FYI, the JavaDoc utility cuts off most of that script which is why I couldn't find it in the online documentation (which looks strangely incomplete as a result). Everything down to the "<XML output> <editted file>" part shows up normally. After that, nothing else gets JavaDoc'd. Is there a bug in Javadoc that anyone is aware of? I didn't notice this until I downloaded the source and looked at the BlastXMLParser directly.
I have seen this as well. The javadoc in 1.4.2 (beta?) seems to silently stop emitting javadoc content when it hits some number of errors, or at the end of the first paragraph with errors, or when there are errors and the starts are aligned with your aura.
Also, I'm not really sure how to go about using the StAX stuff.
Are the biojava and source-forge StAX APIs synchronized now? Anybody know? Perhaps we should write a simple StAX tutorial. I'll see if I get any time in the next week.
Thanks again! DeAngelo
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