[Biojava-l] Re: Questions about ChromatogramGraphic and your Chromatogram Viewer

[Rhett Sutphin]

Hi Andrew,

I'm going to copy this reply to biojava-l in case anyone else has a  
similar question.

On Wednesday, July 16, 2003, at 09:08  AM, Andrew Yates wrote:
> I was searching around the internet for Chromatogram viewers and
> stumbled across your application which I have to say is a very
> impressive piece of kit. I also found your source code for command line
> based image generation of chromatograms.

Thanks.

> I also noticed that you mentioned in an email to the biojava mailing
> list (last month) that the Chromatogram Viewer program can select and
> save a portion of the chromatogram and output into an image. I'm just
> wondering how this is possible and what code you are using to achieve
> this?

How to this in Chromatogram Viewer:
   * Click on the first base you want to have in the image
   * Shift-click on the last base
   * Click "save as image"

"Copy bases to clipboard" also uses the selection.

How to do this programmatically in ChromatogramGraphic:

You need to know the range of trace samples you want to include in the  
graphic.  When you do, you can set the FROM_TRACE_SAMPLE and  
TO_TRACE_SAMPLE options.  See the javadoc for  
ChromatogramGraphic.Option for (slightly) more detail:

http://biojava.org/docs/api/org/biojava/bio/chromatogram/graphic/ 
ChromatogramGraphic.Option.html#FROM_TRACE_SAMPLE

HTH,
Rhett


--
Rhett Sutphin
Research Assistant (Software)
Coordinated Laboratory for Computational Genomics
   and the Center for Macular Degeneration
University of Iowa - Iowa City - Iowa - 52246
mailto:rhett-sutphin at uiowa.edu