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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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class LocalAlignmentEnumerator
// ----------------------------------------------------------------------------
template <typename TScore, typename TSpec>
class LocalAlignmentEnumerator;
/*!
* @class LocalAlignmentEnumerator
* @headerfile <seqan/align.h>
* @brief Enumeration of local alignments.
*
* @signature template <typename TScore, typename TSpec>
* class LocalAlignmentEnumerator;
*
* @tparam TScore The type of the @link Score @endlink to use for the local alignment.
* @tparam TSpec The tag to use for specializing the enumerator.
*
* This is an abstract class that will only be instantiated through its subclasses.
* See the documentation of the specializations for examples.
*
* @section References
*
* <ul>
* <li>Waterman MS, Eggert M: A new algorithm for best subsequence alignments with application to tRNA-rRNA
* comparisons. J Mol Biol 1987, 197(4):723-728.</li>
* </ul>
*/
/*!
* @class UnbandedLocalAlignmentEnumerator
* @extends LocalAlignmentEnumerator
* @headerfile <seqan/align.h>
* @brief Unbanded enumeration of local alignments using the Waterman-Eggert algorithm.
*
* @signature template <typename TScore>
* class LocalAlignmentEnumerator<TScore, Unbanded>;
*
* @tparam TScore The @link Score @endlink type.
*
* @section Examples
*
* Enumerate all alignments into a @link Align @endlink object.
*
* @code{.cpp}
* SimpleScore scoringScheme(2, -1, -1, -2);
* LocalAlignmentEnumerator<SimpleScore, Unbanded> enumerator(scoringScheme, 5);
*
* Dna5String seqH = "CGAGAGAGACCGAGA";
* Dna5String seqV = "TTCTGAGATCCGTTTTT";
*
* Align<Dna5String> align;
* resize(rows(align), 2);@s
* assignSource(row(align), 0, seqH);
* assignSource(row(align), 1, seqV);
*
* int i = 0;
* while (nextLocalAlignment(align, enumerator))
* {
* std::cout << i << "-th alignment:\n";
* std::cout << align << "\n\n";
* std::cout << "score == " << getScore(enumerator) << "\n";
* }
* @endcode
*/
/*!
* @fn UnbandedLocalAlignmentEnumerator::LocalAlignmentEnumerator
* @brief Constructor.
*
* @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme[, cutoff]);
*
* @param[in] scheme The @link Score @endlink object to use for the alignment score.
* @param[in] cutoff Alignments with scores <tt>< cutoff</tt> will be discarded (<tt>int</tt>, default 0).
*/
/*!
* @class BandedLocalAlignmentEnumerator
* @extends LocalAlignmentEnumerator
* @headerfile <seqan/align.h>
* @brief Banded enumeration of local alignments using the Waterman-Eggert algorithm.
*
* @signature template <typename TScore>
* class LocalAlignmentEnumerator<TScore, Banded>;
*
* @tparam TScore The @link Score @endlink type.
*
* @section Examples
*
* Enumerate all alignments in the band between -3 and 0 into an @link Align @endlink object.
*
* @code{.cpp}
* SimpleScore scoringScheme(2, -1, -1, -2);
* LocalAlignmentEnumerator<SimpleScore, Banded> enumerator(scoringScheme, -3, 0, 5);
*
* Dna5String seqH = "CGAGAGAGACCGAGA";
* Dna5String seqV = "TTCTGAGATCCGTTTTT";
*
* Align<Dna5String> align;
* resize(rows(align), 2);
* assignSource(row(align), 0, seqH);
* assignSource(row(align), 1, seqV);
*
* int i = 0;
* while (nextLocalAlignment(align, enumerator))
* {
* std::cout << i << "-th alignment:\n";
* std::cout << align << "\n\n";
* std::cout << "score == " << getScore(enumerator) << "\n";
* }
* @endcode
*/
/*!
* @fn BandedLocalAlignmentEnumerator::LocalAlignmentEnumerator
* @brief Constructor.
*
* @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme, upperDiag, lowerDiag[, cutoff]);
*
* @param[in] scheme The @link Score @endlink object to use for the alignment score.
* @param[in] upperDiag An <tt>int</tt> with the upper diagonal.
* @param[in] lowerDiag An <tt>int</tt> with the lower diagonal.
* @param[in] cutoff Alignments with scores <tt>< cutoff</tt> will be discarded (<tt>int</tt>, default 0).
*/
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function getScore()
// ----------------------------------------------------------------------------
/*!
* @fn LocalAlignmentEnumerator#getScore
* @headerfile <seqan/align.h>
* @brief Get current alignment score.
*
* @signature TScoreVal getScore(enumerator);
*
* @param[in] enumerator The LocalAlignmentEnumerator to query.
*
* @return TScoreVal The current alignment score (@link Score#Value @endlink of <tt>TScore</tt>).
*/
// ----------------------------------------------------------------------------
// Function nextLocalAlignment()
// ----------------------------------------------------------------------------
/*!
* @fn LocalAlignmentEnumerator#nextLocalAlignment
* @headerfile <seqan/align.h>
* @brief Compute next suboptimal local alignment.
*
* @signature bool nextLocalAlignment(align, enumerator);
* @signature bool nextLocalAlignment(gapsH, gapsV, enumerator);
*
* @param[in] align @link Align @endlink object to use for the alignment representation.
* @param[in] gapsH @link Gaps @endlink object to use for the first/horizontal sequence in the alignment matrix.
* @param[in] gapsV @link Gaps @endlink object to use for the second/vertical sequence in the alignment matrix.
* @param[in] enumerator The LocalAlignmentEnumerator to advance.
*
* @return bool <tt>true</tt> if another suboptimal alignment above the given threshold was found and <tt> false
* otherwise.
*/
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
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