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NCBI C++ ToolKit: CAlgorithm_type_Base Class Reference

enum EScoring_Scheme {
  eScoring_Scheme_unassigned = 0 , eScoring_Scheme_percent_id = 1 , eScoring_Scheme_kimura_corrected = 2 , eScoring_Scheme_aligned_score = 3 ,
  eScoring_Scheme_aligned_score_ext = 4 , eScoring_Scheme_aligned_score_filled = 5 , eScoring_Scheme_blast_footprint = 6 , eScoring_Scheme_blast_full = 7 ,
  eScoring_Scheme_hybrid_aligned_score = 8 , eScoring_Scheme_other = 255
} enum EClustering_Method {
  eClustering_Method_unassigned = 0 , eClustering_Method_single_linkage = 1 , eClustering_Method_neighbor_joining = 2 , eClustering_Method_fast_minimum_evolution = 3 ,
  eClustering_Method_other = 255
} enum EScore_Matrix {
  eScore_Matrix_unassigned = 0 , eScore_Matrix_blosum45 = 1 , eScore_Matrix_blosum62 = 2 , eScore_Matrix_blosum80 = 3 ,
  eScore_Matrix_pam30 = 4 , eScore_Matrix_pam70 = 5 , eScore_Matrix_pam250 = 6 , eScore_Matrix_other = 255
} enum ETree_scope { eTree_scope_allDescendants = 0 , eTree_scope_immediateChildrenOnly = 1 , eTree_scope_selfOnly = 2 , eTree_scope_other = 255 } enum EColoring_scope { eColoring_scope_allDescendants = 0 , eColoring_scope_immediateChildrenOnly = 1 , eColoring_scope_other = 255 } enum class E_memberIndex {
  e__allMandatory = 0 , e_scoring_Scheme , e_clustering_Method , e_score_Matrix ,
  e_gapOpen , e_gapExtend , e_gapScaleFactor , e_nTerminalExt ,
  e_cTerminalExt , e_tree_scope , e_coloring_scope
} typedef int TScoring_Scheme typedef int TClustering_Method typedef int TScore_Matrix typedef int TGapOpen typedef int TGapExtend typedef int TGapScaleFactor typedef int TNTerminalExt typedef int TCTerminalExt typedef int TTree_scope typedef int TColoring_scope typedef Tparent::CMemberIndex< E_memberIndex, 11 > TmemberIndex enum EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } Control filling of newly allocated memory. More...
typedef CObjectCounterLocker TLockerType Default locker type for CRef. More...
typedef atomic< Uint8 > TCounter Counter type is CAtomiCounter. More...
typedef Uint8 TCount Alias for value type of counter. More...
CAlgorithm_type_Base (void) virtual ~CAlgorithm_type_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetScoring_Scheme (void) const Check if a value has been assigned to Scoring_Scheme data member. More...
bool CanGetScoring_Scheme (void) const Check if it is safe to call GetScoring_Scheme method. More...
void ResetScoring_Scheme (void) Reset Scoring_Scheme data member. More...
TScoring_Scheme GetScoring_Scheme (void) const Get the Scoring_Scheme member data. More...
void SetScoring_Scheme (TScoring_Scheme value) Assign a value to Scoring_Scheme data member. More...
TScoring_Scheme & SetScoring_Scheme (void) Assign a value to Scoring_Scheme data member. More...
bool IsSetClustering_Method (void) const Check if a value has been assigned to Clustering_Method data member. More...
bool CanGetClustering_Method (void) const Check if it is safe to call GetClustering_Method method. More...
void ResetClustering_Method (void) Reset Clustering_Method data member. More...
TClustering_Method GetClustering_Method (void) const Get the Clustering_Method member data. More...
void SetClustering_Method (TClustering_Method value) Assign a value to Clustering_Method data member. More...
TClustering_Method & SetClustering_Method (void) Assign a value to Clustering_Method data member. More...
bool IsSetScore_Matrix (void) const Check if a value has been assigned to Score_Matrix data member. More...
bool CanGetScore_Matrix (void) const Check if it is safe to call GetScore_Matrix method. More...
void ResetScore_Matrix (void) Reset Score_Matrix data member. More...
TScore_Matrix GetScore_Matrix (void) const Get the Score_Matrix member data. More...
void SetScore_Matrix (TScore_Matrix value) Assign a value to Score_Matrix data member. More...
TScore_Matrix & SetScore_Matrix (void) Assign a value to Score_Matrix data member. More...
bool IsSetGapOpen (void) const 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 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...
bool IsSetGapScaleFactor (void) const Check if a value has been assigned to GapScaleFactor data member. More...
bool CanGetGapScaleFactor (void) const Check if it is safe to call GetGapScaleFactor method. More...
void ResetGapScaleFactor (void) Reset GapScaleFactor data member. More...
TGapScaleFactor GetGapScaleFactor (void) const Get the GapScaleFactor member data. More...
void SetGapScaleFactor (TGapScaleFactor value) Assign a value to GapScaleFactor data member. More...
TGapScaleFactor & SetGapScaleFactor (void) Assign a value to GapScaleFactor data member. More...
bool IsSetNTerminalExt (void) const Check if a value has been assigned to NTerminalExt data member. More...
bool CanGetNTerminalExt (void) const Check if it is safe to call GetNTerminalExt method. More...
void ResetNTerminalExt (void) Reset NTerminalExt data member. More...
TNTerminalExt GetNTerminalExt (void) const Get the NTerminalExt member data. More...
void SetNTerminalExt (TNTerminalExt value) Assign a value to NTerminalExt data member. More...
TNTerminalExt & SetNTerminalExt (void) Assign a value to NTerminalExt data member. More...
bool IsSetCTerminalExt (void) const Check if a value has been assigned to CTerminalExt data member. More...
bool CanGetCTerminalExt (void) const Check if it is safe to call GetCTerminalExt method. More...
void ResetCTerminalExt (void) Reset CTerminalExt data member. More...
TCTerminalExt GetCTerminalExt (void) const Get the CTerminalExt member data. More...
void SetCTerminalExt (TCTerminalExt value) Assign a value to CTerminalExt data member. More...
TCTerminalExt & SetCTerminalExt (void) Assign a value to CTerminalExt data member. More...
bool IsSetTree_scope (void) const Check if a value has been assigned to Tree_scope data member. More...
bool CanGetTree_scope (void) const Check if it is safe to call GetTree_scope method. More...
void ResetTree_scope (void) Reset Tree_scope data member. More...
TTree_scope GetTree_scope (void) const Get the Tree_scope member data. More...
void SetTree_scope (TTree_scope value) Assign a value to Tree_scope data member. More...
TTree_scope & SetTree_scope (void) Assign a value to Tree_scope data member. More...
bool IsSetColoring_scope (void) const Check if a value has been assigned to Coloring_scope data member. More...
bool CanGetColoring_scope (void) const Check if it is safe to call GetColoring_scope method. More...
void ResetColoring_scope (void) Reset Coloring_scope data member. More...
TColoring_scope GetColoring_scope (void) const Get the Coloring_scope member data. More...
void SetColoring_scope (TColoring_scope value) Assign a value to Coloring_scope data member. More...
TColoring_scope & SetColoring_scope (void) Assign a value to Coloring_scope 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

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