[Biojava-l] Serialization and 1.2

[Schreiber, Mark]

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk]
> Sent: Tuesday, January 22, 2002 10:01 PM
> To: Schreiber, Mark
> Cc: biojava-l (E-mail)
> Subject: Re: [Biojava-l] Serialization and 1.2
> 
> 
> On Tue, Jan 22, 2002 at 03:33:54PM +1300, Schreiber, Mark wrote:
> > 
> > A while ago there was some discussion of serialization of biojava
> > objects and the problems of rebuilding things like alphabet 
> indexer. Is
> > it a realistic goal to get this up and running with some 
> jUnit tests for
> > biojava 1.2?
> 
> Um, I should think so.  If turns out that it's going to take
> a while, we can always put it into 1.2.1 instead (aside: I'm
> hoping that the 1.2 branch will be rather more active than 1.1
> was -- I don't think we're going to see the same degree of core
> interface changes which made porting bug fixes between branch-1_1
> and the HEAD difficult).
> 
> As far as I can remember, the problem is not so much
> rebuilding the AlphabetIndexes as ensuring that the serialized
> form isn't dependent on the indexes.  Easiest way would
> seem to be adding explicit writeObject/readObject methods,
> then serializing as a list of (Symbol, double) tuples.
> 
Not quite sure I understand this, are you saying that when an object is
serialized it should record its AlphabetIndexer as a list of Symbol,
integer? tuples that will remake an internal copy of an AlphabetIndexer
post serialization?

If this is the case then wont any class that is serilizable but contains
a reference to an AlphabetIndexer will have to be tweaked individually
to specify writeObject/readObject methods?

Mark
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