NCBI C++ ToolKit
Public Member Functions | Private Member Functions | List of all members
CPHIBlastNuclOptionsHandle Class Reference

Search Toolkit Book for CPHIBlastNuclOptionsHandle

Handle to the nuclein PHI BLAST options. More...

#include <algo/blast/api/phiblast_nucl_options.hpp>

+ Inheritance diagram for CPHIBlastNuclOptionsHandle:
+ Collaboration diagram for CPHIBlastNuclOptionsHandle:

Public Member Functions

 CPHIBlastNuclOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 ~CPHIBlastNuclOptionsHandle ()
 
const char * GetPHIPattern () const
 Retrieves the pattern string option. More...
 
void SetPHIPattern (const char *p)
 Sets the pattern string option. More...
 
- Public Member Functions inherited from CBlastNucleotideOptionsHandle
 CBlastNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastNucleotideOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void SetDefaults ()
 Sets Defaults. More...
 
ELookupTableType GetLookupTableType () const
 Returns LookupTableType. More...
 
void SetLookupTableType (ELookupTableType type)
 Sets LookupTableType. More...
 
int GetWordSize () const
 Returns WordSize. More...
 
void SetWordSize (int ws)
 Sets WordSize. More...
 
objects::ENa_strand GetStrandOption () const
 Returns StrandOption. More...
 
void SetStrandOption (objects::ENa_strand strand)
 Sets StrandOption. More...
 
bool GetDustFiltering () const
 Is dust filtering enabled? More...
 
void SetDustFiltering (bool val)
 Enable dust filtering. More...
 
int GetDustFilteringLevel () const
 Get level parameter for dust. More...
 
void SetDustFilteringLevel (int level)
 Set level parameter for dust. More...
 
int GetDustFilteringWindow () const
 Get window parameter for dust. More...
 
void SetDustFilteringWindow (int window)
 Set window parameter for dust. More...
 
int GetDustFilteringLinker () const
 Get linker parameter for dust. More...
 
void SetDustFilteringLinker (int linker)
 Set linker parameter for dust. More...
 
bool GetRepeatFiltering () const
 Is repeat filtering enabled? More...
 
void SetRepeatFiltering (bool val)
 Enable repeat filtering. More...
 
const char * GetRepeatFilteringDB () const
 Get the repeat filtering database. More...
 
void SetRepeatFilteringDB (const char *db)
 Enable repeat filtering. More...
 
int GetWindowMaskerTaxId () const
 Get the window masker taxid (or 0 if not set). More...
 
void SetWindowMaskerTaxId (int taxid)
 Enable window masker and select a taxid (or 0 to disable). More...
 
const char * GetWindowMaskerDatabase () const
 Get the window masker database name (or NULL if not set). More...
 
void SetWindowMaskerDatabase (const char *db)
 Enable window masker and select a database (or NULL to disable). More...
 
double GetXDropoff () const
 Returns XDropoff. More...
 
void SetXDropoff (double x)
 Sets XDropoff. More...
 
EBlastPrelimGapExt GetGapExtnAlgorithm () const
 Returns GapExtnAlgorithm. More...
 
void SetGapExtnAlgorithm (EBlastPrelimGapExt algo)
 Sets GapExtnAlgorithm. More...
 
EBlastTbackExt GetGapTracebackAlgorithm () const
 Returns GapTracebackAlgorithm. More...
 
void SetGapTracebackAlgorithm (EBlastTbackExt algo)
 Sets GapTracebackAlgorithm. More...
 
int GetMatchReward () const
 Returns MatchReward. More...
 
void SetMatchReward (int r)
 Sets MatchReward. More...
 
int GetMismatchPenalty () const
 Returns MismatchPenalty. More...
 
void SetMismatchPenalty (int p)
 Sets MismatchPenalty. More...
 
const char * GetMatrixName () const
 Returns MatrixName. More...
 
void SetMatrixName (const char *matrix)
 Sets MatrixName. More...
 
int GetGapOpeningCost () const
 Returns GapOpeningCost. More...
 
void SetGapOpeningCost (int g)
 Sets GapOpeningCost. More...
 
int GetGapExtensionCost () const
 Returns GapExtensionCost. More...
 
void SetGapExtensionCost (int e)
 Sets GapExtensionCost. More...
 
void SetTraditionalBlastnDefaults ()
 Sets TraditionalBlastnDefaults. More...
 
void SetTraditionalMegablastDefaults ()
 Sets TraditionalMegablastDefaults. More...
 
void SetVecScreenDefaults ()
 Sets default options for VecScreen. More...
 
- Public Member Functions inherited from CBlastOptionsHandle
 CBlastOptionsHandle (EAPILocality locality)
 Default c-tor. More...
 
bool Validate () const
 Validate the options contained in this object. More...
 
const CBlastOptionsGetOptions () const
 Return the object which this object is a handle for. More...
 
CBlastOptionsSetOptions ()
 Returns a reference to the internal options class which this object is a handle for. More...
 
void DoneDefaults ()
 Returns true if this object needs default values set. More...
 
int GetWindowSize () const
 Returns WindowSize. More...
 
void SetWindowSize (int ws)
 Sets WindowSize. More...
 
int GetOffDiagonalRange () const
 
void SetOffDiagonalRange (int r)
 
void ClearFilterOptions ()
 Clears the filtering options. More...
 
char * GetFilterString () const
 Returns FilterString. More...
 
void SetFilterString (const char *f, bool clear=true)
 Sets FilterString. More...
 
bool GetMaskAtHash () const
 Returns whether masking should only be done for lookup table creation. More...
 
void SetMaskAtHash (bool m=true)
 Sets MaskAtHash. More...
 
double GetGapXDropoff () const
 Returns GapXDropoff. More...
 
void SetGapXDropoff (double x)
 Sets GapXDropoff. More...
 
double GetGapTrigger () const
 Returns GapTrigger. More...
 
void SetGapTrigger (double g)
 Sets GapTrigger. More...
 
double GetGapXDropoffFinal () const
 Returns GapXDropoffFinal. More...
 
void SetGapXDropoffFinal (double x)
 Sets GapXDropoffFinal. More...
 
int GetHitlistSize () const
 Returns HitlistSize. More...
 
void SetHitlistSize (int s)
 Sets HitlistSize. More...
 
int GetMaxNumHspPerSequence () const
 Returns MaxNumHspPerSequence. More...
 
void SetMaxNumHspPerSequence (int m)
 Sets MaxNumHspPerSequence. More...
 
int GetMaxHspsPerSubject () const
 Returns MaxHspsPerSubjectQueryPair. More...
 
void SetMaxHspsPerSubject (int m)
 Sets MaxHspPerSubjectQueryPair. More...
 
double GetEvalueThreshold () const
 Returns EvalueThreshold. More...
 
void SetEvalueThreshold (double eval)
 Sets EvalueThreshold. More...
 
int GetCutoffScore () const
 Returns CutoffScore. More...
 
void SetCutoffScore (int s)
 Sets CutoffScore. More...
 
double GetPercentIdentity () const
 Returns PercentIdentity. More...
 
void SetPercentIdentity (double p)
 Sets PercentIdentity. More...
 
double GetQueryCovHspPerc () const
 Returns QueryCovHspPerc. More...
 
void SetQueryCovHspPerc (double p)
 Sets QueryCovHspPerc. More...
 
int GetMinDiagSeparation () const
 Returns MinDiagSeparation. More...
 
void SetMinDiagSeparation (int d)
 Sets MinDiagSeparation. More...
 
bool GetGappedMode () const
 Returns GappedMode. More...
 
void SetGappedMode (bool m=true)
 Sets GappedMode. More...
 
int GetCullingLimit () const
 Returns Culling limit. More...
 
void SetCullingLimit (int s)
 Sets Culling limit. More...
 
int GetMaskLevel () const
 Returns MaskLevel -RMH-. More...
 
void SetMaskLevel (int ml)
 Sets MaskLevel -RMH-. More...
 
bool GetComplexityAdjMode () const
 Returns Complexity Adjustment Mode -RMH-. More...
 
void SetComplexityAdjMode (bool m=true)
 Sets ComplexityAdjMode -RMH-. More...
 
double GetLowScorePerc () const
 Returns low score percentage for ungapped alignments. More...
 
void SetLowScorePerc (double p)
 Sets low score percentage for ungapped alignments. More...
 
Int8 GetDbLength () const
 Returns DbLength. More...
 
void SetDbLength (Int8 len)
 Sets DbLength. More...
 
unsigned int GetDbSeqNum () const
 Returns DbSeqNum. More...
 
void SetDbSeqNum (unsigned int num)
 Sets DbSeqNum. More...
 
Int8 GetEffectiveSearchSpace () const
 Returns EffectiveSearchSpace. More...
 
void SetEffectiveSearchSpace (Int8 eff)
 Sets EffectiveSearchSpace. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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

 CPHIBlastNuclOptionsHandle (const CPHIBlastNuclOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CPHIBlastNuclOptionsHandleoperator= (const CPHIBlastNuclOptionsHandle &rhs)
 Disallow assignment operator. More...
 

Additional Inherited Members

- Public Types inherited from CBlastOptionsHandle
typedef CBlastOptions::EAPILocality EAPILocality
 Convenience define. 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< Uint8TCounter
 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 CBlastNucleotideOptionsHandle
virtual void SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
virtual void SetLookupTableDefaults ()
 Overrides LookupTableDefaults for nucleotide options. More...
 
virtual void SetMBLookupTableDefaults ()
 Overrides MBLookupTableDefaults for nucleotide options. More...
 
virtual void SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for nucleotide options. More...
 
virtual void SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for nucleotide options. More...
 
virtual void SetMBInitialWordOptionsDefaults ()
 Overrides MBInitialWordOptionsDefaults for nucleotide options. More...
 
virtual void SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for nucleotide options. More...
 
virtual void SetMBGappedExtensionDefaults ()
 Overrides MBGappedExtensionDefaults for nucleotide options. More...
 
virtual void SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for nucleotide options. More...
 
virtual void SetMBScoringOptionsDefaults ()
 Overrides MBScoringOptionsDefaults for nucleotide options. More...
 
virtual void SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for nucleotide options. More...
 
virtual void SetMBHitSavingOptionsDefaults ()
 Overrides MBHitSavingOptionsDefaults for nucleotide options. More...
 
virtual void SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for nucleotide options. More...
 
virtual void SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for nucleotide options. More...
 
- Protected Member Functions inherited from CBlastOptionsHandle
 CBlastOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CBlastOptionsHandle
CRef< CBlastOptionsm_Opts
 Data type this class controls access to. More...
 
bool m_DefaultsMode
 Set to true when 'remote' options should ignore setters. More...
 

Detailed Description

Handle to the nuclein PHI BLAST options.

Adapter class for PHI BLAST search. Exposes an interface to allow manipulation the options that are relevant to this type of search.

Definition at line 53 of file phiblast_nucl_options.hpp.


The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:13 2024 by modify_doxy.py rev. 669887