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marco authored
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2137 5a81b35b-ba03-0410-adc8-b2c5c5119f08
marco authoredgit-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2137 5a81b35b-ba03-0410-adc8-b2c5c5119f08
merge_pairwise_alignments.hh 2.04 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2010 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#ifndef OST_SEQ_ALG_MERGE_PAIRWISE_ALIGNMENTS_HH
#define OST_SEQ_ALG_MERGE_PAIRWISE_ALIGNMENTS_HH
#include <ost/seq/alignment_handle.hh>
#include <ost/seq/alg/module_config.hh>
/*
Author: Marco Biasini
*/
namespace ost { namespace seq { namespace alg {
/// \brief merge a list of pairwise alignments into one multiple sequence
/// alignment
///
/// All sequences in the pairwise sequence alignments are a realigned to the
/// reference sequence. This is useful to merge the results of a BLAST or HMM
/// database search into one multiple sequence alignment.
///
/// The method does not produce the optimal multiple sequence alignemnt for all
/// the sequences.
///
/// \param pairwise_alignments is a list of AlignmentHandles, each containing
/// two sequences
/// \param ref_seq is the reference sequence. The reference sequence must not
/// contain any gaps.
AlignmentHandle DLLEXPORT_OST_SEQ_ALG
MergePairwiseAlignments(const AlignmentList& pairwise_alns,
const SequenceHandle& ref_seq);
}}}
#endif