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bioDS / beast-phylonco

A BEAST2 package for single-cell cancer evolution
GNU Lesser General Public License v2.1
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GT16ErrorModel doesn't have the narrative annotations #32

Closed walterxie closed 1 year ago

walterxie commented 1 year ago

it looks like GT16ErrorModel doesn't have the narrative annotations, so its description in natural language is not very informative.

A simple example is https://github.com/LinguaPhylo/linguaPhylo/blob/d9c49b28aa996c4ed08074f92c2ef439f8e8533f/lphy/src/main/java/lphy/evolution/substitutionmodel/HKY.java#L39

kche309 commented 1 year ago

The narrative annotations are in the code, but not shown on the narrative passage.

After some debugging, it appears an extra empty constructor was suppressing parameters from showing up in the GUI narrative description.

kche309 commented 1 year ago

This is fixed in https://github.com/bioDS/beast-phylonco/pull/33/commits/d595522df1ce211433717afbe5d82e90e7d766a5

Testing with gt16CoalErrModel.lphy from examples in LPhyStudio produces: lphystudio-gt16-errormodel-narrative-fix