local_align.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 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_LOCAL_ALIGN_HH
#define OST_SEQ_ALG_LOCAL_ALIGN_HH

#include <ost/seq/alignment_handle.hh>
#include <ost/seq/alg/subst_weight_matrix.hh>
#include "module_config.hh"

namespace ost { namespace seq { namespace alg {


AlignmentList DLLEXPORT_OST_SEQ_ALG LocalAlign(const ConstSequenceHandle& s1,
                                               const ConstSequenceHandle& s2,
                                               SubstWeightMatrixPtr& subst,
                                               int gap_open=-5, int gap_ext=-2);
}}}

#endif