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stage
include
ost
seq
alg
sequence_identity.hh
Go to the documentation of this file.
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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_SEQUENCE_IDENTITY_HH
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#define OST_SEQ_SEQUENCE_IDENTITY_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/alignment_handle.hh
>
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namespace
ost {
namespace
seq {
namespace
alg {
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struct
RefMode
{
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enum
Type
{
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ALIGNMENT
=0,
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LONGER_SEQUENCE
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};
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};
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Real
DLLEXPORT_OST_SEQ_ALG
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SequenceIdentity
(
const
AlignmentHandle
& aln,
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RefMode::Type
ref_mode=
RefMode::LONGER_SEQUENCE
,
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int
seq_a=0,
int
seq_b=1);
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}}}
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#endif
Real
float Real
Definition:
base.hh:44
ost::seq::alg::RefMode::ALIGNMENT
Definition:
sequence_identity.hh:32
ost::seq::alg::RefMode::Type
Type
Definition:
sequence_identity.hh:31
ost::seq::alg::RefMode::LONGER_SEQUENCE
Definition:
sequence_identity.hh:33
DLLEXPORT_OST_SEQ_ALG
#define DLLEXPORT_OST_SEQ_ALG
Definition:
module_config.hh:27
module_config.hh
alignment_handle.hh
ost::seq::alg::RefMode
Definition:
sequence_identity.hh:30
ost::seq::AlignmentHandle
representation of a multiple sequence alignemnt consisting of two or more sequences ...
Definition:
alignment_handle.hh:53
ost::seq::alg::SequenceIdentity
Real DLLEXPORT_OST_SEQ_ALG SequenceIdentity(const AlignmentHandle &aln, RefMode::Type ref_mode=RefMode::LONGER_SEQUENCE, int seq_a=0, int seq_b=1)
calculate sequence identity for two sequences in an alignment
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