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

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Detailed Description

Implementation of the concrete strategy to obtain PSSM input data for PSI-BLAST from a multiple sequence alignment.

Definition in file msa_pssm_input.cpp.

#include <ncbi_pch.hpp>
#include <algo/blast/api/msa_pssm_input.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include "../core/blast_psi_priv.h"
#include <objtools/readers/aln_reader.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/seqport_util.hpp>
#include <serial/iterator.hpp>

Include dependency graph for msa_pssm_input.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
static const char	kGapChar ('-')
	The representation of a gap in ASCII format.
static void	s_GetQuerySequenceData (const CBioseq &bioseq, size_t query_length, CNCBIstdaa &retval)
	Auxiliary function to retrieve the sequence data in NCBI-stdaa format from the bioseq.
static bool	s_AreSequencesEqual (const CNCBIstdaa &sequence, Uint1 *query)
	Returns true iff sequence is identical to query.
Variables
static char const	rcsid []

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Variable Documentation

char const rcsid[] [static]

Initial value: "$Id: msa_pssm_input.cpp 167659 2009-08-05 13:58:24Z camacho $" Definition at line 2 of file msa_pssm_input.cpp.

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