remove mafft extensions - we do not support them

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / BPPMatrix.hpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/BPPMatrix.hpp b/binaries/src/mafft/extensions/mxscarna_src/BPPMatrix.hpp
deleted file mode 100644 (file)
index 1c16ed7..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/BPPMatrix.hpp
+++ /dev/null
@@ -1,130 +0,0 @@
-//////////////////////////////////////////////////////////////
-// BPPMatrix.hpp
-//
-// save the Base Pairing Probability Matrix for each sequences
-//////////////////////////////////////////////////////////////
-
-#ifndef __BBPMatrix_HPP__
-#define __BBPMatrix_HPP__
-
-#include <iostream>
-#include <string>
-#include "SparseMatrix.h"
-#include "McCaskill.hpp"
-#include "nrutil.h"
-
-
-
-using namespace std;
-
-namespace MXSCARNA{
-class BPPMatrix {
-private:
-
-    int seqLength;       // sequence length;
-    float cutOff;        // the threshold of probability 
-
-    BPPMatrix() {}
-public:
-    SparseMatrix bppMat; // base pairing probability matrix 1-origin(1..seqLength)
-    BPPMatrix(int bppmode, const string &seq, int seqLength, float inCutOff = 0.0001) : seqLength (seqLength), cutOff(inCutOff) {
-      if( bppmode == 'r' ) // by katoh
-        readBPPMatrix(seq);
-      else if( bppmode == 'w' )
-        setandwriteBPPMatrix(seq);
-      else
-        setBPPMatrix(seq);
-    }
-    BPPMatrix(int seqLength, float inCutOff, const Trimat<float> & tmpBppMat) : seqLength(seqLength), cutOff(inCutOff) {
-      bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
-    }
-
-      
-    void setBPPMatrix(const string &seq) {
-       const char *tmpSeq = seq.c_str();
-       McCaskill mc(seqLength, &tmpSeq[1]);
-       mc.calcPartitionFunction();
-       Trimat<float> tmpBppMat(seqLength + 1);
-
-       for (int i = 0; i < seqLength; i++) {
-         for(int j = i; j < seqLength; j++) {
-           tmpBppMat.ref(i+1, j+1) = mc.getProb(i,j);
-         }
-       }
-       bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
-    }
-
-    void setandwriteBPPMatrix(const string &seq) { // by katoh
-        const char *tmpSeq = seq.c_str();
-       McCaskill mc(seqLength, &tmpSeq[1]);
-       mc.calcPartitionFunction();
-       Trimat<float> tmpBppMat(seqLength + 1);
-        float tmpbp;
-
-        fprintf( stdout, ">\n" );
-       for (int i = 0; i < seqLength; i++) {
-         for(int j = i; j < seqLength; j++) {
-        tmpbp = mc.getProb(i,j);
-        if (tmpbp > 0.0001)
-          fprintf( stdout, "%d %d %50.40f\n", i, j, tmpbp );
-           tmpBppMat.ref(i+1, j+1) = tmpbp;
-         }
-       }
-       bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
-    }
-
-    void readBPPMatrix(const string &seq) { // by katoh
-       const char *tmpSeq = seq.c_str();
-       char oneline[1000];
-       int onechar;
-       float prob;
-       int posi, posj;
-       static FILE *bppfp = NULL;
-
-
-       if( bppfp == NULL )
-       {
-               bppfp = fopen( "_bpp", "r" );
-               if( bppfp == NULL )
-               {
-                       fprintf( stderr, "Cannot open _bpp.\n" );
-                       exit( 1 );
-               }
-       }
-
-       Trimat<float> tmpBppMat(seqLength + 1);
-       fgets( oneline, 999, bppfp );
-       if( oneline[0] != '>' )
-       {
-               fprintf( stderr, "Format error\n" );
-               exit( 1 );
-       }
-       while( 1 )
-       {
-               onechar = getc( bppfp ); 
-               ungetc( onechar, bppfp );
-               if( onechar == '>' || onechar == EOF ) break;
-
-               fgets( oneline, 999, bppfp );
-               sscanf( oneline, "%d %d %f", &posi, &posj, &prob );
-//             fprintf( stderr, "%d %d -> %f\n", posi, posj, prob );
-               tmpBppMat.ref(posi+1, posj+1) = prob;
-       }
-
-       bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
-    }
-
-    float GetProb(int i, int j) {
-       return bppMat.GetValue(i,j);
-    }
-
-    float GetLength() const {
-       return seqLength;
-    }
-    
-    void updateBPPMatrix(const Trimat<float> &inbppMat) {
-       bppMat.SetSparseMatrix(seqLength, seqLength, inbppMat, cutOff);
-    }
-};
-}
-#endif // __BPPMatrix_HPP__