/**
>HEADER
    Copyright (c) 2013 Rob Patro robp@cs.cmu.edu

    This file is part of Sailfish.

    Sailfish is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Sailfish is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Sailfish.  If not, see <http://www.gnu.org/licenses/>.
<HEADER
**/


#ifndef TRANSCRIPT_GENE_MAP_HPP
#define TRANSCRIPT_GENE_MAP_HPP

// Allows for the serialization of this class
#include <cereal/archives/binary.hpp>
#include <cereal/types/vector.hpp>
#include <cereal/types/string.hpp>

#include <algorithm>
#include <unordered_map>
#include <vector>

class TranscriptGeneMap {
using Index = size_t;
using Size = size_t;
using NameVector = std::vector<std::string>;
using IndexVector = std::vector<size_t>;
using IndexVectorList = std::vector<std::vector<size_t>>;

private:
    NameVector _transcriptNames;
    NameVector _geneNames;
    IndexVector _transcriptsToGenes;
    IndexVectorList _genesToTranscripts;
    bool _haveReverseMap;

    void _computeReverseMap() {

        _genesToTranscripts.resize( _geneNames.size(), {});

        Index transcriptID = 0;
        size_t maxNumTrans = 0;
        Index maxGene;
        for ( transcriptID = 0; transcriptID < _transcriptsToGenes.size(); ++transcriptID ) {
            _genesToTranscripts[ _transcriptsToGenes[transcriptID] ].push_back( transcriptID );
            if ( maxNumTrans < _genesToTranscripts[ _transcriptsToGenes[transcriptID] ].size() ) {
                maxNumTrans = _genesToTranscripts[ _transcriptsToGenes[transcriptID] ].size();
                maxGene = _transcriptsToGenes[transcriptID];
            }
        }
        std::cerr << "max # of transcripts in a gene was " << maxNumTrans << " in gene " << _geneNames[maxGene] << "\n";
    }

    friend class cereal::access;

    template<class Archive>
    void serialize(Archive & ar, const unsigned int version)
    {
        ar(_transcriptNames, _geneNames, _transcriptsToGenes,
           _genesToTranscripts, _haveReverseMap);
    }

public:
    TranscriptGeneMap() :
        _transcriptNames(NameVector()), _geneNames(NameVector()),
        _transcriptsToGenes(IndexVector()), _haveReverseMap(false) {}


    TranscriptGeneMap( const NameVector &transcriptNames,
                       const NameVector &geneNames,
                       const IndexVector &transcriptsToGenes ) :
        _transcriptNames(transcriptNames), _geneNames(geneNames),
        _transcriptsToGenes(transcriptsToGenes), _haveReverseMap(false) {}


    TranscriptGeneMap(const TranscriptGeneMap& other) = default;
    TranscriptGeneMap& operator=(const TranscriptGeneMap& other) = default;


    Index INVALID { std::numeric_limits<Index>::max() };

    Index findTranscriptID( const std::string &tname ) {
        using std::distance;
        using std::lower_bound;
        auto it = lower_bound( _transcriptNames.begin(), _transcriptNames.end(), tname );
        return ( it == _transcriptNames.end() ) ? INVALID : ( distance(_transcriptNames.begin(), it) );
    }

    Size numTranscripts() {
        return _transcriptNames.size();
    }
    Size numGenes() {
        return _geneNames.size();
    }

    bool needReverse() {
        if ( _haveReverseMap ) {
            return false;
        } else {
            _computeReverseMap();
            return true;
        }
    }

    const IndexVector &transcriptsForGene( Index geneID ) {
        return _genesToTranscripts[geneID];
    }

    inline std::string nameFromGeneID( Index geneID ) {
        return _geneNames[geneID];
    }
    inline Index gene( Index transcriptID ) {
        return _transcriptsToGenes[transcriptID];
    }
    inline std::string geneName( Index transcriptID ) {
        return _geneNames[_transcriptsToGenes[transcriptID]];
    }
    inline std::string geneName (const std::string& transcriptName,
                                 bool complain=true) {
        auto tid = findTranscriptID(transcriptName);
        if (tid != INVALID) {
            return geneName(tid);
        } else {
            std::cerr << "WARNING: couldn't find transcript named ["
                      << transcriptName << "]; returning transcript "
                      << " as it's own gene\n";
            return transcriptName;
        }
    }

    inline std::string transcriptName( Index transcriptID ) {
        return _transcriptNames[transcriptID];
    }
};

#endif // TRANSCRIPT_GENE_MAP_HPP
