[Biojava-l] Chromatogram viewer

[Andy Yates]

If you are working with processed traces i.e. ones which are normalized 
to an intensity of around 1,000 & have very little background noise then 
it is possible to look at the chromatogram's method getBaseCalls(). This 
gives you a base call & the offset in the trace it occurs at. Then it's 
a case of editing the ChromatogramGraphic Option. The ones you need are 
TO_TRACE_SAMPLE and FROM_TRACE_SAMPLE.

So in practice it would look something like this (I haven't compiled 
this so it may not work but you can get the gist of it).

Chromatogram c = getChromatogramFromSomewhere();
ChromatogramGraphic cg = new ChromatogramGraphic(c);
Integer from = new Integer(getScanFromBase(c, 200));
Integer to = new Integer(getScanFromBase(c, 400));
cg.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, from);
cg.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, to);
//Then do the drawing

public int getScanFromBase(Chromatogram c, int base) {
   Alingment align = c.getBaseCalls();
   Symbol baseCall = align.symbolAt(Chromatogram.OFFSETS, base);
   int offset = ((IntegerSymbol)baseCall).intValue();
   return offset;
}

Hope that helps

Andy Yates

King Jordan wrote:
> I would like to be able to display a specific sub-range of a chromatogram.
> For instance, I may have and abi or scf file with 1,000 bp and I would like
> to display only positions 200-400.  Is there some way to modify the abi or
> scf file with biojava to accomplish this?
> 
> Thanks in advance,
> King
> 
> -----------------------
> I. King Jordan
> Associate Professor
> School of Biology
> Georgia Institute of Technology
> 310 Ferst Drive
> Atlanta, GA 30332-0230
> 404-385-2224
> http://esbg.gatech.edu
> 
> 
> 
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