The dynamic character analysis is broken for the L1-norm (additive)

[recursion-ninja]

When a dynamic character is input that uses the L1 norm (additive) metric, runtime exceptions are thrown regarding the specialized handling of this metric. I assume that the error exists in the Ranged instance definition of the DynamicCharacterElement. We need to correct the instance definition (or the calling code) so that this is handled appropriately.

[recursion-ninja]

There appears to be a defect in the decoding from the alphabet.

Alphabets = [ "A", "B", "C" ]

and there exists something like this in the parse result:"AB":[]

We get the empty bitvector when decoding this because notElem "AB" [ "A", "B", "C" ].

[Boarders]

The example in the integration test fails as the read grammar is not specific enough to be able to specify reading the file as a particular alphabet, e.g. protein, instead of as a custom alphabet. The same problem appears in the Sankoff example here #80.

[recursion-ninja]

I corrected a defect in the bit-vector arithmetic used when converting between characters and ranges.

See commit 5e4401e.