Removing old version of mafft to replace with the new

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

diff --git a/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.cpp b/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.cpp
deleted file mode 100644 (file)
index 340353f..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.cpp
+++ /dev/null
@@ -1,211 +0,0 @@
-#include "AlifoldMEA.h"
-
-namespace MXSCARNA{
-
-const int AlifoldMEA::TURN = 3;
-
-void
-AlifoldMEA::
-Run()
-{
-    makeProfileBPPMatrix(alignment);
-    Initialization();
-    DP();
-    TraceBack();
-}
-
-void
-AlifoldMEA::
-makeProfileBPPMatrix(const MultiSequence *Sequences)
-{
-    int length = Sequences->GetSequence(0)->GetLength();
-
-    Trimat<float> *consBppMat = new Trimat<float>(length + 1);
-    fill(consBppMat->begin(), consBppMat->end(), 0);
-
-    for(int i = 1; i <= length; i++) 
-       for (int j = i; j <= length; j++) 
-           bppMat.ref(i, j) = 0;
-
-
-    int number = Sequences->GetNumSequences();
-    for(int seqNum = 0; seqNum < number; seqNum++) {
-       SafeVector<int> *tmpMap = Sequences->GetSequence(seqNum)->GetMappingNumber();
-       int label = Sequences->GetSequence(seqNum)->GetLabel();
-       BPPMatrix *tmpBppMatrix = BPPMatrices[label];
-       
-       for(int i = 1; i <= length ; i++) {
-           int originI = tmpMap->at(i);
-           for(int j = i; j <= length; j++) {
-               int originJ = tmpMap->at(j);
-               if(originI != 0 && originJ != 0) {
-                   float tmpProb = tmpBppMatrix->GetProb(originI, originJ);
-                   bppMat.ref(i, j) += tmpProb;
-               }
-           }
-       }
-    }
-
-       /* compute the mean of base pairing probability  */
-    for(int i = 1; i <= length; i++) {
-       for(int j = i; j <= length; j++) {
-           bppMat.ref(i,j) = bppMat.ref(i,j)/(float)number;
-       }
-    }
-
-    for (int i = 1; i <= length; i++) {
-       float sum = 0;
-       for (int j = i; j <= length; j++) {
-           sum += bppMat.ref(i,j);
-       }
-       Qi[i] = 1 - sum;
-    }
-
-    for (int i = 1; i <= length; i++) {
-       float sum = 0;
-       for (int j = i; j >= 1; j--) {
-           sum += bppMat.ref(j, i);
-       }
-       Qj[i] = 1 - sum;
-    }
-}
-
-void
-AlifoldMEA::
-Initialization()
-{
-    int length = alignment->GetSequence(0)->GetLength();
-
-    for (int i = 1; i <= length; i++) {
-       for (int j = i; j <= length; j++) {
-           M.ref(i,j) = 0;
-           traceI.ref(i,j) = 0;
-           traceJ.ref(i,j) = 0;
-       }
-    }
-
-    for (int i = 1; i <= length; i++) {
-       M.ref(i,i)   = Qi[i]; 
-       traceI.ref(i,i) = 0;
-       traceJ.ref(i,i) = 0;
-    }
-
-    for (int i = 1; i <= length - 1; i++) {
-       M.ref(i, i+1) =  Qi[i+1];
-       traceI.ref(i,i + 1) = 0;
-       traceJ.ref(i,i + 1) = 0;
-    }
-
-    for (int i = 0; i <= length; i++) {
-       ssCons[i] = '.';
-    }
-}
-
-void
-AlifoldMEA::
-DP()
-{
-    float g    = BasePairConst; // see scarna.hpp
-    int length = alignment->GetSequence(0)->GetLength();
-    
-    for (int i = length - 1; i >= 1; i--) {
-       for (int j = i + TURN + 1; j <= length; j++) {
-           float qi       = Qi[i];
-           float qj       = Qj[j];
-           float p        = bppMat.ref(i,j);
-
-           
-           float maxScore = qi + M.ref(i+1, j);
-           int tmpI = i+1;
-           int tmpJ = j;
-           
-           float tmpScore = qj + M.ref(i, j-1);
-           if (tmpScore > maxScore) {
-               maxScore = tmpScore;
-               tmpI     = i;
-               tmpJ     = j - 1;
-           }
-           
-           tmpScore = g*2*p + M.ref(i+1, j-1);
-           if (tmpScore > maxScore) {
-               maxScore = tmpScore;
-               tmpI     = i + 1;
-               tmpJ     = j - 1;
-           }
-           
-           for (int k = i + 1; k < j - 1; k++) {
-               tmpScore = M.ref(i,k) + M.ref(k+1,j);
-               if (tmpScore > maxScore) {
-                   maxScore = tmpScore;
-                   tmpI = i;
-                   tmpJ = j;
-               }
-           }
-           M.ref(i,j)       = maxScore;
-           traceI.ref(i, j) = tmpI;
-           traceJ.ref(i, j) = tmpJ;
-       }
-    }
-}
-
-void
-AlifoldMEA::
-TraceBack()
-{
-
-    int length = alignment->GetSequence(0)->GetLength();
-    SafeVector<int> stackI((length + 1)*(length+1));
-    SafeVector<int> stackJ((length + 1)*(length+1));
-    int pt = 0;
-
-    stackI[pt] = traceI.ref(1, length);
-    stackJ[pt] = traceJ.ref(1, length);
-    ++pt;
-    
-    while(pt != 0) {
-       --pt;
-       int tmpI = stackI[pt];
-       int tmpJ = stackJ[pt];
-       int nextI = traceI.ref(tmpI, tmpJ);
-       int nextJ = traceJ.ref(tmpI, tmpJ);
-
-       if (tmpI < tmpJ) {
-           if (tmpI + 1  == nextI && tmpJ == nextJ) {
-               stackI[pt] = nextI;
-               stackJ[pt] = nextJ;
-               ++pt;
-           }
-           else if (tmpI == nextI && tmpJ - 1 == nextJ) {
-               stackI[pt] = nextI;
-               stackJ[pt] = nextJ;
-               ++pt;
-           }
-           else if (tmpI + 1 == nextI && tmpJ - 1== nextJ) {
-               stackI[pt] = nextI;
-               stackJ[pt] = nextJ;
-               ++pt;
-               ssCons[tmpI] = '(';
-               ssCons[tmpJ] = ')';
-           }
-           else if (tmpI == nextI && tmpJ == nextJ) {
-               float maxScore = IMPOSSIBLE;
-               int maxK = 0;
-
-               for (int k = tmpI + 1; k < tmpJ - 1; k++) {
-                   float tmpScore = M.ref(tmpI,k) + M.ref(k+1,tmpJ);
-                   if (tmpScore > maxScore) {
-                       maxScore = tmpScore;
-                       maxK = k;
-                   }
-               }
-               stackI[pt] = traceI.ref(tmpI, maxK);
-               stackJ[pt] = traceJ.ref(tmpI, maxK);
-               ++pt;
-               stackI[pt] = traceI.ref(maxK+1, tmpJ);
-               stackJ[pt] = traceJ.ref(maxK+1, tmpJ);
-               ++pt;
-           }
-       }
-    }
-}
-}