Search Toolkit Book for CSearchDatabase
Blast Search Subject. More...
#include <algo/blast/api/uniform_search.hpp>
Inheritance diagram for CSearchDatabase:
Collaboration diagram for CSearchDatabase:
Public Types | |
| enum | EMoleculeType { eBlastDbIsProtein , eBlastDbIsNucleotide } |
| Molecule of the BLAST database. More... | |
| typedef vector< TGi > | TGiList |
| Define a list of gis. More... | |
| 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... | |
Public Member Functions | |
| CSearchDatabase (const string &dbname, EMoleculeType mol_type) | |
| Simple constructor. More... | |
| CSearchDatabase (const string &dbname, EMoleculeType mol_type, const string &entrez_query) | |
| Constructor with allows an entrez query to be specified. More... | |
| void | SetDatabaseName (const string &dbname) |
| Mutator for the database name. More... | |
| string | GetDatabaseName () const |
| Accessor for the database name. More... | |
| void | SetMoleculeType (EMoleculeType mol_type) |
| Mutator for the molecule type. More... | |
| EMoleculeType | GetMoleculeType () const |
| Accessor for the molecule type. More... | |
| bool | IsProtein () const |
| Determine whether this database contains protein sequences or not. More... | |
| void | SetEntrezQueryLimitation (const string &entrez_query) |
| Mutator for the entrez query. More... | |
| string | GetEntrezQueryLimitation () const |
| Accessor for the entrez query. More... | |
| void | SetGiList (CSeqDBGiList *gilist) |
| Mutator for the gi list. More... | |
| const CRef< CSeqDBGiList > & | GetGiList () const |
| Accessor for the gi list. More... | |
| const TGiList | GetGiListLimitation () const |
| void | SetNegativeGiList (CSeqDBGiList *gilist) |
| Mutator for the negative gi list. More... | |
| const CRef< CSeqDBGiList > & | GetNegativeGiList () const |
| Accessor for the negative gi list. More... | |
| const TGiList | GetNegativeGiListLimitation () const |
| void | SetFilteringAlgorithm (int filt_algorithm_id) |
| Temporary fix for backwards compatibility with other 6.0 SCs. More... | |
| void | SetFilteringAlgorithm (int filt_algorithm_id, ESubjectMaskingType mask_type) |
| Mutator for the filtering algorithm. More... | |
| void | SetFilteringAlgorithm (const string &filt_algorithm, ESubjectMaskingType mask_type) |
| Mutator for the filtering algorithm. More... | |
| int | GetFilteringAlgorithm () const |
| Accessor for the filtering algorithm ID. More... | |
| string | GetFilteringAlgorithmKey () const |
| Accessor for the filtering algorithm key. More... | |
| ESubjectMaskingType | GetMaskType () const |
| void | SetSeqDb (CRef< CSeqDB > seqdb) |
| Mutator for the seqdb. More... | |
| CRef< CSeqDB > | GetSeqDb () const |
| Obtain a reference to the database. 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 | |
| void | x_TranslateFilteringAlgorithm () const |
| Translate string algorithm id to numeric id. More... | |
| void | x_InitializeDb () const |
| Initialize the database. More... | |
| void | x_ValidateMaskingAlgorithm () const |
| Validates that the specified filtering algorithm ID is supported by the specified BLAST database. More... | |
Private Attributes | |
| string | m_DbName |
| database name More... | |
| EMoleculeType | m_MolType |
| molecule type More... | |
| string | m_EntrezQueryLimitation |
| entrez query More... | |
| CRef< CSeqDBGiList > | m_GiList |
| gi list More... | |
| CRef< CSeqDBGiList > | m_NegativeGiList |
| negative gi list More... | |
| bool | m_GiListSet |
| string | m_FilteringAlgorithmString |
| filtering to apply to database sequences More... | |
| int | m_FilteringAlgorithmId |
| ESubjectMaskingType | m_MaskType |
| bool | m_NeedsFilteringTranslation |
| bool | m_DbInitialized |
| CRef< CSeqDB > | m_SeqDb |
Additional Inherited Members | |
| 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
Blast Search Subject.
Definition at line 109 of file uniform_search.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/uniform_search.hpp
- src/algo/blast/api/uniform_search.cpp
