Design questions:

Use different approaches for sequential data:
 - specify model in terms of slices
 - use for loops instead of recursions
 - use external data strcutures for dynnamic programming tables


For non-sequential data (e.g., phylo-models):

Graphical model specification:

  - Graph structure
  - variable nodes
    o dimension
  - factor nodes:
    o potential
    o variable order


Algorithms:
	
  - sum-product
    - marginal of specific nodes
    - marginal of factor neighbor combinations
  - max-sum
    - max probs
    - arg_max

Support algorithms:

  - Init observed values
    - map from 



---- 

Design questions:

  - Should factors expose their matrix of vector potentials. 
    - (not if algorithms should not make use of them. In other words,
      not if other potential implementations are intended.)
  - Should factors be implemented in terms of an inheritance hirarchy.
    - only if we need to specialize implementations.
  - Do we need a general ordering of the FG nodes (variable and factors).

factorGraph constructor should take

vector<unsigned> dimensions; //
vector<matrix_t> potentials; // matrix_t has one row if potential one-dimensional
vector<vector<unsigned> > varNeighbor;
vector<vector<unsigned> > facNeighbors;


need variable vector

vector< vector< unsigned > > neighbors;

vector<FGBase *> nodes;

vector<unsigned> factors;    // factor indices in nodes

vector<unsigned> variables;  // variable indices in nodes


---
scratch

nodes:
1:
factor neighbors: [1, 2]
dimension: 4

factors:
1:
potential: []
variable neighbors: 1

2:
potential: []
variable neighbors: 2