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Jalview's Groovy API in versions 2.8.x is still very basic. This page is for ideas and wishes which will inform the design of the Jalview 3 scripting API

Why might you use Jalview's Scripting API

  • add/modify functions available from the GUI
  • batch operations
  • delve into Jalview's internals for other reasons

Current lacks in the 'Jalview' scripting object

  1. No 'current focus' variable to get the currently focused alignment panel
    • Could have a new scope variable that gives the current alignframe
  2. No mechanism for attaching functions to buttons on the GUI
    • Relatively easy to implement
    • need to look at how the menu set might be navigated via a Groovy expression
    • need to consider ways for Jalview to store groovy fragments so they can be autoloaded when Jalview launches