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

Search Toolkit Book for CBlastAdvancedProteinOptionsHandle

#include <blast_advprot_options.hpp>

Inheritance diagram for CBlastAdvancedProteinOptionsHandle:

[legend]Collaboration diagram for CBlastAdvancedProteinOptionsHandle:

[legend]List of all members.

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Detailed Description

Handle to the Advanced BLASTP options.

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

Definition at line 56 of file blast_advprot_options.hpp.

Public Member Functions
	CBlastAdvancedProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
ECompoAdjustModes	GetCompositionBasedStats () const
	Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
void	SetCompositionBasedStats (ECompoAdjustModes mode)
	Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
bool	GetSmithWatermanMode () const
	Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
void	SetSmithWatermanMode (bool m=false)
	Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
Protected Member Functions
void	SetGappedExtensionDefaults ()
	Overrides SetGappedExtensionDefaults for advanced blastp options.
void	SetQueryOptionDefaults ()
	Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering.
Private Member Functions
	CBlastAdvancedProteinOptionsHandle (const CBlastAdvancedProteinOptionsHandle &rhs)
	Disallow copy constructor.
CBlastAdvancedProteinOptionsHandle &	operator= (const CBlastAdvancedProteinOptionsHandle &rhs)
	Disallow assignment operator.

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Constructor & Destructor Documentation

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

Disallow copy constructor.

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Member Function Documentation

ECompoAdjustModes CBlastAdvancedProteinOptionsHandle::GetCompositionBasedStats (   )  const [inline]

Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. Definition at line 68 of file blast_advprot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

bool CBlastAdvancedProteinOptionsHandle::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 82 of file blast_advprot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

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

Disallow assignment operator.

void CBlastAdvancedProteinOptionsHandle::SetCompositionBasedStats (  ECompoAdjustModes  mode  )  [inline]

Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. Parameters: mode  composition-based statistics mode [in] Definition at line 75 of file blast_advprot_options.hpp. Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().

void CBlastAdvancedProteinOptionsHandle::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: m  use smith-waterman if true [in] Definition at line 87 of file blast_advprot_options.hpp. Referenced by BOOST_FIXTURE_TEST_CASE().

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

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

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