SequenceAnnotationGenerator in Workflow

jo.stevens

• October 17, 2023 14:29

Hello,

I want to expose options from a SequenceAnnotationGenerator plugin in a workflow, however, I am not sure how to do it. In my plugin I have added the following method:

public DocumentOperation[] getDocumentOperations() {

 DocumentOperation operation = new DocumentOperation() {

 @Override

 public GeneiousActionOptions getActionOptions() {

 GeneiousActionOptions actionOptions = new GeneiousActionOptions("Absawi Plugin", "Absawi Plugin", null, GeneiousActionOptions.Category.None);

 actionOptions.setMainMenuLocation(GeneiousActionOptions.MainMenu.Sequence);

 actionOptions.setInMainToolbar(false);




 return actionOptions;

 }




 @Override

 public String getHelp() {

 return null;

 }




 @Override

 public DocumentSelectionSignature[] getSelectionSignatures() {

 return new DocumentSelectionSignature[0];

 }

 

 //Geneious will display the Options returned from this method as a panel before calling performOperation().

 public Options getOptions(AnnotatedPluginDocument[] docs){

 return new AnnotatorOptions(); 

 }

 

 @Override

 public boolean isDocumentGenerator() {

 return false;

 }

 

 @Override

 public void performOperation(AnnotatedPluginDocument[] annotatedDocuments,

 ProgressListener progressListener, Options options, SequenceSelection sequenceSelection,

 OperationCallback callback) throws DocumentOperationException {

 

 generateAnnotations(annotatedDocuments, null, progressListener, options);

 }

 };

 return new DocumentOperation[] { operation };

 }

 

But somehow, this does not do anything. The workflow annotates, but neither performoperation nor getOptions ever gets called.

0

• Official comment

  

  Jonas Kuhn

  • October 20, 2023 00:37

  Hi Jo,

  you may have to make use of 

  public Options getGeneralOptions() { return new AnnotatorOptions() }

  if you want to make options show up for the workflow. Otherwise it will always run with default options.
• 

  jo.stevens

  • October 20, 2023 15:29

  Hey Jonas,

  Many thanks for this info. I did not realize the solution was so simple. I have implemented the method and can confirm it works like a charm.

  Greetings,

  Jo

  0

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