NCBI C++ ToolKit
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SU_PSSMInput Class Reference

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+ Inheritance diagram for SU_PSSMInput:
+ Collaboration diagram for SU_PSSMInput:

Public Member Functions

 SU_PSSMInput (const BlockMultipleAlignment *b)
 
 ~SU_PSSMInput (void)
 
void Process (void)
 Algorithm to produce multiple sequence alignment structure should be implemented in this method. More...
 
unsigned char * GetQuery (void)
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
unsigned int GetQueryLength (void)
 Get the query's length. More...
 
PSIMsaGetData (void)
 Obtain the multiple sequence alignment structure. More...
 
const PSIBlastOptionsGetOptions (void)
 Obtain the options for the PSSM engine. More...
 
const char * GetMatrixName (void)
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
const PSIDiagnosticsRequestGetDiagnosticsRequest (void)
 Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object. More...
 
- Public Member Functions inherited from IPssmInputData
virtual ~IPssmInputData ()
 virtual destructor More...
 
- Public Member Functions inherited from IPssmInput_Base
virtual ~IPssmInput_Base ()
 virtual destructor 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
 

Private Attributes

const BlockMultipleAlignmentbma
 
unsigned char * masterNCBIStdaa
 
unsigned int masterLength
 
PSIMsadata
 
PSIBlastOptionsoptions
 
PSIDiagnosticsRequest diag
 

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

Definition at line 63 of file su_pssm.cpp.

Constructor & Destructor Documentation

◆ SU_PSSMInput()

SU_PSSMInput::SU_PSSMInput ( const BlockMultipleAlignment b)

◆ ~SU_PSSMInput()

SU_PSSMInput::~SU_PSSMInput ( void  )

Definition at line 434 of file su_pssm.cpp.

References data, masterNCBIStdaa, options, PSIBlastOptionsFree(), and PSIMsaFree().

Member Function Documentation

◆ GetData()

PSIMsa* SU_PSSMInput::GetData ( void  )
inlinevirtual

Obtain the multiple sequence alignment structure.

Implements IPssmInputData.

Definition at line 82 of file su_pssm.cpp.

References data.

◆ GetDiagnosticsRequest()

const PSIDiagnosticsRequest* SU_PSSMInput::GetDiagnosticsRequest ( void  )
inlinevirtual

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object.

Reimplemented from IPssmInputData.

Definition at line 85 of file su_pssm.cpp.

References diag.

Referenced by SU_PSSMInput().

◆ GetMatrixName()

const char* SU_PSSMInput::GetMatrixName ( void  )
inlinevirtual

Obtain the name of the underlying matrix to use when building the PSSM.

Reimplemented from IPssmInput_Base.

Definition at line 84 of file su_pssm.cpp.

Referenced by SU_PSSMInput().

◆ GetOptions()

const PSIBlastOptions* SU_PSSMInput::GetOptions ( void  )
inlinevirtual

Obtain the options for the PSSM engine.

Implements IPssmInputData.

Definition at line 83 of file su_pssm.cpp.

References options.

◆ GetQuery()

unsigned char* SU_PSSMInput::GetQuery ( void  )
inlinevirtual

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

Implements IPssmInput_Base.

Definition at line 80 of file su_pssm.cpp.

References masterNCBIStdaa.

Referenced by SU_PSSMInput().

◆ GetQueryLength()

unsigned int SU_PSSMInput::GetQueryLength ( void  )
inlinevirtual

Get the query's length.

Implements IPssmInput_Base.

Definition at line 81 of file su_pssm.cpp.

References masterLength.

Referenced by SU_PSSMInput().

◆ Process()

void SU_PSSMInput::Process ( void  )
inlinevirtual

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

This will be invoked by the CPssmEngine object before calling GetData()

Implements IPssmInputData.

Definition at line 79 of file su_pssm.cpp.

Member Data Documentation

◆ bma

const BlockMultipleAlignment* SU_PSSMInput::bma
private

Definition at line 66 of file su_pssm.cpp.

Referenced by SU_PSSMInput().

◆ data

PSIMsa* SU_PSSMInput::data
private

Definition at line 70 of file su_pssm.cpp.

Referenced by GetData(), SU_PSSMInput(), and ~SU_PSSMInput().

◆ diag

PSIDiagnosticsRequest SU_PSSMInput::diag
private

Definition at line 72 of file su_pssm.cpp.

Referenced by GetDiagnosticsRequest(), and SU_PSSMInput().

◆ masterLength

unsigned int SU_PSSMInput::masterLength
private

Definition at line 68 of file su_pssm.cpp.

Referenced by GetQueryLength(), and SU_PSSMInput().

◆ masterNCBIStdaa

unsigned char* SU_PSSMInput::masterNCBIStdaa
private

Definition at line 67 of file su_pssm.cpp.

Referenced by GetQuery(), SU_PSSMInput(), and ~SU_PSSMInput().

◆ options

PSIBlastOptions* SU_PSSMInput::options
private

Definition at line 71 of file su_pssm.cpp.

Referenced by GetOptions(), SU_PSSMInput(), and ~SU_PSSMInput().


The documentation for this class was generated from the following file:
Modified on Sun Mar 03 03:10:28 2024 by modify_doxy.py rev. 669887