// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
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// SUCH DAMAGE.

// Author: Patrick Marks, David Alexander

#include <ConsensusCore/Mutation.hpp>

#include <algorithm>
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
#include <cassert>
#include <string>
#include <vector>

#include <iomanip>
#include <iostream>
#include <sstream>

#include <ConsensusCore/Types.hpp>
#include <ConsensusCore/Utils.hpp>
#include <ConsensusCore/Align/PairwiseAlignment.hpp>

using std::max;

namespace ConsensusCore
{
    std::string
    Mutation::ToString() const
    {
        using boost::str;
        using boost::format;

        switch (Type())
        {
            case INSERTION:
                return str(format("Insertion (%s) @%d") % newBases_ % start_);
            case DELETION:
                return str(format("Deletion @%d:%d") % start_ % end_);
            case SUBSTITUTION:
                return str(format("Substitution (%s) @%d:%d") % newBases_ % start_ % end_);
            default: ShouldNotReachHere();
        }
    }

    std::ostream& operator<<(std::ostream& out, const Mutation& m)
    {
        out << m.ToString();
        return out;
    }


    ScoredMutation Mutation::WithScore(float score) const
    {
        return ScoredMutation(*this, score);
    }


    static void
    _ApplyMutationInPlace(const Mutation& mut, int start, std::string* tpl)
    {
        if (mut.IsSubstitution())
        {
            (*tpl).replace(start, mut.End() - mut.Start(), mut.NewBases());
        }
        else if (mut.IsDeletion())
        {
            (*tpl).erase(start, mut.End() - mut.Start());
        }
        else if (mut.IsInsertion())
        {
            (*tpl).insert(start, mut.NewBases());
        }
    }

    std::string
    ApplyMutation(const Mutation& mut, const std::string& tpl)
    {
        std::string tplCopy(tpl);
        _ApplyMutationInPlace(mut, mut.Start(), &tplCopy);
        return tplCopy;
    }

    std::string
    ApplyMutations(const std::vector<Mutation>& muts, const std::string& tpl)
    {
        std::string tplCopy(tpl);
        std::vector<Mutation> sortedMuts(muts);
        std::sort(sortedMuts.begin(), sortedMuts.end());
        int runningLengthDiff = 0;
        foreach (const Mutation& mut, sortedMuts)
        {
            _ApplyMutationInPlace(mut, mut.Start() + runningLengthDiff, &tplCopy);
            runningLengthDiff += mut.LengthDiff();
        }
        return tplCopy;
    }

    std::string MutationsToTranscript(const std::vector<Mutation>& mutations,
                                      const std::string& tpl)
    {
        std::vector<Mutation> sortedMuts(mutations);
        std::sort(sortedMuts.begin(), sortedMuts.end());

        // Build an alignnment transcript corresponding to these mutations.
        int tpos = 0;
        std::string transcript = "";
        foreach (const Mutation& m, sortedMuts)
        {
            for (; tpos < m.Start(); ++tpos)
            {
                transcript.push_back('M');
            }

            if (m.IsInsertion())
            {
                transcript += std::string(m.LengthDiff(), 'I');
            }
            else if (m.IsDeletion())
            {
                transcript += std::string(-m.LengthDiff(), 'D');
                tpos += -m.LengthDiff();
            }
            else if (m.IsSubstitution())
            {
                int len = m.End() - m.Start();
                transcript += std::string(len, 'R');
                tpos += len;
            }
            else
            {
                ShouldNotReachHere();
            }
        }
        for (; tpos < (int)tpl.length(); ++tpos)
        {
            transcript.push_back('M');
        }
        return transcript;
    }

    // MutatedTemplatePositions:
    //  * Returns a vector of length (tpl.length()+1), which, roughly speaking,
    //    indicates the positions in the mutated template tpl' of the characters
    //    in tpl.
    //  * More precisely, for any slice [s, e) of tpl, letting:
    //      - t[s, e) denote the induced substring of the template;
    //      - m[s, e) denote the subvector of mutations with Position
    //        in [s, e);
    //      - t' denote the mutated template; and
    //      - t[s, e)' denote the result of applying mutation m[s, e) to t[s, e),
    //    the resultant vector mtp satisfies t'[mtp[s], mtp[e]) == t[s,e)'.
    //  * Example:
    //               01234567                           0123456
    //              "GATTACA" -> (Del T@2, Ins C@5) -> "GATACCA";
    //    here mtp = 01223567, which makes sense, because for instance:
    //      - t[0,3)=="GAT" has become t'[0,2)=="GA";
    //      - t[0,2)=="GA"  remains "GA"==t'[0,2);
    //      - t[4,7)=="ACA" has become t[3,7)=="ACCA",
    //      - t[5,7)=="CA"  remains "CA"==t'[5,7).
    //
    std::vector<int> TargetToQueryPositions(const std::vector<Mutation>& mutations,
                                            const std::string& tpl)
    {
        return TargetToQueryPositions(MutationsToTranscript(mutations, tpl));
    }


    ScoredMutation::ScoredMutation(const Mutation& m, float score)
        : Mutation(m),
          score_(score)
    {}

    ScoredMutation::ScoredMutation()
        : Mutation(),
          score_(0)
    {}

    float ScoredMutation::Score() const
    {
        return score_;
    }

    std::string ScoredMutation::ToString() const
    {
        std::stringstream ss;
        ss << *this;
        return ss.str();
    }

    std::ostream& operator<<(std::ostream& out, const ScoredMutation& m)
    {
        out << m.Mutation::ToString() << " " << boost::format("%0.2f") % m.Score();
        return out;
    }
}
