#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"

ReadAlign::ReadAlign (Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk) 
                    : mapGen(genomeIn), P(Pin), chunkTr(TrIn) 
{                           
    readNmates=P.readNmates;
    winBin = new uintWinBin* [2];  
    winBin[0] = new uintWinBin [P.winBinN];
    winBin[1] = new uintWinBin [P.winBinN];
    memset(winBin[0],255,sizeof(winBin[0][0])*P.winBinN);
    memset(winBin[1],255,sizeof(winBin[0][0])*P.winBinN);
    //RNGs
    rngMultOrder.seed(P.runRNGseed*(iChunk+1));
    rngUniformReal0to1=std::uniform_real_distribution<double> (0.0, 1.0);
    //transcriptome
    if ( P.quant.trSAM.yes ) {
        alignTrAll=new Transcript [P.alignTranscriptsPerReadNmax];
    };
    //split
    splitR=new uint*[3];
    splitR[0]=new uint[P.maxNsplit]; splitR[1]=new uint[P.maxNsplit]; splitR[2]=new uint[P.maxNsplit];
    //alignments
    PC=new uiPC[P.seedPerReadNmax];
    WC=new uiWC[P.alignWindowsPerReadNmax];
    nWA=new uint[P.alignWindowsPerReadNmax];
    nWAP=new uint[P.alignWindowsPerReadNmax];
    WALrec=new uint[P.alignWindowsPerReadNmax];
    WlastAnchor=new uint[P.alignWindowsPerReadNmax];

#ifdef COMPILE_FOR_LONG_READS
    swWinCov = new uint[P.alignWindowsPerReadNmax];
    scoreSeedToSeed = new intScore [P.seedPerWindowNmax*(P.seedPerWindowNmax+1)/2];
    scoreSeedBest = new intScore [P.seedPerWindowNmax];
    scoreSeedBestInd = new uint [P.seedPerWindowNmax];
    scoreSeedBestMM = new uint [P.seedPerWindowNmax];
    seedChain = new uint [P.seedPerWindowNmax];
#endif

    WA=new uiWA*[P.alignWindowsPerReadNmax];
    for (uint ii=0;ii<P.alignWindowsPerReadNmax;ii++) 
        WA[ii]=new uiWA[P.seedPerWindowNmax];
    WAincl = new bool [P.seedPerWindowNmax];
    trAll = new Transcript**[P.alignWindowsPerReadNmax+1];
    nWinTr = new uint[P.alignWindowsPerReadNmax];
    trArray = new Transcript[P.alignTranscriptsPerReadNmax];
    trArrayPointer =  new Transcript*[P.alignTranscriptsPerReadNmax];
    for (uint ii=0;ii<P.alignTranscriptsPerReadNmax;ii++) 
        trArrayPointer[ii]= &(trArray[ii]);
    trInit = new Transcript;
    //read
    Read0 = new char*[2];
    Read0[0]  = new char [DEF_readSeqLengthMax+1];
    Read0[1]  = new char [DEF_readSeqLengthMax+1];
    Qual0 = new char*[2];
    Qual0[0]  = new char [DEF_readSeqLengthMax+1];
    Qual0[1]  = new char [DEF_readSeqLengthMax+1];
    readNameMates=new char* [P.readNmates];
    for (uint ii=0; ii<P.readNmates; ii++) {
        readNameMates[ii]=new char [DEF_readNameLengthMax];
    };
    readNameExtra.resize(P.readNmates);
    readName = readNameMates[0];
    Read1 = new char*[3];
    Read1[0]=new char[DEF_readSeqLengthMax+1]; Read1[1]=new char[DEF_readSeqLengthMax+1]; Read1[2]=new char[DEF_readSeqLengthMax+1];
    Qual1=new char*[2]; //modified QSs for scoring
    Qual1[0]=new char[DEF_readSeqLengthMax+1]; Qual1[1]=new char[DEF_readSeqLengthMax+1];    
    //outBAM
    outBAMoneAlignNbytes = new uint [P.readNmates+2]; //extra piece for chimeric reads
    outBAMoneAlign = new char* [P.readNmates+2]; //extra piece for chimeric reads
    for (uint ii=0; ii<P.readNmates+2; ii++) {
        outBAMoneAlign[ii]=new char [BAMoutput_oneAlignMaxBytes];
    };
    resetN();
    //chim
    chunkOutChimJunction = new fstream;
    chimDet = new ChimericDetection(P, trAll, nWinTr, Read1, mapGen, chunkOutChimJunction, this);
    //solo
    soloRead = new SoloRead (P, iChunk);
};

void ReadAlign::resetN () {//reset resets the counters to 0 for a new read
    mapMarker=0;
    nA=0;nP=0;nW=0;
    nTr=0;nTrMate=0;
    nUM[0]=0;nUM[1]=0;
    storedLmin=0; uniqLmax=0; uniqLmaxInd=0; multLmax=0; multLmaxN=0; multNminL=0; multNmin=0; multNmax=0; multNmaxL=0;
    chimN=0;

    for (uint ii=0; ii<P.readNmates; ii++) {
        maxScoreMate[ii]=0;
    };

//     for (uint ii=0;ii<P.alignTranscriptsPerReadNmax;ii++) trArrayPointer[ii]= &(trArray[ii]);

};