src/algo/blast/api/psiblast_aux_priv.cpp File Reference

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Detailed Description

Definitions of auxiliary functions/classes for PSI-BLAST.

Definition in file psiblast_aux_priv.cpp.

#include <ncbi_pch.hpp>
#include "psiblast_aux_priv.hpp"
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_encoding.h>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/psi_pssm_input.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/objmgrfree_query_data.hpp>
#include "blast_aux_priv.hpp"
#include "../core/blast_psi_priv.h"
#include <util/format_guess.hpp>
#include <util/math/matrix.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/scoremat/Pssm.hpp>
#include <objects/scoremat/PssmFinalData.hpp>
#include <objects/scoremat/PssmParameters.hpp>
#include <objects/scoremat/FormatRpsDbParameters.hpp>
#include <objects/scoremat/PssmIntermediateData.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <sstream>

Include dependency graph for psiblast_aux_priv.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
void	PsiBlastSetupScoreBlock (BlastScoreBlk *score_blk, CConstRef< objects::CPssmWithParameters > pssm, TSearchMessages &messages, CConstRef< CBlastOptions > options)
	Setup CORE BLAST score block structure with data from the scoremat PSSM.
template<class T>
void	Convert2Matrix (const list< T > &source, CNcbiMatrix< T > &dest, bool by_row, SIZE_TYPE num_rows, SIZE_TYPE num_columns)
	Convert a list of values into a CNcbiMatrix.
void	PsiBlastAddAncillaryPssmData (objects::CPssmWithParameters &pssm, int gap_open, int gap_extend)
	Even though the query sequence and the matrix gap costs are not a product of the PSSM engine, set them as they are required for the PSI-BLAST (query sequence) and RPS-BLAST/formatrpsdb (gap costs).
static void	s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix (objects::CPssmWithParameters &pssm)
	After creating the PSSM from frequency ratios, adjust the frequency ratios matrix to match the dimensions of the score matrix.
void	PsiBlastComputePssmScores (CRef< objects::CPssmWithParameters > pssm, const CBlastOptions &opts)
	Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores.
static double	s_GetEvalue (const CScore &score)
	Returns the evalue from this score object.
static double	s_GetBitScore (const CScore &score)
	Returns the bit_score from this score object.
double	GetLowestEvalue (const objects::CDense_seg::TScores &scores, double *bit_score=NULL)
	Returns the lowest score from the list of scores in CDense_seg::TScores.
Variables
static char const	rcsid []

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Variable Documentation

char const rcsid[] [static]

Initial value: "$Id: psiblast_aux_priv.cpp 161402 2009-05-27 17:35:47Z camacho $" Definition at line 2 of file psiblast_aux_priv.cpp.

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