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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Birte Kehr <birte.kehr@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_
#define SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_
SEQAN_DEFINE_TEST(test_align_integrate_align)
{
using namespace seqan2;
// We do not test the first interface since the second one calls the first
// one implicitely.
// Case: Integration left of existing with leading gaps. Test second
// specialization: One Align of Sequence, one Align of Infix of Sequence.
{
Dna5String seqH = "AAAACGATAAAACGAT";
Dna5String seqV = "CGAT" "CGAT";
// Alignment align:
//
// AAAACGATAAAACGAT
// CGAT----CGAT
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align, 0), seqH);
assignSource(row(align, 1), seqV);
insertGaps(row(align, 1), 4, 4);
// Alignment alignInf
//
// AAAACGAT
// ----CGAT
Align<typename Infix<Dna5String>::Type> alignInf;
resize(rows(alignInf), 2);
assignSource(row(alignInf, 0), infix(seqH, 0, 8));
assignSource(row(alignInf, 1), infix(seqV, 0, 4));
insertGaps(row(alignInf, 1), 0, 4);
integrateAlign(align, alignInf);
std::stringstream ssH, ssV;
ssH << row(align, 0);
ssV << row(align, 1);
SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATAAAACGAT");
SEQAN_ASSERT_EQ(ssV.str(), "----CGAT----CGAT");
}
// Case: Integration left of existing with trailing gaps. Test second
// specialization: One Align of Sequence, one Align of Infix of Sequence.
{
Dna5String seqH = "CGATATAAAAAACGAT";
Dna5String seqV = "CGATT" "CGAT";
// Alignment align:
//
// CGATATAAAAAACGAT
// CGATT----CGAT
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align, 0), seqH);
assignSource(row(align, 1), seqV);
insertGaps(row(align, 1), 5, 4);
// Alignment alignInf
//
// CGATATAA
// CGAT-T--
Align<typename Infix<Dna5String>::Type> alignInf;
resize(rows(alignInf), 2);
assignSource(row(alignInf, 0), infix(seqH, 0, 8));
assignSource(row(alignInf, 1), infix(seqV, 0, 5));
insertGaps(row(alignInf, 1), 5, 2);
insertGaps(row(alignInf, 1), 4, 1);
integrateAlign(align, alignInf);
std::stringstream ssH, ssV;
ssH << row(align, 0);
ssV << row(align, 1);
SEQAN_ASSERT_EQ(ssH.str(), "CGATATAAAAAACGAT");
SEQAN_ASSERT_EQ(ssV.str(), "CGAT-T------CGAT");
}
// Case: Integration right of existing with leading gaps. Test second
// specialization: One Align of Sequence, one Align of Infix of Sequence.
{
Dna5String seqH = "AAAACGATAAAACGAT";
Dna5String seqV = "CGAT" "CGAT";
// Alignment align:
//
// AAAACGATAAAACGAT
// ----CGATCGAT
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align, 0), seqH);
assignSource(row(align, 1), seqV);
insertGaps(row(align, 1), 0, 4);
// Alignment alignInf
//
// AAAACGAT
// ----CGAT
Align<typename Infix<Dna5String>::Type> alignInf;
resize(rows(alignInf), 2);
assignSource(row(alignInf, 0), infix(seqH, 8, 16));
assignSource(row(alignInf, 1), infix(seqV, 4, 8));
insertGaps(row(alignInf, 1), 0, 4);
integrateAlign(align, alignInf);
std::stringstream ssH, ssV;
ssH << row(align, 0);
ssV << row(align, 1);
SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATAAAACGAT");
SEQAN_ASSERT_EQ(ssV.str(), "----CGAT----CGAT");
}
// Case: Integration right of existing with trailing gaps. Test second
// specialization: One Align of Sequence, one Align of Infix of Sequence.
{
Dna5String seqH = "AAAACGATCGATATAA";
Dna5String seqV = "CGATCGATT";
// Alignment align:
//
// AAAACGATCGATATAA
// ----CGATCGATT
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align, 0), seqH);
assignSource(row(align, 1), seqV);
insertGaps(row(align, 1), 0, 4);
// Alignment alignInf
//
// CGATATAA
// CGAT-T--
Align<typename Infix<Dna5String>::Type> alignInf;
resize(rows(alignInf), 2);
assignSource(row(alignInf, 0), infix(seqH, 8, 16));
assignSource(row(alignInf, 1), infix(seqV, 4, 9));
insertGaps(row(alignInf, 1), 5, 2);
insertGaps(row(alignInf, 1), 4, 1);
integrateAlign(align, alignInf);
std::stringstream ssH, ssV;
ssH << row(align, 0);
ssV << row(align, 1);
SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATCGATATAA");
SEQAN_ASSERT_EQ(ssV.str(), "----CGATCGAT-T--");
}
}
SEQAN_DEFINE_TEST(test_align_integrate_align_infix_of_infix)
{
using namespace seqan2;
// Case: both align objects are infixes
{
Dna5String seqH = "NNNANANANANAAAAACGATCGATATAA";
Dna5String seqV = "NNNGGNNAACGATCGATT";
Infix<Dna5String>::Type seqHInf1 = infix(seqH, 3, length(seqH)-1);
Infix<Dna5String>::Type seqVInf1 = infix(seqV, 1, length(seqV));
// ANANANANAAAAACGATCGATATA
// NNGGNNAACGATCGATT
Infix<Dna5String>::Type seqHInf2 = infix(seqHInf1, 3, length(seqHInf1)-1);
Infix<Dna5String>::Type seqVInf2 = infix(seqVInf1, 1, length(seqVInf1));
// NANANAAAAACGATCGATAT
// NGGNNAACGATCGATT
Align<typename Infix<Dna5String>::Type> alignInf1;
resize(rows(alignInf1), 2);
assignSource(row(alignInf1, 0), seqHInf1);
assignSource(row(alignInf1, 1), seqVInf1);
insertGaps(row(alignInf1, 1), 0, 5);
insertGaps(row(alignInf1, 1), length(row(alignInf1, 1)), 2);
// ANANANANAAAAACGATCGATATA
// -----NNGGNNAACGATCGATT--
SEQAN_ASSERT_EQ(row(alignInf1, 0),
CharString("ANANANANAAAAACGATCGATATA"));
SEQAN_ASSERT_EQ(row(alignInf1, 1),
CharString("-----NNGGNNAACGATCGATT--"));
Align<typename Infix<Dna5String>::Type> alignInf2;
resize(rows(alignInf2), 2);
assignSource(row(alignInf2, 0), seqHInf2);
assignSource(row(alignInf2, 1), seqVInf2);
// NANANAAAAACGATCGATAT
// NGGNNAACGATCGATT
insertGaps(row(alignInf2, 0), 5, 2);
insertGaps(row(alignInf2, 1), 7, 2);
// NANAN--AAAAACGATCGATAT
// NGGNNAA--CGATCGATT
SEQAN_ASSERT_EQ(row(alignInf2, 0),
CharString("NANAN--AAAAACGATCGATAT"));
SEQAN_ASSERT_EQ(row(alignInf2, 1),
CharString("NGGNNAA--CGATCGATT"));
integrateAlign(alignInf1, alignInf2);
SEQAN_ASSERT_EQ(row(alignInf1, 0),
CharString("ANANANAN--AAAAACGATCGATATA"));
SEQAN_ASSERT_EQ(row(alignInf1, 1),
CharString("-----NNGGNNAA--CGATCGATT--"));
}
}
#endif // #ifndef SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_
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