[Biojava-l] SAX, DOM, XPath and Flat files

Andy Yates ayates at ebi.ac.uk
Tue Dec 4 10:42:19 UTC 2007

David Huen wrote:
> On Dec 4 2007, Andy Yates wrote:
>> be wanting. It more depends on is there a good enough XPath 
>> implementation that can handle the XML files we'll be pushing through 
>> it (why is it I think the answer is no).
> And why is it I think you are right? :-)

Lol :)

> Some of the XML files used by bioinformaticians can be horrendously 
> large and at least some of the XML packages do appear to behave like 
> they bring the whole file into a memory representation before allowing 
> you to work on it. I think memory use and performance was a major factor 
> in the current BJ implementations adopting an event-based model even 
> though it's more difficult to use usually.

It is one of my biggest concerns that a huge DOM model + BioJava model 
is going to take up a lot of memory. However if a SAX, StAX (either one) 
or DOM based parser is hidden behind a good enough interface hopefully 
the implementation used can be up to the user. That said these goals 
maybe too different & distant for us to be able to do it.


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