Dear Bob, Thanks for the good overview and examples which I found very very useful!
Here is what I am trying to do. Please suggest the best way to handle this. (I remind you that way back in 2005 I made the decision not to use Jmol.js. At this point it seems easiest not to rewrite FirstGlance to use Jmol.js. The lack of Jmol.js has not caused any problem that I am aware of.) I am trying to detect the case when a PDB file is requested (by FirstGlance in Jmol) but is not available. The most likely case is when the PDB file corresponding to a new article in Nature has not been released on the date of publication, which occurs because nobody tells the PDB in advance when publication will occur. The PDB file is in the PDB but has status "HPUB" (hold for publication), so is not publically available. A current example (should remain HPUB at least until next Tuesday's new release batch) is http://www.rcsb.org/pdb/cgi/export.cgi/3IYE.pdb.gz So Jmol applet gets the command load http://www.rcsb.org/pdb/cgi/export.cgi/3IYE.pdb.gz this URL is redirected to http://www.rcsb.org/pdb/nosuchfile.jsp Jmol 11.8.14 generates this in the messageCallback stream: script ERROR: java.io.FileNotFoundException: http://www.rcsb.org/pdb/cgi/export.cgi/3IYE.pdb.gz Jmol displays this in a tiny red font at the top: java.io.FileNotFoundException: http://www.rcsb.org/pdb/nosuchfile.jsp My code watches the messageCallback stream for "FileNotFoundException" in the same line as "error" (ignoring case) and if this occurs, attempts to say something helpful to the user. My current code is confounded by the multiple concurrent messageCallbacks. (FirstGlance is installed together with an Apache server rewrite rule so the unsigned applet can fetch PDB files from other servers.) Thanks, -Eric --- On Sat, 1/23/10, Robert Hanson <hans...@stolaf.edu> wrote: From: Robert Hanson <hans...@stolaf.edu> Subject: Re: [Jmol-users] messageCallback again, before return To: jmol-users@lists.sourceforge.net Date: Saturday, January 23, 2010, 4:57 PM Eric, right,this is the problem with callbacks. Can you give us some examples of why you are using callbacks? If it is to gather information that you really want NOW not later, then a callback is the wrong mechanism. There are three replacement mechanisms we have gone to, leaving callbacks for user action responses. They are very direct, immediate, and useful. I hope one of these will work for you. 1) jmolEvaluate() This extremely useful method returns a value directly. Anything that can be put on a "print" command can be put here. var myJsVar = jmolEvaluate("script('show fileHeader')") alert(jmolEvaluate("{*}.label('%a\\t%n %5.3x\\t%5.3y\\t%5.3z')")) 2) jmolScriptWaitOutput() This function returns exactly what would go to the console synchronously. alert(jmolScriptWaitOutput("show pdbheader")) 3) jmolGetPropertyAsXXXXX() Three functions: jmolGetPropertyAsString(....) jmolGetPropertyAsArray(...) jmolGetPropertyAsJSON(...) allow you to use the "getProperty" command and directly access structured data. alert(jmolGetPropertyAsArray("modelInfo").modelCount) javascript:alert(jmolGetPropertyAsString("fileInfo","remark2")) This "fileInfo" one is all the information in the CIF or PDB file header. alert(jmolGetPropertyAsString("fileinfo.models[1]._cell_length_c") Bob On Sat, Jan 23, 2010 at 2:02 PM, Eric Martz <martze...@yahoo.com> wrote: In FirstGlance in Jmol I am using messageCallback more and more. Today I found why some control javascript that I wrote over a year ago, that relies on messageCallback, has been behaving strangely and basically not working. I have been working with Jmol 11.8.14 applet but upgrading is no problem. It seems that the next messageCallback occurs before the previous messageCallback has returned. My callback function is currently returning nothing. Thus, 6 (or possibly more) callbacks can be executing concurrently and asyncronously with each other. Because I did not anticipate this, the values of my external variables set in the callback function are set in an unpredictable way with unpredictable results. What I observed is that if I put alerts in the callback function, and if those alerts report the number of the callback (1 for the first callback, 2 for the second, and so forth) I see 1, 2, 3, 4, 5, 6, 5, 4, 3, 2, 1. In other words, callback 6 often (but not always?) completes and returns before callback 1 completes and returns. My interpretation of this is in the previous paragraph. Is there some way I can force messageCallback to wait for return of the function it calls before the next messageCallback occurs? If not, I can redesign some code and hopefully get it to work, but it seems to me that in general the "wait for return" would be a good thing. Thanks, -Eric ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
