Always select from vertices table when constructing a graph with `computeGraph`

[grigory93]

Currently, the vertex table is not accessed when neither vertex attributes nor vertex where conditions are specified. This creates problems when auto-assigning ids (from 1 to vertex count) to vertices in a graph.

If we change computeGraph to always select vertices and order them by their names then id-ing vertices becomes consistent across all graph operations. In particular, this helps with clustering graphs and complying with standard community class objects (package igraph) when assigning vertex membership (and its membership element).

35 is related to this.

[grigory93]

This is actually a bug: not selecting vertices by relying on edge table only won't incude vertices with degree 0.

[grigory93]

all changes committed are in computeGraph.R