NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Private Attributes | List of all members

Search Toolkit Book for CPsiBlast

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database. More...

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

+ Inheritance diagram for CPsiBlast:
+ Collaboration diagram for CPsiBlast:

Public Member Functions

 CPsiBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a single sequence against a database of protein sequences. More...
 
 CPsiBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against a database of protein sequences. More...
 
 ~CPsiBlast ()
 Destructor. More...
 
void SetPssm (CConstRef< objects::CPssmWithParameters > pssm)
 This method allows the same object to be reused when performing multiple iterations. More...
 
CConstRef< objects::CPssmWithParameters > GetPssm () const
 Accessor for the most recently used PSSM. More...
 
CRef< CSearchResultSetRun ()
 Run the PSI-BLAST engine for one iteration. 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
 
- Public Member Functions inherited from CThreadable
 CThreadable (void)
 Default ctor. More...
 
virtual ~CThreadable (void)
 Our virtual destructor. More...
 
virtual void SetNumberOfThreads (size_t nthreads)
 Mutator for the number of threads. More...
 
size_t GetNumberOfThreads (void) const
 Accessor for the number of threads to use. More...
 
bool IsMultiThreaded (void) const
 Returns true if more than 1 thread is specified. More...
 

Private Member Functions

 CPsiBlast (const CPsiBlast &rhs)
 Prohibit copy constructor. More...
 
CPsiBlastoperator= (const CPsiBlast &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 atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Public Types inherited from CThreadable
enum  { kMinNumThreads = 1 }
 Never have less than 1 thread. 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...
 
- Protected Attributes inherited from CThreadable
size_t m_NumThreads
 Keep track of how many threads should be used. More...
 

Detailed Description

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

...
/* Run PSI-BLAST starting with a protein query sequence */
CRef<CBioseq> bioseq = ...;
CRef<IQueryFactory> query_factory(new CObjMgrFree_QueryFactory(bioseq));
CRef<CPsiBlast> psiblast(new CPsiBlast(query_factory, db, options));
CSearchResultSet alignment = psiblast->Run();
...
/* Run PSI-BLAST starting with a PSSM */
CRef<CPssmWithParameters> pssm = ...;
psiblast = new CPsiBlast(pssm, db, options);
alignment = psiblast->Run();
...
NCBI C++ Object Manager free implementation of IQueryFactory.
Handle to the protein-protein options to the BLAST algorithm.
Blast Search Subject.
Search Results for All Queries.
CPsiBlast(CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
Constructor to compare a single sequence against a database of protein sequences.
Definition: psiblast.cpp:58
@ eBlastDbIsProtein
protein

Definition at line 78 of file psiblast.hpp.


The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:39:56 2024 by modify_doxy.py rev. 669887