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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: Birte Kehr <birte.kehr@fu-berlin.de>
// ==========================================================================
// Operations on alignments such as integration
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
template <typename TSource0, typename TGapSpec0,
typename TSource1, typename TGapSpec1,
typename TPos>
inline void
integrateGaps(Gaps<TSource0, TGapSpec0> & targetRow,
Gaps<TSource1, TGapSpec1> const & sourceRow,
TPos const viewPos)
{
typedef typename Iterator<Gaps<TSource0, TGapSpec0>, Standard>::Type TTargetIt;
typedef typename Iterator<Gaps<TSource1, TGapSpec1> const, Standard>::Type TSourceIt;
// This assertion ensures that the number of sequence characters after viewPos is greater than or equal to
// the number of source characters in the clipped infix row.
SEQAN_ASSERT_GEQ(endPosition(targetRow) - toSourcePosition(targetRow, viewPos),
endPosition(sourceRow) - beginPosition(sourceRow));
// init iterators
TTargetIt it = iter(targetRow, viewPos);
// walk through Gaps containers and copy gaps
for (TSourceIt sIt = begin(sourceRow, Standard()), sItEnd = end(sourceRow, Standard()); sIt != sItEnd;)
{
TPos gapSize = countGaps(sIt);
insertGaps(it, gapSize);
goFurther(it, gapSize+1);
goFurther(sIt, gapSize+1);
}
}
template <typename TSource0, typename TGapSpec0,
typename TSource1, typename TGapSpec1>
inline void
integrateGaps(Gaps<TSource0, TGapSpec0> & targetRow,
Gaps<TSource1, TGapSpec1> const & sourceRow)
{
typename Position<TSource0>::Type viewPos = beginPosition(source(sourceRow)) // correct for infixes
- beginPosition(source(targetRow)) // ...
+ beginPosition(sourceRow); // respect source clipping
integrateGaps(targetRow, sourceRow, toViewPosition(targetRow, viewPos));
}
// ----------------------------------------------------------------------------
// Function integrateAlign()
// ----------------------------------------------------------------------------
/*!
* @fn integrateAlign
* @headerfile <seqan/align.h>
* @brief Integrates an alignment into another by copying the gaps.
*
* @signature void integrateAlign(align1, align2[, positions]);
*
* @param[in,out] align1 Target Alignment object into which align2 is to be integrated.
* @param[in] align2 Alignment object that is to be integrated into align1.
* @param[in] positions The integration positions in align1 for all rows (view positions), String of positions.
*
* @section Examples
*
* @include demos/dox/align/integrate_align.cpp
*
* The output is as follows:
*
* @include demos/dox/align/integrate_align.cpp.stdout
*/
template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2, typename TPos>
void integrateAlign(Align<TSource1, TSpec1> & align,
Align<TSource2, TSpec2> const & infixAlign,
String<TPos> const & viewPos)
{
SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows.");
typedef typename Size<Align<TSource1, TSpec1> >::Type TSize;
//NOTE(h-2): could be parallelized
for (TSize i = 0; i < length(rows(align)); ++i)
integrateGaps(row(align, i), row(infixAlign, i), viewPos[i]);
}
template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2>
void integrateAlign(Align<TSource1, TSpec1> & align,
Align<TSource2, TSpec2> const & infixAlign)
{
SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows.");
typedef typename Size<Align<TSource1, TSpec1> >::Type TSize;
//NOTE(h-2): could be parallelized
for (TSize i = 0; i < length(rows(align)); ++i)
integrateGaps(row(align, i), row(infixAlign, i));
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
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