From: Miguel <mi...@jm...> - 2005-01-25 20:22:40
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Nico, I see that you released the current build to the /jmol directory on www.jmol.org Unfortunately, some of the development code breaks 1.1 JVMs (MSFT IE & NS= 4.7). I had not had a chance to review the Folding support that you added to org.jmol.adapter.smarter.Resolver. In your modifications you are using th= e method String.split(String regex) ... which only was introduced with 1.4 JVMs. So, we need to do a few things. 1. re-release the 10.00 release to www.jmol.org/jmol 2. fix the Resolver. a. it should not use 'split' b. determine if the lexical parsing mechanism you are using to recognize Folding should be generalized so that other readers could use that mechanism in the future. 3. Test the FoldingReader on 1.1 jvms to confirm no other use of newer methods. 4. Release your new www.jmol.org/fah with a test version of the JmolApplet ... until we can do a full release that will support Folding. Do not feel bad ... none of this is a big problem. Miguel |
From: Miguel <mi...@jm...> - 2005-01-25 21:38:05
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>> 1. re-release the 10.00 release to www.jmol.org/jmol > > Done OK >> 2. fix the Resolver. >> a. it should not use 'split' >> b. determine if the lexical parsing mechanism you are using >> to recognize Folding should be generalized so that other >> readers could use that mechanism in the future. >> >> 3. Test the FoldingReader on 1.1 jvms to confirm no other use >> of newer methods. > > Ok Try to do these things. Let me know if you need advice/assistance. >> 4. Release your new www.jmol.org/fah with a test version of the >> JmolApplet ... until we can do a full release that will support >> Folding. > > For the moment, I have created as you suggested in your other mail a > jmolPrerelease and I have modified the fah page to point to it. OK. I suggest that you use the new Jmol.js *and* the new JmolApplet*.jar file= s. >> Do not feel bad ... none of this is a big problem. > > Thanks, I will think of 1.1 jvms in the future. I know that it is difficult to do. Q: Do you have access to a machine with a 1.1 JVM? Win98/WinME/Win2K? If not, you can try using Netscape 4.8. Otherwise, let me know when you have releases and I will test for you. Miguel ----- Open Source Molecular Visualization www.jmol.org miguel=40jmol.org ----- |
From: Nicolas V. <nve...@cl...> - 2005-01-25 22:26:32
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From: "Miguel" <mi...@jm...> >>> 2. fix the Resolver. >>> a. it should not use 'split' >>> b. determine if the lexical parsing mechanism you are using >>> to recognize Folding should be generalized so that other >>> readers could use that mechanism in the future. >>> >>> 3. Test the FoldingReader on 1.1 jvms to confirm no other use >>> of newer methods. >> >> Ok > >Try to do these things. Let me know if you need advice/assistance. I have fixed the Resolver and the FoldingReader by replacing split() with StringTokenizer. I have tested the new applet with IE6 configured to use MS JVM, it is now working. It is a lot slower to load the applet than before, is it normal ? > I suggest that you use the new Jmol.js *and* the new JmolApplet*.jar files. Ok > Q: Do you have access to a machine with a 1.1 JVM? Win98/WinME/Win2K? Win2K with IE6. |
From: Miguel <mi...@jm...> - 2005-01-25 22:47:04
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> I have fixed the Resolver and the FoldingReader by replacing split() wi= th > StringTokenizer. > I have tested the new applet with IE6 configured to use MS JVM, it is n= ow > working. Good. > It is a lot slower to load the applet than before, is it normal ? Slower? I was hoping that it would be faster. Remember that since you have your own copy of JmolApplet?.jar in the fah directory then it must be downloaded the first time you visit the page. Previously it would come up right away, once you had gone to www.jmol.org= >> I suggest that you use the new Jmol.js *and* the new JmolApplet*.jar > files. > Ok I am hoping to switch to the new applet loader code that will display the= Jmol logo and then download the separate pieces. >> Q: Do you have access to a machine with a 1.1 JVM? Win98/WinME/Win2K? > > Win2K with IE6. Tres bien. Miguel ----- Open Source Molecular Visualization www.jmol.org miguel=40jmol.org ----- |
From: Peter Murray-R. <pm...@ca...> - 2005-02-07 11:13:59
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I have filed the following Jmol problem as a bug, but I think it warrants greater discussion: The following "CML" file from our Xindice database <entry src:col="/db/wwmm/nci/entry" src:key="nci_006229.xml"> <identifier tautomeric="0" version="0.932Beta"> <basic>C10H8,1H-2H-6H-10-8H-4H-3H-7H-9(10)5H-1</basic> <charge/> </identifier> <molecule formalCharge="0" id="NSC6229"> <formula>C 10 H 8</formula> ... snipped ... </entry> has namespaced prefixes added by Xindice but without the namespace URI (xmlns:src). This is an invalid file if validation is enforced but I think is otherwise OK. Under java1.4 there is no problem but under 1.5 the applet stops at a black background with the Java console error: SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml SmarterJmolAdapter:The Resolver thinks:Cml Using JAXP/SAX XML parser. Using JAXP/SAX XML parser. Using JAXP/SAX XML parser. SAX FATAL:The prefix "src" for attribute "src:col" associated with an element type "molecule" is not bound. org.xml.sax.SAXParseException: The prefix "src" for attribute "src:col" associated with an element type "molecule" is not bound. at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source) at org.jmol.adapter.smarter.CmlReader.readAtomSetCollection(CmlReader.java:71) ...... and more I think this should be trapped and reported as it fooled us for at least a day! In the future it is almost certain that people will submit "invalid" files on a regular basis and so validation should be switched off by default. I think this problem is intermediate between validation and non-validation. Without a schema there can be no validation so it's not a validation error, but it is certainly well-formed. I am not quite sure whether it is reasonable for a parser to throw a fatal error with the above file (It is also not very helpful for Xindice to emit it like this, although it is possible it is our fault). I suppose we shall retrofit the namespaceURI. Even advance brings its own crop of problems! P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |