OK - using a fully quailfied FILE url worked. Also, I got rid of the
capabilities message by ading sax/ to the capability names in
Pdb2XMLConverter lines 97/98
oParser.setFeature("http://xml.org/sax/features/namespaces",true);
oParser.setFeature("http://xml.org/sax/features/namespace-prefixes";,
true);
Thanks,
Matthew
Simon Brocklehurst wrote:
>
> Matthew Pocock wrote:
>
>
>>Hi.
>>
>>I've tried to run the PDB parser example, but hit a snag.
>>
>>C:\stuff\biojava\biojava-live\demos>java eventbasedparsing.Pdb2XML
>>files\pdb\hgh_ori.pdb
>>WARNING: ignoring attempt to set illegal combination of parser features
>><?xml version="1.0"?>
>>no protocol: files\pdb\hgh_ori.pdb
>>Couldn't open file
>>
>>Am I being stupid (typing something wrong, incorrect xml parser,
>>generaly fooling around) or is it broken?
>>
>
> I don't think it's broken [ce n'est pas possible ;-)] - I think this is due
> to the modifications put in by to make the SAX drivers compatible with XSLT
> out of the box which removed the ability to resolve simple file paths.
>
> In other words, you can't specify pathnames as a simple string. Rather, you
> need to specify the path to the file as some kind of URI/URL just as you
> would in a web browser e.g. file://files/pdb/hgh_ori.pdb
>
> At least I think this is likely to be the problem... let me know...
>
> S.
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:[EMAIL PROTECTED]
>
>
>
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