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local_align.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_SEQ_ALG_LOCAL_ALIGN_HH
20 #define OST_SEQ_ALG_LOCAL_ALIGN_HH
21 
24 #include "module_config.hh"
25 
26 namespace ost { namespace seq { namespace alg {
27 
28 
29 AlignmentList DLLEXPORT_OST_SEQ_ALG LocalAlign(const ConstSequenceHandle& s1,
30  const ConstSequenceHandle& s2,
31  SubstWeightMatrixPtr& subst,
32  int gap_open=-5, int gap_ext=-2);
33 }}}
34 
35 #endif
AlignmentList DLLIMPORT LocalAlign(const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)
#define DLLEXPORT_OST_SEQ_ALG
std::vector< AlignmentHandle > AlignmentList
boost::shared_ptr< SubstWeightMatrix > SubstWeightMatrixPtr