Egon Willighagen wrote:
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On Monday 27 September 2004 18:01, Bob Hanson wrote:
I also checked out Jmol-web and CVSROOT, so I think I now have pretty much the whole thing.
CVSROOT is not something you need to have a look at. It contains stuff enabling CVS commands to be tracked... e.g. there are scripts that will ensure that the CVS commits gets loged to the jmol-commits@ mailing list, which I can recommend to subscribe to, and loged to the #cdk IRC chat channel on the irc.freenode.net network, where CDK developers get together (and Miguel too in the past, but not lately...)
Right, I see that now. Interesting, but not something I would ever deal with directly. I see that it's all unused except checkoutlist, ciabot_cvs, loginfo, and syncmail. That makes sense. What a slick system.
OK, let's talk a bit about how/where you see the documentation fitting in. I think I need to incorporate your header in there, for example.
Yes, it would need a header with some information: license, and some CVS tracking info. E.g.:
/* $RCSfile: JmolApplet.java,v $ * $Author: migueljmol $ * $Date: 2004/07/30 11:50:57 $ * $Revision: 1.89 $ * * ... etc
The $RCSfile: $ etc. gets updated whenever you do a commit.
I see. The keywords $RCSfile $Author $Date $Revision define fields that will be updated. What's the ",v" in $RCSfile? Or don't I worry about that, because these will be updated automatically? I presume that if this information is not present, then that's OK (I see it isn't in every .js file, for example). But it makes sense for me to put it in. I notice that it also isn't in the xml files in the Jmol-web/doc/source area.
Is there a specific directory that this needs to go into? Basically it's a couple of .htm files and .js files in a main directory and a set of examples in a subdirectory. In addition, there is a .xls file that generates all the code.
I assume that it's quite standalone, but will get placed on www.jmol.org. The Jmol-web modules might apply, but am not sure if it would conflict with the current dir structure... Miguel?
Directories:
I see
Jmol-web/source/doc/demo/
subdirectories for topics; no obvious introductory or explanatory HTML contains jmol/
Jmol-web/source/doc/docs/index.xml
this seems the logical place to introduce this as a fourth resource.
XML:
OK, I'm catching on. I haven't used XML before, but this is slick.
I can see right now that
http://jmol.sourceforge.net/scripting/index.xml
needs some updating. (I'm not volunteering.)
Q: What provision is in place to allow this site to be house-tested prior to going "live" with users?
Also, am I right that "codebase" can't refer to "../../applet" that is, two levels up and one over? When I tried that I got an error.
How on the project site are you maintaining reference all to the same .jar file?
When on www.jmol.org we have the option to say something like codebase="/jmol/Jmol.jar" which would point to www.jmol.org/jmol/Jmol.jar
But ../ in codebase="" should work too, see http://jmol.sourceforge.net/applet/
I see how [codebase] is working:
<applet name="anim" code="JmolApplet" archive="JmolApplet.jar"
codebase="[codebase]"
width="350" height="350" mayscript="true">
<param name="load" value="SN1_reaction.xyz">
</applet>does the trick. This is getting integrated using build.xml
I also see in build.xml how that gets replaced differently depending upon the location of the file. Fabulous.
I'm curious where http://jmol.sourceforge.net/jmol/ comes from, as I don't see it under Jmol-web. Oh, wait. I see. It's created in the build. OK. It looks to me like the demos in
http://jmol.sourceforge.net/demo/
are using their own private version. Hmm:
http://jmol.sourceforge.net/jmol/ JmolApplet.jar 21-Sep-2004 13:24 620k JmolApplet.properties 21-Sep-2004 13:24 1k
http://jmol.sourceforge.net/demo/jmol/ Jmol.js 21-Sep-2004 13:23 17k JmolApplet.jar 21-Sep-2004 13:23 516k
How do you explain the two different file sizes? Created just a minute apart?
OK, so I presume the demo pages are using their own applet. Maybe there's a reason for this.... I'd rather just use the main applet.
Is that because you can't use the relative reference ../../jmol/ as a codebase in demo/aminoacids ?
Is this the way it should be?
suggestion:
I suggest that I compose the page as XML within the /demo/ directory. (Do you just do this by hand, or do you have an XML writer? It would be good for me to do it by hand. I'll learn XML. I realize I have to be far more careful with my tags and such. Most of it is in .js files, anyway. But it would be interesting to code the example pages as XML. That might be a later project.)
What are people's feelings about the demos currently in /demo/? Should I try to integrate them into the documentation somehow?
Bob
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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