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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: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_FIND_INDEX_LAMBDA_H
#define SEQAN_FIND_INDEX_LAMBDA_H
namespace seqan2 {
// ============================================================================
// Metafunction
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction DefaultFind<Index>
// ----------------------------------------------------------------------------
template <typename THaystack, typename THaystackSpec, typename TPattern>
struct DefaultFind<Index<THaystack, THaystackSpec>, TPattern>
{
typedef Backtracking<Exact> Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _findImpl(indexText, sequenceNeedle, Backtracking<Exact>)
// ----------------------------------------------------------------------------
template <typename TState, typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TSpec>
SEQAN_FUNC_ENABLE_IF(IsSequence<TNeedle>, void)
_findImpl(TState & /* state */,
TIndex & index,
TNeedle const & needle,
TThreshold /* threshold */,
TDelegate && delegate,
Backtracking<Exact, TSpec>)
{
typedef typename Iterator<TIndex, TopDown<> >::Type TIndexIt;
TIndexIt indexIt(index);
if (goDown(indexIt, needle))
{
delegate(indexIt, TThreshold());
}
}
// ----------------------------------------------------------------------------
// Function _findImpl(trieText, sequenceNeedle, Backtracking<Edit/HammingDistance>)
// ----------------------------------------------------------------------------
template <typename TIndexIt, typename TNeedle, typename TNeedleIt,
typename TThreshold, typename TDelegate, typename TDistance>
inline void
_findBacktracking(TIndexIt indexIt,
TNeedle const & needle,
TNeedleIt needleIt,
TThreshold errors,
TThreshold threshold,
TDelegate && delegate,
TDistance)
{
// Exact case.
if (errors == threshold)
{
if (goDown(indexIt, suffix(needle, position(needleIt, needle))))
delegate(indexIt, errors);
}
// Approximate case.
else if (errors < threshold)
{
// Base case.
if (atEnd(needleIt, needle))
{
delegate(indexIt, errors);
}
// Recursive case.
else
{
// Insertion.
SEQAN_IF_CONSTEXPR (IsSameType<TDistance, EditDistance>::VALUE)
{
_findBacktracking(indexIt, needle, needleIt + 1,
static_cast<TThreshold>(errors + 1), threshold, delegate, TDistance());
}
if (goDown(indexIt))
{
do
{
// Mismatch.
TThreshold delta = !ordEqual(parentEdgeLabel(indexIt), value(needleIt));
_findBacktracking(indexIt, needle, needleIt + 1,
static_cast<TThreshold>(errors + delta), threshold, delegate, TDistance());
// Deletion.
SEQAN_IF_CONSTEXPR (IsSameType<TDistance, EditDistance>::VALUE)
{
_findBacktracking(indexIt, needle, needleIt,
static_cast<TThreshold>(errors + 1), threshold, delegate, TDistance());
}
}
while (goRight(indexIt));
}
}
}
}
template <typename TState, typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
SEQAN_FUNC_ENABLE_IF(And<Is<StringTrieConcept<TIndex> >, IsSequence<TNeedle> >, void)
_findImpl(TState & /* indexIt */,
TIndex & index,
TNeedle const & needle,
TThreshold threshold,
TDelegate && delegate,
Backtracking<TDistance, TSpec>)
{
typedef typename Iterator<TIndex, TopDown<> >::Type TIndexIt;
typedef typename Iterator<TNeedle const, Standard>::Type TNeedleIt;
TIndexIt indexIt(index);
TNeedleIt needleIt = begin(needle, Standard());
TThreshold errors = 0;
_findBacktracking(indexIt, needle, needleIt, errors, threshold, delegate, TDistance());
}
// ----------------------------------------------------------------------------
// Function _findImpl(treeText, sequenceNeedle, Backtracking<HammingDistance>());
// ----------------------------------------------------------------------------
template <typename TState, typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TSpec>
SEQAN_FUNC_ENABLE_IF(And<Is<StringTreeConcept<TIndex> >, IsSequence<TNeedle> >, void)
_findImpl(TState & /* indexIt */,
TIndex & index,
TNeedle const & needle,
TThreshold threshold,
TDelegate && delegate,
Backtracking<HammingDistance, TSpec>)
{
typedef typename Iterator<TIndex, TopDown<> >::Type TIndexIt;
TIndexIt indexIt(index);
// This lambda is stored locally because approximateStringSearch() does not accept rvalue delegates.
std::function<void(TNeedle const &, TIndexIt const &)> delegator = [&](TNeedle const &, TIndexIt const & it)
{
// NOTE(esiragusa): the approximateStringSearch() functor doesn't know the score...
delegate(it, threshold);
};
approximateStringSearch(delegator, needle, indexIt, threshold);
}
// ----------------------------------------------------------------------------
// Function find(treeText, trieNeedle, Backtracking<TDistance>());
// ----------------------------------------------------------------------------
template <typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
SEQAN_FUNC_ENABLE_IF(And<Is<StringTreeConcept<TIndex> >, Is<StringTrieConcept<TNeedle> > >, void)
find(TIndex & text,
TNeedle & needle,
TThreshold threshold,
TDelegate && delegate,
Backtracking<TDistance, TSpec>)
{
typedef typename Iterator<TIndex, TopDown<> >::Type TTextIt;
typedef typename Iterator<TNeedle, TopDown<> >::Type TNeedleIt;
TTextIt textIt(text);
TNeedleIt needleIt(needle);
// This lambda is stored locally because approximateTreeSearch() does not accept rvalue delegates.
std::function<void(TNeedleIt const &, TTextIt const &)> delegator =
[&](TNeedleIt const & nIt, TTextIt const & tIt)
{
// NOTE(esiragusa): the approximateTreeSearch() functor doesn't know the score...
delegate(tIt, nIt, threshold);
};
approximateTreeSearch(delegator, needleIt, textIt, threshold);
}
// ----------------------------------------------------------------------------
// Function find(indexText, treeNeedle, errors, [](...){}, Backtracking<TDistance>());
// ----------------------------------------------------------------------------
template <typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
SEQAN_FUNC_ENABLE_IF(And<Is<StringIndexConcept<TIndex> >, Is<StringTreeConcept<TNeedle> > >, void)
find(TIndex & index,
TNeedle & needle,
TThreshold threshold,
TDelegate && delegate,
Backtracking<TDistance, TSpec>)
{
typedef Backtracking<TDistance, TSpec> TAlgorithm;
typedef Finder<TIndex, TAlgorithm> TFinder_;
typedef Pattern<TNeedle, TAlgorithm> TPattern_;
TFinder_ _finder(index);
TPattern_ _pattern(needle, length(back(host(needle))));
while (_resume(_finder, _pattern, threshold))
{
delegate(_finder.index_iterator, _pattern.index_iterator, _pattern.prefix_aligner.errors);
}
}
// ----------------------------------------------------------------------------
// Function find(trieText, trieNeedle, errors, [](...){}, Backtracking<TDistance>());
// ----------------------------------------------------------------------------
template <typename TIndex, typename TNeedle,
typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
SEQAN_FUNC_ENABLE_IF(And<Is<StringTrieConcept<TIndex> >, Is<StringTrieConcept<TNeedle> > >, void)
find(TIndex & index,
TNeedle & needle,
TThreshold threshold,
TDelegate && delegate,
Backtracking<TDistance, TSpec>)
{
typedef Backtracking<TDistance, TSpec> TAlgorithm;
typedef Finder_<TIndex, TNeedle, TAlgorithm> TFinder;
TFinder finder;
// This lambda is stored locally because _find() does not accept rvalue delegates.
std::function<void(TFinder const &)> delegator = [&](TFinder const &)
{
delegate(_textIterator(finder), _patternIterator(finder), _getScore(finder));
};
_find(finder, index, needle, threshold, delegator);
}
}
#endif // #ifndef SEQAN_FIND_INDEX_LAMBDA_H
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