[Biojava-l] writing SCF

[Rhett Sutphin]

Hi Shameek,

On Monday, July 7, 2003, at 04:38  AM, Shameek Chakravarty wrote:
> I cant see any support for *writing* SCF or ABI files.
> Is there a module in works for the same ?

You are correct:  the current chromatogram package does not support 
writing chromatograms at all.  I do not intend to add this support in 
the near term.  This is due to constraints on my time, not any 
fundamental opposition to the idea.

If you'd like to do this yourself, here are some pointers:

* Documentation on the SCF format is included in the Staden io_lib 
library source.  This library is available from 
http://www.mrc-lmb.cam.ac.uk/pubseq/downloads.html#io_lib .  The 
documentation is in the scf/ directory of the source archive.

* The ABI format is not documented by ABI; however, Clark Tibbets 
reverse engineered several different data streams surrounding the ABI 
377.  The ABIF format was one of them and so is documented in his paper 
"Raw Data, File Formats, and the Digital and Analog Raw Data Streams of 
the ABI PRISM  377 DNA Sequencer."
(There's a link to a current online location for this paper in the 
javadoc for ABIFParser.)  The ABIFParser class might also be useful to 
get some ideas, but I don't think it could be easily converted into a 
writer.

* The SimpleChromatogram class provides a Chromatogram implementation 
with public mutators.  This could be useful if you want to create the 
chromatograms programatically.

Rhett