objects::CScope &scope, string &prot_name, GetFeatureFunc get_mrna, GetFeatureFunc get_cds) |
| CConstRef< objects::CSuspect_rule_set > | GetOrganelleProductRules (const string &name="") |
| CConstRef< objects::CSuspect_rule_set > | GetProductRules (const string &name="") |
| std::ostream & | operator<< (std::ostream &str, NDiscrepancy::eTestNames name) |
Macro Definition Documentation
◆ NEW_DISCREPANCY_API
| #define NEW_DISCREPANCY_API |
Definition at line 37 of file discrepancy.hpp.
Typedef Documentation
◆ GetFeatureFunc
| typedef std::function< CRef<objects::CSeq_feat>) > GetFeatureFunc |
Definition at line 292 of file discrepancy.hpp.
◆ TDiscrepancyCaseMap
| typedef map<eTestNames, CRef<CDiscrepancyCase> > TDiscrepancyCaseMap |
Definition at line 179 of file discrepancy.hpp.
◆ TGroup
| typedef unsigned short TGroup |
Definition at line 276 of file discrepancy.hpp.
◆ TReportItemList
| typedef vector<CRef<CReportItem> > TReportItemList |
Definition at line 149 of file discrepancy.hpp.
◆ TReportObjectList
| typedef vector<CRef<CReportObj> > TReportObjectList |
Definition at line 100 of file discrepancy.hpp.
◆ TTestNamesSet
| using TTestNamesSet = ct::const_bitset<static_cast<size_t>(eTestNames::max_test_names), eTestNames> |
Definition at line 70 of file discrepancy.hpp.
◆ TTypeTag
| using TTypeTag = std::integral_constant<eTestTypes, _type> |
Definition at line 72 of file discrepancy.hpp.
Enumeration Type Documentation
◆ EGroup
| enum EGroup |
| Enumerator | |
|---|---|
| eAll | |
| eDisc | |
| eOncaller | |
| eSubmitter | |
| eSmart | |
| eBig | |
| eTSA | |
| eFatal | |
| eAutofix | |
Definition at line 265 of file discrepancy.hpp.
◆ eTestTypes
|
strong |
| Enumerator | |
|---|---|
| SEQUENCE | |
| FEAT | |
| STRING | |
| SEQ_SET | |
| DESC | |
| BIOSRC | |
| AUTHORS | |
| SUBMIT | |
| PUBDESC | |
| max_num_types | |
Definition at line 56 of file discrepancy.hpp.
Function Documentation
◆ FixProductName()
| string FixProductName | ( | const objects::CSuspect_rule * | rule, |
| objects::CScope & | scope, | ||
| string & | prot_name, | ||
| GetFeatureFunc | get_mrna, | ||
| GetFeatureFunc | get_cds | ||
| ) |
◆ GetDiscrepancyAliases()
| vector<string_view> GetDiscrepancyAliases | ( | eTestNames | name | ) |
Definition at line 155 of file discrepancy_core.cpp.
References CDiscrepancyCaseProps::Aliases, and CCaseRegistry::GetProps().
Referenced by CDiscRepArgDescriptions::PrintUsage().
◆ GetDiscrepancyCaseName() [1/2]
| string_view GetDiscrepancyCaseName | ( | eTestNames | name | ) |
Definition at line 150 of file discrepancy_core.cpp.
References CCaseRegistry::GetProps(), and CDiscrepancyCaseProps::sName.
◆ GetDiscrepancyCaseName() [2/2]
| eTestNames GetDiscrepancyCaseName | ( | string_view | name | ) |
Definition at line 131 of file discrepancy_core.cpp.
References map_checker< Container >::find(), g_test_registry, CCaseRegistry::GetAliasMap(), i, CDiscrepancyCaseProps::sName, and NStr::StartsWith().
Referenced by CDiscrepancyContext::AddTest(), AutofixCommandHugeMode(), BOOST_AUTO_TEST_CASE(), CDiscrepancyGroup::CDiscrepancyGroup(), CReportItemFactory::Create(), CReportItem::CreateReportItem(), GetDiscrepancyDescr(), GetDiscrepancyGroup(), GetDiscrepancyNames(), CDiscrepancyDlg::LoadSettings(), CDiscrepancyConf::OnOk(), operator<<(), CDiscRepArgDescriptions::PrintUsage(), CDiscRepApp::Run(), CDiscrepancyConf::UpdateList(), CDiscrepancyList::UpdateList(), and CDiscrepancyAutofixTreeItemData::x_AddParamPanel().
◆ GetDiscrepancyDescr() [1/2]
| string_view GetDiscrepancyDescr | ( | eTestNames | name | ) |
Definition at line 175 of file discrepancy_core.cpp.
References CDiscrepancyCaseProps::Descr, and CCaseRegistry::GetProps().
Referenced by BOOST_AUTO_TEST_CASE(), and CDiscrepancyList::UpdateList().
◆ GetDiscrepancyDescr() [2/2]
| NCBI_DISCREPANCY_EXPORT string_view GetDiscrepancyDescr | ( | string_view | name | ) |
Definition at line 170 of file discrepancy_core.cpp.
References GetDiscrepancyCaseName().
◆ GetDiscrepancyGroup() [1/2]
| TGroup GetDiscrepancyGroup | ( | eTestNames | name | ) |
Definition at line 180 of file discrepancy_core.cpp.
References CCaseRegistry::GetProps(), and CDiscrepancyCaseProps::Group.
Referenced by GetDiscrepancyGroup(), and CDiscrepancyPanel::UpdateTestList().
◆ GetDiscrepancyGroup() [2/2]
| NCBI_DISCREPANCY_EXPORT TGroup GetDiscrepancyGroup | ( | string_view | name | ) |
Definition at line 185 of file discrepancy_core.cpp.
References GetDiscrepancyCaseName(), and GetDiscrepancyGroup().
◆ GetDiscrepancyNames()
| NCBI_DISCREPANCY_EXPORT vector<string> GetDiscrepancyNames | ( | TGroup | group = EGroup::eAll | ) |
Definition at line 190 of file discrepancy_core.cpp.
References GetDiscrepancyCaseName(), GetDiscrepancyTests(), names, string, and tests.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDiscrepancyTests()
| TTestNamesSet GetDiscrepancyTests | ( | TGroup | group | ) |
Definition at line 201 of file discrepancy_core.cpp.
References eAutofix, g_test_registry, CCaseRegistry::GetAutofixTests(), and names.
Referenced by BOOST_AUTO_TEST_CASE(), GetDiscrepancyNames(), CDiscRepArgDescriptions::PrintUsage(), CDiscRepApp::Run(), CDiscrepancyConf::UpdateList(), CDiscrepancyList::UpdateList(), CDiscrepancyPanel::UpdateTestList(), CDiscrepancyAutofixTreeItemData::x_AddParamPanel(), and CTable2AsnValidator::x_PopulateDiscrepancy().
◆ GetOrganelleProductRules()
Definition at line 116 of file fsm_statics.cpp.
Referenced by CDiscrepancyContext::GetOrganelleProductRules().
◆ GetProductRules()
Definition at line 123 of file fsm_statics.cpp.
Referenced by CDiscrepancyContext::GetProductRules(), and CDiscrepancyContext::SetSuspectRules().
◆ IsShortrRNA()
◆ operator<<()
| std::ostream& operator<< | ( | std::ostream & | str, |
| NDiscrepancy::eTestNames | name | ||
| ) |
Definition at line 125 of file discrepancy_core.cpp.
References GetDiscrepancyCaseName(), and str().
