// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
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// 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.
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//       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"
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// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================

#ifndef SEQAN_HEADER_FIND_BEGIN_H
#define SEQAN_HEADER_FIND_BEGIN_H


//////////////////////////////////////////////////////////////////////////////

namespace seqan2
{

//////////////////////////////////////////////////////////////////////////////
// Forward declarations of Pattern Specs that could be used prefix search

//see find_score.h
template <typename TScore, typename TSpec, typename TFindBeginPatternSpec>
struct DPSearch;

//see finder_myers_ukkonen.h
template <typename TSpec, typename THasState, typename TFindBeginPatternSpec>
struct Myers;


//____________________________________________________________________________

/*!
 * @mfn DefaultFindBeginPatternSpec
 * @headerfile <seqan/find.h>
 * @brief Type of the default <tt>findBegin</tt> pattern specialization, given a score.
 *
 * @signature DefaultBeginPatternSpec<TScore>::Type;
 *
 * @tparam TScore The score to query.
 *
 * @return Type The pattern specialization to use as a default.
 */

template <typename TScore = EditDistanceScore, typename THasState = True>
struct DefaultFindBeginPatternSpec
{
    typedef DPSearch<TScore, FindPrefix, void> Type;
};

template <typename THasState>
struct DefaultFindBeginPatternSpec<EditDistanceScore, THasState>
{
    // typedef Myers<FindPrefix, void, True> Type;
    typedef Myers<FindPrefix, THasState, void> Type;
};

//____________________________________________________________________________
//must be implemented for all patterns that do approximate infix finding

template <typename TPattern>
struct FindBeginPatternSpec
{
    typedef void Type; //void means: no find begin (see FindBegin_)
};

//____________________________________________________________________________
// Metafunction FindBeginPattern: pattern used to find the begin of an approximate match

template <typename TPattern>
struct FindBeginPattern
{
    typedef typename Needle<TPattern>::Type TNeedle_;
    typedef ModifiedString<TNeedle_, ModReverse> TReverseNeedle_;
    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec_;
    typedef Pattern<TReverseNeedle_, TFindBeginPatternSpec_> Type;
};

//////////////////////////////////////////////////////////////////////////////
// Base class for approximate finders that manages findBegin stuff

template <typename TPattern, typename TFindBeginPatternSpec = typename FindBeginPatternSpec<TPattern>::Type >
struct FindBegin_
{
    typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern_;

    TFindBeginPattern_ data_findBeginPattern;
};

template <typename TPattern>
struct FindBegin_ <TPattern, void>
{
//need no findBegin if FindBeginPatternSpec is void
};


//////////////////////////////////////////////////////////////////////////////

template <typename TFindBeginPatternSpec>
struct FindBeginImpl_
{
    template <typename TPattern, typename TNeedle>
    static inline void
    _findBeginInit(TPattern & pattern, TNeedle & needle_)
    {
//        setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
        // TODO(rrahn): Mhmm, is this really intended here, or is it due to a wrong design of setHost of patterns which always copies instread of strong the reference where it can?
        // It could happen, that we are really overwriting the original needle, if it was passed as non-const lvalue reference.
        // The version above would be safer, as reverseString always returns a copy.
        // But maybe the set function of ModifiedStrings is overloaded such that we will do a copy anyway in the holder class.
        setHost(needle(pattern.data_findBeginPattern), needle_);
        setScoringScheme(pattern.data_findBeginPattern, scoringScheme(pattern));
    }
//____________________________________________________________________________

    template <typename TFinder, typename TPattern, typename TLimit>
    static inline bool
    findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
    {
        typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
        typedef typename Haystack<TFinder>::Type THaystack;
        typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
        typedef Finder<TReverseHaystack> TBeginFinder;
        typedef typename Position<THaystack>::Type TPosition;

        TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
        setScoreLimit(find_begin_pattern, limit);

        //build begin_finder
        TBeginFinder begin_finder;
        THaystack & hayst = haystack(finder);
        setContainer(host(hostIterator(begin_finder)), hayst);
        TPosition begin_finder_beginPosition = position(finder);
        TPosition begin_finder_position;

        if (!finder._beginFind_called)
        {//start finding
            finder._beginFind_called = true;
            _setFinderLength(finder, 0);
            clear(begin_finder);
            begin_finder_position = begin_finder_beginPosition;
        }
        else
        {//resume finding
            _finderSetNonEmpty(begin_finder);
            SEQAN_ASSERT_GT(length(finder), 0u);
            begin_finder_position = endPosition(finder) - length(finder);
        }
        setPosition(host(hostIterator(begin_finder)), begin_finder_position);
        _setFinderEnd(begin_finder);
        _setFinderLength(begin_finder, length(finder));

        bool begin_found = find(begin_finder, find_begin_pattern);
        if (begin_found)
        {//new begin found: report in finder
            _setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
        }
        return begin_found;
    }
    template <typename TFinder, typename TPattern>
    static inline bool
    findBegin(TFinder & finder, TPattern & pattern)
    {
        return findBegin(finder, pattern, scoreLimit(pattern));
    }

//____________________________________________________________________________

    template <typename TPattern>
    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
    getBeginScore(TPattern & pattern)
    {
        return getScore(pattern.data_findBeginPattern);
    }
};


// TODO(holtgrew): Copy-and-paste code from above.
template <typename THasState>
struct FindBeginImpl_<Myers<FindPrefix, THasState, void> >
{
    template <typename TPattern, typename TNeedle>
    static inline void
    _findBeginInit(TPattern & pattern, TNeedle & needle_)
    {
//        setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
        setHost(pattern.data_findBeginPattern, reverseString(needle_));
//         _patternFirstInit(pattern.data_findBeginPattern, host(pattern));
    }
//____________________________________________________________________________

    template <typename TFinder, typename TPattern, typename TLimit>
    static inline bool
    findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
    {
        typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
        typedef typename Haystack<TFinder>::Type THaystack;
        typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
        typedef Finder<TReverseHaystack> TBeginFinder;
        typedef typename Position<THaystack>::Type TPosition;

        TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
        setScoreLimit(find_begin_pattern, limit);

        //build begin_finder
        TBeginFinder begin_finder;
        typename Parameter_<THaystack>::Type hayst = haystack(finder);
        setContainer(host(hostIterator(begin_finder)), hayst);
        TPosition begin_finder_beginPosition = position(finder);
        TPosition begin_finder_position;

        if (!finder._beginFind_called)
        {//start finding
            finder._beginFind_called = true;
            _setFinderLength(finder, 0);
            clear(begin_finder);
            begin_finder_position = begin_finder_beginPosition;
        }
        else
        {//resume finding
            _finderSetNonEmpty(begin_finder);
            SEQAN_ASSERT_GT(length(finder), 0u);
            begin_finder_position = endPosition(finder) - length(finder);
        }
        setPosition(host(hostIterator(begin_finder)), begin_finder_position);
        _setFinderEnd(begin_finder);
        _setFinderLength(begin_finder, length(finder));

        bool begin_found = find(begin_finder, find_begin_pattern);
        if (begin_found)
        {//new begin found: report in finder
            _setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
        }
        return begin_found;
    }
    template <typename TFinder, typename TPattern>
    static inline bool
    findBegin(TFinder & finder, TPattern & pattern)
    {
        return findBegin(finder, pattern, scoreLimit(pattern));
    }

//____________________________________________________________________________

    template <typename TPattern>
    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
    getBeginScore(TPattern & pattern)
    {
        return getScore(pattern.data_findBeginPattern);
    }
};

//default implementation of findBegin emulates the behaviour
//of findBegin for approximate string matching algorithms
//for exact algorithms:
//the first call returns true ("begin position found")
//the next calls return false ("no further begin position found")
//no searching needed, since the exact algorithms set the
//match length manually via "_setFinderLength" (it's the needle length)

template <>
struct FindBeginImpl_<void>
{
    template <typename TPattern, typename TNeedle>
    static inline void
    _findBeginInit(TPattern &, TNeedle &)
    {
    }

    template <typename TFinder, typename TPattern, typename TLimit>
    static inline bool
    findBegin(TFinder & finder, TPattern &, TLimit)
    {
        if (!finder._beginFind_called)
        {
            finder._beginFind_called = true;
            return true;
        }
        return false;
    }
    template <typename TFinder, typename TPattern>
    static inline bool
    findBegin(TFinder & finder, TPattern & pattern)
    {
        return findBegin(finder, pattern, 0);
    }

    template <typename TPattern>
    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
    getBeginScore(TPattern & pattern)
    {
        return getScore(pattern);
    }
};


//////////////////////////////////////////////////////////////////////////////

//initialize pattern of begin finding
template <typename TPattern, typename TNeedle>
inline void
_findBeginInit(TPattern & pattern, TNeedle & needle_)
{
    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
    return FindBeginImpl_<TFindBeginPatternSpec>::_findBeginInit(pattern, needle_);
}

//////////////////////////////////////////////////////////////////////////////

//find begin main interface

/*!
 * @fn Finder#findBegin
 * @headerfile <seqan/find.h>
 * @brief Search the begin of an approximate match.
 *
 * @signature bool findBegin(finder, pattern[, limit]);
 *
 * @param[in,out] finder  The Finder object to search through.
 * @param[in,out] pattern The Pattern object to search for.  This must be a pattern for approximate string matching.
 * @param[in]     limit   The score limit.  The default is the limit used during the last <tt>find</tt> call, see
 *                        <tt>getScore</tt>.  All occurrences that score at least <tt>limit</tt> are reported.
 *
 * @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no match.
 *
 * The function <tt>find</tT> successfully called be called - that is an end position was found - before calling
 * findBegin to find a begin position.
 */

template <typename TFinder, typename TPattern>
inline bool
findBegin(TFinder & finder,
          TPattern & pattern)
{
    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
    return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern);
}
template <typename TFinder, typename TPattern, typename TLimit>
inline bool
findBegin(TFinder & finder,
          TPattern & pattern,
          TLimit limit)
{
    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
    return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern, limit);
}

//////////////////////////////////////////////////////////////////////////////

/*!
 * @fn Pattern#getBeginScore
 * @headerfile <seqan/find.h>
 * @brief Score of the last match found by @link Finder#findBegin @endlink during approximate searching.
 *
 * @signature TScoreValue getBeginScore(pattern);
 *
 * @param[in] pattern A Pattern that can be used for approximate searching.
 *
 * @return TScoreValue The score of the lst match found using <tt>pattern</tt>.  The value is set after successfully
 *                     call of @link Finder#findBegin @endlink.  If no match was found, the value is undefined.
 */

template <typename TPattern>
inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
getBeginScore(TPattern & pattern)
{
    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
    return FindBeginImpl_<TFindBeginPatternSpec>::getBeginScore(pattern);
}

//////////////////////////////////////////////////////////////////////////////

}// namespace seqan2

#endif //#ifndef SEQAN_HEADER_...
