This proved to be rather easy MUCH to my surprise.  It became clear to me that the only time my train would hit a photocell was if that cell was allocated to me already.  So, if a cell got covered up and it was not allocated to the train, the allocation array[cell#] would be set to 2.  2 meant that something other than the train had the cell.  It could be a shadow of someone leaning over the track or a hand or a tree.  If when the train requested the next cell, the allocation for that cell was already 2, then the train would be blocked.  A flag was set in the train object that it was blocked and the OS kept track of what cell blocked it.  This way, when there was a departure on a cell that was allocated to 2, a check could be made to see if the train was blocked on that cell.  If so, the train would become unblocked and it would be granted that photocell as a resource.  If the train was not blocked on that cell, then the allocation table simply de-allocated it.  As long as a train was blocked, it is unable to move.

I originally had intentions of making a small language for the train to obey that would have a simple if blocked statement.  This way, the train would be able to follow an alternate path if it was blocked.  But the scope of this project ruled that possibility out.