From: Joe G. <jmg@SeiraD.com> - 2009-11-04 20:16:01
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GREAT _____ From: Robert Hanson [mailto:ha...@st...] Sent: Wednesday, November 04, 2009 1:06 PM To: jmo...@li... Subject: Re: [Jmol-developers] inline clarification I have a similar idea, but it will be more integrated. Cannot work on this for 5 hours now, but I'm sure I can get it. Definitely not quite that simple, but close. Bob On Wed, Nov 4, 2009 at 1:19 PM, Joe Gatewood <jm...@se...> wrote: Bob, I was looking though the code and found viewer.openReader calling FileManager.createAtomSetCollectionFromReader I created a Reader extension than read an array. I was able to wrap my class with a BufferedReader and read the array. I thought I had a solution but createAtomSetCollectionFromReader opens the file that Reader is accessing to determine the file type, I think. The need to access the file to determine type when the Reader is at hand seems very odd. Anyway if I could pass the data type ie "pdb" ,etc to openReader and then createAtomSetCollectionFromReader used that type instead of setting type to null as currently implemented I think I would be OK. On the other hand I could hand you a String[] or List<String> and leave the details to you. Whatever you think best is fine with me. Joe _____ From: Robert Hanson [mailto:ha...@st...] Sent: Wednesday, November 04, 2009 11:46 AM To: jmo...@li... Subject: Re: [Jmol-developers] inline clarification It's certainly an interesting idea. The reader is a linear reader, so it should not matter. I think the method might exclude XML formats and, of course binary formats, just because those aren't line oriented, but all the rest are. I wonder.... So what you suggest is replacing a "BufferedReader" with a "StringArrayReader" in effect. I probably have just enough time to try that. So you will give me a String[] or a Vector? Bob On Wed, Nov 4, 2009 at 10:53 AM, Joe Gatewood <jm...@se...> wrote: Bob, I managed to get the data sets with multiple models to load inline. I had to increase the heap size. I am currently of the opinion however that loading files from arrays could be made more efficient. As you obviously know using the inline approach includes Convert the array of lines to a "really big string" with some form of line delimiters Pass this "really big string" to Jmol which then looks for the delimiters and breaks the string back into an array. All this is just to get the data back into the starting form. Is there a reason we can not just pass an array of data directly to Jmol? Thanks, Joe _____ From: Robert Hanson [mailto:ha...@st...] Sent: Monday, November 02, 2009 12:01 PM To: jmo...@li... Subject: Re: [Jmol-developers] inline clarification Joe, there shouldn't be any need to write a file - you are correct; you should be able to use those directly. The Java StringBuffer is a very efficient mechanism. Don't use String = String + line. Use StringBuffer sb = new StringBuffer(); int nLines = myArrayList.size(); for (int i = 0; i < nLines; i++) sb.append(myArrayList.get(nLines)).append('\n'); viewer.loadInline(sb.toString()); That should be equivalent to loading the multiple models as separate models -- it will automatically create a model for each MODEL statement. Bob ---------------------------------------------------------------------------- -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 ---------------------------------------------------------------------------- -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 |