// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
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//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
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// ==========================================================================
// 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_
