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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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_STORE_INTERVALTREE_H
#define SEQAN_HEADER_STORE_INTERVALTREE_H
//#define DEBUG_TREE
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
// Create IntervallTreeStores
//////////////////////////////////////////////////////////////////////////////
template<typename TSpec, typename TConfig>
inline void
createIntervalTreeStore(FragmentStore<TSpec, TConfig> & me, const bool &unknownO)
{
typedef typename FragmentStore<TSpec, TConfig>::TAnnotationStore TAnnotationStore;
typedef typename Value<TAnnotationStore>::Type TAnnotationStoreElement;
typedef typename TAnnotationStoreElement::TId TId;
typedef typename Iterator<TAnnotationStore>::Type TAnnotationIterator;
typedef typename FragmentStore<TSpec, TConfig>::TIntervalTreeStore TIntervalTreeStore;
typedef typename Value<TIntervalTreeStore>::Type TIntervalTree;
typedef typename TIntervalTree::TInterval TInterval;
typedef String<TInterval> TIntervals;
typedef typename Iterator<String<TIntervals> >::Type TCIter;
static const TId INVALID_ID = TAnnotationStoreElement::INVALID_ID;
// get intervals for each contig (R- and F-strand):
if (!empty(me.annotationStore) && !unknownO)
{
resize(me.intervalTreeStore_F, length(me.contigStore) );
resize(me.intervalTreeStore_R, length(me.contigStore) );
String<TIntervals> contigIntervals_F;
String<TIntervals> contigIntervals_R;
resize(contigIntervals_F, length(me.contigStore));
resize(contigIntervals_R, length(me.contigStore));
TAnnotationIterator itAnno = begin(me.annotationStore);
TAnnotationIterator itAnnoEnd = end(me.annotationStore);
TId beginPos;
TId endPos;
TInterval interval;
for ( ; itAnno != itAnnoEnd; goNext(itAnno))
{
if (getValue(itAnno).contigId != INVALID_ID)
{
beginPos = getValue(itAnno).beginPos;
endPos = getValue(itAnno).endPos;
if (beginPos != INVALID_ID && beginPos <= endPos)
{
interval.i1 = beginPos;
interval.i2 = endPos;
interval.cargo = position(itAnno, me.annotationStore);
appendValue(value(contigIntervals_F, getValue(itAnno).contigId), interval, Generous());
}
else if (beginPos != INVALID_ID && beginPos > endPos)
{
interval.i1 = endPos;
interval.i2 = beginPos;
interval.cargo = position(itAnno, me.annotationStore);
appendValue(value(contigIntervals_R, getValue(itAnno).contigId), interval, Generous() );
}
}
}
// build trees for each contig and each strand:
TCIter itF = begin(contigIntervals_F);
TCIter itFEnd = end(contigIntervals_F);
TCIter itR = begin(contigIntervals_R);
for ( ; itF != itFEnd; goNext(itF), goNext(itR))
{
TIntervalTree intervalTree_F(getValue(itF), ComputeCenter());
TIntervalTree intervalTree_R(getValue(itR), ComputeCenter());
assignValue(me.intervalTreeStore_F, position(itF, contigIntervals_F), intervalTree_F);
assignValue(me.intervalTreeStore_R, position(itR, contigIntervals_R), intervalTree_R);
}
}
// if read orientation is not known:
// get intervals for each contig:
if (!empty(me.annotationStore) && unknownO)
{
resize(me.intervalTreeStore_F, length(me.contigStore) );
clear(me.intervalTreeStore_R);
String<TIntervals> contigIntervals;
resize(contigIntervals, length(me.contigStore));
TAnnotationIterator itAnno = begin(me.annotationStore);
TAnnotationIterator itAnnoEnd = end(me.annotationStore);
TId beginPos;
TId endPos;
TInterval interval;
for ( ; itAnno != itAnnoEnd; goNext(itAnno))
{
if (getValue(itAnno).contigId != INVALID_ID)
{
beginPos = getValue(itAnno).beginPos;
endPos = getValue(itAnno).endPos;
if (beginPos != INVALID_ID)
{
if (beginPos <= endPos)
{
interval.i1 = beginPos;
interval.i2 = endPos;
}
else
{
interval.i1 = endPos;
interval.i2 = beginPos;
}
interval.cargo = position(itAnno, me.annotationStore);
appendValue(value(contigIntervals, getValue(itAnno).contigId), interval, Generous());
}
}
}
// build trees for each contig:
TCIter itC = begin(contigIntervals);
TCIter itCEnd = end(contigIntervals);
for ( ; itC != itCEnd; goNext(itC))
{
TIntervalTree intervalTree(getValue(itC), ComputeCenter());
assignValue(me.intervalTreeStore_F, position(itC, contigIntervals), intervalTree);
}
}
}
//////////////////////////////////////////////////////////////////////////////
// find intervals containing one interval
//////////////////////////////////////////////////////////////////////////////
template<typename TIntervalTree, typename TInterval, typename TCargo>
inline void
findIntervalsForInterval(String<TCargo> & result, TIntervalTree & intervalTree, TInterval & interval, unsigned offsetInterval)
{
String<TCargo> result1;
String<TCargo> result2;
findIntervals(result1, intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval);
findIntervals(result2, intervalTree.g, intervalTree.pm, interval.i2 - offsetInterval);
interSec(result, result1, result2);
}
//////////////////////////////////////////////////////////////////////////////
}// namespace seqan2
#endif //#ifndef SEQAN_HEADER_...
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