remove mafft extensions - we do not support them

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / AlifoldMEA.h

diff --git a/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h b/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h
deleted file mode 100644 (file)
index 02c06c5..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#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_