Search Toolkit Book for CPssmEngine
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... | |
| CObject & | operator= (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 | |
| BlastQueryInfo * | x_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... | |
| CPssmEngine & | operator= (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 | |
| IPssmInputData * | m_PssmInput |
| Handle to strategy to process raw PSSM input data. More... | |
| IPssmInputFreqRatios * | m_PssmInputFreqRatios |
| Pointer to input data to create PSSM from frequency ratios. More... | |
| CBlastScoreBlk | m_ScoreBlk |
| Blast score block structure. More... | |
| IPssmInputCdd * | m_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< Uint8 > | TCounter |
| 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();
...
Definition at line 99 of file pssm_engine.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/pssm_engine.hpp
- src/algo/blast/api/pssm_engine.cpp
