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 _______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l
