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Setting the String Value for Blast plugin option is not working

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

Matthew Shum

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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.

Hilary Miller 0 votes
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