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// Author: David Alexander

#include <ConsensusCore/Poa/PoaConsensus.hpp>

#include <boost/algorithm/string.hpp>
#include <boost/foreach.hpp>
#include <boost/tuple/tuple.hpp>
#include <string>
#include <utility>
#include <vector>

#include <ConsensusCore/Align/AlignConfig.hpp>
#include <ConsensusCore/Utils.hpp>

using boost::tie;

namespace ConsensusCore
{
    AlignConfig DefaultPoaConfig(AlignMode mode)
    {
        AlignParams params(3, -5, -4, -4);
        AlignConfig config(params, mode);
        return config;
    }

    PoaConsensus::PoaConsensus(const std::string& css,
                               const PoaGraph& g,
                               const std::vector<size_t>& cssPath)
        : Sequence(css), Graph(g), Path(cssPath)
    {}

    PoaConsensus::PoaConsensus(const std::string& css,
                               const detail::PoaGraphImpl& gi,
                               const std::vector<size_t>& cssPath)
        : Sequence(css), Graph(gi), Path(cssPath)
    {}

    PoaConsensus::~PoaConsensus()
    {}

    const PoaConsensus*
    PoaConsensus::FindConsensus(const std::vector<std::string>& reads)
    {
        return FindConsensus(reads, DefaultPoaConfig(GLOBAL), -INT_MAX);
    }

    const PoaConsensus*
    PoaConsensus::FindConsensus(const std::vector<std::string>& reads,
                                const AlignConfig& config,
                                int minCoverage)
    {
        PoaGraph pg;
        foreach (const std::string& read, reads)
        {
            if (read.length() == 0)
            {
                throw InvalidInputError("Input sequences must have nonzero length.");
            }
            pg.AddRead(read, config);
        }
        return pg.FindConsensus(config, minCoverage);
    }

    const PoaConsensus*
    PoaConsensus::FindConsensus(const std::vector<std::string>& reads,
                                AlignMode mode,
                                int minCoverage)
    {
        return FindConsensus(reads, DefaultPoaConfig(mode), minCoverage);
    }

    std::string
    PoaConsensus::ToGraphViz(int flags) const
    {
        return Graph.ToGraphViz(flags, this);
    }

    void
    PoaConsensus::WriteGraphVizFile(std::string filename, int flags) const
    {
        Graph.WriteGraphVizFile(filename, flags, this);
    }
}
