[Biojava-l] Serialization of SimpleSequences

[Schreiber, Mark]

This problem is now resolved in the biojava1.3 branch, Features are serializing nicely and still behaiving like features at the end of it all.
 
I'm still working on a solution in biojava-live which involves delving into the bowels of the ontology Term implementations to find out why they won't deserialize. Some problem with a HashSet throwing a wobbly when it calls hashcode() on Term$Impl and getting a null pointer exception which shouldn't be possible as far as I can tell. Matthew, do you know what might be going on? Might need to write a ReadObject method for Term$Impl to hold its hand but hopefull not.
 
- Mark
 

	-----Original Message----- 
	From: Schreiber, Mark 
	Sent: Tue 28/10/2003 3:40 p.m. 
	To: Vasa Curcin; biojava-l at biojava.org 
	Cc: 
	Subject: RE: [Biojava-l] Serialization of SimpleSequences
	
	

	Hi -
	
	I thought we had fixed that one although it turns out the unit test was a bit inadequate. Generally its not a good idea to make an interface implement serializable as there may be a perfectly valid implementation that can't implement serializable. Probably better to make as many of the implementations as possible serializable. I'll have a look at this.
	
	- Mark
	
	
	        -----Original Message-----
	        From: Vasa Curcin [mailto:vc100 at doc.ic.ac.uk]
	        Sent: Tue 28/10/2003 2:06 p.m.
	        To: biojava-l at biojava.org
	        Cc:
	        Subject: [Biojava-l] Serialization of SimpleSequences
	       
	       
	
	        Hello,
	       
	        While transferring some sequences via serialization, I noticed that all
	        my Features are getting lost. After some digging around, it seems as if
	        Java doesn't serialize the FeatureHolder inside the sequence (I was
	        working with SimpleSequence objects). Even though a
	        NotSerializableException is not thrown, the FeatureHolder is missing.
	        After making the FeatureHolder interface in Biojava extend Serializable,
	        the problem disappeared. How much will this change affect the rest of
	        the code - ie. is there a good reason why FeatureHolders are not
	        serializable?
	       
	        Cheers,
	        Vasa
	       
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