// ==========================================================================
//                 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
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// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
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// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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// 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_...
