NCBI C++ ToolKit
Public Member Functions | List of all members
ISearchFactory Class Referenceabstract

Search Toolkit Book for ISearchFactory

Factory for ISearch. More...

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

+ Inheritance diagram for ISearchFactory:
+ Collaboration diagram for ISearchFactory:

Public Member Functions

virtual CRef< ISeqSearchGetSeqSearch ()=0
 Create a new search object with a sequence-based query. More...
 
virtual CRef< IPssmSearchGetPssmSearch ()=0
 Create a new search object with a pssm-based query. More...
 
virtual CRef< CBlastOptionsHandleGetOptions (EProgram program)=0
 Create a CBlastOptionsHandle. 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
 

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

Factory for ISearch.

This class is an abstract factory class for the ISearch class. Concrete subclasses of this class will create and return concrete subclasses of the ISearch class. Use this class when you need to write code that decribes an algorithm over the abstract ISearch API, and is ignorant of the concrete type of search it is performing (i.e.: local vs. remote search).

Definition at line 285 of file uniform_search.hpp.

Member Function Documentation

virtual CRef<CBlastOptionsHandle> ISearchFactory::GetOptions ( EProgram  program)
pure virtual

Create a CBlastOptionsHandle.

This creates a CBlastOptionsHandle for the specified program value. The options can be used to configure a search created by the GetSeqSearch() or GetPssmSearch() methods. The search object and the CBlastOptionsHandle object should be created by the same ISearchFactory subclass.

Parameters
programThe program type for this search.
Returns
An options handle object for this program and factory type.

Implemented in CRemoteSearchFactory, and CLocalSearchFactory.

Referenced by BOOST_AUTO_TEST_CASE(), RunMultipleProteinSearch(), and CTracebackSearchTestFixture::x_Traceback().

virtual CRef<IPssmSearch> ISearchFactory::GetPssmSearch ( )
pure virtual

Create a new search object with a pssm-based query.

A search object will be constructed and configured for a search using a PSSM query.

Returns
A search object for a PSSM search.

Implemented in CRemoteSearchFactory, and CLocalSearchFactory.

virtual CRef<ISeqSearch> ISearchFactory::GetSeqSearch ( )
pure virtual

Create a new search object with a sequence-based query.

A search object will be constructed and configured for a search using a query that consists of one or more sequences.

Returns
A search object for a sequence search.

Implemented in CRemoteSearchFactory, and CLocalSearchFactory.

Referenced by RunMultipleProteinSearch().


The documentation for this class was generated from the following file:
Modified on Tue May 22 12:45:48 2018 by modify_doxy.py rev. 546573