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CBlastxOptionsHandle Class Reference

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Handle to the translated nucleotide-protein options to the BLAST algorithm. More...

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

+ Inheritance diagram for CBlastxOptionsHandle:
+ Collaboration diagram for CBlastxOptionsHandle:

Public Member Functions

 CBlastxOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
objects::ENa_strand GetStrandOption () const
 Returns StrandOption. More...
 
void SetStrandOption (objects::ENa_strand strand)
 Sets StrandOption. More...
 
int GetQueryGeneticCode () const
 Returns QueryGeneticCode. More...
 
void SetQueryGeneticCode (int gc)
 Sets QueryGeneticCode. More...
 
bool GetOutOfFrameMode () const
 Returns OutOfFrameMode. More...
 
void SetOutOfFrameMode (bool m=true)
 Sets OutOfFrameMode. More...
 
int GetFrameShiftPenalty () const
 Returns FrameShiftPenalty. More...
 
void SetFrameShiftPenalty (int p)
 Sets FrameShiftPenalty. More...
 
int GetLongestIntronLength () const
 Returns LongestIntronLength. More...
 
void SetLongestIntronLength (int l)
 Sets LongestIntronLength. More...
 
ECompoAdjustModes GetCompositionBasedStats () const
 Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
void SetCompositionBasedStats (ECompoAdjustModes mode)
 Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
bool GetSmithWatermanMode () const
 Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. More...
 
void SetSmithWatermanMode (bool m=false)
 Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. More...
 
- Public Member Functions inherited from CBlastProteinOptionsHandle
 CBlastProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastProteinOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
double GetWordThreshold () const
 Returns WordThreshold. More...
 
void SetWordThreshold (double wt)
 Sets WordThreshold. More...
 
int GetWordSize () const
 Returns WordSize. More...
 
void SetWordSize (int ws)
 Sets WordSize. More...
 
double GetXDropoff () const
 Returns XDropoff. More...
 
void SetXDropoff (double x)
 Sets XDropoff. More...
 
bool GetSegFiltering () const
 Is SEG filtering enabled? More...
 
void SetSegFiltering (bool val)
 Enable SEG filtering. More...
 
int GetSegFilteringWindow () const
 Get window parameter for seg. More...
 
void SetSegFilteringWindow (int window)
 Set window parameter for seg. More...
 
double GetSegFilteringLocut () const
 Get locut parameter for seg. More...
 
void SetSegFilteringLocut (double locut)
 Set locut parameter for seg. More...
 
double GetSegFilteringHicut () const
 Get hicut parameter for seg. More...
 
void SetSegFilteringHicut (double hicut)
 Set hicut parameter for seg. 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...
 
- 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...
 
virtual void SetDefaults ()
 Resets the state of the object to all default values. 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
 

Protected Member Functions

virtual void SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
void SetLookupTableDefaults ()
 Overrides LookupTableDefaults for blastx options. More...
 
void SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for blastx options. More...
 
void SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for blastx options. More...
 
void SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for blastx options. More...
 
void SetGappedExtensionDefaults ()
 Overrides SetGappedExtensionDefaults for blastx option. More...
 
- Protected Member Functions inherited from CBlastProteinOptionsHandle
virtual void SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for protein options. More...
 
virtual void SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for protein options. More...
 
virtual void SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for protein 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...
 

Private Member Functions

 CBlastxOptionsHandle (const CBlastxOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastxOptionsHandleoperator= (const CBlastxOptionsHandle &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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 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 translated nucleotide-protein options to the BLAST algorithm.

Adapter class for translated nucleotide-protein BLAST comparisons. Exposes an interface to allow manipulation the options that are relevant to this type of search.

Definition at line 54 of file blastx_options.hpp.

Constructor & Destructor Documentation

CBlastxOptionsHandle::CBlastxOptionsHandle ( const CBlastxOptionsHandle rhs)
private

Disallow copy constructor.

Member Function Documentation

ECompoAdjustModes CBlastxOptionsHandle::GetCompositionBasedStats ( void  ) const
inline

Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.

Definition at line 104 of file blastx_options.hpp.

int CBlastxOptionsHandle::GetFrameShiftPenalty ( ) const
inline

Returns FrameShiftPenalty.

Definition at line 88 of file blastx_options.hpp.

int CBlastxOptionsHandle::GetLongestIntronLength ( ) const
inline

Returns LongestIntronLength.

Definition at line 94 of file blastx_options.hpp.

bool CBlastxOptionsHandle::GetOutOfFrameMode ( ) const
inline

Returns OutOfFrameMode.

Definition at line 82 of file blastx_options.hpp.

int CBlastxOptionsHandle::GetQueryGeneticCode ( ) const
inline

Returns QueryGeneticCode.

Definition at line 74 of file blastx_options.hpp.

bool CBlastxOptionsHandle::GetSmithWatermanMode ( ) const
inline

Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.

into account when calculating expect values.

Definition at line 118 of file blastx_options.hpp.

objects::ENa_strand CBlastxOptionsHandle::GetStrandOption ( ) const
inline

Returns StrandOption.

Definition at line 64 of file blastx_options.hpp.

CBlastxOptionsHandle& CBlastxOptionsHandle::operator= ( const CBlastxOptionsHandle rhs)
private

Disallow assignment operator.

void CBlastxOptionsHandle::SetCompositionBasedStats ( ECompoAdjustModes  mode)
inline

Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.

Parameters
modecomposition-based statistics mode [in]

Definition at line 111 of file blastx_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastxOptionsHandle::SetFrameShiftPenalty ( int  p)
inline

Sets FrameShiftPenalty.

Parameters
pFrameShiftPenalty [in]

Definition at line 91 of file blastx_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastxOptionsHandle::SetLongestIntronLength ( int  l)
inline

Sets LongestIntronLength.

Parameters
lLongestIntronLength [in]

Definition at line 97 of file blastx_options.hpp.

void CBlastxOptionsHandle::SetOutOfFrameMode ( bool  m = true)
inline

Sets OutOfFrameMode.

Parameters
mOutOfFrameMode [in]

Definition at line 85 of file blastx_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastxOptionsHandle::SetQueryGeneticCode ( int  gc)
inline

Sets QueryGeneticCode.

Parameters
gcQueryGeneticCode [in]

Definition at line 77 of file blastx_options.hpp.

virtual void CBlastxOptionsHandle::SetRemoteProgramAndService_Blast3 ( )
inlineprotectedvirtual

Set the program and service name for remote blast.

Reimplemented from CBlastProteinOptionsHandle.

Definition at line 127 of file blastx_options.hpp.

void CBlastxOptionsHandle::SetSmithWatermanMode ( bool  m = false)
inline

Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.

Parameters
muse smith-waterman if true [in]

Definition at line 123 of file blastx_options.hpp.

void CBlastxOptionsHandle::SetStrandOption ( objects::ENa_strand  strand)
inline

Sets StrandOption.

Parameters
strandStrandOption [in]

Definition at line 69 of file blastx_options.hpp.


The documentation for this class was generated from the following files:
Modified on Sat Mar 25 15:50:05 2017 by modify_doxy.py rev. 506947