Example #1
0
  virtual void processNode(InternalNode &u) {
    int id=u.getID();
    PhylogenyNode *left=u.getLeft(), *right=u.getRight();
    NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
    NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
    Array2D<double>::RowIn2DArray<double> row=L[id];
    for(Symbol a=0 ; a<numAlpha ; ++a) {
      row[a]=
	processInternalChild(a,left,leftPt,&u)+
	processInternalChild(a,right,rightPt,&u);
    }
  }
Example #2
0
  virtual void processNode(InternalNode &u) {
    int id=u.getID();
    int left=u.getLeft()->getID(), right=u.getRight()->getID();
    NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
    NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
    Array2D<double>::RowIn2DArray<double> row=L[id];
    for(Symbol a=0 ; a<numAlpha ; ++a) {
      if(gapSymbols.isMember(a)) continue;
      row[a]=
	processInternalChild(a,left,leftPt,0,0)+
	processInternalChild(a,right,rightPt,0,0);
    }
  }
Example #3
0
  virtual void processNode(InternalNode &u) {
    int id=u.getID();
    Array2D<double>::RowIn2DArray<double> row=L[id];
    int left=u.getLeft()->getID(), right=u.getRight()->getID();
    NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
    NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
    Sequence nmer;
    for(int i=0 ; i<numNmers ; ++i) {
      nmer.fromInt(i,numCols,alphabetMap);
      row[i]=
	processInternalChild(nmer,left,leftPt)+
	processInternalChild(nmer,right,rightPt);
    }
  }
Example #4
0
  virtual void processNode(InternalNode &u) {
    int id=u.getID();
    NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
    NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
    int left=u.getLeft()->getID(), right=u.getRight()->getID();
    Array2D<double>::RowIn2DArray<double> row=L[id];
    Symbol a=A.getIthTrack(id)[column];
    if(gapSymbols.isMember(a))
      for(a=0 ; a<numAlpha ; ++a) {
	if(gapSymbols.isMember(a)) continue;
	row[a]=
	  processInternalChild(a,id,left,leftPt)+
	  processInternalChild(a,id,right,rightPt);
      }
    else {
      for(Symbol b=0 ; b<numAlpha ; ++b) row[b]=NEGATIVE_INFINITY;
      double l=processInternalChild(a,id,left,leftPt);
      double r=processInternalChild(a,id,right,rightPt);
      row[a]=l+r;
    }
  }