[cml/ccml-discuss] Re: [Bioclipse-devel] CMLRSS plugin

[Egon W. <e.w...@sc...>]

On Tuesday 07 March 2006 12:31, peter murray-rust wrote:
> At 09:26 07/03/2006, Egon Willighagen wrote:
> > But after that transition back to 5.0, I still had that 
> >ClassCastException in this piece of code:
> >
> >CMLBuilder builder = new CMLBuilder();
> >CMLElement cmlElement = null;
> >// cmlElement = (CMLElement) builder.build(file).getRootElement();
> >cmlElement = (CMLElement)builder.parseString(localResourceString);
> >
> >The cast to a CMLElement is failing. This caused trouble for me and for
> >Tobias, with both Jumbo 5.1 and 5.0... Peter, ideas?
>
> This only works if the rootElement is a NAMESPACED CMLElement, else
> it produces a simple Element. My guess is that you need to change the
> namespace.

I'm quite positive that this indeed is the problem. For some reason the 
namespace of the XOM Node was not set, while it did use "cml" prefix.

I can imagine this to be the case for Tobias as well, because Bioclipse 
actually interprets CML at the Resource level, and splits up a CML file with 
a <molecule> and a <spectrum> on the same level into two childs below the 
CMLReource... and I can very well imagine that in this case too, XOM does not 
set the namespace for these Element's specifically, if set at a parent Node.

:(

> Namespaces are a problem since we haven't been very consistent in
> CML. The current suggestion is that we always use
> "http://www.xml-cml.org/schema". What we could then do is strip off
> all other old CML namespaces at start of parse and replace by this one.

Yes, stripping might be a good idea. At least they have the above in common.

Egon

-- 
e.w...@sc...
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
Blog: http://chem-bla-ics.blogspot.com/
http://www.cac.science.ru.nl/people/egonw/
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