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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 INCLUDE_SEQAN_JOURNALED_STRING_TREE_JST_EXTENSION_SHIFT_OR_H_
#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_JST_EXTENSION_SHIFT_OR_H_
namespace seqan2
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class PatternStateShiftOr_
// ----------------------------------------------------------------------------
template <typename TPattern>
struct PatternStateShiftOr_
{
using TWord = typename TPattern::TWord;
String<TWord> prefSufMatch; // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
};
// ----------------------------------------------------------------------------
// Class JstExtension; ShiftOr
// ----------------------------------------------------------------------------
template <typename TNeedle>
class JstExtension<Pattern<TNeedle, ShiftOr> > :
public JstExtensionBase<JstExtension<Pattern<TNeedle, ShiftOr> >, ContextEnd>
{
public:
using TPattern = Pattern<TNeedle, ShiftOr>;
using TBase = JstExtensionBase<JstExtension<Pattern<TNeedle, ShiftOr> >, ContextEnd>;
using TWord = typename TPattern::TWord;
static constexpr TWord WORD_INDEX_HIGH_BIT = BitsPerValue<TWord>::VALUE - 1;
TPattern& _pattern;
TWord carry;
TWord mask;
bool isLongNeedle;
JstExtension(TPattern & pattern) : TBase(*this), _pattern(pattern)
{
// Explicitly force to initialize pattern due to implementation detail.
_patternInit(_pattern);
state(*this).prefSufMatch = _pattern.prefSufMatch;
mask = static_cast<TWord>(1) << (_pattern.needleLength - 1) % BitsPerValue<TWord>::VALUE;
isLongNeedle = _pattern.blockCount > 1;
}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction GetPatternState
// ----------------------------------------------------------------------------
template <typename TNeedle>
struct GetPatternState<JstExtension<Pattern<TNeedle, ShiftOr> > >
{
using Type = PatternStateShiftOr_<Pattern<TNeedle, ShiftOr> >;
};
template <typename TNeedle>
struct GetPatternState<JstExtension<Pattern<TNeedle, ShiftOr> > const>
{
using Type = PatternStateShiftOr_<Pattern<TNeedle, ShiftOr> > const;
};
// ----------------------------------------------------------------------------
// Metafunction ProxySelectionMethod
// ----------------------------------------------------------------------------
template <typename TNeedle>
struct ProxySelectionMethod<JstExtension<Pattern<TNeedle, ShiftOr> > >
{
using Type = SelectFirstProxy;
};
// ============================================================================
// Functions
// ============================================================================
namespace impl
{
// ----------------------------------------------------------------------------
// Function impl::runLongNeedle()
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TIterator>
inline std::pair<size_t, bool>
runLongNeedle(JstExtension<Pattern<TNeedle, ShiftOr> > & me,
TIterator const hystkIt)
{
using TWord = typename Pattern<TNeedle, ShiftOr>::TWord;
using TValue = typename Value<TNeedle>::Type;
me.carry = 0;
for(TWord block = 0; block < me._pattern.blockCount; ++block)
{
bool newCarry = isBitSet(state(me).prefSufMatch[block], me.WORD_INDEX_HIGH_BIT);
state(me).prefSufMatch[block] = ((state(me).prefSufMatch[block] << 1) | me.carry) |
me._pattern.bitMasks[me._pattern.blockCount * ordValue(convert<TValue>(getValue(hystkIt))) +
block];
me.carry = newCarry;
}
return std::pair<size_t, bool>(1, !(state(me).prefSufMatch[me._pattern.blockCount - 1] & me.mask));
}
// ----------------------------------------------------------------------------
// Function impl::runShortNeedle()
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TIterator>
inline std::pair<size_t, bool>
runShortNeedle(JstExtension<Pattern<TNeedle, ShiftOr> > & me,
TIterator const hystkIt)
{
using TValue = typename Value<TNeedle>::Type;
state(me).prefSufMatch[0] = (state(me).prefSufMatch[0] << 1) |
me._pattern.bitMasks[ordValue(convert<TValue>(getValue(hystkIt)))];
return std::pair<size_t, bool>(1, !(state(me).prefSufMatch[0] & me.mask));
}
} // namespace impl
template <typename TNeedle, typename TIterator>
inline std::pair<size_t, bool>
run(JstExtension<Pattern<TNeedle, ShiftOr> > & me,
TIterator hystkIt)
{
return (me.isLongNeedle) ? impl::runLongNeedle(me, hystkIt) : impl::runShortNeedle(me, hystkIt);
}
} // namespace seqan2
#endif // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JST_EXTENSION_SHIFT_OR_H_
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