NCBI C++ ToolKit
Functions
msa_pssm_input.cpp File Reference

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

#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 <objtools/readers/reader_exception.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.

Go to the SVN repository for this file.

Functions

 USING_SCOPE (objects)
 
static const char kGapChar ('-')
 The representation of a gap in ASCII format. More...
 
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. More...
 
static bool s_AreSequencesEqual (const CNCBIstdaa &sequence, Uint1 *query)
 Returns true iff sequence is identical to query. More...
 

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.

Modified on Wed Jul 17 13:19:17 2024 by modify_doxy.py rev. 669887