//------------------------------------------------------------------------------ // 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_GLOBAL_ALIGN_HH #define OST_SEQ_ALG_GLOBAL_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 GlobalAlign(const ConstSequenceHandle& s1, const ConstSequenceHandle& s2, SubstWeightMatrixPtr& subst, int gap_open=-5,int gap_ext=-2); }}} #endif