Search Toolkit Book for CMagicBlast
BLAST RNA-Seq mapper. More...
#include <algo/blast/api/magicblast.hpp>
Inheritance diagram for CMagicBlast:
Collaboration diagram for CMagicBlast:
Public Member Functions | |
| CMagicBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CMagicBlastOptionsHandle > options) | |
| Constructor to map short reads as queries to a genome as BLAST database. More... | |
| ~CMagicBlast () | |
| Destructor. More... | |
| CRef< CSeq_align_set > | Run (void) |
| Run the RNA-Seq mapping. More... | |
| CRef< CMagicBlastResultSet > | RunEx (void) |
| TSearchMessages | GetSearchMessages (void) const |
| 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 |
| Public Member Functions inherited from CThreadable | |
| CThreadable (void) | |
| Default ctor. More... | |
| virtual | ~CThreadable (void) |
| Our virtual destructor. More... | |
| virtual void | SetNumberOfThreads (size_t nthreads) |
| Mutator for the number of threads. More... | |
| size_t | GetNumberOfThreads (void) const |
| Accessor for the number of threads to use. More... | |
| bool | IsMultiThreaded (void) const |
| Returns true if more than 1 thread is specified. More... | |
Protected Member Functions | |
| CMagicBlast (const CMagicBlast &rhs) | |
| Prohibit copy constructor. More... | |
| CMagicBlast & | operator= (const CMagicBlast &rhs) |
| Prohibit assignment operator. More... | |
| void | x_Validate (void) |
| Perform sanity checks on input arguments. More... | |
| int | x_Run (void) |
| CRef< CSeq_align_set > | x_BuildSeqAlignSet (const BlastMappingResults *results) |
| CRef< CMagicBlastResultSet > | x_BuildResultSet (const BlastMappingResults *results) |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Static Protected Member Functions | |
| static CRef< CSeq_align_set > | x_CreateSeqAlignSet (const HSPChain *results, CRef< ILocalQueryData > qdata, CRef< IBlastSeqInfoSrc > seqinfo_src, const BlastQueryInfo *query_info, bool btop_splice_signals) |
| Create results. More... | |
Private Attributes | |
| CRef< IQueryFactory > | m_Queries |
| Queries. More... | |
| CRef< CLocalDbAdapter > | m_LocalDbAdapter |
| Reference to a BLAST subject/database object. More... | |
| CRef< CBlastOptions > | m_Options |
| Options to configure the search. More... | |
| CRef< CBlastPrelimSearch > | m_PrelimSearch |
| Object that runs BLAST search. More... | |
| CRef< SInternalData > | m_InternalData |
| Internal data strctures. More... | |
| TSearchMessages | m_Messages |
| Warning and error messages. More... | |
| bool | m_BtopSpliceSignals |
| Should BTOP strings be formatted with splice signals. 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... | |
| Public Types inherited from CThreadable | |
| enum | { kMinNumThreads = 1 } |
| Never have less than 1 thread. 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 Attributes inherited from CThreadable | |
| size_t | m_NumThreads |
| Keep track of how many threads should be used. More... | |
Detailed Description
BLAST RNA-Seq mapper.
Definition at line 57 of file magicblast.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/magicblast.hpp
- src/algo/blast/api/magicblast.cpp
