CBlastProteinOptionsHandle Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CBlastProteinOptionsHandle

#include <blast_prot_options.hpp>

Inheritance diagram for CBlastProteinOptionsHandle:

[legend]Collaboration diagram for CBlastProteinOptionsHandle:

[legend]List of all members.

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Detailed Description

Handle to the protein-protein options to the BLAST algorithm.

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

Definition at line 53 of file blast_prot_options.hpp.

Public Member Functions
	CBlastProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
double	GetWordThreshold () const
	Returns WordThreshold.
void	SetWordThreshold (double wt)
	Sets WordThreshold.
int	GetWordSize () const
	Returns WordSize.
void	SetWordSize (int ws)
	Sets WordSize.
double	GetXDropoff () const
	Returns XDropoff.
void	SetXDropoff (double x)
	Sets XDropoff.
bool	GetSegFiltering () const
	Is SEG filtering enabled?
void	SetSegFiltering (bool val)
	Enable SEG filtering.
int	GetSegFilteringWindow () const
	Get window parameter for seg.
void	SetSegFilteringWindow (int window)
	Set window parameter for seg.
double	GetSegFilteringLocut () const
	Get locut parameter for seg.
void	SetSegFilteringLocut (double locut)
	Set locut parameter for seg.
double	GetSegFilteringHicut () const
	Get hicut parameter for seg.
void	SetSegFilteringHicut (double hicut)
	Set hicut parameter for seg.
const char *	GetMatrixName () const
	Returns MatrixName.
void	SetMatrixName (const char *matrix)
	Sets MatrixName.
int	GetGapOpeningCost () const
	Returns GapOpeningCost.
void	SetGapOpeningCost (int g)
	Sets GapOpeningCost.
int	GetGapExtensionCost () const
	Returns GapExtensionCost.
void	SetGapExtensionCost (int e)
	Sets GapExtensionCost.
Protected Member Functions
virtual void	SetRemoteProgramAndService_Blast3 ()
	Set the program and service name for remote blast.
virtual void	SetLookupTableDefaults ()
	Overrides LookupTableDefaults for protein options.
virtual void	SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for protein options.
virtual void	SetInitialWordOptionsDefaults ()
	Overrides InitialWordOptionsDefaults for protein options.
virtual void	SetGappedExtensionDefaults ()
	Overrides GappedExtensionDefaults for protein options.
virtual void	SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for protein options.
virtual void	SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for protein options.
virtual void	SetEffectiveLengthsOptionsDefaults ()
	Overrides EffectiveLengthsOptionsDefaults for protein options.
virtual void	SetSubjectSequenceOptionsDefaults ()
	Overrides SubjectSequenceOptionsDefaults for protein options.
Private Member Functions
	CBlastProteinOptionsHandle (const CBlastProteinOptionsHandle &rhs)
	Disallow copy constructor.
CBlastProteinOptionsHandle &	operator= (const CBlastProteinOptionsHandle &rhs)
	Disallow assignment operator.

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Constructor & Destructor Documentation

CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (  const CBlastProteinOptionsHandle &  rhs  )  [private]

Disallow copy constructor.

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Member Function Documentation

int CBlastProteinOptionsHandle::GetGapExtensionCost (   )  const [inline]

Returns GapExtensionCost. Definition at line 122 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE(), and PsiBlastComputePssmFromAlignment().

int CBlastProteinOptionsHandle::GetGapOpeningCost (   )  const [inline]

Returns GapOpeningCost. Definition at line 116 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE(), and PsiBlastComputePssmFromAlignment().

const char* CBlastProteinOptionsHandle::GetMatrixName (   )  const [inline]

Returns MatrixName. Definition at line 110 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and PsiBlastComputePssmFromAlignment().

bool CBlastProteinOptionsHandle::GetSegFiltering (   )  const [inline]

Is SEG filtering enabled? Definition at line 84 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastProteinOptionsHandle::GetSegFilteringHicut (   )  const [inline]

Get hicut parameter for seg. Definition at line 102 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastProteinOptionsHandle::GetSegFilteringLocut (   )  const [inline]

Get locut parameter for seg. Definition at line 96 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastProteinOptionsHandle::GetSegFilteringWindow (   )  const [inline]

Get window parameter for seg. Definition at line 90 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastProteinOptionsHandle::GetWordSize (   )  const [inline]

Returns WordSize. Definition at line 69 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().

double CBlastProteinOptionsHandle::GetWordThreshold (   )  const [inline]

Returns WordThreshold. Definition at line 63 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastProteinOptionsHandle::GetXDropoff (   )  const [inline]

Returns XDropoff. Definition at line 77 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

CBlastProteinOptionsHandle& CBlastProteinOptionsHandle::operator= (  const CBlastProteinOptionsHandle &  rhs  )  [private]

Disallow assignment operator.

void CBlastProteinOptionsHandle::SetGapExtensionCost (  int  e  )  [inline]

Sets GapExtensionCost. Parameters: e  GapExtensionCost [in] Definition at line 125 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and SetScoringOptionsDefaults().

void CBlastProteinOptionsHandle::SetGapOpeningCost (  int  g  )  [inline]

Sets GapOpeningCost. Parameters: g  GapOpeningCost [in] Definition at line 119 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and SetScoringOptionsDefaults().

void CBlastProteinOptionsHandle::SetMatrixName (  const char *  matrix  )  [inline]

Sets MatrixName. Parameters: matrix  MatrixName [in] Definition at line 113 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and SetScoringOptionsDefaults().

virtual void CBlastProteinOptionsHandle::SetRemoteProgramAndService_Blast3 (   )  [inline, protected, virtual]

Set the program and service name for remote blast. Implements CBlastOptionsHandle. Reimplemented in CBlastxOptionsHandle, CPSIBlastOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Definition at line 129 of file blast_prot_options.hpp.

void CBlastProteinOptionsHandle::SetSegFiltering (  bool  val  )  [inline]

Enable SEG filtering. Parameters: val  enable SEG filtering [in] Definition at line 87 of file blast_prot_options.hpp. Referenced by CDUpdater::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), SetQueryOptionDefaults(), and CBlastAdvancedProteinOptionsHandle::SetQueryOptionDefaults().

void CBlastProteinOptionsHandle::SetSegFilteringHicut (  double  hicut  )  [inline]

Set hicut parameter for seg. Acceptable values are greater than Locut (see SetSegFilteringLocut). Parameters: hicut  seg filtering parameter hicut [in] Definition at line 106 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

void CBlastProteinOptionsHandle::SetSegFilteringLocut (  double  locut  )  [inline]

Set locut parameter for seg. Acceptable values are greater than 0. Parameters: locut  seg filtering parameter locut [in] Definition at line 99 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

void CBlastProteinOptionsHandle::SetSegFilteringWindow (  int  window  )  [inline]

Set window parameter for seg. Acceptable value are > 0. Parameters: window  seg filtering parameter window [in] Definition at line 93 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

void CBlastProteinOptionsHandle::SetWordSize (  int  ws  )  [inline]

Sets WordSize. Parameters: ws  WordSize [in] Definition at line 72 of file blast_prot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and SetLookupTableDefaults().

void CBlastProteinOptionsHandle::SetWordThreshold (  double  wt  )  [inline]

Sets WordThreshold. Parameters: wt  WordThreshold [in] Definition at line 66 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE(), CTBlastnOptionsHandle::SetLookupTableDefaults(), and SetLookupTableDefaults().

void CBlastProteinOptionsHandle::SetXDropoff (  double  x  )  [inline]

Sets XDropoff. Parameters: x  XDropoff [in] Definition at line 80 of file blast_prot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE(), and SetInitialWordOptionsDefaults().

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The documentation for this class was generated from the following files:

• include/algo/blast/api/blast_prot_options.hpp
• src/algo/blast/api/blast_prot_options.cpp

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