I have two main comments on this.
1. Back in the summer I produced my own modifications of the
jmolCheckbox() function, as indicated by the comments in my modified
version of Jmol.js for 10.2:
The jmolCheckbox() function has been cloned and modified to give:
jmolCheckboxMaster() and jmolCheckboxSlave(), which have their own
counters and generate ids of the type jmolChkboxMaster0 and
jmolChkboxSlave0, ..1, ...2. These generate checkboxes with one
additional
function for onClick(). In the case of the 'master' the updateSlaves()
funtion sets all the 'slave' checkboxes to the same state as the master
after the master has been clicked. In the case of the 'slaves' the
notifyMaster() function determines whether the change of state of
the slave
has resulted in a situation in which all slaves are now checked
(when the
master must be likewise updated) or a situation in which not all
slaves are
checked (in which case the master should be unchecked).
It is in use on my web app at http://doolittle.ibls.gla.ac.uk/motif
and notified the developers group about it (unfortunately I have not
the email to hand) and was told that it would be incorporated in the
next release. It is not in 11.0.RC3. I think it would be a useful
addition, but if it is not going to be included, I need to know so
that I can mount a branch on my own website and reference it in
publications.
2. The SourceForge page at http://jmol.sourceforge.net/jslibrary/
needs the following modifications to make it intelligible to non-
cognoscenti. In making these modifications you should treat users
like adults and tell them what the alternative are.
a. The first section entitled "Why should you use Jmol.js?" should be
replaced by a section entitled "What is Jmol.js?" explaining what
Jmol.js provides. As I understand it, it provides two rather distinct
things, which should be clearly differentiated and spelled out. In
brief:
(i) Jmol.js provides a way of providing user controls to the Jmol
applet on the web page. You can set up a page to load a molecule of
interest and then provide buttons and checkboxes to allow the user to
change specific features of the appearance of the molecule, its
background, cause it to rotate etc. (This is possible through a
technology called LiveConnect that allows web pages to interact with
applets.) The alternative is to leave the user to manipulate the
molecule through the inbuilt applet controls or console commands,
which are only really suitable for users familiar with Jmol.
(ii) Jmol.js also provides functions to control the html and css
layout of the applet on the web page. Even if you prefer to write
your own css, the basic javascript for displaying the applet is
highly recommended. If you prefer to manage your own html and css,
you can leave the css parameters blank in the functions that accept
them.
b. General Recommendations
REMOVE THE CHILDISH AND MISLEADING NONSENSE ABOUT ABSOLUTE REFERENCES
BEING EVIL!
And that's shouting. But I've raised this point before.
The sentence: "Absolute URLs which start with http:// are evil and
should never be used."
should be replaced by:
"Absolute URLs (those starting with http:/)" are generally considered
bad practice and should be replaced by references relative to the
calling page wherever possible. It is, however, sometimes impossible
to avoid them (e.g. when pages are generated on the fly from servlets
etc.)" or something of the sort.
I have to use absolute references for my servlets, and they work, and
I resent being presented with dogmatic statements with no explanation
involving severe misuse of English. Computer geeks may know that when
they use the word 'evil' they don't mean 'evil' in the biblical
sense, but who the hell do you think you are writing these pages for?
The pages are meant to help people us Jmol.js. This you do by
explaining the reason for recommendations, not by blanket statement
to try to enforce your own html prejudices on people. Honi soit qui
mal y pense.
c. Link (but there isn't one)
How about a statement that Jmol.js is part of the Jmol download
package, and a link to where you can download the Jmol.js. After all,
isn't that what one would expect? And let's make it accurate, unlike
the link on the present download page which states that the current
official release is version 10.2, and then leads you to a page in
which 10.2 is nowhere to be found, and all the versions available
seem to developmental versions.
David Leader
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