On Jun 23, 2006, at 10:49 PM, Bob Hanson wrote:
> simple things like this are possible; the bitset idea or atom  
> expression
> idea provides flexibility. If null, then it could certainly default to
> "replace all" but I thought we were interested in something that  
> didn't
> necessarily replace all.
>

true, something more generally applicable would be better. still,  
what about the case where an atom may be added or deleted? i suppose  
that at the beginning of the method we could have something like this:

   void replaceCoords(BitSet atomList, Point3f[] coordList) {
     int newAtomCount = atomList.size();
     if (newAtomCount > atomCount) {
       for(int i = atomCount; i < newAtomCount; i++) {
         addAtom(); // the syntax for this method baffles me at the  
moment
       }
       atomCount = newAtomCount;
     }
     else if (newAtomCount < atomCount) {
       for(int i = atomCount - 1; i >= newAtomCount; i--)
         deleteAtom(i);
       atomCount = newAtomCount;
     }
     // rest of code
   }

though clearly i don't understand all the fields of addAtom() yet.  
would this be the best way to go about this?

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