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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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#ifndef TESTS_MODIFIER_MODIFIER_STRING_PADDING_H_
#define TESTS_MODIFIER_MODIFIER_STRING_PADDING_H_
SEQAN_DEFINE_TEST(test_modified_string_padding_construction)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
SEQAN_ASSERT(modString._host == &seq);
SEQAN_ASSERT(modString._cargo._paddedValue == 'A');
SEQAN_ASSERT(modString._cargo._numPaddedChar == 0u);
SEQAN_ASSERT(modString._cargo._remainingSteps == 0u);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_expand)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
ModifiedString<DnaString, ModPadding> modString2(seq);
expand(modString, 5);
expand(modString2, 5, 'C');
for (unsigned i = 0; i < 5; ++i)
{
SEQAN_ASSERT(modString[length(seq) + i] == 'A');
SEQAN_ASSERT(modString2[length(seq) + i] == 'C');
}
}
SEQAN_DEFINE_TEST(test_modified_string_padding_length)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
SEQAN_ASSERT(length(modString) == length(seq));
expand(modString, 5);
SEQAN_ASSERT(length(modString) == length(seq) + 5);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_begin)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
auto it = begin(modString, Standard());
SEQAN_ASSERT(host(it) == begin(seq, Rooted()));
SEQAN_ASSERT_EQ(cargo(it)._remainingSteps, 0u);
SEQAN_ASSERT_EQ(cargo(it)._numPaddedChar, 0u);
expand(modString, 5);
it = begin(modString, Standard());
SEQAN_ASSERT(host(it) == begin(seq, Rooted()));
SEQAN_ASSERT_EQ(cargo(it)._remainingSteps, 5u);
SEQAN_ASSERT_EQ(cargo(it)._numPaddedChar, 5u);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_end)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
auto itEnd = end(modString, Standard());
SEQAN_ASSERT(host(itEnd) == end(seq, Rooted()));
SEQAN_ASSERT_EQ(cargo(itEnd)._remainingSteps, 0u);
SEQAN_ASSERT_EQ(cargo(itEnd)._numPaddedChar, 0u);
expand(modString, 5);
itEnd = end(modString, Standard());
SEQAN_ASSERT(host(itEnd) == end(seq, Rooted()));
SEQAN_ASSERT_EQ(cargo(itEnd)._remainingSteps, 0u);
SEQAN_ASSERT_EQ(cargo(itEnd)._numPaddedChar, 5u);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_difference)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
expand(modString, 5);
auto itB = begin(modString, Standard());
auto itE = end(modString, Standard());
auto pos = 0;
for (auto it = itB; it != itE; ++it, ++pos)
SEQAN_ASSERT(it - itB == pos);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_iterator)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
ModifiedString<DnaString, ModPadding> modString(seq);
expand(modString, 5, static_cast<Dna>('T'));
// Test begin, end, increment, decrement and dereference
auto itSeq = begin(seq, Standard());
auto it = begin(modString, Standard());
for (; it != end(modString, Standard()); ++it)
{
if (itSeq < end(seq, Standard()))
SEQAN_ASSERT_EQ(*it, *(itSeq++));
else
SEQAN_ASSERT_EQ(*it, static_cast<Dna>('T'));
}
while (it != begin(modString, Standard()))
{
--it;
if (it - begin(modString, Standard()) < static_cast<typename Difference<decltype(it)>::Type>(length(seq)))
SEQAN_ASSERT_EQ(*it, *(--itSeq));
else
SEQAN_ASSERT_EQ(*it, static_cast<Dna>('T'));
}
// Test advance.
SEQAN_ASSERT(it == begin(modString, Standard()));
it += 4;
SEQAN_ASSERT_EQ(*it, seq[4]);
it -= 2;
SEQAN_ASSERT_EQ(*it, seq[2]);
it += 13;
SEQAN_ASSERT_EQ(*it, static_cast<Dna>('T'));
it -= 15;
SEQAN_ASSERT_EQ(*it, seq[0]);
it = it + 17;
SEQAN_ASSERT_EQ(*it, static_cast<Dna>('T'));
it += 3;
SEQAN_ASSERT(it == end(modString, Standard()));
it -= 5;
SEQAN_ASSERT_EQ(*it, static_cast<Dna>('T'));
SEQAN_ASSERT_EQ(*(it - 3), seq[12]);
}
SEQAN_DEFINE_TEST(test_modified_string_padding_defect_2190)
{
using namespace seqan2;
DnaString seq = "ACGTGGATAGCATCG";
auto seqInf = infix(seq, 0, length(seq));
auto test_const = [](auto const & modifier)
{
// using TRef = typename Reference<decltype(modifier)>::Type;
auto x = value(modifier, 1);
SEQAN_ASSERT_EQ(x, 'C');
};
{ // Test working case, when reference of const modifier gives back a const reference to the value
ModifiedString<decltype(seq), ModPadding> modString(seq);
test_const(modString);
}
{ // Test defect, when reference of const modifier gives back a non-const reference to the value
ModifiedString<decltype(seqInf), ModPadding> modString(seqInf);
test_const(modString);
}
}
#endif // #ifndef TESTS_MODIFIER_MODIFIER_STRING_PADDING_H_
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