Walter

Import GUI related classes into studio core from LPhyBEAST

1

Some useful GUI related classes, for example: - interface Progress Allow the progress of a method to show in progressBar. - TextPaneOutputStream Send System out or err to JTextPane.

Prefer to use MethodCall than to use Function

1

For example: `D.nchar()` not `nchar(D)`; `ψ.nodeCount()` not `nodecount(tree=ψ)`; => yuleRelaxed.lphy

should java.awt.geom.Point2D or java.awt.Color be in the core?

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I think lphy core should be "awt and swing free". The following classes may be refactored to move awt code to `studio`. java.awt.geom.Point2D: - `interface TimeTreeNodeVisitor` - `interface LayeredNode` -...

Store column names to ContinuousCharacterData: The `Double[][] continuousCharacterData` has row names which are insider `Taxa`, but no column names which are trait names. I suggest to create String[] traitNames in...

Citation is missing for some models

1

Citation is missing for some models

Need log4j or similar to disable debug messages after release.

BactrianRandomWalkOperator should use "windowSize" not "scaleFactor". I have a chat with Remco about this, because it will affect all XMLs and BEAUti templates, it'd better to include it in a...