NCBI C++ ToolKit
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Search Toolkit Book for CPsiBl2Seq

Runs a single iteration of the PSI-BLAST algorithm between 2 sequences. More...

#include <algo/blast/api/psibl2seq.hpp>

+ Inheritance diagram for CPsiBl2Seq:
+ Collaboration diagram for CPsiBl2Seq:

Public Member Functions

 CPsiBl2Seq (CRef< objects::CPssmWithParameters > pssm, CRef< IQueryFactory > subject, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against protein sequences. More...
 
 CPsiBl2Seq (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > subject, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against protein sequences. More...
 
 CPsiBl2Seq (CRef< IQueryFactory > query, CRef< IQueryFactory > subject, CConstRef< CBlastProteinOptionsHandle > options)
 Constructor to compare protein sequences in an object manager-free manner. More...
 
 ~CPsiBl2Seq ()
 Destructor. More...
 
CRef< CSearchResultSetRun ()
 Run the PSI-BLAST 2 Sequences engine. 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 Member Functions

void x_InitSubject (CRef< IQueryFactory > subject, const CBlastOptionsHandle *options)
 Auxiliary method to initialize the subject. More...
 
 CPsiBl2Seq (const CPsiBl2Seq &rhs)
 Prohibit copy constructor. More...
 
CPsiBl2Seqoperator= (const CPsiBl2Seq &rhs)
 Prohibit assignment operator. More...
 

Private Attributes

CRef< CLocalDbAdapterm_Subject
 Reference to a BLAST subject/database object. More...
 
class CPsiBlastImplm_Impl
 Implementation class. More...
 

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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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

Runs a single iteration of the PSI-BLAST algorithm between 2 sequences.

Definition at line 57 of file psibl2seq.hpp.

Constructor & Destructor Documentation

CPsiBl2Seq::CPsiBl2Seq ( const CPsiBl2Seq rhs)
private

Prohibit copy constructor.

Member Function Documentation

CPsiBl2Seq& CPsiBl2Seq::operator= ( const CPsiBl2Seq rhs)
private

Prohibit assignment operator.

Member Data Documentation

class CPsiBlastImpl* CPsiBl2Seq::m_Impl
private

Implementation class.

Definition at line 119 of file psibl2seq.hpp.

Referenced by CPsiBl2Seq(), Run(), and ~CPsiBl2Seq().

CRef<CLocalDbAdapter> CPsiBl2Seq::m_Subject
private

Reference to a BLAST subject/database object.

Definition at line 116 of file psibl2seq.hpp.

Referenced by CPsiBl2Seq(), and x_InitSubject().


The documentation for this class was generated from the following files:
Modified on Mon Oct 16 16:17:55 2017 by modify_doxy.py rev. 546573