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Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | List of all members
CQualLookupMap Class Referenceabstract

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#include <objtools/validator/tax_validation_and_cleanup.hpp>

+ Inheritance diagram for CQualLookupMap:
+ Collaboration diagram for CQualLookupMap:

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< CQualifierRequestx_MakeNewRequest (const string &orig_val, const COrg_ref &org)=0
 

Protected Attributes

TQualifierRequests m_Map
 
COrgMod::ESubtype m_Subtype
 
bool m_Populated
 

Detailed Description

Definition at line 187 of file tax_validation_and_cleanup.hpp.

Member Typedef Documentation

◆ TQualifierRequests

Definition at line 243 of file tax_validation_and_cleanup.hpp.

Constructor & Destructor Documentation

◆ CQualLookupMap()

CQualLookupMap::CQualLookupMap ( COrgMod::ESubtype  subtype)
inline

Definition at line 190 of file tax_validation_and_cleanup.hpp.

◆ ~CQualLookupMap()

virtual CQualLookupMap::~CQualLookupMap ( )
inlinevirtual

Definition at line 191 of file tax_validation_and_cleanup.hpp.

Member Function Documentation

◆ AddDesc()

void CQualLookupMap::AddDesc ( CConstRef< CSeqdesc desc,
CConstRef< CSeq_entry ctx 
)

◆ AddFeat()

void CQualLookupMap::AddFeat ( CConstRef< CSeq_feat feat)

◆ AddOrg()

void CQualLookupMap::AddOrg ( const COrg_ref org)

◆ AddString()

void CQualLookupMap::AddString ( const string val)

◆ ApplyToOrg()

virtual bool CQualLookupMap::ApplyToOrg ( COrg_ref org) const
pure virtual

◆ Check()

virtual bool CQualLookupMap::Check ( const COrg_ref ) const
inlinevirtual

Reimplemented in CStrainMap.

Definition at line 208 of file tax_validation_and_cleanup.hpp.

Referenced by AddDesc(), AddFeat(), and AddOrg().

◆ Clear()

void CQualLookupMap::Clear ( void  )

◆ GetKey()

virtual string CQualLookupMap::GetKey ( const string orig_val,
const COrg_ref org 
) const
pure virtual

Implemented in CStrainMap, CSpecificHostMapForFix, and CSpecificHostMap.

Referenced by AddDesc(), AddFeat(), and AddOrg().

◆ GetRequestList()

vector< CRef< COrg_ref > > CQualLookupMap::GetRequestList ( )

◆ IncrementalUpdate()

string CQualLookupMap::IncrementalUpdate ( const vector< CRef< COrg_ref > > &  input,
const CTaxon3_reply reply,
TTaxId  descTaxID = ZERO_TAX_ID 
)

◆ IsPopulated()

bool CQualLookupMap::IsPopulated ( ) const
inline

◆ IsUpdateComplete()

bool CQualLookupMap::IsUpdateComplete ( ) const

◆ ListErrors()

void CQualLookupMap::ListErrors ( vector< TTaxError > &  errs) const
virtual

◆ PostErrors()

void CQualLookupMap::PostErrors ( CValidError_imp imp)

◆ x_FindRequest()

CQualLookupMap::TQualifierRequests::iterator CQualLookupMap::x_FindRequest ( const string val)
protected

◆ x_MakeNewRequest()

virtual CRef<CQualifierRequest> CQualLookupMap::x_MakeNewRequest ( const string orig_val,
const COrg_ref org 
)
protectedpure virtual

Member Data Documentation

◆ m_Map

TQualifierRequests CQualLookupMap::m_Map
protected

◆ m_Populated

bool CQualLookupMap::m_Populated
protected

Definition at line 247 of file tax_validation_and_cleanup.hpp.

Referenced by AddDesc(), AddFeat(), AddOrg(), AddString(), Clear(), and IsPopulated().

◆ m_Subtype

COrgMod::ESubtype CQualLookupMap::m_Subtype
protected

Definition at line 246 of file tax_validation_and_cleanup.hpp.

Referenced by AddDesc(), AddFeat(), AddOrg(), and IncrementalUpdate().


The documentation for this class was generated from the following files:
Modified on Sun Mar 03 03:16:56 2024 by modify_doxy.py rev. 669887