Re: [Jmol-developers] JUMBO4.6 and implications for communal libraries (chemjars)

[Peter Murray-R. <pm...@ca...>]

At 08:46 17/02/2005 -0500, Miguel wrote:
> > gnujaxp, xerces, and other XML parsers (a real problem)
>
>I don't really understand why XML parsers are a problem for your purposes.

In principle things should be better (especially with Java 1.5 where it is 
builtin). There are several current problems:
- Java 1.5 uses a different W3C DOM API from Java 1.4. Our DOM was 
1.4-compatible. If we make it 1.5-compatible it won't be 1.4 compatible
- we haven't managed to get the XML Validator technology to work on Java 
1.5. If anyone has, please let us know how. The old validator (Apache 
DomBuilder) no longer works

but the main problems is that if there are several XML parsers *in the 
distrib*, then they interact in horrible ways.


> > The major remaining problem seems to be XML. This continues to drive us
> > wild. So far it seems:
> > - XML is OS dependent. Am I right that Jmol requires gnujaxp if it is to
> > run XML on Mac, for example
>
>The Java 1.4 class libraries include an XML parser. On Mac OSX, just like
>every other platform.

Yes. But there are - see above - serious changes for 1.5


>Jmol requires gnujaxp for the Microsoft 1.1 JVM for IE/Win32 ... but this
>is an anomoly that should not affect people working on chemical
>applications in Java 1.4/1.5.

Thanks.

> > - Xerces (at least) has a new version every new moon. They are all
> > incompatible AFAICS. I can no longer run validation on XML - the last tool
> > (ASBuilder) disappeared and the new XML validation language in Java 1.5
> > tells us that it doesn't understand the XML Schema namespace!!!
> > - Xerces is now embedded in Java 1.5 and causes additional interactions
> > with any Xerces in the distrib. (I think JUMBO has at least two if not 3
> > xerces from other thirdparties!).
> >
> > Any of you checking out JUMBO will see the problem. I'd be grateful for
> > - Jmol (Miguel) - how does Jmol parse XML (CML) - what parser does it use,
> > etc?
>
>Jmol uses whatever is included in the Java class libraries. Jmol
>successfully reads CML files on both Java 1.4 & 1.5

Excellent

>Java 1.2 & Java 1.3 are *not* supported by Jmol.
>
>Jmol will fall back to trying gnujaxp.jar on the Java 1.1 platform ... IE
>+ Win32 + Microsoft 1.1 JVM

Thanks very much

P.


>Miguel
>
>
>
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Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069