Re: [Jmol-developers] Problems with openStringInline() & memory

[Robert H. <ha...@st...>]

Frankly, I can't help you with 11.2. That was so long ago, and the code has
changed so much, who knows what bug that could be. So this discussion
assumes at least 11.6; I'm using 11.7. I don't think you can use
JmolSimpleViewer for these purposes. Any particular reason you are using
that rather than JmolViewer itself? JmolViewer includes a method,
setModeMouse(int mode) that allows you to close out the viewer and start a
new one; JmolSimpleViewer does not.

  /**
   * NOTE: for APPLICATION AND APPLET call
   *
   *   setModeMouse(JmolConstants.MOUSE_NONE);
   *
   * before setting viewer=null
   *
   * in order to remove references to display window in listeners and
hoverWatcher


Failure to do that will certainly cause the effect you describe.

As for openStringInline(), that should work fine. But the sequence you
describe really should not work:

           viewer.openStringInline("<cif string>", true));
           viewer.evalString(strScript);
           String strError = viewer.getOpenFileError();


The first creates a model, the second adds a script to a queue, and the
third -- well, here's the note I made to myself:

  // The following was NOT what you think it was:
  //   abstract public String getOpenFileError();
  // Somewhere way back when, "openFile" became a method that did not create
  // the model set, but just an intermediary AtomSetCollection called the
"clientFile"
  // (and did not necessarily close the file)
  // then "getOpenFileError()" actually created the model set, deallocated
the file open thread,
  // and closed the file.

That could be 11.2.... I took that out, because it should never be used, at
least not in any recent version of Jmol.

In Jmol 11.6 or 11.7 it's way easier than this. All you would need is:

           viewer.evalString("data \"model\"\n" + cifString + "\nend
\"model\"\n" + strScript);

There should be no memory issues, provided you use

   viewer.setModeMouse(JmolConstants.MOUSE_NONE);

prior to disposing of the frame.


Bob

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900