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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>
// ==========================================================================
// Code for journal entries.
// ==========================================================================
#ifndef SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRY_H_
#define SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRY_H_
namespace seqan2 {
// ============================================================================
// Enums, Classes
// ============================================================================
enum SegmentSource
{
SOURCE_NULL,
SOURCE_ORIGINAL,
SOURCE_PATCH
};
template <typename TPos_, typename TSize_>
struct JournalEntry
{
typedef TPos_ TPos;
typedef TSize_ TSize;
// Flag for where the segment comes from.
SegmentSource segmentSource;
// Position in the original string or the insertion buffer,
// depending on segmentSource.
TPos physicalPosition;
// Position in the virtual string.
TPos virtualPosition;
// Physical position in the host string. For SOURCE_PATCH entries, this is the position of the closest
// SOURCE_ORIGINAL entry left of it. If there is no such entry then this is 0. Unused and always 0 for unbalanced
// tree.
TPos physicalOriginPosition;
// Length of the segment.
TSize length;
JournalEntry()
: segmentSource(SOURCE_NULL),
physicalPosition(0),
virtualPosition(0),
physicalOriginPosition(0),
length(0)
{}
JournalEntry(SegmentSource const & segmentSource,
TPos physicalPosition,
TPos virtualPosition,
TPos physicalHostPosition,
TSize length)
: segmentSource(segmentSource),
physicalPosition(physicalPosition),
virtualPosition(virtualPosition),
physicalOriginPosition(physicalHostPosition),
length(length)
{}
};
template <typename TPos, typename TSize>
struct JournalEntryLtByVirtualPos
{
bool operator()(JournalEntry<TPos, TSize> const & a,
JournalEntry<TPos, TSize> const & b) const
{
return a.virtualPosition < b.virtualPosition;
}
};
// TODO (rmaerker): Note that this comparison only makes sense if the nodes are sorted
// in ascending order according to their physical position - this might be violated
// if rearrangements are included.
template <typename TPos, typename TSize>
struct JournalEntryLtByPhysicalOriginPos
{
bool operator()(JournalEntry<TPos, TSize> const & a, JournalEntry<TPos, TSize> const & b) const
{
return a.physicalOriginPosition < b.physicalOriginPosition;
}
};
// ============================================================================
// Metafunctions
// ============================================================================
template <typename TPos, typename TSize>
struct Size<JournalEntry<TPos, TSize> >
{
typedef TSize Type;
};
template <typename TPos, typename TSize>
struct Size<JournalEntry<TPos, TSize> const>
: Size<JournalEntry<TPos, TSize> > {};
template <typename TPos, typename TSize>
struct Position<JournalEntry<TPos, TSize> >
{
typedef TPos Type;
};
template <typename TPos, typename TSize>
struct Position<JournalEntry<TPos, TSize> const>
: Position<JournalEntry<TPos, TSize> > {};
// ============================================================================
// Functions
// ============================================================================
template <typename TStream, typename TPos, typename TSize>
TStream & operator<<(TStream & stream, JournalEntry<TPos, TSize> const & entry)
{
return stream << "{segmentSource=" << entry.segmentSource
<< ", virtualPosition=" << entry.virtualPosition
<< ", physicalPosition=" << entry.physicalPosition
<< ", physicalOriginPosition=" << entry.physicalOriginPosition
<< ", length=" << entry.length
<< "}";
}
} // namespace seqan2
#endif // SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRY_H_
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