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

[peter murray-r. <pm...@ca...>]

At 09:26 07/03/2006, Egon Willighagen wrote:
>On Monday 06 March 2006 22:11, peter murray-rust wrote:
> > At 19:07 06/03/2006, Egon Willighagen wrote:
> > >with quite some help from Ola, I made good progress with the CMLRSS
> > > plugin. The screenshot is at:
> > >
> > >http://wiki.bioclipse.net/index.php?title=CMLRSS_plugin
> >
> > Looks nice...
>
>Will soon make a nicer screenshot with the chemistry in the Jmol/JChemPaint
>Views of Bioclipse.
>
> > I assume that we still have to fix them problems we had
> > yesterday to get the molecules displayed
>
>Yes, and no :)
>
>1. Ola fixed that run link and showed me how to run it using the Run menu
>item. So, that works again.
>2. CMLResources are extracted from the feeds, and are in principle viewable
>too
>
>However,
>
>3. Tobias had trouble with the CMLBuilder which now returned a XOM Node,
>instead of a CMLElement ... since he is not able to discuss this problem in
>detail until thursday, he backed out Jumbo 5.1 and replaced it with 5.0
>again... 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.

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.

Tobias, can you check that the rootElement is a valid CML local name 
and that it has this namespace?

>But this is something that should be easily solvable, I assume. And, pending
>this fix, I can't make screenshots with the Jmol view.
>
>BTW, some interesting advantages of the new plugin over the old plugin:
>
>- multiple items are supported
>- any CML is supported, so including CMLSpect is fine, as is any other CML
>supported by Bioclipse

Brilliant.

P.

I am getting more and more anecdotal feel that things are starting to 
change for the better. I think the Bioclipse plugin will catch a mood...

P.


>Egon
>
>PS. Henry, are you subscribed to this list too?

Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069