virtual void processNode(InternalNode &u) 
  {
    int id=u.getID();
    Array2D<double>::RowIn2DArray<double> row=L[id];
    Taxon *taxon=static_cast<Taxon*>(u.getDecoration());
    SubstitutionMatrix &leftPt=getMatrix(*taxon,LEFT);
    SubstitutionMatrix &rightPt=getMatrix(*taxon,RIGHT);
    int left=u.getLeft()->getID(), right=u.getRight()->getID();
    for(Symbol a=0 ; a<numAlpha ; ++a)
	if(a!=gap) row[a]=
	  processInternalChild(a,left,leftPt)+
	  processInternalChild(a,right,rightPt);
  }
Beispiel #2
0
 void processNode(InternalNode &v) {
   Taxon &taxon=*static_cast<Taxon*>(v.getDecoration());
   cout<<"  LLL "<<taxon.getName()<<"="<<taxon.getSeqLen()<<endl;
 }
Beispiel #3
0
      void processNode(InternalNode &v) {
	Taxon &taxon=*static_cast<Taxon*>(v.getDecoration());
	//cout<<"extending "<<taxon.getName()<<" "<<taxon.getSeqLen()<<endl;
	taxon.getSeq()=Sequence(gapSymbol,taxon.getSeqLen());
      }