NCBI C++ ToolKit
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CPssmInputWithNoCDs Class Reference

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Simple PSSM computation strategy with one CD. More...

+ Inheritance diagram for CPssmInputWithNoCDs:
+ Collaboration diagram for CPssmInputWithNoCDs:

Public Member Functions

 CPssmInputWithNoCDs (void)
 
virtual ~CPssmInputWithNoCDs ()
 
virtual PSICdMsaGetData (void)
 Get CD data for PSSM computation. More...
 
virtual const PSIBlastOptionsGetOptions (void)
 Get CDD-related PSI-BLAST options. More...
 
virtual void Process (void)
 Pre-process CDs used for PSSM computation. More...
 
virtual unsigned char * GetQuery (void)
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
virtual unsigned int GetQueryLength (void)
 Get the query's length. More...
 
- Public Member Functions inherited from IPssmInputCdd
virtual ~IPssmInputCdd ()
 
virtual const PSIDiagnosticsRequestGetDiagnosticsRequest (void)
 Get diagnostics options. More...
 
- Public Member Functions inherited from IPssmInput_Base
virtual ~IPssmInput_Base ()
 virtual destructor More...
 
virtual const char * GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
virtual int GetGapExistence ()
 Obtain the gap existence value for the underlying matrix used to build the PSSM. More...
 
virtual int GetGapExtension ()
 Obtain the gap extension value for the underlying matrix used to build the PSSM. More...
 
virtual CRef< objects::CBioseq > GetQueryForPssm ()
 Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). 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...
 
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
 

Protected Attributes

PSICdMsa m_CdMsa
 
PSIMsaDimensions m_Dimensions
 
CPSIBlastOptions m_Options
 
vector< unsigned char > m_Query
 
vector< PSICdMsaCell * > m_Msa
 

Static Protected Attributes

static const int kQueryLength = 6
 

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 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 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 Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Simple PSSM computation strategy with one CD.

Definition at line 154 of file pssmcreate_cdd_unit_test.cpp.

Constructor & Destructor Documentation

◆ CPssmInputWithNoCDs()

CPssmInputWithNoCDs::CPssmInputWithNoCDs ( void  )

Definition at line 1212 of file pssmcreate_cdd_unit_test.cpp.

References NULL, and PSIBlastOptionsNew().

◆ ~CPssmInputWithNoCDs()

virtual CPssmInputWithNoCDs::~CPssmInputWithNoCDs ( )
inlinevirtual

Definition at line 160 of file pssmcreate_cdd_unit_test.cpp.

Member Function Documentation

◆ GetData()

virtual PSICdMsa* CPssmInputWithNoCDs::GetData ( void  )
inlinevirtual

Get CD data for PSSM computation.

Implements IPssmInputCdd.

Definition at line 162 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetOptions()

virtual const PSIBlastOptions* CPssmInputWithNoCDs::GetOptions ( void  )
inlinevirtual

Get CDD-related PSI-BLAST options.

Implements IPssmInputCdd.

Definition at line 164 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetQuery()

virtual unsigned char* CPssmInputWithNoCDs::GetQuery ( void  )
inlinevirtual

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

Implements IPssmInput_Base.

Definition at line 168 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetQueryLength()

virtual unsigned int CPssmInputWithNoCDs::GetQueryLength ( void  )
inlinevirtual

Get the query's length.

Implements IPssmInput_Base.

Definition at line 170 of file pssmcreate_cdd_unit_test.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ Process()

virtual void CPssmInputWithNoCDs::Process ( void  )
inlinevirtual

Pre-process CDs used for PSSM computation.

Implements IPssmInputCdd.

Definition at line 166 of file pssmcreate_cdd_unit_test.cpp.

Member Data Documentation

◆ kQueryLength

const int CPssmInputWithNoCDs::kQueryLength = 6
staticprotected

Definition at line 181 of file pssmcreate_cdd_unit_test.cpp.

◆ m_CdMsa

PSICdMsa CPssmInputWithNoCDs::m_CdMsa
protected

Definition at line 175 of file pssmcreate_cdd_unit_test.cpp.

◆ m_Dimensions

PSIMsaDimensions CPssmInputWithNoCDs::m_Dimensions
protected

Definition at line 176 of file pssmcreate_cdd_unit_test.cpp.

◆ m_Msa

vector<PSICdMsaCell*> CPssmInputWithNoCDs::m_Msa
protected

Definition at line 179 of file pssmcreate_cdd_unit_test.cpp.

◆ m_Options

CPSIBlastOptions CPssmInputWithNoCDs::m_Options
protected

Definition at line 177 of file pssmcreate_cdd_unit_test.cpp.

◆ m_Query

vector<unsigned char> CPssmInputWithNoCDs::m_Query
protected

Definition at line 178 of file pssmcreate_cdd_unit_test.cpp.


The documentation for this class was generated from the following file:
Modified on Mon Feb 26 03:59:32 2024 by modify_doxy.py rev. 669887