binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h

   1 #ifndef _ALIFOLDMEA_H_
   2 #define _ALIFOLDMEA_H_
   3
   4 #include <iostream>
   5 #include <string>
   6 #include <cassert>
   7 #include "scarna.hpp"
   8 #include "nrutil.h"
   9 #include "Util.hpp"
  10 #include "Beta.hpp"
  11 #include "BPPMatrix.hpp"
  12 #include "MultiSequence.h"
  13 #include "Sequence.h"
  14 #include "SafeVector.h"
  15
  16 using namespace std;
  17
  18 namespace MXSCARNA {
  19 class AlifoldMEA {
  20     MultiSequence *alignment;
  21     SafeVector<BPPMatrix*> BPPMatrices;
  22     float BasePairConst;
  23     Trimat<float> M;
  24     Trimat<int> traceI;
  25     Trimat<int> traceJ;
  26     Trimat<float> bppMat;
  27     NRVec<float>  Qi;
  28     NRVec<float>  Qj;
  29     NRVec<char> ssCons;
  30
  31     static const int TURN;
  32
  33     void Initialization();
  34     void makeProfileBPPMatrix(const MultiSequence *Sequences);
  35     void DP();
  36     void TraceBack();
  37  public:
  38     AlifoldMEA(MultiSequence *inalignment, SafeVector<BPPMatrix*> &inBPPMatrices, float inBasePairConst = 6) :
  39         alignment(inalignment), BPPMatrices(inBPPMatrices),
  40         BasePairConst(inBasePairConst),
  41         M(inalignment->GetSequence(0)->GetLength()+1),
  42         traceI(inalignment->GetSequence(0)->GetLength()+1),
  43         traceJ(inalignment->GetSequence(0)->GetLength()+1),
  44         bppMat(inalignment->GetSequence(0)->GetLength() + 1),
  45         Qi(inalignment->GetSequence(0)->GetLength() + 1),
  46         Qj(inalignment->GetSequence(0)->GetLength() + 1),
  47         ssCons(inalignment->GetSequence(0)->GetLength() + 1){}
  48
  49     void Run();
  50
  51     string *getSScons() {
  52         string *sscons = new string();
  53         sscons->push_back(' ');
  54         int length = alignment->GetSequence(0)->GetLength();
  55         for (int i = 1; i <= length; i++) {
  56             sscons->push_back(ssCons[i]);
  57         }
  58
  59         return sscons;
  60     }
  61 };
  62 }
  63 #endif // _ALIFOLDMEA_H_