source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/AlifoldMEA.h

#ifndef _ALIFOLDMEA_H_
#define _ALIFOLDMEA_H_

#include <iostream>
#include <string>
#include <cassert>
#include "scarna.hpp"
#include "nrutil.h"
#include "Util.hpp"
#include "Beta.hpp"
#include "BPPMatrix.hpp"
#include "MultiSequence.h"
#include "Sequence.h"
#include "SafeVector.h"

using namespace std;

namespace MXSCARNA {
class AlifoldMEA {
    MultiSequence *alignment;
    SafeVector<BPPMatrix*> BPPMatrices;
    float BasePairConst;
    Trimat<float> M;
    Trimat<int> traceI;
    Trimat<int> traceJ;
    Trimat<float> bppMat;
    NRVec<float>  Qi;
    NRVec<float>  Qj;
    NRVec<char> ssCons;
    
    static const int TURN;

    void Initialization();
    void makeProfileBPPMatrix(const MultiSequence *Sequences);
    void DP();
    void TraceBack();
 public:
    AlifoldMEA(MultiSequence *inalignment, SafeVector<BPPMatrix*> &inBPPMatrices, float inBasePairConst = 6) :
        alignment(inalignment), BPPMatrices(inBPPMatrices),
        BasePairConst(inBasePairConst),
        M(inalignment->GetSequence(0)->GetLength()+1), 
        traceI(inalignment->GetSequence(0)->GetLength()+1),
        traceJ(inalignment->GetSequence(0)->GetLength()+1),
        bppMat(inalignment->GetSequence(0)->GetLength() + 1), 
        Qi(inalignment->GetSequence(0)->GetLength() + 1), 
        Qj(inalignment->GetSequence(0)->GetLength() + 1), 
        ssCons(inalignment->GetSequence(0)->GetLength() + 1){}

    void Run();

    string *getSScons() {
        string *sscons = new string();
        sscons->push_back(' ');
        int length = alignment->GetSequence(0)->GetLength();
        for (int i = 1; i <= length; i++) {
            sscons->push_back(ssCons[i]);
        }
        
        return sscons;
    }
};
}
#endif // _ALIFOLDMEA_H_