[Biojava-dev] Contributing chromatogram support to BioJava

[Rhett Sutphin]

Hi,

Rhett Sutphin wrote:

 > On Wednesday, March 5, 2003, at 03:29  AM, Matthew Pocock wrote:
 >
 >> Sounds great! I for one could realy use this stuff.
 >> Could you dump the javadoc somewhere so that we can
 >> just double-check the API, and then we can sort you
 >> out. Are you intending to dump the code into biojava
 >
 >
 > I'll do this sometime this weekend.

The API is up at 
http://www.detailedbalance.net/~rhett/dev/biojava/chromat-contrib/doc/ .
The package structure is still the original structure that I described 
in my last message, except with org.biojava.bio prepended.  I'm ready to 
change it if you folks recommend.

I've ported almost all the code over to using biojava Symbols (etc.) -- 
only ChromatogramGraphic is left to go.  I ran into one snag during this 
conversion:  SimpleBasisSymbol is a package-level class.  You'll see in 
the API that I would like to represent base calls as a type of 
BasisSymbol (since they're a concatenation of a DNA symbol [the call] 
and an integer [the sample offset of the peak]).  Subclassing 
SimpleBasisSymbol seems like the best way to do this -- in fact, I 
already did it by modifying a local copy of BioJava 1.3pre1.

Is there a strong reason for this access restriction?  Looking through 
the mailing list archives, I see that this has been mentioned, but not 
explained.  The API is inconsistent -- AbstractSymbol and 
SimpleAtomicSymbol are public while SimpleSymbol and SimpleBasisSymbol 
are not.

If there is a strong reason for this, is there a recommended path to 
implementing BasisSymbol without a lot of redundant code?

Rhett

-- 
Rhett Sutphin
Research Assistant (Software)
Coordinated Laboratory for Computational Genomics
   and the Center for Macular Degeneration
University of Iowa - Iowa City, IA 52242 - USA
4111 MEBRF - email: rhett-sutphin at uiowa.edu