[Biococoa-dev] BCSymbolList replacement

Charles PARNOT charles.parnot at stanford.edu
Mon Jan 31 19:03:05 EST 2005

OK, I finally took the time to write some code yesterday. I have done 
the most difficult part of it, I think, which was to refactor the 
BCSequence class tree:
* Superclass = BCAbstractSequence (Koen won the vote on the name, 100%!)
	that includes annotations (no code yet, though!!)
* BCSymbolList thus gone; sorry Koen, it seems that I had to undo 
most of what you did when adding that class;  the vote was for 
removal of that hierarchy for simplification purpose; we don't have 
to, we can also keep BCSymbolList as the super-superclass and then 
* BCSequence = one of the subclass of BCAbstractSequence (I have not 
added all the code, yet, I have more questions to ask to you guys... 
next email!)
* BCSequenceDNA, BCSequenceRNA,... : same as before, they are simply 
now subclasses of BCAbstractSequence

Before commiting, I just wanted to check one last time, because I had 
to modify ~30 classes to replace the 'symbolList'  namings with 
'sequence', also in method names (several 'Find and Replace' were 
necessary). The compilation is fine and everything seems to work OK. 
I don't know if you want to add a tag before such major refactoring 
(this is probably ~ the same as when you added the BCSymbolList, 
Koen?). I suppose such major refactoring is bound to happen at early 
stages of a project, and are a good thing? :-)


Help science go fast forward:

Charles Parnot
charles.parnot at stanford.edu

Room  B157 in Beckman Center
279, Campus Drive
Stanford University
Stanford, CA 94305 (USA)

Tel +1 650 725 7754
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