// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Tobias Rausch <rausch@embl.de>
// Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_

namespace seqan2 {

//////////////////////////////////////////////////////////////////////////////
// Adaptations so that the alignment graph works like any other graph
//////////////////////////////////////////////////////////////////////////////





//////////////////////////////////////////////////////////////////////////////
// Alignment Graph OutEdgeIterator
//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////
// Graph InternalOutEdgeIterator for Alignment
//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TIteratorSpec>
class Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > >
{
public:
    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph_;
    typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
    typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;

    TGraph_ const* data_host;
    TVertexDescriptor_ data_source;
    TEdgeDescriptor_ data_edge{};

    Iter() = default;

    Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) :
        data_host(&_graph),
        data_source(v)
    {
        if (empty(_graph)) data_edge = 0;
        else data_edge = getValue(_graph.data_align.data_vertex,v);
    }

    Iter(Iter const& _iter) :
        data_host(_iter.data_host),
        data_source(_iter.data_source),
        data_edge(_iter.data_edge)
    {
    }

    ~Iter() {
    }

    Iter const&    operator = (Iter const & _other) {
        if (this == &_other) return *this;
        data_host = _other.data_host;
        data_source = _other.data_source;
        data_edge = _other.data_edge;
        return *this;
    }
//____________________________________________________________________________
};


//////////////////////////////////////////////////////////////////////////////
// Graph InternalOutEdgeIterator - Metafunctions
//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec>
struct Iterator<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, OutEdgeIterator>
{
    typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
};

template<typename TStringSet, typename TCargo, typename TGraphSpec>
struct Iterator<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > const, OutEdgeIterator>
{
    typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > const, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
};


//////////////////////////////////////////////////////////////////////////////
// Graph InternalOutEdgeIterator - Functions
//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline typename GetValue<Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
getValue(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    return it.data_edge;
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline typename Reference<Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
value(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    return it.data_edge;
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline bool
atBegin(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    return (it.data_edge == getValue(_getVertexString(*it.data_host), it.data_source));
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline void
goBegin(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    it.data_edge = getValue(_getVertexString(*it.data_host),it.data_source);
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline bool
atEnd(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    return (it.data_edge == 0);
}


//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline void
goEnd(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    it.data_edge = 0;
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline void
goNext(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    if (!atEnd(it)) {
        if (it.data_source == getSource(it.data_edge)) it.data_edge = getNextS(it.data_edge);
        else it.data_edge = getNextT(it.data_edge);
    }
}


//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline void
goPrevious(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
    typedef typename EdgeType<TGraph>::Type TEdge;
    TEdge* current = getValue(_getVertexString(*it.data_host), it.data_source);
    if (current == it.data_edge) return;
    while (current != 0) {
        if (it.data_source == getSource(current)) {
            if (it.data_edge == getNextS(current)) break;
            else current = getNextS(current);
        } else {
            if (it.data_edge == getNextT(current)) break;
            else current = getNextT(current);
        }
    }
    it.data_edge = current;
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline bool
operator ==(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
            Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
{
    return ((it1.data_edge==it2.data_edge) &&
            (it1.data_source==it2.data_source));
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline bool
operator !=(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
            Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
{
    return ((it1.data_edge!=it2.data_edge) ||
            (it1.data_source!=it2.data_source));
}

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > >::Type
targetVertex(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
{
    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
    TVertexDescriptor target = targetVertex(*it.data_host, it.data_edge);
    if (target != it.data_source) return target;
    else return sourceVertex(*it.data_host, it.data_edge);
}



//////////////////////////////////////////////////////////////////////////////
// Go Next function for EdgeIterator
//////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////

template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
inline void
goNext(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
{
    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
    _goNextInternal(it);
    TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
    while((!atEnd(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
        _goNextInternal(it);
        sourceV = sourceVertex(it.data_edge_it);
    }
}




//////////////////////////////////////////////////////////////////////////////
// Graph drawing adaptations
//////////////////////////////////////////////////////////////////////////////



//////////////////////////////////////////////////////////////////////////////

template <typename TStringSet, typename TCargo, typename TSpec, typename TNodeAttributes>
inline void
_createNodeAttributes(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
                      TNodeAttributes& nodeMap)
{
    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
    typedef typename Id<TGraph>::Type TIdType;
    resizeVertexMap(nodeMap, g);

    unsigned int scaling = 20 / length(value(g.data_sequence));
    if (scaling == 0) scaling = 1;

    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
    TConstIter it(g);
    for(;!atEnd(it);++it) {
        TIdType id = sequenceId(g, *it);
        std::ostringstream outs;
        outs << "label = \"";
        outs << "[" << fragmentBegin(g, *it) << "," << fragmentBegin(g, *it)+fragmentLength(g, *it) << ")";
        // the lower command outputs the fragemtn of the string it is replaced by the interval
        //outs << label(g, *it);
        outs << "\", group = ";
        outs << id;
        append(property(nodeMap, *it), outs.str().c_str());
        //std::cout << property(nodeMap, *it) << std::endl;
    }
}

//////////////////////////////////////////////////////////////////////////////

template <typename TStringSet, typename TSpec, typename TEdgeAttributes>
inline void
_createEdgeAttributes(Graph<Alignment<TStringSet, void, TSpec> > const& g,
                      TEdgeAttributes& edgeMap)
{
    _createEmptyEdgeAttributes(g.data_align,edgeMap);
}

//////////////////////////////////////////////////////////////////////////////

template <typename TStringSet, typename TCargo, typename TSpec, typename TEdgeAttributes>
inline void
_createEdgeAttributes(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
                      TEdgeAttributes& edgeMap)
{
    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
    resizeEdgeMap(edgeMap, g);

    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
    TConstEdIter itEd(g);
    for(;!atEnd(itEd);++itEd) {
        TCargo c = getCargo(*itEd);
        std::ostringstream outs;
        outs << "label = \"";
        outs << (TCargo) c;
        outs << "\",";
        outs << "len = 10.0";
        append(property(edgeMap, *itEd), outs.str().c_str());
    }
}

//////////////////////////////////////////////////////////////////////////////

template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
inline void
_writeGraphFooter(TTarget & iter,
                  Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
                  DotDrawing)
{
    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
    typedef typename Size<TGraph>::Type TSize;
    typedef typename Id<TGraph>::Type TId;
    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;

    TStringSet& str = stringSet(g);
    TSize len = length(str);
    for(TSize i = 0; i<len; ++i) {
        TId seqId = positionToId(str, i);
        TSize j = 0;
        TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
        TVertexDescriptor previousVertex = nilVertex;
        while(j<length(str[i]))
        {
            TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, j);
            if (nextVertex == nilVertex) {
                ++j;
                continue;
            }
            if (previousVertex != nilVertex)
            {
                appendNumber(iter, previousVertex);
                write(iter, " -- ");
                appendNumber(iter, nextVertex);
                write(iter, " [len=3.0, arrowhead=vee];\n");
            }
            previousVertex = nextVertex;
            j += fragmentLength(g, nextVertex);
        }
    }
    writeValue(iter, '\n');
}

//////////////////////////////////////////////////////////////////////////////

template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
inline void
_writeGraphType(TTarget & iter,
                Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
                DotDrawing)
{
    write(iter, "graph");
}

//////////////////////////////////////////////////////////////////////////////

template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
inline void
_writeEdgeType(TTarget & iter,
               Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
               DotDrawing)
{
    write(iter, " -- ");
}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_