Haven't deleted anything so should still be backwards compatible with old code. The major change is the new PositionParadigmFramework class which consolidates a lot of information so it doesn't need to be passed around to do simple things. Should be a lot easier to use and to test.
The long term goal is to move everything into the PositionParadigmFramework class, or make new classes with functions that accept a PositionParadigmFramework instance. Also started a Genome class which will allow a nicer syntax, printing etc for dealing with entire genomes (as cosets of permutations)
Haven't deleted anything so should still be backwards compatible with old code. The major change is the new
PositionParadigmFrameworkclass which consolidates a lot of information so it doesn't need to be passed around to do simple things. Should be a lot easier to use and to test.The long term goal is to move everything into the
PositionParadigmFrameworkclass, or make new classes with functions that accept aPositionParadigmFrameworkinstance. Also started aGenomeclass which will allow a nicer syntax, printing etc for dealing with entire genomes (as cosets of permutations)