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NCBI C++ ToolKit: CPssmFinalData_Base Class Reference
Represents ASN.1 type PssmFinalData defined in file scoremat.asn
Search Toolkit Book for CPssmFinalData_Base
=========================================================================== PSI-BLAST, formatrpsdb, RPS-BLAST workflow: =========================================== More...
#include <objects/scoremat/PssmFinalData_.hpp>
enum class E_memberIndex {
e__allMandatory = 0 , e_scores , e_lambda , e_kappa ,
e_h , e_scalingFactor , e_lambdaUngapped , e_kappaUngapped ,
e_hUngapped , e_wordScoreThreshold
} typedef list< int > TScores typedef double TLambda typedef double TKappa typedef double TH typedef int TScalingFactor typedef double TLambdaUngapped typedef double TKappaUngapped typedef double THUngapped typedef double TWordScoreThreshold typedef Tparent::CMemberIndex< E_memberIndex, 10 > 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...
CPssmFinalData_Base (void) virtual ~CPssmFinalData_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetScores (void) const PSSM's scores Check if a value has been assigned to Scores data member. More...
bool CanGetScores (void) const Check if it is safe to call GetScores method. More...
void ResetScores (void) Reset Scores data member. More...
const TScores & GetScores (void) const Get the Scores member data. More...
TScores & SetScores (void) Assign a value to Scores data member. More...
bool IsSetLambda (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to Lambda data member. More...
bool CanGetLambda (void) const Check if it is safe to call GetLambda method. More...
void ResetLambda (void) Reset Lambda data member. More...
TLambda GetLambda (void) const Get the Lambda member data. More...
void SetLambda (TLambda value) Assign a value to Lambda data member. More...
TLambda & SetLambda (void) Assign a value to Lambda data member. More...
bool IsSetKappa (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to Kappa data member. More...
bool CanGetKappa (void) const Check if it is safe to call GetKappa method. More...
void ResetKappa (void) Reset Kappa data member. More...
TKappa GetKappa (void) const Get the Kappa member data. More...
void SetKappa (TKappa value) Assign a value to Kappa data member. More...
TKappa & SetKappa (void) Assign a value to Kappa data member. More...
bool IsSetH (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to H data member. More...
bool CanGetH (void) const Check if it is safe to call GetH method. More...
void ResetH (void) Reset H data member. More...
TH GetH (void) const Get the H member data. More...
void SetH (TH value) Assign a value to H data member. More...
TH & SetH (void) Assign a value to H data member. More...
bool IsSetScalingFactor (void) const scaling factor used to obtain more precision when building the PSSM. More...
bool CanGetScalingFactor (void) const Check if it is safe to call GetScalingFactor method. More...
void ResetScalingFactor (void) Reset ScalingFactor data member. More...
void SetDefaultScalingFactor (void) Assign default value to ScalingFactor data member. More...
TScalingFactor GetScalingFactor (void) const Get the ScalingFactor member data. More...
void SetScalingFactor (TScalingFactor value) Assign a value to ScalingFactor data member. More...
TScalingFactor & SetScalingFactor (void) Assign a value to ScalingFactor data member. More...
bool IsSetLambdaUngapped (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to LambdaUngapped data member. More...
bool CanGetLambdaUngapped (void) const Check if it is safe to call GetLambdaUngapped method. More...
void ResetLambdaUngapped (void) Reset LambdaUngapped data member. More...
TLambdaUngapped GetLambdaUngapped (void) const Get the LambdaUngapped member data. More...
void SetLambdaUngapped (TLambdaUngapped value) Assign a value to LambdaUngapped data member. More...
TLambdaUngapped & SetLambdaUngapped (void) Assign a value to LambdaUngapped data member. More...
bool IsSetKappaUngapped (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to KappaUngapped data member. More...
bool CanGetKappaUngapped (void) const Check if it is safe to call GetKappaUngapped method. More...
void ResetKappaUngapped (void) Reset KappaUngapped data member. More...
TKappaUngapped GetKappaUngapped (void) const Get the KappaUngapped member data. More...
void SetKappaUngapped (TKappaUngapped value) Assign a value to KappaUngapped data member. More...
TKappaUngapped & SetKappaUngapped (void) Assign a value to KappaUngapped data member. More...
bool IsSetHUngapped (void) const Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to HUngapped data member. More...
bool CanGetHUngapped (void) const Check if it is safe to call GetHUngapped method. More...
void ResetHUngapped (void) Reset HUngapped data member. More...
THUngapped GetHUngapped (void) const Get the HUngapped member data. More...
void SetHUngapped (THUngapped value) Assign a value to HUngapped data member. More...
THUngapped & SetHUngapped (void) Assign a value to HUngapped data member. More...
bool IsSetWordScoreThreshold (void) const Word score threshold Check if a value has been assigned to WordScoreThreshold data member. More...
bool CanGetWordScoreThreshold (void) const Check if it is safe to call GetWordScoreThreshold method. More...
void ResetWordScoreThreshold (void) Reset WordScoreThreshold data member. More...
TWordScoreThreshold GetWordScoreThreshold (void) const Get the WordScoreThreshold member data. More...
void SetWordScoreThreshold (TWordScoreThreshold value) Assign a value to WordScoreThreshold data member. More...
TWordScoreThreshold & SetWordScoreThreshold (void) Assign a value to WordScoreThreshold 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
=========================================================================== PSI-BLAST, formatrpsdb, RPS-BLAST workflow: ===========================================
Two possible inputs to PSI-BLAST and formatrpsdb: 1) PssmWithParams where pssm field contains intermediate PSSM data (matrix of frequency ratios) 2) PssmWithParams where pssm field contains final PSSM data (matrix of scores and statistical parameters) - such as written by cddumper
In case 1, PSI-BLAST's PSSM engine is invoked to create the PSSM and perform the PSI-BLAST search or build the PSSM to then build the RPS-BLAST database. In case 2, PSI-BLAST's PSSM engine is not invoked and the matrix of scores statistical parameters are used to perform the search in PSI-BLAST and the same data and the data in PssmWithParams::params::rpsdbparams is used to build the PSSM and ultimately the RPS-BLAST database
reads ++++++++++++++ writes PssmWithParams ====> + PSI-BLAST + =====> PssmWithParams ++++++++++++++ | ^ ^ | | | | | +===========================================+ | | | +===========================================+ | | | reads | | v | +++++++++++++++ writes +++++++++++++++++++++++ | | formatrpsdb | =====> | RPS-BLAST databases | | +++++++++++++++ +++++++++++++++++++++++ | ^ | | | | reads | +++++++++++++ | | RPS-BLAST | | +++++++++++++ | | reads ++++++++++++ writes | Cdd ======> | cddumper | =============================+ ++++++++++++
=========================================================================== Contains the PSSM's scores and its associated statistical parameters. Dimensions and order in which scores are stored must be the same as that specified in Pssm::numRows, Pssm::numColumns, and Pssm::byrow
CPssmFinalData_Base –
Definition at line 119 of file PssmFinalData_.hpp.
The documentation for this class was generated from the following files:
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