Question about accessing different option values via "custom java code"

Matthew Shum

• November 22, 2016 13:02

Hello,

I am trying to invoke the Geneious Assembler plugin in the "custom java code" step using varying levels of sensitivities. There are a total of 6 different available sensitivities (see picture 1).
The problem I am facing is that I can only call: "low", "medium", "high", and "highest" via:

DocumentOperation deNovo = PluginUtilities.getDocumentOperation("com.biomatters.plugins.alignment.AssemblyOperation_Denovo");

options = deNovo.getOptions(documents);

options.setStringValue("method.Geneious.deNovo.sensitivity", "medium");

I tried to use options.getDescriptionAndState() to find option values but all I get is (see picture 2): 

Can someone help me identify the last two sensitivity option values?

Thank you

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  Geneious Team

  • November 22, 2016 19:54

  Hi Matthew,

  The problem is that getDescriptionAndState() contains html tags which are interpreted in the dialog being displayed. To see the options, you need to do this instead:

  Dialogs.showMessageDialog(StringUtilities.escapeHtmlCharacters(options.getDescriptionAndState()))

  The names of the two sensitivity settings you are missing are mediumLow and lowWithLowMemoryUsage. The only difference between low and lowWithLowMemoryUsage is performance vs memory usage. Those two settings should produce identical results.

  Best regards,
  Matt.

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  Matthew Shum

  • November 22, 2016 19:59

  Thank you Matt! This answers my question exactly!

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