Can't see in Annotate & Predict the new menu item

Andi Shobash

• August 12, 2024 06:01

I follow the tutorial in Phobos Plugin Development Example. And when I added the code:

@Override
public GeneiousActionOptions getActionOptions() {
// Put the menu item in the Find/Locate part of the Sequence menu
return new GeneiousActionOptions("Locate Tandem Repeat(s) with Phobos...")
.setMainMenuLocation(GeneiousActionOptions.MainMenu.AnnotateAndPredict);
}

After that I check it in the Annotate & Predict menu I cant see the "Locate Tandem Repeat(s) with Phobos...". How do I fix that?

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• 

  Matthew Cheung

  • August 19, 2024 03:39

  Hi Andi,

  Are you able to share your current code?  You can send it to support@geneious.com if you like and we can take a look at what is going wrong.

  The tutorial is a bit out of date (uses Geneious from about a decade ago) but should still be applicable.  I've just tried running through the start of it quickly and the steps required for running differ depending on the IDE.  Could you tell us which IDE you're using?

  Completely guessing here, but one thing that might be going wrong is that your new plugin isn't being loaded.  Two things you could double check:

  1. Check that the new PhobosPlugin class returns your new SequenceAnnotationGenerator like so 

     public SequenceAnnotationGenerator[] getSequenceAnnotationGenerators() { return new SequenceAnnotationGenerator[] { new PhobosAnnotationGenerator() }; }

      

  2. Check that the plugin is being specified in arguments supplied to Geneious, this will differ based on your IDE but should be a line like:
     extraPlugins="com.example.phobos.PhobosPlugin"

   

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