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NCBI C++ ToolKit: CFormatRpsDbParameters_Base Class Reference
This structure is used to create the RPS-BLAST database auxiliary file (*.aux) and it contains parameters set at creation time of the PSSM. More...
CFormatRpsDbParameters_Base (void) virtual ~CFormatRpsDbParameters_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetMatrixName (void) const name of the underlying score matrix whose frequency ratios were used in PSSM construction (e.g. More...
bool CanGetMatrixName (void) const Check if it is safe to call GetMatrixName method. More...
void ResetMatrixName (void) Reset MatrixName data member. More...
const TMatrixName & GetMatrixName (void) const Get the MatrixName member data. More...
void SetMatrixName (const TMatrixName &value) Assign a value to MatrixName data member. More...
void SetMatrixName (TMatrixName &&value) TMatrixName & SetMatrixName (void) Assign a value to MatrixName data member. More...
bool IsSetGapOpen (void) const gap opening penalty corresponding to the matrix above Check if a value has been assigned to GapOpen data member. More...
bool CanGetGapOpen (void) const Check if it is safe to call GetGapOpen method. More...
void ResetGapOpen (void) Reset GapOpen data member. More...
TGapOpen GetGapOpen (void) const Get the GapOpen member data. More...
void SetGapOpen (TGapOpen value) Assign a value to GapOpen data member. More...
TGapOpen & SetGapOpen (void) Assign a value to GapOpen data member. More...
bool IsSetGapExtend (void) const gap extension penalty corresponding to the matrix above Check if a value has been assigned to GapExtend data member. More...
bool CanGetGapExtend (void) const Check if it is safe to call GetGapExtend method. More...
void ResetGapExtend (void) Reset GapExtend data member. More...
TGapExtend GetGapExtend (void) const Get the GapExtend member data. More...
void SetGapExtend (TGapExtend value) Assign a value to GapExtend data member. More...
TGapExtend & SetGapExtend (void) Assign a value to GapExtend data member. More...
virtual void Reset (void) Reset the whole object. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Set object to copy of another one. More...
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const Check if both objects contain the same values. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
void ThrowUnassigned (TMemberIndex index) const void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const bool HasNamespaceName (void) const Check if object data type has namespace name. More...
const string & GetNamespaceName (void) const Get namespace name. More...
bool HasNamespacePrefix (void) const Check if data type has namespace prefix. More...
const string & GetNamespacePrefix (void) const Get namespace prefix. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (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...
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
This structure is used to create the RPS-BLAST database auxiliary file (*.aux) and it contains parameters set at creation time of the PSSM.
Also, the matrixName field is used by formatrpsdb to build a PSSM from a Pssm structure which only contains PssmIntermediateData.
CFormatRpsDbParameters_Base –
Definition at line 76 of file FormatRpsDbParameters_.hpp.
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