Hi Shirley,
I am not really familiar with this code but I think
AlternateTokenization was introduced after the Logo code and that is
why you do not find it there. Can you fill a bug report? Also I'll be
happy to add any patch you submit.
Thank you.
George
Quoting Shirley Hui <[email protected]>:
Thanks George. It looks like using alternate tokenization works if you are
"stringifying" a Sequence explicitly using the alphabet.getTokenization()
method.
But presumably this gets done within the DistributionLogo class or some
other class down the line and I don't want to modify any Biojava classes
unless I really have to.
The way I am constructing the DNA sequences is like this:
Sequences seq =DNATools.createDNASequence(sequence, name);
The list sequences is used to make a SimpleWeightMatrix wm.
Then the call to DistributionLogo is like this:
Distribution dist = wm.getColumn(columnNumber);
DistributionLogo dl = new DistributionLogo();
dl.setRenderingHints(hints);
dl.setOpaque(false);
dl.setDistribution(dist);
dl.setPreferredSize(new Dimension((int) columnWidth, (int) columnHeight));
dl.setLogoPainter(new TextLogoPainter());
dl.setStyle(symbolColorStyle);
There no way that I can tell right now in the DNATools API to make the
DNATools use the alternate string tokenization via the call to
createDNASequence()
or another type of set method?
shirley
On Fri, May 27, 2011 at 12:15 PM, George Waldon
<[email protected]>wrote:
Hello Shirley,
I think you need to use AlternateTokenisation at some point; check BJ1.8.1
Cookbook at http://www.biojava.org/wiki/BioJava:Cookbook:Sequence
regards,
George
Quoting Shirley Hui <[email protected]>:
Hi,
I am using DNATools to generate dna Sequences.
I noticed that the static methods in DNATools a(),c(),t(),g() map to lower
case characters.
I am using using DistributionLogo class to draw sequences logos for a set
of
dna Sequences.
I think DistributionLogo is calling the static methods to map the
nucleotides which is lower case.
But I want the logo output the nucleotides in uppercase. How can I do
this?
Thanks for your help
shirley
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