NCBI C++ ToolKit
Public Member Functions | Static Public Member Functions | Static Private Member Functions | Private Attributes | List of all members
CStrainRequest Class Reference

Search Toolkit Book for CStrainRequest

#include <objtools/validator/tax_validation_and_cleanup.hpp>

+ Inheritance diagram for CStrainRequest:
+ Collaboration diagram for CStrainRequest:

Public Member Functions

 CStrainRequest (const string &strain, const COrg_ref &org)
 
void AddReply (const CT3Reply &reply) override
 
void ListErrors (vector< TTaxError > &errs) const override
 
- Public Member Functions inherited from CQualifierRequest
 CQualifierRequest ()
 
void AddParent (CConstRef< CSeqdesc > desc, CConstRef< CSeq_entry > ctx)
 
void AddParent (CConstRef< CSeq_feat > feat)
 
void AddRequests (vector< CRef< COrg_ref > > &request_list) const
 
bool MatchTryValue (const string &val) const
 
size_t NumRemainingReplies () const
 
void PostErrors (CValidError_imp &imp)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Member Functions

static string MakeKey (const string &strain, const string &taxname)
 
static bool RequireTaxname (const string &taxname)
 
static bool Check (const COrg_ref &org)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Static Private Member Functions

static bool x_IsUnwanted (const string &str)
 
static bool x_IgnoreStrain (const string &str)
 

Private Attributes

string m_Strain
 
string m_Taxname
 
bool m_IsInvalid
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Types inherited from CQualifierRequest
typedef pair< CConstRef< CSeqdesc >, CConstRef< CSeq_entry > > TDescPair
 
- Protected Member Functions inherited from CQualifierRequest
void x_Init ()
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CQualifierRequest
vector< stringm_ValuesToTry
 
size_t m_RepliesProcessed
 
vector< TDescPairm_Descs
 
vector< CConstRef< CSeq_feat > > m_Feats
 

Detailed Description

Definition at line 161 of file tax_validation_and_cleanup.hpp.

Constructor & Destructor Documentation

◆ CStrainRequest()

CStrainRequest::CStrainRequest ( const string strain,
const COrg_ref org 
)

Member Function Documentation

◆ AddReply()

void CStrainRequest::AddReply ( const CT3Reply reply)
overridevirtual

◆ Check()

bool CStrainRequest::Check ( const COrg_ref org)
static

◆ ListErrors()

void CStrainRequest::ListErrors ( vector< TTaxError > &  errs) const
overridevirtual

◆ MakeKey()

string CStrainRequest::MakeKey ( const string strain,
const string taxname 
)
static

Definition at line 294 of file tax_validation_and_cleanup.cpp.

References RequireTaxname().

Referenced by CStrainRequest(), and CStrainMap::GetKey().

◆ RequireTaxname()

bool CStrainRequest::RequireTaxname ( const string taxname)
static

Definition at line 304 of file tax_validation_and_cleanup.cpp.

References NStr::EndsWith().

Referenced by CStrainRequest(), and MakeKey().

◆ x_IgnoreStrain()

bool CStrainRequest::x_IgnoreStrain ( const string str)
staticprivate

Definition at line 240 of file tax_validation_and_cleanup.cpp.

References isalpha(), isdigit(), and str().

Referenced by CStrainRequest().

◆ x_IsUnwanted()

bool CStrainRequest::x_IsUnwanted ( const string str)
staticprivate

Definition at line 314 of file tax_validation_and_cleanup.cpp.

References NStr::FindNoCase(), NPOS, and str().

Referenced by Check().

Member Data Documentation

◆ m_IsInvalid

bool CStrainRequest::m_IsInvalid
private

Definition at line 177 of file tax_validation_and_cleanup.hpp.

Referenced by AddReply(), CStrainRequest(), and ListErrors().

◆ m_Strain

string CStrainRequest::m_Strain
private

Definition at line 175 of file tax_validation_and_cleanup.hpp.

Referenced by AddReply(), and ListErrors().

◆ m_Taxname

string CStrainRequest::m_Taxname
private

Definition at line 176 of file tax_validation_and_cleanup.hpp.

Referenced by CStrainRequest().


The documentation for this class was generated from the following files:
Modified on Wed Feb 28 07:11:58 2024 by modify_doxy.py rev. 669887