Search Toolkit Book for CMagicBlastResults
Magic-BLAST results for a single query/read or a pair of reads. More...
#include <algo/blast/api/magicblast.hpp>
Inheritance diagram for CMagicBlastResults:
Collaboration diagram for CMagicBlastResults:
Public Types | |
| enum | EResultsInfo { fUnaligned = 1 , fFiltered = 1 << 1 } |
| Information flags about mapping results. More... | |
| enum | EOrdering { eFwRevFirst = 0 , eRevFwFirst } |
| Ordering of alignments. More... | |
| typedef int | TResultsInfo |
| 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 | |
| CMagicBlastResults (CConstRef< CSeq_id > query_id, CConstRef< CSeq_id > mate_id, CRef< CSeq_align_set > aligns, const TMaskedQueryRegions *query_mask=NULL, const TMaskedQueryRegions *mate_mask=NULL, int query_length=0, int mate_length=0) | |
| Constructor for a pair. More... | |
| CMagicBlastResults (CConstRef< CSeq_id > query_id, CRef< CSeq_align_set > aligns, const TMaskedQueryRegions *query_mask=NULL, int query_length=0) | |
| Constructor for a single read. More... | |
| CConstRef< CSeq_align_set > | GetSeqAlign (void) const |
| Get alignments. More... | |
| CRef< CSeq_align_set > | SetSeqAlign (void) |
| Get non-const alignments. More... | |
| bool | IsPaired (void) const |
| Are alignments computed for paired reads. More... | |
| bool | IsConcordant (void) const |
| Are an aligned pair concordant? More... | |
| TResultsInfo | GetFirstInfo (void) const |
| Get alignment flags for the query. More... | |
| TResultsInfo | GetLastInfo (void) const |
| Get alignment flags for the mate. More... | |
| const CSeq_id & | GetQueryId (void) const |
| Get query sequence id. More... | |
| const CSeq_id & | GetFirstId (void) const |
| Get sequence id of the first segment of a paired read. More... | |
| const CSeq_id & | GetLastId (void) const |
| Get sequence id of the last sequence of a paired read. More... | |
| bool | FirstAligned (void) const |
| Is the query aligned. More... | |
| bool | LastAligned (void) const |
| Is the mate aligned. More... | |
| void | SortAlignments (EOrdering order) |
| Sort alignments by selected criteria (pair configuration) 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_SetInfo (int first_length, const TMaskedQueryRegions *first_masks, int last_length=0, const TMaskedQueryRegions *last_masks=NULL) |
Private Attributes | |
| CConstRef< CSeq_id > | m_QueryId |
| Query id. More... | |
| CConstRef< CSeq_id > | m_MateId |
| Mate id if results are for paired reads. More... | |
| CRef< CSeq_align_set > | m_Aligns |
| Alignments for a single or a pair of reads. More... | |
| bool | m_Paired |
| True if results are for paired reads. More... | |
| bool | m_Concordant |
| True if results are concordant pair. More... | |
| TResultsInfo | m_FirstInfo |
| Alignment flags for the query. More... | |
| TResultsInfo | m_LastInfo |
| Alignment flags for the mate. 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
Magic-BLAST results for a single query/read or a pair of reads.
Definition at line 136 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
