[Biojava-l] Upper case symbols

[Eric Haugen]

Andreas Draeger wrote:
> Dear all,
> 
> Thank you for this very quick answer regarding Sequence logos! The code 
> works fine. However, would it also be possible to tell the DNATools 
> class that upper case letters should be used instead of lower case "a", 
> "c", "g", and "t"? I think it is more common to apply upper case symbols 
> in sequence logos.
> 
> Cheers
> Andreas
> 

Hi Andreas,

The way I did it was to uppercase the letters in the AlphabetManager.xml file,
replacing the AlphabetManager.xml inside my biojava.jar.  See the attached version.
Maybe there's an easier way I don't know about...

Best regards,

Eric

-- 
Eric Haugen
Software Engineer
Stam lab, UW Genome Sciences
University of Washington
2211 Elliott Avenue, 6th Floor
Seattle, WA 98121
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