NCBI C++ ToolKit
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Search Toolkit Book for CImportStrategy
Class to return parts of the CBlast4_request, or data associated with a CBlast4_request, such as options. More...
#include <algo/blast/api/search_strategy.hpp>
Public Member Functions | |
CImportStrategy (CRef< objects::CBlast4_request > request, bool ignore_unsupported_options=false) | |
Constructor, imports the CBlast4_request. More... | |
CRef< blast::CBlastOptionsHandle > | GetOptionsHandle () |
Builds and returns the OptionsHandle. More... | |
string | GetTask () |
Fetches task, such as "megablast", "blastn", etc. More... | |
string | GetService () const |
Fetches service, such as psiblast, plain, megablast. More... | |
string | GetProgram () const |
Fetches program, one of blastn, blastp, blastx, tblastn, tblastx. More... | |
string | GetCreatedBy () const |
Returns ident field from a Blast4-request. More... | |
TSeqRange | GetQueryRange () |
The start and stop on the query (if applicable) More... | |
int | GetDBFilteringID () |
The DB filter ID. More... | |
string | GetDBFilteringKey () |
The DB filter key. More... | |
ESubjectMaskingType | GetSubjectMaskingType () |
Get Subject Masking Type. More... | |
CRef< objects::CBlast4_queries > | GetQueries () |
The queries either as Bioseq, seqloc, or pssm. More... | |
CRef< objects::CBlast4_subject > | GetSubject () |
Returns the target sequences. More... | |
objects::CBlast4_parameters * | GetAlgoOptions () |
Options specific to blast searches (e.g, threshold, expect value). More... | |
objects::CBlast4_parameters * | GetProgramOptions () |
Options for controlling program execution and database filtering. More... | |
objects::CBlast4_parameters * | GetWebFormatOptions () |
Options for controlling formatting (psi blast iteration number also). More... | |
unsigned int | GetPsiNumOfIterations () |
Get number of iteration for psi blast, return 0 if num of iterations not available. More... | |
CBlastOptionsBuilder & | GetOptionsBuilder () |
Return the BlastOptions builder used in this class. More... | |
set< int > | GetTaxidList () |
set< int > | GetNegativeTaxidList () |
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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... | |
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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 | FetchData () |
Fills in CImportStrategyData and m_OptionsBuilder. More... | |
void | x_GetProgramOptionIntegerList (EBlastOptIdx idx, list< int > &list) |
CImportStrategy (const CImportStrategy &rhs) | |
Prohibit copy constructor. More... | |
CImportStrategy & | operator= (const CImportStrategy &rhs) |
Prohibit assignment operator. More... | |
Private Attributes | |
unique_ptr< CImportStrategyData > | m_Data |
CRef< objects::CBlast4_request > | m_Request |
string | m_Service |
unique_ptr< CBlastOptionsBuilder > | m_OptionsBuilder |
bool | m_IgnoreUnsupportedOptions |
ignore unsupported options when creating blast options builder object More... | |
Additional Inherited Members | |
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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... | |
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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... | |
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static void | EnableDebugDump (bool on) |
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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... | |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Class to return parts of the CBlast4_request, or data associated with a CBlast4_request, such as options.
Definition at line 100 of file search_strategy.hpp.