NCBI C++ ToolKit
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Search Toolkit Book for CQualLookupMap
#include <objtools/validator/tax_validation_and_cleanup.hpp>
Public Member Functions | |
CQualLookupMap (COrgMod::ESubtype subtype) | |
virtual | ~CQualLookupMap () |
bool | IsPopulated () const |
void | Clear () |
virtual string | GetKey (const string &orig_val, const COrg_ref &org) const =0 |
virtual bool | Check (const COrg_ref &) const |
void | AddDesc (CConstRef< CSeqdesc > desc, CConstRef< CSeq_entry > ctx) |
void | AddFeat (CConstRef< CSeq_feat > feat) |
void | AddOrg (const COrg_ref &org) |
void | AddString (const string &val) |
vector< CRef< COrg_ref > > | GetRequestList () |
string | IncrementalUpdate (const vector< CRef< COrg_ref > > &input, const CTaxon3_reply &reply, TTaxId descTaxID=ZERO_TAX_ID) |
bool | IsUpdateComplete () const |
void | PostErrors (CValidError_imp &imp) |
virtual void | ListErrors (vector< TTaxError > &errs) const |
virtual bool | ApplyToOrg (COrg_ref &org) const =0 |
Protected Types | |
typedef map< string, CRef< CQualifierRequest > > | TQualifierRequests |
Protected Member Functions | |
TQualifierRequests::iterator | x_FindRequest (const string &val) |
virtual CRef< CQualifierRequest > | x_MakeNewRequest (const string &orig_val, const COrg_ref &org)=0 |
Protected Attributes | |
TQualifierRequests | m_Map |
COrgMod::ESubtype | m_Subtype |
bool | m_Populated |
Definition at line 214 of file tax_validation_and_cleanup.hpp.
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protected |
Definition at line 270 of file tax_validation_and_cleanup.hpp.
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inline |
Definition at line 217 of file tax_validation_and_cleanup.hpp.
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inlinevirtual |
Definition at line 218 of file tax_validation_and_cleanup.hpp.
void CQualLookupMap::AddDesc | ( | CConstRef< CSeqdesc > | desc, |
CConstRef< CSeq_entry > | ctx | ||
) |
Definition at line 902 of file tax_validation_and_cleanup.cpp.
References Check(), ctx, map_checker< Container >::end(), map_checker< Container >::find(), GetKey(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CSeqdesc_Base::GetSource(), CBioSource_Base::IsSetOrg(), COrg_ref::IsSetOrgMod(), CSeqdesc_Base::IsSource(), ncbi::grid::netcache::search::fields::key, m_Map, m_Populated, m_Subtype, and x_MakeNewRequest().
Definition at line 934 of file tax_validation_and_cleanup.cpp.
References Check(), map_checker< Container >::end(), map_checker< Container >::find(), CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), GetKey(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CSeqFeatData_Base::IsBiosrc(), CSeq_feat_Base::IsSetData(), CBioSource_Base::IsSetOrg(), COrg_ref::IsSetOrgMod(), ncbi::grid::netcache::search::fields::key, m_Map, m_Populated, m_Subtype, and x_MakeNewRequest().
Definition at line 967 of file tax_validation_and_cleanup.cpp.
References Check(), map_checker< Container >::end(), map_checker< Container >::find(), GetKey(), COrgName_Base::GetMod(), COrg_ref_Base::GetOrgname(), COrg_ref::IsSetOrgMod(), ncbi::grid::netcache::search::fields::key, m_Map, m_Populated, m_Subtype, and x_MakeNewRequest().
Referenced by CTaxValidationAndCleanup::CheckOneOrg().
Definition at line 994 of file tax_validation_and_cleanup.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), m_Map, m_Populated, val, and x_MakeNewRequest().
Referenced by CTaxValidationAndCleanup::FixOneSpecificHost(), and CTaxValidationAndCleanup::IsOneSpecificHostValid().
Implemented in CSpecificHostMapForFix, CStrainMap, and CSpecificHostMap.
Reimplemented in CStrainMap.
Definition at line 235 of file tax_validation_and_cleanup.hpp.
void CQualLookupMap::Clear | ( | void | ) |
Definition at line 895 of file tax_validation_and_cleanup.cpp.
References map_checker< Container >::clear(), m_Map, and m_Populated.
Referenced by CTaxValidationAndCleanup::FixOneSpecificHost(), CTaxValidationAndCleanup::IsOneSpecificHostValid(), and CTaxValidationAndCleanup::x_ClearMaps().
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pure virtual |
Implemented in CStrainMap, CSpecificHostMapForFix, and CSpecificHostMap.
Definition at line 1007 of file tax_validation_and_cleanup.cpp.
References m_Map, and map_checker< Container >::size().
Referenced by CTaxValidationAndCleanup::FixOneSpecificHost(), CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), CTaxValidationAndCleanup::GetStrainLookupRequest(), CTaxValidationAndCleanup::IsOneSpecificHostValid(), and CTaxValidationAndCleanup::ReportSpecificHostErrors().
string CQualLookupMap::IncrementalUpdate | ( | const vector< CRef< COrg_ref > > & | input, |
const CTaxon3_reply & | reply, | ||
TTaxId | descTaxID = ZERO_TAX_ID |
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) |
Definition at line 1035 of file tax_validation_and_cleanup.cpp.
References map_checker< Container >::end(), CTaxon3_reply_Base::GetReply(), COrgMod::GetSubtypeName(), input(), kEmptyStr, m_Map, m_Subtype, and x_FindRequest().
Referenced by CTaxValidationAndCleanup::AdjustOrgRefsWithSpecificHostReply(), CTaxValidationAndCleanup::IncrementalSpecificHostMapUpdate(), CTaxValidationAndCleanup::IncrementalStrainMapUpdate(), and CTaxValidationAndCleanup::ReportSpecificHostErrors().
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inline |
Definition at line 220 of file tax_validation_and_cleanup.hpp.
References m_Populated.
Referenced by CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), CTaxValidationAndCleanup::IncrementalSpecificHostMapUpdate(), and CTaxValidationAndCleanup::IsSpecificHostMapUpdateComplete().
bool CQualLookupMap::IsUpdateComplete | ( | ) | const |
Definition at line 1061 of file tax_validation_and_cleanup.cpp.
References m_Map.
Referenced by CTaxValidationAndCleanup::AdjustOrgRefsWithSpecificHostReply(), CTaxValidationAndCleanup::IsSpecificHostMapUpdateComplete(), CTaxValidationAndCleanup::IsStrainMapUpdateComplete(), and CTaxValidationAndCleanup::ReportSpecificHostErrors().
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virtual |
Definition at line 1083 of file tax_validation_and_cleanup.cpp.
References m_Map.
Referenced by CTaxValidationAndCleanup::CheckOneOrg(), and CTaxValidationAndCleanup::IsOneSpecificHostValid().
void CQualLookupMap::PostErrors | ( | CValidError_imp & | imp | ) |
Definition at line 1073 of file tax_validation_and_cleanup.cpp.
References m_Map.
Referenced by CTaxValidationAndCleanup::ReportSpecificHostErrors(), and CTaxValidationAndCleanup::ReportStrainErrors().
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protected |
Definition at line 1018 of file tax_validation_and_cleanup.cpp.
References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::find(), m_Map, and val.
Referenced by IncrementalUpdate().
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protectedpure virtual |
Implemented in CStrainMap, CSpecificHostMapForFix, and CSpecificHostMap.
Referenced by AddDesc(), AddFeat(), AddOrg(), and AddString().
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protected |
Definition at line 272 of file tax_validation_and_cleanup.hpp.
Referenced by AddDesc(), AddFeat(), AddOrg(), AddString(), CSpecificHostMapForFix::ApplyToOrg(), Clear(), GetRequestList(), IncrementalUpdate(), IsUpdateComplete(), ListErrors(), PostErrors(), and x_FindRequest().
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protected |
Definition at line 274 of file tax_validation_and_cleanup.hpp.
Referenced by AddDesc(), AddFeat(), AddOrg(), AddString(), Clear(), and IsPopulated().
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protected |
Definition at line 273 of file tax_validation_and_cleanup.hpp.
Referenced by AddDesc(), AddFeat(), AddOrg(), and IncrementalUpdate().