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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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Specific tests for the combination of seeds. This header should
// contain explicit tests for each combination type (i.e. merging,
// different chaining) for both Simple and Chained Seeds. The code is
// already rudimentarily tested in test_seeds_seed_set_base.h.
// However, we only test the later begin/end dimensions there and not
// the diagonals for the seed sets.
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/stream.h> // for printing seqan2::String<>
#include <seqan/seeds.h>
SEQAN_DEFINE_TEST(test_seeds_combination_seeds_combineable_merge_chained)
{
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
//typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Case: Is Mergeable, partial overlap.
{
TSeed left(0, 0, 3);
TSeed right(2, 2, 3);
SEQAN_ASSERT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Is Mergeable, complete overlap.
{
TSeed left(0, 0, 3);
TSeed right(0, 0, 3);
SEQAN_ASSERT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Is Mergeable, prefix overlap.
{
TSeed left(0, 0, 3);
TSeed right(0, 0, 4);
SEQAN_ASSERT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Is Mergeable, suffix overlap.
{
TSeed left(0, 0, 4);
TSeed right(1, 1, 3);
SEQAN_ASSERT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Not Mergeable, too large diagonal distance.
{
TSeed left(0, 0, 4);
TSeed right(2, 0, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Not Mergeable, no overlap.
{
TSeed left(0, 0, 4);
TSeed right(5, 5, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
// Case: Not Mergeable, second starts right of first one.
{
TSeed left(2, 2, 3);
TSeed right(0, 0, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 1, Nothing(), Merge()));
}
}
SEQAN_DEFINE_TEST(test_seeds_combination_seeds_combineable_simple_chaining_chained)
{
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
//typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Case: Chaineable.
{
TSeed left(0, 0, 3);
TSeed right(4, 5, 3);
SEQAN_ASSERT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
// Case: Not Chaineable, overlap.
{
TSeed left(0, 0, 3);
TSeed right(1, 0, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
// Case: Not Chainable, too far away.
{
TSeed left(0, 0, 3);
TSeed right(6, 7, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
}
SEQAN_DEFINE_TEST(test_seeds_combination_seeds_combineable_simple_chaos_chaining_chained)
{
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
//typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Case: Chaineable.
{
TSeed left(0, 0, 3);
TSeed right(4, 5, 3);
SEQAN_ASSERT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
// Case: Not Chaineable, overlap.
{
TSeed left(0, 0, 3);
TSeed right(1, 0, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
// Case: Not Chainable, too far away.
{
TSeed left(0, 0, 3);
TSeed right(6, 7, 3);
SEQAN_ASSERT_NOT(_seedsCombineable(left, right, 3, Nothing(), SimpleChain()));
}
}
SEQAN_DEFINE_TEST(test_seeds_combination_combine_seeds_merge_chained)
{
// TODO(holtgrew): Add scoring to the tests.
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Case: Each has one diagonal, first one is shortened.
{
TSeed left;
appendDiagonal(left, TDiagonal(0, 0, 3));
TSeed right;
appendDiagonal(right, TDiagonal(2, 1, 3));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), Nothing(), Nothing(), Merge());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 1));
appendDiagonal(expected, TDiagonal(2, 1, 3));
SEQAN_ASSERT_EQ(expected, left);
// TODO(holtgrew): Check lower and upper diagonal.
}
// Case: First has two diagonals, one must be deleted, one shortened.
{
TSeed left;
appendDiagonal(left, TDiagonal(0, 0, 3));
appendDiagonal(left, TDiagonal(4, 5, 3));
TSeed right;
appendDiagonal(right, TDiagonal(6, 6, 3));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), Nothing(), Nothing(), Merge());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 3));
appendDiagonal(expected, TDiagonal(4, 5, 1));
appendDiagonal(expected, TDiagonal(6, 6, 3));
SEQAN_ASSERT_EQ(expected, left);
// TODO(holtgrew): Check lower and upper diagonal.
}
// Case: First has two diagonals, one must be deleted, first one is kept.
{
TSeed left;
appendDiagonal(left, TDiagonal(0, 0, 3));
appendDiagonal(left, TDiagonal(4, 5, 3));
TSeed right;
appendDiagonal(right, TDiagonal(4, 5, 3));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), Nothing(), Nothing(), Merge());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 3));
appendDiagonal(expected, TDiagonal(4, 5, 3));
SEQAN_ASSERT_EQ(expected, left);
// TODO(holtgrew): Check lower and upper diagonal.
}
// Case: First has two diagonals, all are kept.
{
TSeed left;
appendDiagonal(left, TDiagonal(0, 0, 3));
appendDiagonal(left, TDiagonal(4, 5, 3));
TSeed right;
appendDiagonal(right, TDiagonal(7, 7, 3));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), Nothing(), Nothing(), Merge());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 3));
appendDiagonal(expected, TDiagonal(4, 5, 2));
appendDiagonal(expected, TDiagonal(7, 7, 3));
SEQAN_ASSERT_EQ(expected, left);
// TODO(holtgrew): Check lower and upper diagonal.
}
}
SEQAN_DEFINE_TEST(test_seeds_combination_combine_seeds_simple_chaining_chained)
{
// TODO(holtgrew): Also test score updates...
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Simple chaining is easy, the diagonals are simply copied over.
TSeed left;
appendDiagonal(left, TDiagonal(1, 2, 3));
appendDiagonal(left, TDiagonal(5, 6, 3));
TSeed right;
appendDiagonal(right, TDiagonal(10, 10, 3));
appendDiagonal(right, TDiagonal(15, 14, 3));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), Nothing(), Nothing(), SimpleChain());
TSeed expected;
appendDiagonal(expected, TDiagonal(1, 2, 3));
appendDiagonal(expected, TDiagonal(5, 6, 3));
appendDiagonal(expected, TDiagonal(10, 10, 3));
appendDiagonal(expected, TDiagonal(15, 14, 3));
SEQAN_ASSERT_EQ(expected, left);
}
SEQAN_DEFINE_TEST(test_seeds_combination_combine_seeds_simple_chaos_chaining_chained)
{
// TODO(holtgrew): Also test score updates...
using namespace seqan2;
typedef Seed<ChainedSeed> TSeed;
typedef Value<Seed<ChainedSeed> >::Type TDiagonal;
// Simple case: Both seeds have one diagonal.
{
DnaString sequence0 = "ACAAAC";
DnaString sequence1 = "ACACCAAC";
TSeed left(0, 0, 2);
TSeed right(6, 4, 2);
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), sequence0, sequence1, Chaos());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 3));
appendDiagonal(expected, TDiagonal(5, 3, 3));
SEQAN_ASSERT_EQ(expected, left);
}
// Each seed has two diagonals. The same example as above but CC
// prepended and appended to both sequences.
{
DnaString sequence0 = "CCACAAACCC";
DnaString sequence1 = "CCACACCAACCC";
TSeed left;
appendDiagonal(left, TDiagonal(0, 0, 2));
appendDiagonal(left, TDiagonal(2, 2, 2));
TSeed right;
appendDiagonal(right, TDiagonal(8, 6, 2));
appendDiagonal(right, TDiagonal(10, 8, 2));
_combineSeeds(left, right, Score<int, Simple>(0, -1, -1), sequence0, sequence1, Chaos());
TSeed expected;
appendDiagonal(expected, TDiagonal(0, 0, 2));
appendDiagonal(expected, TDiagonal(2, 2, 3));
appendDiagonal(expected, TDiagonal(7, 5, 3));
appendDiagonal(expected, TDiagonal(10, 8, 2));
SEQAN_ASSERT_EQ(expected, left);
}
}
SEQAN_BEGIN_TESTSUITE(test_seeds_combination)
{
SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_merge_chained);
SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_simple_chaining_chained);
SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_simple_chaos_chaining_chained);
SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_merge_chained);
SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_simple_chaining_chained);
SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_simple_chaos_chaining_chained);
}
SEQAN_END_TESTSUITE
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