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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
//------------------------------------------------------------------------------
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/mol/mol.hh>
#include <ost/invalid_handle.hh>
#include <ost/integrity_error.hh>
#include <ost/mol/mol.hh>
#include <ost/seq/alignment_handle.hh>
#include <ost/seq/aligned_region.hh>
#include <ost/seq/sequence_handle.hh>
#include <ost/seq/sequence_list.hh>
#include <ost/seq/impl/sequence_list_impl.hh>
#include <ost/seq/impl/sequence_impl.hh>
#include <ost/seq/sequence_list.hh>
using namespace ost;
using namespace ost::seq;
using namespace ost::mol;
BOOST_AUTO_TEST_SUITE( aligned_region );
BOOST_AUTO_TEST_CASE(aligned_region_triv)
{
AlignmentHandle a = CreateAlignment();
SequenceHandle seq1 = CreateSequence("S1","ab-cdef");
SequenceHandle seq2 = CreateSequence("S2","ghijk-l");
a.AddSequence(seq1);
a.AddSequence(seq2);
AlignedRegion ar = AlignedRegion(a,0,2,1);
BOOST_CHECK(ar.GetAlignmentHandle()==a);
BOOST_CHECK_EQUAL(ar.GetStart(),0);
BOOST_CHECK_EQUAL(ar.GetEnd(),2);
BOOST_CHECK_EQUAL(ar.GetLength(),2);
BOOST_CHECK_EQUAL(ar.GetMaster(),1);
ar.SetMaster(0);
BOOST_CHECK_EQUAL(ar.GetMaster(),0);
ar.SetMaster(-1);
BOOST_CHECK_EQUAL(ar.GetMaster(),-1);
BOOST_CHECK_THROW(ar.SetMaster(2),IntegrityError);
BOOST_CHECK_THROW(ar.SetMaster(-2),IntegrityError);
AlignedRegion ar_same = a.MakeRegion(0,2);
BOOST_CHECK(ar==ar_same);
}
BOOST_AUTO_TEST_CASE(aligned_region_delete)
{
AlignmentHandle a = CreateAlignment();
SequenceHandle seq1 = CreateSequence("S1","ab-cdef");
SequenceHandle seq2 = CreateSequence("S2","ghijk-l");
a.AddSequence(seq1);
a.AddSequence(seq2);
AlignedRegion ar = a.MakeRegion(1,2);
ar.Delete();
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"acdef");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"gjk-l");
a = CreateAlignment();
seq1 = CreateSequence("S1","ab-cdef");
seq2 = CreateSequence("S2","ghijk-l");
a.AddSequence(seq1);
a.AddSequence(seq2);
ar = a.MakeRegion(0,7);
ar.Delete();
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"");
a = CreateAlignment();
seq1 = CreateSequence("S1","ab-cdef");
seq2 = CreateSequence("S2","ghijk-l");
a.AddSequence(seq1);
a.AddSequence(seq2);
ar = a.MakeRegion(0,0);
ar.Delete();
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"ab-cdef");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"ghijk-l");
}
BOOST_AUTO_TEST_CASE(aligned_region_replace)
{
AlignmentHandle a1 = CreateAlignment();
SequenceHandle seq11 = CreateSequence("S1","ab-cdef");
SequenceHandle seq12 = CreateSequence("S2","ghijk-l");
a1.AddSequence(seq11);
a1.AddSequence(seq12);
AlignedRegion ar1 = a1.MakeRegion(2,2);
AlignmentHandle a2 = CreateAlignment();
SequenceHandle seq21 = CreateSequence("S1","zzzzzzz");
SequenceHandle seq22 = CreateSequence("S2","ee-----");
a2.AddSequence(seq21);
a2.AddSequence(seq22);
AlignedRegion ar2 = a2.MakeRegion(2,2);
ar1.Replace(ar2);
BOOST_CHECK_EQUAL(a1.GetSequence(0).GetString(),"abzzdef");
BOOST_CHECK_EQUAL(a1.GetSequence(1).GetString(),"gh--k-l");
a1 = CreateAlignment();
seq11 = CreateSequence("S1","ab-cdef");
seq12 = CreateSequence("S2","ghijk-l");
a1.AddSequence(seq11);
a1.AddSequence(seq12);
ar1 = a1.MakeRegion(1,2);
a2 = CreateAlignment();
seq21 = CreateSequence("S1","zzzzzzz");
seq22 = CreateSequence("S2","ee-----");
a2.AddSequence(seq21);
a2.AddSequence(seq22);
ar2 = a2.MakeRegion(1,0);
ar1.Replace(ar2);
BOOST_CHECK_EQUAL(a1.GetSequence(0).GetString(),"acdef");
BOOST_CHECK_EQUAL(a1.GetSequence(1).GetString(),"gjk-l");
a1 = CreateAlignment();
seq11 = CreateSequence("S1","ab-cdef");
seq12 = CreateSequence("S2","ghijk-l");
a1.AddSequence(seq11);
a1.AddSequence(seq12);
ar1 = a1.MakeRegion(1,2);
a2 = CreateAlignment();
seq21 = CreateSequence("S1","zzzzzzz");
seq22 = CreateSequence("S2","ee-----");
a2.AddSequence(seq21);
a2.AddSequence(seq22);
ar2 = a2.MakeRegion(1,3);
ar1.Replace(ar2);
BOOST_CHECK_EQUAL(a1.GetSequence(0).GetString(),"azzzcdef");
BOOST_CHECK_EQUAL(a1.GetSequence(1).GetString(),"ge--jk-l");
}
BOOST_AUTO_TEST_CASE(aligned_region_shift)
{
AlignmentHandle a = CreateAlignment();
SequenceHandle seq1 = CreateSequence("S1","ab-c");
SequenceHandle seq2 = CreateSequence("S2","ghij");
a.AddSequence(seq1);
a.AddSequence(seq2);
AlignedRegion ar = a.MakeRegion(1,2);
BOOST_CHECK_NO_THROW(ar.ShiftLeft(1));
BOOST_CHECK_EQUAL(ar.GetStart(),0);
BOOST_CHECK_EQUAL(ar.GetEnd(),2);
BOOST_CHECK_EQUAL(ar.GetLength(),2);
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"b-ac");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"higj");
BOOST_CHECK_NO_THROW(ar.ShiftLeft(0));
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"b-ac");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"higj");
BOOST_CHECK_THROW(ar.ShiftLeft(1),IntegrityError);
BOOST_CHECK_NO_THROW(ar.ShiftRight(2));
BOOST_CHECK_EQUAL(ar.GetStart(),2);
BOOST_CHECK_EQUAL(ar.GetEnd(),4);
BOOST_CHECK_EQUAL(ar.GetLength(),2);
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"acb-");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"gjhi");
BOOST_CHECK_NO_THROW(ar.ShiftRight(0));
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"acb-");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"gjhi");
BOOST_CHECK_THROW(ar.ShiftRight(1),IntegrityError);
}
BOOST_AUTO_TEST_SUITE_END();
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