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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>
// ==========================================================================
#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
namespace seqan2
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// TODO(rrahn): Redesign interface.
template <typename TJst>
class JstTraversalNode
{
public:
typedef typename Member<TJst, JstSourceMember>::Type TSequence;
typedef typename Iterator<TSequence, Standard>::Type TSeqIterator;
typedef typename Position<TSequence>::Type TPosition;
typedef typename MakeSigned<TPosition>::Type TSignedPos;
typedef typename Member<TJst, JstDeltaMapMember>::Type TDeltaMap;
typedef typename Iterator<TDeltaMap, Standard>::Type TDeltaIterator;
typedef typename DeltaCoverage<TDeltaMap>::Type TCoverage;
typedef typename Size<TJst>::Type TSize;
// __ Mapping Resources ___________________________________________________
TSignedPos headSrcPos; // Head of the context pointing into base sequence. Can be negative in the initialization phase.
TSize remainingSize;
TSize proxyId;
TDeltaIterator headDelta; // Iterator to first delta in context.
TDeltaIterator branchRoot; // Iterator to root of current branch.
// __ Navigation Resources ________________________________________________
TDeltaIterator curDelta; // current delta iterator.
TDeltaIterator nextDelta;
TSeqIterator begEdgeIt; // Current iterator of this edge.
TSeqIterator curEdgeIt; // Current iterator of this edge.
TSeqIterator endEdgeIt; // End of this edge.
TCoverage coverage; // Coverage of this node.
bool isBase;
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
template <typename TJstLhs, typename TJstRhs>
inline void
swap(JstTraversalNode<TJstLhs> & lhs,
JstTraversalNode<TJstRhs> & rhs)
{
std::swap(lhs.remainingSize, rhs.remainingSize);
std::swap(lhs.headSrcPos, rhs.headSrcPos);
std::swap(lhs.proxyId, rhs.proxyId);
std::swap(lhs.headDelta, rhs.headDelta);
std::swap(lhs.branchRoot, rhs.branchRoot);
std::swap(lhs.curDelta, rhs.curDelta);
std::swap(lhs.nextDelta, rhs.nextDelta);
std::swap(lhs.begEdgeIt, rhs.begEdgeIt);
std::swap(lhs.curEdgeIt, rhs.curEdgeIt);
std::swap(lhs.endEdgeIt, rhs.endEdgeIt);
swap(lhs.coverage, rhs.coverage);
std::swap(lhs.isBase, rhs.isBase);
}
template <typename TStream, typename TJst>
inline TStream&
operator<<(TStream & stream, JstTraversalNode<TJst> const & node)
{
stream << "<HEA: " << node.headSrcPos;
stream << " REM: " << node.remainingSize;
stream << " CUR: (" << *node.curDelta << ")";
stream << " NXT: (" << *node.nextDelta << ")";
stream << " SEQ: " << infix(container(node.begEdgeIt), position(node.begEdgeIt), position(node.endEdgeIt));
stream << " POS: " << position(node.curEdgeIt) - position(node.begEdgeIt);
stream << " PID: " << node.proxyId;
stream << " COV: " << _printCoverage(node.coverage);
if (node.isBase)
stream << " Base: true";
else
stream << " Base: false";
stream << ">";
return stream;
}
}
#endif // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
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