// ==========================================================================
//                 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_ALGORITHM_REFINE_ANNOTATION_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_

//SEQAN_NO_DDDOC: do not generate documentation for this file

namespace seqan2 {


template<typename TSequence, typename TValue, typename TSpec = Simple>
class Annotation;



template<typename TSequence,typename TValue>
class Annotation<TSequence,TValue,Simple>{

public:
    typedef typename Id<TSequence>::Type TId_;
    typedef typename Position<TSequence>::Type TPos_;
    typedef typename Size<TSequence>::Type TSize_;

    TId_ data_seq_id;
    TPos_ data_begin;
    TSize_ data_length;
    //String<char> data_label;
    TValue data_label;

    Annotation()
    {
    }


    Annotation(TId_ seqId, TPos_ begin, TSize_ len, TValue label) :
            data_seq_id(seqId),
            data_begin(begin),
            data_length(len),
            data_label(label)
    {
    }

    ~Annotation()
    {
    }

};



template<typename TSequence,typename TValue,typename TSpec>
typename Id<TSequence>::Type&
sequenceId(Annotation<TSequence,TValue,TSpec> & me)
{
    return me.data_seq_id;
}

template<typename TSequence,typename TValue,typename TSpec>
typename Position<TSequence>::Type&
fragmentBegin(Annotation<TSequence,TValue,TSpec> & me)
{
    return me.data_begin;
}

template<typename TSequence,typename TValue,typename TSpec>
typename Size<TSequence>::Type&
fragmentLength(Annotation<TSequence,TValue,TSpec> & me)
{
    return me.data_length;
}

template<typename TSequence,typename TValue,typename TSpec>
TValue
label(Annotation<TSequence,TValue,TSpec> & me)
{
    return me.data_label;
}


template<typename TSequence,typename TValue,typename TSpec>
struct Value<Annotation<TSequence,TValue,TSpec> >
{
    typedef TValue Type;
};


// default: no annotation given, do nothing
template<typename TValue, typename TAliString, typename TGraph, typename TPropertyMap, typename TStringSet, typename TMap, typename TTagSpec>
inline void
_addAnnotationCuts(String<std::set<TValue> > &,
                   TAliString &,
                   String<TGraph> &,
                   String<TPropertyMap> &,
                   TStringSet &,
                   TMap &,
                   bool,
                   TValue,
                   Tag<TTagSpec>)
{
    return;
}




//refine positions where annotation changes (borders of annotated stretches)
template<typename TValue, typename TAliString, typename TGraph, typename TPropertyMap, typename TStringSet, typename TMap, typename TAnnoString, typename TTagSpec>
inline void
_addAnnotationCuts(String<std::set<TValue> > & all_nodes,
                   TAliString & alis,
                   String<TGraph> & gs,
                   String<TPropertyMap> & pms,
                   TStringSet & seq,
                   TMap & seq_map,
                   TAnnoString & annotation,
                   TValue min_fragment_len,
                   Tag<TTagSpec> tag)
{

    //typedef typename Value<TAnnoString>::Type TAnnotation;
    typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
    typedef typename std::set<TValue>::iterator TSetIterator;
    //call function _refine for each position that annotation is given for (the borders of annotated stretches)
    TAnnoIter anno_it = begin(annotation,Standard());
    TAnnoIter anno_end = end(annotation,Standard());
    //for each annotated stretch
    while(anno_it != anno_end)
    {

        TValue seq_i_id = sequenceId(*anno_it);
        TValue begin_i = fragmentBegin(*anno_it);
        TValue end_i = begin_i + fragmentLength(*anno_it);
        TValue seq_i_pos = idToPosition(seq,seq_i_id);

        //refine begin
        TSetIterator iter = all_nodes[seq_i_pos].find(begin_i);
        if(_cutIsValid(all_nodes,seq_i_pos,begin_i,iter,min_fragment_len,tag))
        {
            all_nodes[seq_i_pos].insert(begin_i);
            _refine(begin_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
        }
        //and end position
        iter = all_nodes[seq_i_pos].find(end_i);
        if(_cutIsValid(all_nodes,seq_i_pos,end_i,iter,min_fragment_len,tag))
        {
            all_nodes[seq_i_pos].insert(end_i);
            _refine(end_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
        }
        ++anno_it;
    }

}


// add annotation labels to nodes, as given in annotation, store as node properties in pm
template<typename TPropertyMap, typename TStringSet, typename TMap, typename TAnnoString, typename TAliGraph,typename TTagSpec>
inline void
_addNodeAnnotation(TStringSet &,
                   TMap &,
                   TAnnoString & annotation,
                   TPropertyMap & pm,
                   TAliGraph & ali_g,
                   Tag<TTagSpec>)
{

    resizeVertexMap(pm, ali_g);

    typedef typename Value<TAnnoString>::Type TAnnotation;
    typedef typename Id<TAnnotation>::Type TId;
    typedef typename Position<TAnnotation>::Type TPos;
    typedef typename Value<TAnnotation>::Type TLabel;
    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;

    typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
    TAnnoIter anno_it = begin(annotation,Standard());
    TAnnoIter anno_end = end(annotation,Standard());

    //for each annotated stretch
    while(anno_it != anno_end)
    {
        TLabel label_ = label(*anno_it);
        TId seq_id = sequenceId(*anno_it);
        TPos act_pos = fragmentBegin(*anno_it);
        TPos end_pos = act_pos + fragmentLength(*anno_it);

        //for each interval that lies within the current segment/fragement/alignment
        while(act_pos < end_pos)
        {
            //get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
            TVertexDescriptor act_knot = findVertex(ali_g,seq_id,act_pos);

            String<TLabel> property = getProperty(pm, act_knot);
            appendValue(property,label_);
            assignProperty(pm, act_knot, property);
            SEQAN_ASSERT(fragmentBegin(ali_g,act_knot)==act_pos);

            //prepare for next interval
            act_pos += fragmentLength(ali_g,act_knot);
        }
        ++anno_it;

    }



}

// edgescore = alignmentscore * annoscore
// compute annotation score: 2 if vd1 and vd2 share same annotation
// 1 if they are not the same (--> edgescore = alignmentscore)
template<typename TAliGraph,typename TScore, typename TPropertyMap>
typename Value<TScore>::Type
_getRefinedAnnoScore(TAliGraph &,
             TPropertyMap & pm,
             typename VertexDescriptor<TAliGraph>::Type vd1,
             typename VertexDescriptor<TAliGraph>::Type vd2,
             TScore &)
{
    typedef typename Value<TPropertyMap>::Type TProperty;
    //typedef typename Value<TProperty>::Type TChar;
    typedef typename Iterator<TProperty,Standard>::Type TIterator;

    TIterator prop1_it = begin(property(pm,vd1),Standard());
    TIterator prop1_end = end(property(pm,vd1),Standard());
    while(prop1_it != prop1_end)
    {
        TIterator prop2_it = begin(property(pm,vd2),Standard());
        TIterator prop2_end = end(property(pm,vd2),Standard());
        while(prop2_it != prop2_end)
        {
            if(*prop2_it==*prop1_it)
                return 2;/*scoreMatch(score_type);*/
            ++prop2_it;
        }
        ++prop1_it;
    }
    return 1;

}

// default score 1 --> edgescore = alignmentscore
template<typename TAliGraph,typename TScore>
typename Value<TScore>::Type
_getRefinedAnnoScore(TAliGraph &,
             bool,
             typename VertexDescriptor<TAliGraph>::Type,
             typename VertexDescriptor<TAliGraph>::Type,
             TScore &)
{
    return (typename Value<TScore>::Type) 1;
}




//annotation given,exact refinement, score type given
template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TAnnoString,typename TOutGraph, typename TSequence, typename TSetSpec>
void
matchRefinement(TAlignmentString & alis,
                TAnnoString & anno,
                StringSet<TSequence, TSetSpec> & seq,
                Score<TScoreValue,TScoreSpec> & score_type,
                TOutGraph & ali_graph)
{
    //min_fragment_len = 1   ==> Exact cutting
    matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
}


//annotation given,score type given, min fragment length given, if > 1 ==> inexact refinement
template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TAnnoString, typename TOutGraph, typename TSequence, typename TSetSpec>
void
matchRefinement(TAlignmentString & alis,
                TAnnoString & anno,
                StringSet<TSequence, TSetSpec> & seq,
                Score<TScoreValue,TScoreSpec> & score_type,
                TOutGraph & ali_graph,
                unsigned int min_frag_len)
{
    if(min_frag_len > 1)
        matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,InexactRefinement());
    else
        matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,ExactRefinement());
}



//annotation given,score type not given, min fragment length given, if > 1 ==> inexact refinement
template<typename TAlignmentString, typename TOutGraph, typename TAnnoString, typename TSequence, typename TSetSpec>
void
matchRefinement(TAlignmentString & alis,
                TAnnoString & anno,
                StringSet<TSequence, TSetSpec> & seq,
                TOutGraph & ali_graph,
                unsigned int min_frag_len)
{
//    Score<int,FakeScore > fake_score;
    typename Cargo<TOutGraph>::Type fake_score = 1;
    if(min_frag_len > 1)
        matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,InexactRefinement());
    else
        matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,ExactRefinement());
}



//annotation given,exact refinement, score type not given
template<typename TAlignmentString,typename TAnnoString, typename TOutGraph, typename TSequence, typename TSetSpec>
void
matchRefinement(TAlignmentString & alis,
                TAnnoString & anno,
                StringSet<TSequence, TSetSpec> & seq,
                TOutGraph & ali_graph)
{
//    Score<int,FakeScore > fake_score;
    typename Cargo<TOutGraph>::Type fake_score = 1;
    matchRefinement(alis,seq,fake_score,ali_graph,1,anno,ExactRefinement());
}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
