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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: Christopher Pockrandt <christopher.pockrandt@fu-berlin.de>
// ==========================================================================
#include <seqan/index.h>
#include <ctime>
#include "test_index_helpers.h"
using namespace seqan2;
template <typename TSpec = void, typename TLengthSum = size_t>
struct FMIndexConfigLevelsPrefix
{
typedef TLengthSum LengthSum;
typedef Levels<TSpec, LevelsPrefixRDConfig<TLengthSum, Alloc<>, 1, 0> > Bwt;
typedef Levels<TSpec, LevelsRDConfig<TLengthSum, Alloc<>, 1, 0> > Sentinels;
static const unsigned SAMPLING = 10;
};
template <typename TSpec = void, typename TLengthSum = size_t>
struct FMIndexWTConfig
{
typedef TLengthSum LengthSum;
typedef WaveletTree<TSpec, WTRDConfig<TLengthSum, Alloc<>, 1, 0> > Bwt;
typedef Levels<TSpec, LevelsRDConfig<TLengthSum, Alloc<>, 1, 0> > Sentinels;
static const unsigned SAMPLING = 10;
};
typedef
TagList<Index<String<bool>, BidirectionalIndex<FMIndex<void, FMIndexConfigLevelsPrefix<> > > >,
TagList<Index<DnaString, BidirectionalIndex<FMIndex<void, FMIndexConfigLevelsPrefix<> > > >,
TagList<Index<Dna5String, BidirectionalIndex<FMIndex<void, FMIndexConfigLevelsPrefix<> > > >,
TagList<Index<String<bool>, BidirectionalIndex<FMIndex<void, FMIndexWTConfig<> > > >,
TagList<Index<DnaString, BidirectionalIndex<FMIndex<void, FMIndexWTConfig<> > > >,
TagList<Index<Dna5String, BidirectionalIndex<FMIndex<void, FMIndexWTConfig<> > > >
> > > > > >
FMIndices;
// ==========================================================================
// Test Classes
// ==========================================================================
// --------------------------------------------------------------------------
// Class RankDictionaryTest
// --------------------------------------------------------------------------
template <typename TIndex_>
class BidirectionalFMIndexTest : public Test
{
public:
typedef TIndex_ TIndex;
};
SEQAN_TYPED_TEST_CASE(BidirectionalFMIndexTest, FMIndices);
// testing the bidirectional FM index by comparing ranges and hits against two stand-alone
// FM indices of the original and the reversed text
template <typename TBiFMIndex, typename TText, typename TPattern>
inline bool
testBidirectionalIndex(TBiFMIndex & bifmIndex, TText & text, TText & revText, TPattern & pattern)
{
typedef Index<TText, FMIndex<> > TFMIndex;
typedef typename Iterator<TFMIndex, TopDown<> >::Type TFMIter;
typedef typename Iterator<TBiFMIndex, TopDown<> >::Type TBiFMIter;
ModifiedString<TPattern, ModReverse> revPattern(pattern);
TFMIndex indexFwd(text);
TFMIndex indexRev(revText);
TFMIter itFwd(indexFwd);
TFMIter itRev(indexRev);
TBiFMIter bifm(bifmIndex);
bool res1 = goDown(itFwd, revPattern);
bool res2 = goDown(itRev, pattern);
std::mt19937 rng(time(nullptr));
unsigned left = rng() % length(pattern);
unsigned right = left;
bool res3 = goDown(bifm, pattern[left]);
while (res3 && (0 < left || right < length(pattern) - 1))
{
if (rng() % 2 && 0 < left)
{
--left;
res3 = goDown(bifm, pattern[left], Fwd());
}
else if (right < length(pattern) - 1)
{
++right;
res3 = goDown(bifm, pattern[right], Rev());
}
}
SEQAN_ASSERT_EQ(res1, res2);
SEQAN_ASSERT_EQ(res1, res3);
if (res1) // if pattern was found in index
{
SEQAN_ASSERT(getOccurrences(itFwd) == getOccurrences(bifm, Fwd()));
SEQAN_ASSERT(getOccurrences(itRev) == getOccurrences(bifm, Rev()));
}
return 0;
}
SEQAN_TYPED_TEST(BidirectionalFMIndexTest, SearchInString)
{
typedef typename TestFixture::TIndex TIndex;
typedef typename Host<TIndex>::Type TText;
std::mt19937 rng(time(nullptr));
TText text;
generateText(rng, text, 3947);
TText revText(text);
reverse(revText);
TIndex index(text);
for (unsigned patternLength = 1; patternLength <= 10; ++patternLength)
{
TText pattern;
generateText(rng, pattern, patternLength);
testBidirectionalIndex(index, text, revText, pattern);
}
}
#ifndef __alpha__ // NOTE(h-2): fails on alpha for unknown reasons
SEQAN_TYPED_TEST(BidirectionalFMIndexTest, SearchInStringSet)
{
typedef typename TestFixture::TIndex TIndex;
typedef typename Host<TIndex>::Type TText;
typedef typename Spec<TIndex>::Type TIndexSpec;
typedef StringSet<TText, Owner<ConcatDirect<void> > > TStringSet;
typedef Index<TStringSet, TIndexSpec> TStringSetIndex;
std::mt19937 rng(time(nullptr));
unsigned textLength = 3947;
TStringSet stringSet;
TStringSet revStringSet;
for (unsigned stringSetSize = 1; stringSetSize <= 3; ++stringSetSize)
{
TText text;
generateText(rng, text, textLength);
ModifiedString<TText, ModReverse> revText(text);
appendValue(stringSet, text);
appendValue(revStringSet, revText);
TStringSetIndex index(stringSet);
for (unsigned patternLength = 1; patternLength <= 20; ++patternLength)
{
TText pattern;
if (rng() % 2) // guaranteed hit
pattern = infixWithLength(text, rng() % (textLength - patternLength), patternLength);
else // likely to have no hits (for longer pattern and short texts)
generateText(rng, pattern, patternLength);
testBidirectionalIndex(index, stringSet, revStringSet, pattern);
}
}
}
#endif // __alpha__
// ==========================================================================
// Functions
// ==========================================================================
int main(int argc, char const ** argv)
{
TestSystem::init(argc, argv);
return TestSystem::runAll();
}
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