Fix: Change backing datastructure of graphs

* Replaces List with Dictionary with the node index being the key and
  the GraphNode (also containing the index) the value
* This dramatically speeds up the MatrixMarket string to graph
  transformation in MatrixMarketReader since adding edges and in
  particular nodes to the graph is much faster
* This is because the nodes are added to the graph as needes i.e. the
  graph searches for them in the existing node list and if not present
  adds them. This search is significant the larger the graph gets. This
  is also why the transformation of larger graphs took exponentially
  longer.