On Sat, Feb 23, 2013 at 8:28 AM, Egon Willighagen <
[email protected]> wrote:
>
> I very briefly tried to upgrade Jmol in Bioclipse last week; Bioclipse
> 2.6.0 uses 11.8.17. I tried upgrading to 13.x but there were too many
> API changes. Is there an migration help page, by any change? And,
> would it already be worth upgrading to the latest 11.x? That would be
> easier and still perhaps improve Bioclipse 2.6.1 ?
>
>
Yes, I'm sure that's an issue. Most notably might be that we are no longer
using javax.vecmath -- don't know how much of an issue that is for you, as
there are no references to these classes in JmolViewer, I think.
As you can imagine, there was a tremendous amount of refactoring to do to
make this all compatible with JavaScript. Doing a compare of JmolViewer to
11.7.45, I see that these references are all gone:
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Event;
import java.awt.Graphics;
import java.awt.Image;
import java.awt.Rectangle;
import java.util.BitSet;
import javax.vecmath.Matrix4f;
import javax.vecmath.Point3f;
All the java.awt references are now Object, because Android and JavaScript
can't deal with java.awt. java.util.BitSet is now jmol.org.util.BS;
Matrix4f is now jmol.org.util.Matrix4f, and Point3f is now
jmol.org.util.P3.
I can imagine that it will be quite a job to adjust to that.
One thing you could to would be to go to 13.0. That doesn't make any
changes in vecmath and just moves all those awt references to Object.
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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