Search Toolkit Book for ILocalQueryData
Provides access (not ownership) to the C structures used to configure local BLAST search class implementations. More...
#include <algo/blast/api/query_data.hpp>
Inheritance diagram for ILocalQueryData:
Collaboration diagram for ILocalQueryData:
Public Member Functions | |
| ILocalQueryData () | |
| Default constructor. More... | |
| virtual | ~ILocalQueryData () |
| virtual destructor More... | |
| virtual BLAST_SequenceBlk * | GetSequenceBlk ()=0 |
| Accessor for the BLAST_SequenceBlk structure. More... | |
| virtual BlastQueryInfo * | GetQueryInfo ()=0 |
| Accessor for the BlastQueryInfo structure. More... | |
| virtual size_t | GetNumQueries ()=0 |
| Get the number of queries. More... | |
| virtual CConstRef< objects::CSeq_loc > | GetSeq_loc (size_t index)=0 |
| Get the Seq_loc for the sequence indicated by index. More... | |
| virtual size_t | GetSeqLength (size_t index)=0 |
| Get the length of the sequence indicated by index. More... | |
| size_t | GetSumOfSequenceLengths () |
| Compute the sum of all the sequence's lengths. More... | |
| void | GetMessages (TSearchMessages &messages) const |
| Retrieve all error/warning messages. More... | |
| void | GetQueryMessages (size_t index, TQueryMessages &qmsgs) |
| Retrieve error/warning messages for a specific query. More... | |
| bool | IsValidQuery (size_t index) |
| Determine if a given query sequence is valid or not. More... | |
| bool | IsAtLeastOneQueryValid () |
| Determine if at least one query sequence is valid or not. More... | |
| void | FlushSequenceData () |
| Frees the cached sequence data structure (as this is usually the larger data structure). 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 |
Protected Attributes | |
| CBLAST_SequenceBlk | m_SeqBlk |
| Data member to cache the BLAST_SequenceBlk. More... | |
| CBlastQueryInfo | m_QueryInfo |
| Data member to cache the BlastQueryInfo. More... | |
| TSearchMessages | m_Messages |
| Error/warning messages are stored here. More... | |
Private Member Functions | |
| void | x_ValidateIndex (size_t index) |
Private Attributes | |
| size_t | m_SumOfSequenceLengths |
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
Provides access (not ownership) to the C structures used to configure local BLAST search class implementations.
Definition at line 54 of file query_data.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/query_data.hpp
- src/algo/blast/api/query_data.cpp
