Search Toolkit Book for CBlastQueryFilteredFrames
Collection of BlastSeqLoc lists for filtering processing. More...
#include "blast_setup.hpp"
(Private to src/algo/blast/api.)
Inheritance diagram for CBlastQueryFilteredFrames:
Collaboration diagram for CBlastQueryFilteredFrames:
Public Types | |
| typedef CSeqLocInfo::ETranslationFrame | ETranslationFrame |
| Data type for frame value, however inputs to methods use "int" instead of this type for readability and brevity. 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 | |
| CBlastQueryFilteredFrames (EBlastProgramType program) | |
| Construct container for frame values and BlastSeqLocs for the specified search program. More... | |
| CBlastQueryFilteredFrames (EBlastProgramType program, const TMaskedQueryRegions &mqr) | |
| Construct container for frame values and BlastSeqLocs from a TMaskedQueryRegions vector. More... | |
| ~CBlastQueryFilteredFrames () | |
| Destructor; frees any BlastSeqLoc lists not released by the caller. More... | |
| void | AddSeqLoc (const objects::CSeq_interval &intv, int frame) |
| Add a masked interval to the specified frame. More... | |
| BlastSeqLoc ** | operator[] (int frame) |
| Access the BlastSeqLocs for a given frame. More... | |
| void | Release (int frame) |
| Release the BlastSeqLocs for a given frame. More... | |
| bool | QueryHasMultipleFrames () const |
| Check whether the query is multiframe for this type of search. More... | |
| const set< ETranslationFrame > & | ListFrames () |
| Returns the list of frame values for which this object contains masking information. More... | |
| bool | Empty () |
| Returns true if this object contains any masking information. More... | |
| void | UseProteinCoords (TSeqPos dna_length) |
| Adjusts all stored masks from nucleotide to protein offsets. More... | |
| size_t | GetNumFrames () 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 |
Private Types | |
| typedef map< ETranslationFrame, BlastSeqLoc * > | TFrameSet |
| Frame and BlastSeqLoc* info type. More... | |
Private Member Functions | |
| CBlastQueryFilteredFrames (CBlastQueryFilteredFrames &f) | |
| Prevent copy construction. More... | |
| CBlastQueryFilteredFrames & | operator= (CBlastQueryFilteredFrames &f) |
| Prevent assignment. More... | |
| void | x_VerifyFrame (int frame) |
| Verify the specified frame value. More... | |
| bool | x_NeedsTrans () |
| Returns true if this program needs coordinate translation. More... | |
Private Attributes | |
| EBlastProgramType | m_Program |
| The type of search being done. More... | |
| TFrameSet | m_Seqlocs |
| Frame and BlastSeqLoc* data. More... | |
| TFrameSet | m_SeqlocTails |
| Frame and tail of BlastSeqLoc* linked list (to speed up appending) More... | |
| set< ETranslationFrame > | m_Frames |
| Frames for masked locations. More... | |
| bool | m_TranslateCoords |
| True if this object's masked regions store DNA coordinates that will later be translated into protein coordinates. More... | |
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
Collection of BlastSeqLoc lists for filtering processing.
This class acts as a container for frame values and collections of BlastSeqLoc objects used by the blast filtering processing code. The support for filtering of blastx searches adds complexity and creates more opportunities for errors to occur. This class was designed to handle some of that complexity, and guard against some of those possible errors.
Definition at line 428 of file blast_setup.hpp.
The documentation for this class was generated from the following files:
- src/algo/blast/api/blast_setup.hpp
- src/algo/blast/api/blast_setup_cxx.cpp
