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yat-0.10.x
yat
utility
Alignment.h
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#ifndef _theplu_yat_utility_alignment_
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#define _theplu_yat_utility_alignment_
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// $Id: Alignment.h 2815 2012-08-28 02:38:36Z peter $
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/*
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Copyright (C) 2004 Jari Häkkinen, Peter Johansson
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Copyright (C) 2005 Peter Johansson
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Copyright (C) 2006 Jari Häkkinen
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Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
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Copyright (C) 2012 Peter Johansson
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This file is part of the yat library, http://dev.thep.lu.se/yat
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The yat library is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License as
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published by the Free Software Foundation; either version 3 of the
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License, or (at your option) any later version.
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The yat library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with yat. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include "
deprecate.h
"
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#include <string>
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#include <utility>
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#include <vector>
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namespace
theplu {
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namespace
yat {
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namespace
utility {
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class
Matrix;
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double
NeedlemanWunsch
(
const
utility::Matrix& s,
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std::vector<std::pair<size_t, size_t> >& path,
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const
double
gap);
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double
SmithWaterman
(
const
utility::Matrix& s,
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double
gap,
double
open_gap) YAT_DEPRECATE;
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double
ssearch
(std::string first, std::string second,
double
gap,
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double
open_gap,
double
mismatch=0.0);
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}}}
// of namespace utility, yat, and theplu
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#endif
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