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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2015, 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>
// ==========================================================================
// Tests for the journaled string tree find module.
// ==========================================================================
#ifndef TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_FIND_H_
#define TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_FIND_H_
#include <sstream>
#include <vector>
#include <seqan/find.h>
#include <seqan/basic.h>
#include <seqan/journaled_string_tree.h>
#include <seqan/stream.h>
#include "test_journaled_string_tree_mock.h"
using namespace seqan;
template <typename TTraverser>
struct TestHelperHitCollector_
{
TTraverser* travPtr;
StringSet<String<unsigned> > positions;
TestHelperHitCollector_(TTraverser & trav) : travPtr(&trav)
{
resize(positions, length(JstMockGenerator::_createComplexTestSet()), Exact());
}
inline void
operator()()
{
auto pos = position(*travPtr);
for (auto p : pos)
{
appendValue(positions[p.i1], p.i2);
}
}
};
template <typename TNeedle, typename TSpec, typename TSize>
inline void _testFindJst(Pattern<TNeedle, TSpec> & p,
TSize contextLength,
TSize windowLength)
{
typedef JournaledStringTree<DnaString> TJst;
auto jst = JstMockGenerator::_createComplexJst<TJst>();
typename Traverser<TJst>::Type trav(jst, contextLength, windowLength);
JstExtension<Pattern<TNeedle, TSpec> > ext(p);
TestHelperHitCollector_<decltype(trav)> delegate(trav);
#if defined(JST_FIND_DEBUG)
clear(__testSet);
resize(__testSet, length(jst));
#endif
find(trav, ext, delegate);
auto _compareTestSetM = JstMockGenerator::_createComplexTestSet();
for (unsigned pos = 0; pos < length(_compareTestSetM); ++pos)
{
Finder<DnaString> finder(_compareTestSetM[pos]);
unsigned counter = 0;
while (find(finder, p))
{
if (IsSameType<TSpec, Horspool>::VALUE)
SEQAN_ASSERT_EQ(delegate.positions[pos][counter], position(finder) + length(needle(p)) - 1);
else
SEQAN_ASSERT_EQ(delegate.positions[pos][counter], finder.data_endPos - 1);
++counter;
}
SEQAN_ASSERT(counter == length(delegate.positions[pos]));
}
}
SEQAN_DEFINE_TEST(test_journaled_string_tree_find_horspool)
{
for (auto ndl : JstMockGenerator::generateNeedles())
{
Pattern<DnaString, Horspool> p(ndl);
_testFindJst(p, length(needle(p)), length(needle(p)));
}
}
SEQAN_DEFINE_TEST(test_journaled_string_tree_find_shiftand)
{
for (auto ndl : JstMockGenerator::generateNeedles())
{
Pattern<DnaString, ShiftAnd> p(ndl);
_testFindJst(p, length(needle(p)), length(needle(p)));
}
}
SEQAN_DEFINE_TEST(test_journaled_string_tree_find_shiftor)
{
for (auto ndl : JstMockGenerator::generateNeedles())
{
Pattern<DnaString, ShiftOr> p(ndl);
_testFindJst(p, length(needle(p)), length(needle(p)));
}
}
SEQAN_DEFINE_TEST(test_journaled_string_tree_find_myers)
{
for (auto ndl : JstMockGenerator::generateNeedles())
{
Pattern<DnaString, MyersUkkonen> p(ndl, -2);
_testFindJst(p, length(needle(p)) + 2, length(needle(p)) + 2);
}
#if defined(JST_FIND_DEBUG)
_printTestSet();
for(unsigned i = 0; i < length(__testSet); ++i)
if (__testSet[i] != JstMockGenerator::_createComplexTestSet()[i])
std::cout << i << std::endl;
#endif
}
#endif // TESTS_JOURNALED_STRING_TREE_TEST_JOURNALED_STRING_TREE_FIND_H_
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