How to add a child of "Cloning"

Weixi Liao

• June 16, 2014 08:13

I wonder if it is possible to add a child of "Cloning" in the toolbar.

I try to use GeneiousActionOptions.createSubmenuActionOptions(PluginUtilities.getDocumentOperation("XX").getActionOptions().getParentOptions(),new GeneiousActionOptions("","")), but when Geneious is launching and loading plugins, it seems that user plugins are loaded before "Cloning", and cannot locate the action of "Cloning".

 

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  Richard Moir

  • June 16, 2014 23:32

  No, unfortunately we haven't made the Cloning menu available through the public api. Your next best option is probably the Tools menu.

  What plugin are you working on if you don't mind me asking? We could be interested in listing it on our plugins page if you're interested.

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  Weixi Liao

  • June 20, 2014 15:54

  Thanks for answering.

  I am working on a plugin importing a list to run a series of cloning operation, used in library construction for example. Another problem I meet is that I cannot set the options and perform the operation of digestion, and I am trying to rewrite a simple one.

  The inputs of "workflow" cannot be customed other than document selection, is it?

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  Richard Moir

  • June 21, 2014 15:07

  Ok, what kind of digest are you doing? Restriction enzyme?

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  Weixi Liao

  • June 23, 2014 05:14

  Yes, like golden gate.

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  Richard Moir

  • June 23, 2014 15:38

  Unfortunately our digest operation is not set up that well for scripting. What you need to do is annotate your sequence with "restriction site" type annotations for the enzymes you want to use then run our digest operation on that with default options. Here is an example BsaI restriction site which the digest operation will recognize:

  SequenceAnnotation anno = new SequenceAnnotation("BsaI", "restriction site");
  anno.addQualifier("Recognition pattern", "GGTCTC(1/5)");
  anno.addInterval(new SequenceAnnotationInterval(472,477));

  Alternatively you can digest the sequence manually using SequenceExtractionUtilities or by creating new sequence documents from scratch.

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  Weixi Liao

  • June 24, 2014 09:23

  Thanks, but I meet a new problem.

  I add the annotations of "restriction site", and it works tested by "Digest ..." in "workflow", but when I call "performOperation", it fails.

   

  DocumentOperation digest=PluginUtilities.getDocumentOperation("com.biomatters.plugins.restrictionAnalysis.DigestOperation");

  List<AnnotatedPluginDocument> list=digest.performOperation(doclist, ProgressListener.EMPTY, digest.getOptions(doclist));

   

  Is there anything wrong?

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  Richard Moir

  • June 25, 2014 21:54

  Are you getting the assertion about running in the swing thread? If so, you need to invokeAndWait like this:

  DocumentOperation digest=PluginUtilities.getDocumentOperation("com.biomatters.plugins.restrictionAnalysis.DigestOperation");
  final AtomicReference<Options> options = new AtomicReference<Options>();
  ThreadUtilities.invokeNowOrWait(new Runnable() {
    public void run() {
      options.set(digest.getOptions(doclist));
    }
  });
  List<AnnotatedPluginDocument> list=digest.performOperation(doclist, ProgressListener.EMPTY, options.get());

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  Weixi Liao

  • July 07, 2014 13:26

  Finally it is working now.

  Thanks very much!

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