[Biojava-l] New idea for alignment parsing and Re: Parser for MrBayes output

[Ben Stöver]

Hi,

> To me the whole idea sounds great. Especially if it can be made
> compatible with the existing Biojava interfaces. If I understand what
> you propose, you would only introduce a new way of parsing things
> which
> could even live alongside the current parsers. It could even go to
> its
> own package (sequence.nio ?). For me this is a +1 too.

Yes, it would be 100 % compatible with the current classes and code relying on
them. But additionally to a new way of parsing, the editable sequences alone
would be an additional new feature, since it was not possible to change the
contents of a sequence without creating a new instance before, to use it e.g.
as the data source for an alignment editor (as one of many possible examples).

Just to avoid confusion: I was thinking about implementing the new sequence
and parser interfaces and some initial parsers (e.g. FASTA, Phylip, MEGA, ...)
and implementations for the new editable sequences. For the whole Nexus stuff
which is going far beyond sequences (and MrBayes focus would probably be on
trees anyway) I was thinking that Pola will possibly be taking care of that.

Best
Ben