#ifndef MATCHER_H
#define MATCHER_H

//
// Written by Martin Steinegger & Maria Hauser, mhauser@genzentrum.lmu.de
//
// Calls SSE2 parallelized calculation of Smith-Waterman alignment and non-parallelized traceback afterwards.
//

#include <cfloat>
#include <algorithm>
#include <vector>
#include "itoa.h"

#include "Sequence.h"
#include "BaseMatrix.h"
#include "StripedSmithWaterman.h"
#include "EvalueComputation.h"
#include "BandedNucleotideAligner.h"

class Matcher{

public:
    static const unsigned int SCORE_ONLY = 0;
    static const unsigned int SCORE_COV = 1;
    static const unsigned int SCORE_COV_SEQID = 2;
    const static int ALN_RES_WITH_OUT_BT_COL_CNT = 10;

    const static int ALN_RES_WITH_BT_COL_CNT = 11;

    struct result_t {
        unsigned int dbKey;
        int score;
        float qcov;
        float dbcov;
        float seqId;
        double eval;
        unsigned int alnLength;
        int qStartPos;
        int qEndPos;
        unsigned int qLen;
        int dbStartPos;
        int dbEndPos;
        unsigned int dbLen;
        std::string backtrace;
        result_t(unsigned int dbkey,int score,
                 float qcov, float dbcov,
                 float seqId, double eval,
                 unsigned int alnLength,
                 int qStartPos,
                 int qEndPos,
                 unsigned int qLen,
                 int dbStartPos,
                 int dbEndPos,
                 unsigned int dbLen,
                 std::string backtrace) : dbKey(dbkey), score(score), qcov(qcov),
                                          dbcov(dbcov), seqId(seqId), eval(eval), alnLength(alnLength),
                                          qStartPos(qStartPos), qEndPos(qEndPos), qLen(qLen),
                                          dbStartPos(dbStartPos), dbEndPos(dbEndPos), dbLen(dbLen),
                                          backtrace(backtrace) {};
        
        result_t(){};

        static void swapResult(result_t & res, EvalueComputation &evaluer, bool hasBacktrace){
            double rawScore = evaluer.computeRawScoreFromBitScore(res.score);
            res.eval = evaluer.computeEvalue(rawScore, res.dbLen);

            unsigned int qstart = res.qStartPos;
            unsigned int qend = res.qEndPos;
            unsigned int qLen = res.qLen;
            res.qStartPos = res.dbStartPos;
            res.qEndPos = res.dbEndPos;
            res.qLen = res.dbLen;
            res.dbStartPos = qstart;
            res.dbEndPos = qend;
            res.dbLen = qLen;
            if (hasBacktrace) {
                for (size_t j = 0; j < res.backtrace.size(); j++) {
                    if (res.backtrace.at(j) == 'I') {
                        res.backtrace.at(j) = 'D';
                    } else if (res.backtrace.at(j) == 'D') {
                        res.backtrace.at(j) = 'I';
                    }
                }
            }
        }

        static void protein2nucl(std::string & backtrace, std::string &newBacktrace) {
            char buffer[256];
            for (size_t pos = 0; pos < backtrace.size(); pos++) {
                int cnt =0;
                if (isdigit(backtrace[pos])){
                    cnt += Util::fast_atoi<int>(backtrace.c_str()+pos);
                    while (isdigit(backtrace[pos])){
                        pos++;
                    }
                }
                bool update = false;
                switch (backtrace[pos]) {
                    case 'M':
                    case 'D':
                    case 'I':
                        update = true;
                        break;
                }
                if (update) {
                    char *buffNext = Itoa::i32toa_sse2(cnt*3, buffer);
                    size_t len = buffNext - buffer;
                    newBacktrace.append(buffer, len - 1);
                    newBacktrace.push_back(backtrace[pos]);
                }
            }
        }
    };

    Matcher(int querySeqType, int maxSeqLen, BaseMatrix *m,
            EvalueComputation * evaluer, bool aaBiasCorrection,
            int gapOpen, int gapExtend, int zdrop = 40);

    ~Matcher();

    // run SSE2 parallelized Smith-Waterman alignment calculation and traceback
    result_t getSWResult(Sequence* dbSeq, const int diagonal, bool isReverse, const int covMode, const float covThr, const double evalThr,
                         unsigned int alignmentMode, unsigned int seqIdMode, bool isIdentical, bool wrappedScoring=false);

    // need for sorting the results
    static bool compareHits (const result_t &first, const result_t &second){
        //return (first.eval < second.eval);
        if(first.eval < second.eval )
            return true;
        if(second.eval < first.eval )
            return false;
        if(first.score > second.score )
            return true;
        if(second.score > first.score )
            return false;
        if(first.dbLen < second.dbLen )
            return true;
        if(second.dbLen < first.dbLen )
            return false;
        if(first.dbKey < second.dbKey )
            return true;
        if(second.dbKey < first.dbKey )
            return false;
        return false;
    }
    static bool compareHitByPos(const result_t &first, const result_t &second){

        int firstQStartPos  = std::min( first.qStartPos, first.qEndPos);
        int secondQStartPos = std::min( second.qStartPos, second.qEndPos);
        if(secondQStartPos < firstQStartPos )
            return false;
        if(firstQStartPos < secondQStartPos)
            return true;
        return false;

    }
    // need for sorting the results
    static bool compareHitsByPosAndStrand (const result_t &first, const result_t &second){
        //return (first.eval < second.eval);
        if(second.dbKey < first.dbKey)
            return false;
        if(first.dbKey < second.dbKey)
            return true;
        bool qFirstRev = (first.qStartPos > first.qEndPos);
        bool qSecondRev = (second.qStartPos > second.qEndPos);
        if(qSecondRev < qFirstRev)
            return false;
        if(qFirstRev < qSecondRev)
            return true;
        bool dbFirstRev = (first.dbStartPos > first.dbEndPos);
        bool dbSecondRev = (second.dbStartPos > second.dbEndPos);
        if(dbSecondRev < dbFirstRev)
            return false;
        if(dbFirstRev < dbSecondRev)
            return true;
        int firstQStartPos  = std::min( first.qStartPos, first.qEndPos);
        int secondQStartPos = std::min( second.qStartPos, second.qEndPos);
        int firstDbStart    = std::min( first.dbStartPos, first.dbEndPos);
        int secondDbStart   = std::min( second.dbStartPos, second.dbEndPos);
        int firstDiagonal  = firstQStartPos - firstDbStart;
        int secondDiagonal = secondQStartPos - secondDbStart;
        if(secondDiagonal < firstDiagonal)
            return false;
        if(firstDiagonal < secondDiagonal)
            return true;
        if(secondDbStart < firstDbStart )
            return false;
        if(firstDbStart < secondDbStart)
            return true;
        return false;
    }

    // map new query into memory (create queryProfile, ...)
    void initQuery(Sequence* query);

    static result_t parseAlignmentRecord(const char *data, bool readCompressed=false);

    static void readAlignmentResults(std::vector<result_t> &result, char *data, bool readCompressed = false);

    static float estimateSeqIdByScorePerCol(uint16_t score, unsigned int qLen, unsigned int tLen);

    static std::string compressAlignment(const std::string &bt);

    static std::string uncompressAlignment(const std::string &cbt);


    static size_t resultToBuffer(char * buffer, const result_t &result, bool addBacktrace, bool compress  = true);

    static int computeAlnLength(int anEnd, int start, int dbEnd, int dbStart);


private:

    // costs to open a gap
    int gapOpen;
    // costs to extend a gap
    int gapExtend;

    // holds values of the current active query
    Sequence * currentQuery;

    // aligner Class
    SmithWaterman * aligner;
    // aligner for nucl
    BandedNucleotideAligner * nuclaligner;
    // substitution matrix
    BaseMatrix* m;
    // evalue
    EvalueComputation * evaluer;
    // byte version of substitution matrix
    int8_t * tinySubMat;
    // set substituion matrix
    void setSubstitutionMatrix(BaseMatrix *m);

};

#endif
