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stage
include
ost
seq
alg
alignment_opts.hh
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//------------------------------------------------------------------------------
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// This file is part of the OpenStructure project <www.openstructure.org>
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//
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// Copyright (C) 2008-2011 by the OpenStructure authors
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//
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// This library is free software; you can redistribute it and/or modify it under
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// the terms of the GNU Lesser General Public License as published by the Free
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// Software Foundation; either version 3.0 of the License, or (at your option)
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// any later version.
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// This library is distributed in the hope that it will be useful, but WITHOUT
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// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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// details.
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//
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// You should have received a copy of the GNU Lesser General Public License
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// along with this library; if not, write to the Free Software Foundation, Inc.,
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// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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//------------------------------------------------------------------------------
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#ifndef OST_SEQ_ALG_ALIGNMENT_OPTS_HH
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#define OST_SEQ_ALG_ALIGNMENT_OPTS_HH
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/*
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Author: Marco Biasini
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*/
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#include <
ost/seq/alg/module_config.hh
>
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#include <
ost/seq/alg/subst_weight_matrix.hh
>
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namespace
ost {
namespace
seq {
namespace
alg {
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struct
DLLEXPORT_OST_SEQ_ALG
AlignmentOpts
{
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AlignmentOpts
(
int
gap_open,
int
gap_ext,
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const
SubstWeightMatrixPtr
& weights):
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gap_open_penalty(gap_open), gap_extension_penalty(gap_ext),
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subst_weights(weights)
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{
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}
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int
gap_open_penalty
;
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int
gap_extension_penalty
;
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SubstWeightMatrixPtr
subst_weights
;
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};
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}}}
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#endif
ost::seq::alg::AlignmentOpts::gap_extension_penalty
int gap_extension_penalty
Definition:
alignment_opts.hh:40
DLLEXPORT_OST_SEQ_ALG
#define DLLEXPORT_OST_SEQ_ALG
Definition:
module_config.hh:27
subst_weight_matrix.hh
module_config.hh
ost::seq::alg::AlignmentOpts::AlignmentOpts
AlignmentOpts(int gap_open, int gap_ext, const SubstWeightMatrixPtr &weights)
Definition:
alignment_opts.hh:33
ost::seq::alg::AlignmentOpts::gap_open_penalty
int gap_open_penalty
Definition:
alignment_opts.hh:39
ost::seq::alg::SubstWeightMatrixPtr
boost::shared_ptr< SubstWeightMatrix > SubstWeightMatrixPtr
Definition:
subst_weight_matrix.hh:33
ost::seq::alg::AlignmentOpts::subst_weights
SubstWeightMatrixPtr subst_weights
Definition:
alignment_opts.hh:41
ost::seq::alg::AlignmentOpts
options for local and global sequence alignment algorithms
Definition:
alignment_opts.hh:32
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