NCBI C++ ToolKit
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CPssm Class Reference

Represents ASN.1 type Pssm defined in file scoremat.asn

Search Toolkit Book for CPssm

#include <objects/scoremat/Pssm.hpp>

+ Inheritance diagram for CPssm:
+ Collaboration diagram for CPssm:

Public Member Functions

 CPssm (void)
 
 ~CPssm (void)
 
SIZE_TYPE GetQueryLength () const
 Return the query length or 0 if no query is available. More...
 
void GetQuerySequenceData (CNCBIstdaa &sequence) const
 Retrieve the query sequence data in ncbistdaa format. More...
 
double GetLambda () const
 
double GetKappa () const
 
double GetH () const
 
double GetLambdaUngapped () const
 
double GetKappaUngapped () const
 
double GetHUngapped () const
 
void SetLambda (double val)
 
void SetKappa (double val)
 
void SetH (double val)
 
void SetLambdaUngapped (double val)
 
void SetKappaUngapped (double val)
 
void SetHUngapped (double val)
 
- Public Member Functions inherited from CPssm_Base
 CPssm_Base (void)
 
virtual ~CPssm_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetIsProtein (void) const
 Is the this a protein or nucleotide scoring matrix? Check if a value has been assigned to IsProtein data member. More...
 
bool CanGetIsProtein (void) const
 Check if it is safe to call GetIsProtein method. More...
 
void ResetIsProtein (void)
 Reset IsProtein data member. More...
 
void SetDefaultIsProtein (void)
 Assign default value to IsProtein data member. More...
 
TIsProtein GetIsProtein (void) const
 Get the IsProtein member data. More...
 
void SetIsProtein (TIsProtein value)
 Assign a value to IsProtein data member. More...
 
TIsProteinSetIsProtein (void)
 Assign a value to IsProtein data member. More...
 
bool IsSetIdentifier (void) const
 PSSM identifier Check if a value has been assigned to Identifier data member. More...
 
bool CanGetIdentifier (void) const
 Check if it is safe to call GetIdentifier method. More...
 
void ResetIdentifier (void)
 Reset Identifier data member. More...
 
const TIdentifierGetIdentifier (void) const
 Get the Identifier member data. More...
 
void SetIdentifier (TIdentifier &value)
 Assign a value to Identifier data member. More...
 
TIdentifierSetIdentifier (void)
 Assign a value to Identifier data member. More...
 
bool IsSetNumRows (void) const
 The dimensions of the matrix are returned so the client can verify that all data was received. More...
 
bool CanGetNumRows (void) const
 Check if it is safe to call GetNumRows method. More...
 
void ResetNumRows (void)
 Reset NumRows data member. More...
 
TNumRows GetNumRows (void) const
 Get the NumRows member data. More...
 
void SetNumRows (TNumRows value)
 Assign a value to NumRows data member. More...
 
TNumRowsSetNumRows (void)
 Assign a value to NumRows data member. More...
 
bool IsSetNumColumns (void) const
 number of columns Check if a value has been assigned to NumColumns data member. More...
 
bool CanGetNumColumns (void) const
 Check if it is safe to call GetNumColumns method. More...
 
void ResetNumColumns (void)
 Reset NumColumns data member. More...
 
TNumColumns GetNumColumns (void) const
 Get the NumColumns member data. More...
 
void SetNumColumns (TNumColumns value)
 Assign a value to NumColumns data member. More...
 
TNumColumnsSetNumColumns (void)
 Assign a value to NumColumns data member. More...
 
bool IsSetRowLabels (void) const
 row-labels is given to note the order of residue types so that it can be cross-checked between applications. More...
 
bool CanGetRowLabels (void) const
 Check if it is safe to call GetRowLabels method. More...
 
void ResetRowLabels (void)
 Reset RowLabels data member. More...
 
const TRowLabelsGetRowLabels (void) const
 Get the RowLabels member data. More...
 
TRowLabelsSetRowLabels (void)
 Assign a value to RowLabels data member. More...
 
bool IsSetByRow (void) const
 are matrices stored row by row? Check if a value has been assigned to ByRow data member. More...
 
bool CanGetByRow (void) const
 Check if it is safe to call GetByRow method. More...
 
void ResetByRow (void)
 Reset ByRow data member. More...
 
void SetDefaultByRow (void)
 Assign default value to ByRow data member. More...
 
TByRow GetByRow (void) const
 Get the ByRow member data. More...
 
void SetByRow (TByRow value)
 Assign a value to ByRow data member. More...
 
TByRowSetByRow (void)
 Assign a value to ByRow data member. More...
 
bool IsSetQuery (void) const
 PSSM representative sequence (master) Check if a value has been assigned to Query data member. More...
 
bool CanGetQuery (void) const
 Check if it is safe to call GetQuery method. More...
 
void ResetQuery (void)
 Reset Query data member. More...
 
const TQueryGetQuery (void) const
 Get the Query member data. More...
 
void SetQuery (TQuery &value)
 Assign a value to Query data member. More...
 
TQuerySetQuery (void)
 Assign a value to Query data member. More...
 
bool IsSetIntermediateData (void) const
 both intermediateData and finalData can be provided, but at least one of them must be provided. More...
 
bool CanGetIntermediateData (void) const
 Check if it is safe to call GetIntermediateData method. More...
 
void ResetIntermediateData (void)
 Reset IntermediateData data member. More...
 
const TIntermediateDataGetIntermediateData (void) const
 Get the IntermediateData member data. More...
 
void SetIntermediateData (TIntermediateData &value)
 Assign a value to IntermediateData data member. More...
 
TIntermediateDataSetIntermediateData (void)
 Assign a value to IntermediateData data member. More...
 
bool IsSetFinalData (void) const
 Final representation for the PSSM Check if a value has been assigned to FinalData data member. More...
 
bool CanGetFinalData (void) const
 Check if it is safe to call GetFinalData method. More...
 
void ResetFinalData (void)
 Reset FinalData data member. More...
 
const TFinalDataGetFinalData (void) const
 Get the FinalData member data. More...
 
void SetFinalData (TFinalData &value)
 Assign a value to FinalData data member. More...
 
TFinalDataSetFinalData (void)
 Assign a value to FinalData data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- 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...
 
- 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 Attributes

static const double kInvalidStat = 0.0
 
- Static Public Attributes inherited from CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- 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...
 

Private Types

typedef CPssm_Base Tparent
 

Private Member Functions

 CPssm (const CPssm &value)
 
CPssmoperator= (const CPssm &value)
 

Additional Inherited Members

- Public Types inherited from CPssm_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_isProtein , e_identifier , e_numRows ,
  e_numColumns , e_rowLabels , e_byRow , e_query ,
  e_intermediateData , e_finalData
}
 
typedef bool TIsProtein
 
typedef CObject_id TIdentifier
 
typedef int TNumRows
 
typedef int TNumColumns
 
typedef list< stringTRowLabels
 
typedef bool TByRow
 
typedef CSeq_entry TQuery
 
typedef CPssmIntermediateData TIntermediateData
 
typedef CPssmFinalData TFinalData
 
typedef Tparent::CMemberIndex< E_memberIndex, 10 > TmemberIndex
 
- 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 Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- 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)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 54 of file Pssm.hpp.

Member Typedef Documentation

◆ Tparent

typedef CPssm_Base CPssm::Tparent
private

Definition at line 56 of file Pssm.hpp.

Constructor & Destructor Documentation

◆ CPssm() [1/2]

CPssm::CPssm ( void  )
inline

Definition at line 97 of file Pssm.hpp.

◆ ~CPssm()

CPssm::~CPssm ( void  )

Definition at line 57 of file Pssm.cpp.

◆ CPssm() [2/2]

CPssm::CPssm ( const CPssm value)
private

Member Function Documentation

◆ GetH()

double CPssm::GetH ( void  ) const

◆ GetHUngapped()

double CPssm::GetHUngapped ( ) const

◆ GetKappa()

double CPssm::GetKappa ( void  ) const

◆ GetKappaUngapped()

double CPssm::GetKappaUngapped ( ) const

◆ GetLambda()

double CPssm::GetLambda ( void  ) const

◆ GetLambdaUngapped()

double CPssm::GetLambdaUngapped ( ) const

◆ GetQueryLength()

SIZE_TYPE CPssm::GetQueryLength ( void  ) const

◆ GetQuerySequenceData()

void CPssm::GetQuerySequenceData ( CNCBIstdaa sequence) const

Retrieve the query sequence data in ncbistdaa format.

Parameters
sequenceobject on which to store the sequence, it will be empty if there is no sequence data available [in|out]

Definition at line 77 of file Pssm.cpp.

References CPssm_Base::CanGetQuery(), CSeqportUtil::Convert(), copy(), CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetNcbistdaa(), CPssm_Base::GetQuery(), GetQueryLength(), CSeq_entry_Base::GetSeq(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsNcbistdaa(), and CAliasBase< TPrim >::Set().

Referenced by CMakeProfileDBApp::x_RPSUpdateStatistics().

◆ operator=()

CPssm& CPssm::operator= ( const CPssm value)
private

◆ SetH()

void CPssm::SetH ( double  val)

◆ SetHUngapped()

void CPssm::SetHUngapped ( double  val)

◆ SetKappa()

void CPssm::SetKappa ( double  val)

◆ SetKappaUngapped()

void CPssm::SetKappaUngapped ( double  val)

◆ SetLambda()

void CPssm::SetLambda ( double  val)

◆ SetLambdaUngapped()

void CPssm::SetLambdaUngapped ( double  val)

Member Data Documentation

◆ kInvalidStat

const double CPssm::kInvalidStat = 0.0
static

The documentation for this class was generated from the following files:
Modified on Sat Mar 02 10:53:00 2024 by modify_doxy.py rev. 669887