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 <[email protected]> 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:[email protected]]
> *Sent:* Wednesday, November 04, 2009 11:46 AM
>
> *To:* [email protected]
> *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 <[email protected]> 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:[email protected]]
> *Sent:* Monday, November 02, 2009 12:01 PM
>
>
> *To:* [email protected]
> *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
>
>
>
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>
>
>
> --
> 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
>
>
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> trial. Simplify your report design, integration and deployment - and focus
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> what you do best, core application coding. Discover what's new with
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>
--
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
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