LocARNA-1.8.11
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constructors ensure name uniqueness; if constructing as alignment of alignments, names are made unique if needed.
because this class does not know whether it contains RNA, it would be useful to have a derived class RNAMultipleAlignment. This class could guarantee that its sequences are normalized RNA sequences. Consequently, we could enforce by the type system that RnaEnsemble is generated only from RNAMultipleAlignment etc.
automatically adapt output width for sequence names to longest name
support constraints for in loop probabilities
split up RnaEnsemble into two classes; one with and one without in-loop probabilities (like RnaData and ExtRnaData)