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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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
//------------------------------------------------------------------------------
/*
* Authors: Marco Biasini
*/
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/seq/alg/sequence_identity.hh>
using namespace ost;
using namespace ost::seq;
BOOST_AUTO_TEST_SUITE(ost_seq_alg);
BOOST_AUTO_TEST_CASE(seqid_one)
{
SequenceHandle s1=CreateSequence("S1", "abcdefgh");
SequenceHandle s2=CreateSequence("S2", "abcd----");
AlignmentHandle aln=CreateAlignment();
aln.AddSequence(s1);
aln.AddSequence(s2);
Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
// check the default sequence indices
seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
// check the default value for reference mode
seqid=alg::SequenceIdentity(aln);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
BOOST_CHECK_CLOSE(seqid, Real(100.0), Real(1e-6));
}
BOOST_AUTO_TEST_CASE(seqid_two)
{
SequenceHandle s1=CreateSequence("S1", "abcd");
SequenceHandle s2=CreateSequence("S2", "xbcx");
AlignmentHandle aln=CreateAlignment();
aln.AddSequence(s1);
aln.AddSequence(s2);
Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
// check the default sequence indices
seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
// check the default value for reference mode
seqid=alg::SequenceIdentity(aln);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
BOOST_CHECK_CLOSE(seqid, Real(50.0), Real(1e-6));
}
BOOST_AUTO_TEST_CASE(seqid_three)
{
SequenceHandle s1=CreateSequence("S1", "a--d");
SequenceHandle s2=CreateSequence("S2", "x--x");
AlignmentHandle aln=CreateAlignment();
aln.AddSequence(s1);
aln.AddSequence(s2);
Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
// check the default sequence indices
seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
// check the default value for reference mode
seqid=alg::SequenceIdentity(aln);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
}
BOOST_AUTO_TEST_CASE(seqid_empty)
{
SequenceHandle s1=CreateSequence("S1", "---");
SequenceHandle s2=CreateSequence("S2", "---");
AlignmentHandle aln=CreateAlignment();
aln.AddSequence(s1);
aln.AddSequence(s2);
Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
// check the default sequence indices
seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
// check the default value for reference mode
seqid=alg::SequenceIdentity(aln);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
BOOST_CHECK_CLOSE(seqid, Real(0.0), Real(1e-6));
}
BOOST_AUTO_TEST_SUITE_END();
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