Setting the String Value for Blast plugin option is not working

Matthew Shum

• December 02, 2016 13:10

I am trying to set the String Value for the blast parameter nucleotideQueryOption.manualQuery.subsequence.useSubsequence to "true". However, every time, I utilize options.setStringValue("nucleotideQueryOption.manualQuery.subsequence.useSubsequence", "true"), options.getNamesAndValues(true) returns "false".

Is there another parameter I need to change in order to change the above parameter?

Thanks!

Matt

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  Hilary Miller

  • December 05, 2016 01:18

  Hi Matt, 

  You can only use a subsequence on manual queries, so that needs to be set first. The sequence of options to set is:

  options.setStringValue("queryInputMethod.queryInputMethod", "specifyQuery")

  options.setStringValue("manualQuery.manuallySpecifiedQuery", "GATTACA")

  options.setStringValue("manualQuery.subsequence.useSubsequence", "true")

   

  Alternatively, if you want to use a region on a selected document, you should create a sequence selection first, then get the options and set:

  options.setStringValue("queryInputMethod.queryInputMethod", "useSelectedRegion")

   

  Hope that helps for what you want to achieve.

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  Matthew Shum

  • December 05, 2016 22:02

  Thanks Jonas! This helps!

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