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

Search Toolkit Book for CBlastAncillaryData

#include <blast_results.hpp>

Inheritance diagram for CBlastAncillaryData:

[legend]Collaboration diagram for CBlastAncillaryData:

[legend]List of all members.

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Detailed Description

Class used to return ancillary data from a blast search, i.e.

information that is not the list of alignment found

Definition at line 51 of file blast_results.hpp.

Public Member Functions
	CBlastAncillaryData (EBlastProgramType program_type, int query_number, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info)
	constructor
	CBlastAncillaryData (pair< double, double > lambda, pair< double, double > k, pair< double, double > h, Int8 effective_search_space, bool is_psiblast=false)
	Parametrized constructor taking pairs of values for ungapped and gapped Karlin-Altschul parameters as well as the effective search space.
	~CBlastAncillaryData ()
	Destructor.
	CBlastAncillaryData (const CBlastAncillaryData &rhs)
	Copy-constructor.
CBlastAncillaryData &	operator= (const CBlastAncillaryData &rhs)
	Assignment operator.
const Blast_KarlinBlk *	GetUngappedKarlinBlk () const
	Retrieve ungapped Karlin parameters.
const Blast_KarlinBlk *	GetGappedKarlinBlk () const
	Retrieve gapped Karlin parameters.
const Blast_KarlinBlk *	GetPsiUngappedKarlinBlk () const
	Retrieve PSI-BLAST ungapped Karlin parameters.
const Blast_KarlinBlk *	GetPsiGappedKarlinBlk () const
	Retrieve PSI-BLAST gapped Karlin parameters.
Int8	GetSearchSpace () const
	Retrieve the search space for this query sequence.
Private Member Functions
void	do_copy (const CBlastAncillaryData &other)
	Workhorse for copy constructor and assignment operator.
Private Attributes
Blast_KarlinBlk *	m_UngappedKarlinBlk
	Ungapped Karlin parameters for one query.
Blast_KarlinBlk *	m_GappedKarlinBlk
	Gapped Karlin parameters for one query.
Blast_KarlinBlk *	m_PsiUngappedKarlinBlk
	PSI-BLAST ungapped Karlin parameters for one query (if applicable).
Blast_KarlinBlk *	m_PsiGappedKarlinBlk
	PSI-BLAST gapped Karlin parameters for one query (if applicable).
Int8	m_SearchSpace
	Search space used when calculating e-values for one query.

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Constructor & Destructor Documentation

CBlastAncillaryData::CBlastAncillaryData (  const CBlastAncillaryData &  rhs  )  [inline]

Copy-constructor. Definition at line 86 of file blast_results.hpp.

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Member Function Documentation

const Blast_KarlinBlk* CBlastAncillaryData::GetGappedKarlinBlk (   )  const [inline]

Retrieve gapped Karlin parameters. Definition at line 102 of file blast_results.hpp.

const Blast_KarlinBlk* CBlastAncillaryData::GetPsiGappedKarlinBlk (   )  const [inline]

Retrieve PSI-BLAST gapped Karlin parameters. Definition at line 112 of file blast_results.hpp.

const Blast_KarlinBlk* CBlastAncillaryData::GetPsiUngappedKarlinBlk (   )  const [inline]

Retrieve PSI-BLAST ungapped Karlin parameters. Definition at line 107 of file blast_results.hpp.

Int8 CBlastAncillaryData::GetSearchSpace (   )  const [inline]

Retrieve the search space for this query sequence. If the results correspond to a blastx search, the search space will refer to protein letters Definition at line 118 of file blast_results.hpp.

const Blast_KarlinBlk* CBlastAncillaryData::GetUngappedKarlinBlk (   )  const [inline]

Retrieve ungapped Karlin parameters. Definition at line 97 of file blast_results.hpp.

CBlastAncillaryData& CBlastAncillaryData::operator= (  const CBlastAncillaryData &  rhs  )  [inline]

Assignment operator. Definition at line 91 of file blast_results.hpp.

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Member Data Documentation

Blast_KarlinBlk* CBlastAncillaryData::m_GappedKarlinBlk [private]

Gapped Karlin parameters for one query. Definition at line 127 of file blast_results.hpp. Referenced by CBlastAncillaryData(), do_copy(), and ~CBlastAncillaryData().

Blast_KarlinBlk* CBlastAncillaryData::m_PsiGappedKarlinBlk [private]

PSI-BLAST gapped Karlin parameters for one query (if applicable). Definition at line 133 of file blast_results.hpp. Referenced by CBlastAncillaryData(), do_copy(), and ~CBlastAncillaryData().

Blast_KarlinBlk* CBlastAncillaryData::m_PsiUngappedKarlinBlk [private]

PSI-BLAST ungapped Karlin parameters for one query (if applicable). Definition at line 130 of file blast_results.hpp. Referenced by CBlastAncillaryData(), do_copy(), and ~CBlastAncillaryData().

Int8 CBlastAncillaryData::m_SearchSpace [private]

Search space used when calculating e-values for one query. Definition at line 137 of file blast_results.hpp. Referenced by CBlastAncillaryData(), and do_copy().

Blast_KarlinBlk* CBlastAncillaryData::m_UngappedKarlinBlk [private]

Ungapped Karlin parameters for one query. Definition at line 124 of file blast_results.hpp. Referenced by CBlastAncillaryData(), do_copy(), and ~CBlastAncillaryData().

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

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

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