Jmol devs...
I apologize for "breaking the build" over the weekend by checking stuff
into the main trunk erroneously. Luckily Miguel spotted the error and
asked me to revert the changes, hopefully before anyone was inconvenienced
by this. I am truely sorry about t hat.
Miguel - I already *am* on this mailing list from [EMAIL PROTECTED],
and I
had thought my Pfizer email would be fixed by now, but alas no.
So the work I was trying to do was...
I work on the open source project PFAAT, a protein alignment tool. We
have switched over
to using Jmol as the 3D molecule viewer for this project and have been
very happy with it. I have
modified Jmol in a few small ways to make it easier to use Jmol as a
viewer for an existing application.
Some of the changes that I made, such as the JmolSelectionListener
stuff, have already been merged
in by Miguel already prevoiusly. I am ready to merge in the few
remaining features that we added.
Some of the features do not cause any problems - such as making some
private data members protected,
adding a feature to not do System.exit() when the last Jmol window is
closed, etc.
There is one feature we added that represents a more significant change
and this is the one I added that
"broke the build" or more property "broke the applet". We added a
SelectWithin dialog to help
visually construct a script statement for selecting atoms withing a
given range of some atomic feature, such
as other atoms, the protein backbone, etc.
I added code to Eval.java etc. to allow for a command:
selectWithinDialog. This dialog was in the
package org.openscience.jmol.app. Ie...it is a feature that is intended
for the standalone application, but
not for the Applet. I belive this was one of the mistakes I made:
checking in these chagnes to Eval.java,
because it referred to code that is meant only for the standalone app.
The other mistake I made was I was checking things into the main trunk,
not into a branch created for
the purpose of exploring these features and how they should be merged
into Jmol.
As for the selectWithinDialog command - what Miguel and I had talked
about was creating a more generic
command for launching dialogs created by end -user / programmers for use
with standalone Jmol. Something
maybe like...
open dialog XXXX
The idea is the standalone app would register a "handler" with the core
that listed what dialogs it could open
and have the core Eval stuff call on that handler when a script is
executed to open one of those dialogs.
So...if anyone has any ideas they think I should keep in mind while
building this, let me know.
And Miguel - am I allowed to make my own branch or do I ask you or Egon
to create it for me? If I cannot do
it would you please create a branch for me to work in?
- Paul Dana
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