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Computes a PSSM as specified in PSI-BLAST. More...

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

+ Inheritance diagram for CPssmEngine:
+ Collaboration diagram for CPssmEngine:

Public Member Functions

 CPssmEngine (IPssmInputData *input)
 Constructor to configure the PSSM engine with a PSSM input data strategy object Checks that no data returned by the IPssmInputData interface is NULL. More...
 
 CPssmEngine (IPssmInputFreqRatios *input)
 Constructor to perform the last 2 stages of the PSSM creation algorithm Checks that no data returned by the IPssmInputFreqRatios interface is NULL. More...
 
 CPssmEngine (IPssmInputCdd *input)
 Constructor to configure the PSSM engine with a PSSM input data strategy object for CDD-based PSSM computation. More...
 
 ~CPssmEngine ()
 Destructor. More...
 
void SetUngappedStatisticalParams (CConstRef< CBlastAncillaryData > ancillary_data)
 Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation. More...
 
CRef< objects::CPssmWithParameters > Run ()
 Runs the PSSM engine to compute the PSSM. 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

BlastQueryInfox_InitializeQueryInfo (unsigned int query_length)
 Initialiazes the core BlastQueryInfo structure for a single protein sequence. More...
 
void x_InitializeScoreBlock (const unsigned char *query, unsigned int query_length, const char *matrix_name, int gap_existence, int gap_extension)
 Initializes the BlastScoreBlk data member required to run the PSSM engine. More...
 
unsigned char * x_GetQuery () const
 Private interface to retrieve query sequence from its data source interface. More...
 
unsigned int x_GetQueryLength () const
 Private interface to retrieve query length from its data source interface. More...
 
const char * x_GetMatrixName () const
 Private interface to retrieve matrix name from its data source interface. More...
 
int x_GetGapExistence () const
 Private interface to retrieve gap existence cost from data source. More...
 
int x_GetGapExtension () const
 Private interface to retrieve gap extension cost from data source. More...
 
CRef< objects::CPssmWithParameters > x_CreatePssmFromMsa ()
 Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment, creates a PSSM using the CORE C PSSM engine API. More...
 
CRef< objects::CPssmWithParameters > x_CreatePssmFromFreqRatios ()
 Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios, creates a PSSM using the CORE C PSSM engine API. More...
 
CRef< objects::CPssmWithParameters > x_CreatePssmFromCDD ()
 Using IPssmInputCdd as a delegate to provide data in the form of multiple alignment of CDs, creates PSSM using the CORE C PSSM engine API. More...
 
 CPssmEngine ()
 Default constructor available for derived test classes. More...
 
 CPssmEngine (const CPssmEngine &rhs)
 Prohibit copy constructor. More...
 
CPssmEngineoperator= (const CPssmEngine &rhs)
 Prohibit assignment operator. More...
 

Static Private Member Functions

static unsigned char * x_GuardProteinQuery (const unsigned char *query, unsigned int query_length)
 Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence. More...
 
static CRef< objects::CPssmWithParameters > x_PSIMatrix2Asn1 (const PSIMatrix *pssm, const char *matrix_name, const PSIBlastOptions *opts=NULL, const PSIDiagnosticsResponse *diagnostics=NULL)
 Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object. More...
 
static std::string x_ErrorCodeToString (int error_code)
 Convert a PSSM return status into a string. More...
 

Private Attributes

IPssmInputDatam_PssmInput
 Handle to strategy to process raw PSSM input data. More...
 
IPssmInputFreqRatiosm_PssmInputFreqRatios
 Pointer to input data to create PSSM from frequency ratios. More...
 
CBlastScoreBlk m_ScoreBlk
 Blast score block structure. More...
 
IPssmInputCddm_PssmInputCdd
 Pointer to strategy to process raw PSSM input data Note: Only one m_PssmInput* should be non-NULL. More...
 

Friends

class ::CPssmCreateTestFixture
 unit test 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...
 
- 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

Computes a PSSM as specified in PSI-BLAST.

This class must be configured with a concrete strategy for it to obtain its input data. The following example uses the CPsiBlastInputData concrete strategy:

...
CPsiBlastInputData pssm_strategy(query, query_length, alignment,
object_manager_scope, psi_blast_options);
CPssmEngine pssm_engine(&pssm_strategy);
CRef<CPssmWithParameters> scoremat = pssm_engine.Run();
...
Computes a PSSM as specified in PSI-BLAST.
static string query

Definition at line 99 of file pssm_engine.hpp.


The documentation for this class was generated from the following files:
Modified on Wed Jul 17 13:21:56 2024 by modify_doxy.py rev. 669887