[Biojava-l] Blast XML + XSL = HTML

Richard Holland holland at ebi.ac.uk
Mon Jul 23 11:40:29 UTC 2007

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Hi Dmitry.

Thanks for your efforts and offer to contribute your code to the BioJava

You say that the existing Blast2HTMLHanlder handler is inflexible, which
is true enough. However I don't see how substituting the handler for an
XSL stylesheet would make it any more flexible - the user would still
have to live with an HTML format specified by the designer of the
stylesheet unless the wrapping code that calls the stylesheet could
somehow dynamically modify the XML based on method calls.

I'm also unsure as to whether the whole transformation is appropriate
for BioJava (the Blast2HTMLHandler itself is on borderline territory -
saved only by the fact that it creates the reports based on SAX events
that can potentially come from non-BlastXML sources). BioJava is a Java
toolkit, and the transformation from XML to HTML via an XSL stylesheet
doesn't require Java at all.

Mark - if you're reading this - guidance, please?


Dmitry Repchevsky wrote:
> Hello!
> I used biojava Blast2HTMLHandler, but found it unflexible and slow (?).
> Finally I made an xsl stylesheet  to convert blast output into html 
> <div> element.
> Also I have a class BlastXML2HTML to make the transform , it's pretty 
> simple.
> May I contribute it?
> Best regards,
> Dmitry
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