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CSeqTest Class Referenceabstract

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Class CSeqTest provides a general API for performing a given test on. More...

#include <algo/seqqa/seqtest.hpp>

+ Inheritance diagram for CSeqTest:
+ Collaboration diagram for CSeqTest:

Public Member Functions

virtual bool CanTest (const CSerialObject &obj, const CSeqTestContext *ctx) const =0
 Test to see whether the given object *can* be used in this test. More...
 
virtual CRef< objects::CSeq_test_result_set > RunTest (const CSerialObject &obj, const CSeqTestContext *ctx)=0
 RunTest() is called for each registered object. 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 Types

typedef void(* TCdregionTester) (const objects::CSeq_id &, const CSeqTestContext *ctx, objects::CFeat_CI, objects::CSeq_test_result &)
 A fuction type that analyzes coding regions. More...
 

Protected Member Functions

CRef< objects::CSeq_test_result > x_SkeletalTestResult (const string &test_name)
 Create a Seq-test-result with some fields filled in, including a name for this test, which must be supplied as an argument. More...
 
CRef< objects::CSeq_test_result_set > x_TestAllCdregions (const CSerialObject &obj, const CSeqTestContext *ctx, const string &test_name, TCdregionTester cdregion_tester)
 Given a Seq-id and a context, analyze all coding regions by calling a supplied function. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. 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...
 
- 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...
 

Detailed Description

Class CSeqTest provides a general API for performing a given test on.

Definition at line 95 of file seqtest.hpp.

Member Typedef Documentation

◆ TCdregionTester

typedef void(* CSeqTest::TCdregionTester) (const objects::CSeq_id &, const CSeqTestContext *ctx, objects::CFeat_CI, objects::CSeq_test_result &)
protected

A fuction type that analyzes coding regions.

Definition at line 113 of file seqtest.hpp.

Member Function Documentation

◆ CanTest()

virtual bool CSeqTest::CanTest ( const CSerialObject obj,
const CSeqTestContext ctx 
) const
pure virtual

Test to see whether the given object *can* be used in this test.

Implemented in CTestTranscript, CTestSingleAln, CTestSeqId, CTestProtProd_EntrezNeighbors, CTestProtProd, and CTestBlastp.

◆ RunTest()

virtual CRef<objects::CSeq_test_result_set> CSeqTest::RunTest ( const CSerialObject obj,
const CSeqTestContext ctx 
)
pure virtual

◆ x_SkeletalTestResult()

CRef< CSeq_test_result > CSeqTest::x_SkeletalTestResult ( const string test_name)
protected

◆ x_TestAllCdregions()

CRef< CSeq_test_result_set > CSeqTest::x_TestAllCdregions ( const CSerialObject obj,
const CSeqTestContext ctx,
const string test_name,
TCdregionTester  cdregion_tester 
)
protected

The documentation for this class was generated from the following files:
Modified on Wed May 15 15:09:51 2024 by modify_doxy.py rev. 669887