Indices - clean up the validation etc API

[GoogleCodeExporter]

The API to access the various indices object properties is in need of a 
cleanup.  Much of the API is not fully logical.  

The simplest solution is to rebuild the system, with Biodiverse::Calculations 
being clear and also a more logical name given how the naming scheme has 
evolved.  

Original issue reported on code.google.com by shawnlaffan on 6 Oct 2014 at 6:28