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

Search Toolkit Book for CPsiBlastInputData

#include <psi_pssm_input.hpp>

Inheritance diagram for CPsiBlastInputData:

[legend]Collaboration diagram for CPsiBlastInputData:

[legend]List of all members.

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Detailed Description

This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST algorithm for building a multiple sequence alignment from a list of pairwise alignments using the C++ object manager.

Definition at line 122 of file psi_pssm_input.hpp.

Public Member Functions
	CPsiBlastInputData (const unsigned char *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > sset, CRef< objects::CScope > scope, const PSIBlastOptions &opts, const char *matrix_name=NULL, const PSIDiagnosticsRequest *diags=NULL)
	Construct a concrete strategy, used to configure the CPssmEngine object.
virtual	~CPsiBlastInputData ()
	virtual destructor
void	Process ()
	The work to process the alignment is done here.
unsigned char *	GetQuery ()
	Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.
unsigned int	GetQueryLength ()
	Get the query's length.
PSIMsa *	GetData ()
	Obtain the multiple sequence alignment structure.
const PSIBlastOptions *	GetOptions ()
	Obtain the options for the PSSM engine.
const char *	GetMatrixName ()
	Obtain the name of the underlying matrix to use when building the PSSM.
const PSIDiagnosticsRequest *	GetDiagnosticsRequest ()
	Obtain the diagnostics data that is requested from the PSSM engine.
CRef< objects::CBioseq >	GetQueryForPssm ()
	Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). This is required for any PSSM which is intended to be used as a starting point for a PSI-BLAST iteration
Private Member Functions
unsigned int	x_CountAndSelectQualifyingAlignments ()
	Examines the sequence alignment and keeps track of those hits which have an HSP with an e-value below the inclusion threshold specified in the PSIBlastOptions structure.
void	x_ExtractAlignmentData ()
	Populates the multiple alignment data structure.
void	x_CopyQueryToMsa ()
	Copies query sequence data to multiple alignment data structure.
unsigned int	GetNumAlignedSequences () const
	Returns the number of sequences that make up the multiple sequence alignment Exceptions: CBlastException  if this number hasn't been calculated yet (need to invoke Process() first!).
void	x_ProcessDenseg (const objects::CDense_seg &denseg, unsigned int msa_index, double evalue, double bit_score)
	Iterates over the Dense-seg passed in and extracts alignment information to multiple alignment data structure.
void	x_ExtractQueryForPssm ()
	Extracts the query bioseq from m_SeqAlignSet.
	CPsiBlastInputData (const CPsiBlastInputData &)
	prohibit copy constructor
CPsiBlastInputData &	operator= (const CPsiBlastInputData &)
	prohibit assignment operator
Static Private Member Functions
static void	x_GetSubjectSequence (const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
	Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg.
Private Attributes
unsigned char *	m_Query
	Pointer to query sequence.
CRef< objects::CScope >	m_Scope
	Scope where to retrieve the sequences in the aligment from.
PSIMsa *	m_Msa
	Structure representing the multiple sequence alignment.
PSIMsaDimensions	m_MsaDimensions
	Multiple sequence alignment dimensions.
CConstRef< objects::CSeq_align_set >	m_SeqAlignSet
	Pairwise alignment result of a BLAST search.
PSIBlastOptions	m_Opts
	Algorithm options.
PSIDiagnosticsRequest *	m_DiagnosticsRequest
	Diagnostics request structure.
string	m_MatrixName
	Underlying matrix to use.
CRef< objects::CBioseq >	m_QueryBioseq
	Query as CBioseq for PSSM.
Friends
class	::CPssmCreateTestFixture
	unit test class

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Constructor & Destructor Documentation

CPsiBlastInputData::CPsiBlastInputData (  const CPsiBlastInputData &   )  [private]

prohibit copy constructor

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Member Function Documentation

CRef<objects::CBioseq> CPsiBlastInputData::GetQueryForPssm (   )  [inline, virtual]

Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). This is required for any PSSM which is intended to be used as a starting point for a PSI-BLAST iteration Reimplemented from IPssmInput_Base. Definition at line 171 of file psi_pssm_input.hpp. References m_QueryBioseq.

CPsiBlastInputData& CPsiBlastInputData::operator= (  const CPsiBlastInputData &   )  [private]

prohibit assignment operator

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Friends And Related Function Documentation

friend class ::CPssmCreateTestFixture [friend]

unit test class Definition at line 249 of file psi_pssm_input.hpp.

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Member Data Documentation

PSIDiagnosticsRequest* CPsiBlastInputData::m_DiagnosticsRequest [private]

Diagnostics request structure. Definition at line 190 of file psi_pssm_input.hpp. Referenced by GetDiagnosticsRequest().

string CPsiBlastInputData::m_MatrixName [private]

Underlying matrix to use. Definition at line 192 of file psi_pssm_input.hpp. Referenced by GetMatrixName().

PSIMsa* CPsiBlastInputData::m_Msa [private]

Structure representing the multiple sequence alignment. Definition at line 182 of file psi_pssm_input.hpp. Referenced by GetData(), Process(), x_CopyQueryToMsa(), x_ProcessDenseg(), and ~CPsiBlastInputData().

PSIMsaDimensions CPsiBlastInputData::m_MsaDimensions [private]

Multiple sequence alignment dimensions. Definition at line 184 of file psi_pssm_input.hpp. Referenced by GetNumAlignedSequences(), GetQueryLength(), and Process().

PSIBlastOptions CPsiBlastInputData::m_Opts [private]

Algorithm options. Definition at line 188 of file psi_pssm_input.hpp. Referenced by GetOptions(), x_CountAndSelectQualifyingAlignments(), and x_ExtractAlignmentData().

unsigned char* CPsiBlastInputData::m_Query [private]

Pointer to query sequence. Definition at line 178 of file psi_pssm_input.hpp.

CRef<objects::CBioseq> CPsiBlastInputData::m_QueryBioseq [private]

Query as CBioseq for PSSM. Definition at line 194 of file psi_pssm_input.hpp. Referenced by GetQueryForPssm(), and x_ExtractQueryForPssm().

CRef<objects::CScope> CPsiBlastInputData::m_Scope [private]

Scope where to retrieve the sequences in the aligment from. Definition at line 180 of file psi_pssm_input.hpp. Referenced by x_ProcessDenseg().

CConstRef<objects::CSeq_align_set> CPsiBlastInputData::m_SeqAlignSet [private]

Pairwise alignment result of a BLAST search. Definition at line 186 of file psi_pssm_input.hpp. Referenced by x_CountAndSelectQualifyingAlignments(), x_ExtractAlignmentData(), and x_ExtractQueryForPssm().

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

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

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