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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>
// ==========================================================================
// Basic defintions and forwards used globally for this module.
// ==========================================================================
#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Tag Traversal Tags
// ----------------------------------------------------------------------------
struct ForwardTraversal_;
typedef Tag<ForwardTraversal_> ForwardTraversal;
struct BidirectionalTraversal_;
typedef Tag<BidirectionalTraversal_> BidirectionalTraversal;
// ----------------------------------------------------------------------------
// Tag JSTree
// ----------------------------------------------------------------------------
template <typename TSpec = ForwardTraversal>
struct JSTree;
// ----------------------------------------------------------------------------
// Tag JstBufferMember
// ----------------------------------------------------------------------------
struct JstBufferMember_;
typedef Tag<JstBufferMember_> JstBufferMember;
// ----------------------------------------------------------------------------
// Tag JstSourceMember
// ----------------------------------------------------------------------------
struct JstSourceMember_;
typedef Tag<JstSourceMember_> JstSourceMember;
// ----------------------------------------------------------------------------
// Tag JstDeltaMapMember
// ----------------------------------------------------------------------------
struct JstDeltaMapMember_;
typedef Tag<JstDeltaMapMember_> JstDeltaMapMember;
// ----------------------------------------------------------------------------
// Class DefaultJstConfig
// ----------------------------------------------------------------------------
/*!
* @class DefaultJstConfig
* @headerfile <seqan/journaled_string_tree.h>
* @brief The default Journaled-String-Tree configuration object.
*
* @signature template <typename TSequence>
* class DefaultJstConfig<TDeltaStore>
*
* @tparam TSequence Type of the underlying base sequence.
*
* Defines the follwoing types used to configure the @link DeltaMap @endlink:
* @code{.cpp}
* typedef typename Size<TSequence>::Type TDeltaPos;
* typedef typename Value<TSequence>::Type TSnpValue;
* typedef String<TSnpValue> TInsValue;
* typedef typename Size<TSequence>::Type TDelValue;
* typedef Pair<TDelValue, TInsValue> TSVValue;
* @endcode
*/
template <typename TSequence>
struct DefaultJstConfig
{
typedef typename Size<TSequence>::Type TDeltaPos; // Position type for delta entry.
typedef typename Value<TSequence>::Type TSnpValue; // Value type of the SNPs.
typedef String<TSnpValue> TInsValue; // Value type of insertions.
typedef typename Size<TSequence>::Type TDelValue; // Value type of deletions.
typedef Pair<TDelValue, TInsValue> TSVValue; // Value type of structural variants (combination of deletion and insertion).
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction Traverser
// ----------------------------------------------------------------------------
template <typename TContainer, typename TObserverList = ObserverList<> >
struct Traverser;
// ----------------------------------------------------------------------------
// Metafunction ContextIterator
// ----------------------------------------------------------------------------
template <typename TObj>
struct ContextIterator;
// ============================================================================
// Functions
// ============================================================================
} // namespace seqan2
#endif // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
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