// ==========================================================================
//                 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
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================

#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_
#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_

namespace seqan2 {

// ============================================================================
// Forwards
// ============================================================================

// ============================================================================
// Tags, Classes, Enums
// ============================================================================

// ============================================================================
// Metafunctions
// ============================================================================

// ============================================================================
// Functions
// ============================================================================

// ----------------------------------------------------------------------------
// Function _joinInternal()                     [GlobalAlign<JournaledCompact>]
// ----------------------------------------------------------------------------

// TODO(rmaerker): Change the orientation of reference and journal.
template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec, typename TJournalString2>
inline void
_joinInternal(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journal,
              StringSet<TJournalString2, Owner<JournaledSet> > const & journalSet,
              JoinConfig<GlobalAlign<JournaledCompact> > const & joinConfig)
{
    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;

    // TODO(rmaerker): Check the correct behavior here.
    TJournalString tmpJournal;
    setHost(tmpJournal, value(journalSet._globalRefHolder));

    if (isBandSet(joinConfig))
        globalAlignment(tmpJournal, host(journalSet), journal, scoringScheme(joinConfig), joinConfig._alignConfig,
                        lowerDiagonal(joinConfig), upperDiagonal(joinConfig));
    else
        globalAlignment(tmpJournal, host(journalSet), journal, scoringScheme(joinConfig), joinConfig._alignConfig);

    // Apply the alignment to the journal.
    set(journal, tmpJournal);
}

}  // namespace seqan2

#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_
