Hmm. I don't think it's Jmol. The only way that can happen is if the file
reader somehow has no file path. But we have in AtomSetCollectionReader:
filePath = "" + htParams.get("fullPathName");
Ah, wait, this could be:
public Object getInfo(int modelIndex, String key) {
return (modelIndex < 0 ? null : am[modelIndex].auxiliaryInfo.get(key));
}
maybe your modelIndex < 0.
So I don't see how that can become null.
Try taking a look at viewer.ms.msInfo and seeing what its keys are.
It's public. You are basically saying that in that Hashtable there is no
"modelFile" key.
Hard to believe....
On Thu, Aug 25, 2016 at 12:23 PM, Charles Ofoegbu (Staff) <
[email protected]> wrote:
> Dear Bob,
>
> We are updating Jalview’s Jmol from version 14.2.14_2015 to
> 14.6.1_2016.08.11. So far everything seems to work well. However, a new bug
> showed up when superposing structures. I’ve tracked it down to the method
> getModelFileName(modelIndex) in ModelSet class which usually returns
> the absolute file path in version 14.2.14_2015 but now returns a null
> string in 14.6.1_2016.08.11.
>
> I’m wondering if this is a bug or if a there is a new method for getting
> the FileName for a loaded model?
>
> Thanks and regards,
> Charles
>
>
>
> Ofoegbu Tochukwu Charles
> Jalview Visual Analytics Developer/Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK.
> Skype: cofoegbu
> www.jalview.org
> www.compbio.dundee.ac.uk
>
>
>
>
>
>
>
>
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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