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If in a translation block there is a taxa name that is an integer, say "1", and if we have the same integer as a code for some other taxa name then getLabelIndex method recognise code 1 as a taxa name…
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Java 7 has some methods to more conveniently access Files and deal with class paths, and generic code can be made a bit cleaner, etc... Also, Java 8 is already on the horizon, so packages tend to be w…
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Hi all,
I will start working on implementing some of the common univariate distributions missing in the bayonet.distributions package and implementing tests for them. I plan to focus on implementing …
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I vote for getting rid of the int system.
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Currently TaxonSet has a constructor which takes a list of Taxon objects and uses this to set the relevant input. There is no constructor to set alternative Alignment input.
Additionally, it would b…
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I could be wrong, but I believe `DataType.isAmbiguous(state)` should return true if the integer variable state represents an ambiguous character. (For nucleotide data, the "state" corresponding to a c…
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If the requirement of deriving from BEASTObject could be relaxed, while still having BEASTObject like behaviour (Inputs as members, initAndValidate to initialise, Description annotation, etc) a class …
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MASTER used it once, but switched to JBLAS. Does anything else use it? Can we remove it?
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Coalescent likelihood is tested, but the coalescent tree generation code is not. This is important, as its predominant use as a state initialiser means that it's very possible for errors to creep in …
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When editing a value of a parameter -- which is a list of primitives -- in the init panel, nothing suitable is found. A table editor matching dimensions would be nice.