Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

I think it gets back to the issue of what is embedded in what. The magic of
the Jmol applet, of course, is that you can embed it in whatever context
you want -- Jena3D, for example. This is not directly possible for the Jmol
application. (It can be done, but you have to be a Java programmer to do
it.) So I am not seeing a solution for people who want to embed the Jmol
applet in a larger context. JavaFX is the other way around -- embed a web
page in a devoted Java project.

Bob

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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rolf Huehne]

Am 09.06.17 um 15:21 schrieb Robert Hanson:

Yes. By "felt" you mean that the browser will manage its threads
relating to tabs and other dyanamic content (e.g. ads), and it may shift
a running JavaScript app to a lower priority more likely than a running
Java application would or, in particular, then a running Java applet would.

When I tested this outside of Jmol with some Javascript it even seemed 
to me that a script run repeatedly was slowed down by the browser 
deliberately, although nothing else did change what would require to 
change the priority.


Regards,
Rolf

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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rolf Huehne]

Am 09.06.17 um 15:21 schrieb Robert Hanson:

I think we're one level off here. You can always run Jmol.jar if you
want Jmol's desktop application, and nothing is going to change about
that. It isn't an applet, so there is no browser issue.

I don't think that Jmol's current desktop application can replace the 
applet. Besides the rich functionality and powerful scripting language 
of Jmol in general, the strength of the applet is the flexibility to 
build any interface for Jmol you want.


Take for example the Jena3D Viewer (http://jena3d.leibniz-fli.de). 
Almost nothing of it's special functionalities could be transferred to 
the current desktop application.



My quick read of the JavaFX tutorial
[docs.oracle.com/javafx/2/overview/jfxpub-overview.htm
] suggests
that it is simply a newer way to build an independent Java desktop
application like Jmol.jar, but it has a wider set of user interface
capability than what we use now (Swing). Thus, they talk about being
able to insert a full-fledged webkit browser into the application, to
use CSS for styling, to dynamically create a user interface -- that sort
of thing.

And although the general Javascript performance is catching up with
Java, my observation is that it the performance is less stable. This
means that a task for example took anything from 60 seconds to 120
seconds (or even more) in the Javascript version, depending on how
the browser 'felt'. In contrast the Java version stably needed about
ten seconds, run on the same system before and after the Javascript
version.

Yes. By "felt" you mean that the browser will manage its threads
relating to tabs and other dyanamic content (e.g. ads), and it may shift
a running JavaScript app to a lower priority more likely than a running
Java application would or, in particular, then a running Java applet would.

A 1:12 performance ratio seems on the outside of what I have observed,
but I am sure that can happen. We are seeing 1:3 to 1:6 commonly.

I'm pretty sure the real benefit would be to use the WebGL option in
JSmol, or at least to develop that further. For example, by merging
NGL's excellent 3D capabilities into JSmol.

Rolf, do you have a sense of whether these slow-downs are rendering
issues? Or do they happen in relation to file opening, model
construction, or surface construction?

Rendering speed differences are rather difficult to quantify. If I 
rotate or zoom into a large structure with many translucent bonds, it is 
rather a qualitative shift: from almost unusable to totally unusable for 
most interactive work.


My quantitative observations are related to running times of Jmol 
scripts. In the Javascript version they run up to about 50 times slower 
than in the Java version. My general impression (a few month ago) was 
that built-in functions were running about 5 times slower than in Java, 
while user-defined functions were running up to 50 times slower.


Regards,
Rolf


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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

I don't know anything about JavaFX, but it's not clear to me there has
>> been any development on it since 2012 or 2014. Maybe just an idea that
>> never took off? Do you see some advantage to this?
>>
>> Since I don't have done any Java programming I will know even less. When
> I spoke to a computer scientist about the problem of dropped NPAPI plugin
> support by an increasing number of browsers, he suggested to become
> independent of any browser by combining the applet with already existing
> Java HTML5/CSS/Javascript engines. I have chosen the example engines just
> to illustrate the idea, not because I know anything particular about their
> suitability.
>
> It seems that Oracle still recommends JavaFX for Desktop applications.
> At last that is what the following post about the future of JavaFX from
> 2016 (unfortunately in German) suggests: https://jaxenter.de/hart-aber-
> fair-welche-zukunft-hat-javafx-37199 . Among other things it describes
> the reaction of Oracle to a request of an interest group of german Java
> users (iJUG) about the future of JavaFX. According to this Oracle
> recommends it and has an official roadmap for it until 2028.
>
> The advantage I see with the general idea is that each Jmol-based web
> service, running in the future with the Javascript version, could also be
> run as a Java desktop application.
>
>
I think we're one level off here. You can always run Jmol.jar if you want
Jmol's desktop application, and nothing is going to change about that. It
isn't an applet, so there is no browser issue.

My quick read of the JavaFX tutorial [
docs.oracle.com/javafx/2/overview/jfxpub-overview.htm] suggests that it is
simply a newer way to build an independent Java desktop application like
Jmol.jar, but it has a wider set of user interface capability than what we
use now (Swing). Thus, they talk about being able to insert a full-fledged
webkit browser into the application, to use CSS for styling, to dynamically
create a user interface -- that sort of thing.

And although the general Javascript performance is catching up with Java,
> my observation is that it the performance is less stable. This means that a
> task for example took anything from 60 seconds to 120 seconds (or even
> more) in the Javascript version, depending on how the browser 'felt'. In
> contrast the Java version stably needed about ten seconds, run on the same
> system before and after the Javascript version.
>
> Yes. By "felt" you mean that the browser will manage its threads relating
to tabs and other dyanamic content (e.g. ads), and it may shift a running
JavaScript app to a lower priority more likely than a running Java
application would or, in particular, then a running Java applet would.

A 1:12 performance ratio seems on the outside of what I have observed, but
I am sure that can happen. We are seeing 1:3 to 1:6 commonly.

I'm pretty sure the real benefit would be to use the WebGL option in JSmol,
or at least to develop that further. For example, by merging NGL's
excellent 3D capabilities into JSmol.

Rolf, do you have a sense of whether these slow-downs are rendering issues?
Or do they happen in relation to file opening, model construction, or
surface construction?

Bob



>
> Regards,
> Rolf
>
> 
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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-- 
Robert M. Hanson
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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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rolf Huehne]

Am 08.06.17 um 19:44 schrieb Robert Hanson:



On Thu, Jun 8, 2017 at 10:58 AM, Rolf Huehne > wrote:

Am 08.06.17 um 14:41 schrieb Robert Hanson:

RIP,  Java applets.

Since there still are many situations where the superior Java
performance would be helpful (large structures; surfaces; complex
Jmol scripts that are running about 50 times slower in the
Javascript version) it would still be good to have a Java version
with the flexibility of the applet to build customized user interfaces.

sorry, didn't mean to imply that we were dropping applet production.
It's all produced in a few clicks of a button -- Jmol app, Jmol applet,
JmolData, JSmol. So I will keep that happening the same.

I havn't misunderstood that. But an applet can only be of public use if 
there are systems available supporting it.



I am wondering how much effort it would be to extend the applet by a
HTML/CSS rendering and Javascript engine like it is provided by
systems like 'JavaFX - WebView Component
(https://docs.oracle.com/javase/8/javafx/api/toc.htm


https://stackoverflow.com/questions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane

),
Oracle Nashorn
(http://www.oracle.com/technetwork/articles/java/jf14-nashorn-2126515.html

),
and HtmlUnit (http://htmlunit.sourceforge.net/
).

I woud guess one of the critical points would be how much of the
Javascript/Applet communication would still be possible in such
application.


I don't know anything about JavaFX, but it's not clear to me there has
been any development on it since 2012 or 2014. Maybe just an idea that
never took off? Do you see some advantage to this?

Since I don't have done any Java programming I will know even less. When 
I spoke to a computer scientist about the problem of dropped NPAPI 
plugin support by an increasing number of browsers, he suggested to 
become independent of any browser by combining the applet with already 
existing Java HTML5/CSS/Javascript engines. I have chosen the example 
engines just to illustrate the idea, not because I know anything 
particular about their suitability.


It seems that Oracle still recommends JavaFX for Desktop applications.
At last that is what the following post about the future of JavaFX from 
2016 (unfortunately in German) suggests: 
https://jaxenter.de/hart-aber-fair-welche-zukunft-hat-javafx-37199 . 
Among other things it describes the reaction of Oracle to a request of 
an interest group of german Java users (iJUG) about the future of 
JavaFX. According to this Oracle recommends it and has an official 
roadmap for it until 2028.


The advantage I see with the general idea is that each Jmol-based web 
service, running in the future with the Javascript version, could also 
be run as a Java desktop application.


And although the general Javascript performance is catching up with 
Java, my observation is that it the performance is less stable. This 
means that a task for example took anything from 60 seconds to 120 
seconds (or even more) in the Javascript version, depending on how the 
browser 'felt'. In contrast the Java version stably needed about ten 
seconds, run on the same system before and after the Javascript version.


Regards,
Rolf

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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

On Thu, Jun 8, 2017 at 10:58 AM, Rolf Huehne 
wrote:

> Am 08.06.17 um 14:41 schrieb Robert Hanson:
>
>> RIP,  Java applets.
>>
>> Since there still are many situations where the superior Java performance
> would be helpful (large structures; surfaces; complex Jmol scripts that are
> running about 50 times slower in the Javascript version) it would still be
> good to have a Java version with the flexibility of the applet to build
> customized user interfaces.
>
> sorry, didn't mean to imply that we were dropping applet production.  It's
all produced in a few clicks of a button -- Jmol app, Jmol applet,
JmolData, JSmol. So I will keep that happening the same.



> I am wondering how much effort it would be to extend the applet by a
> HTML/CSS rendering and Javascript engine like it is provided by systems
> like 'JavaFX - WebView Component (https://docs.oracle.com/javas
> e/8/javafx/api/toc.htm https://stackoverflow.com/ques
> tions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane),
> Oracle Nashorn (http://www.oracle.com/technetwork/articles/java/jf14-
> nashorn-2126515.html), and HtmlUnit (http://htmlunit.sourceforge.net/).
>
> I woud guess one of the critical points would be how much of the
> Javascript/Applet communication would still be possible in such application.
>

I don't know anything about JavaFX, but it's not clear to me there has been
any development on it since 2012 or 2014. Maybe just an idea that never
took off? Do you see some advantage to this?

Bob
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rolf Huehne]

Am 08.06.17 um 14:41 schrieb Robert Hanson:

RIP,  Java applets.

Since there still are many situations where the superior Java 
performance would be helpful (large structures; surfaces; complex Jmol 
scripts that are running about 50 times slower in the Javascript 
version) it would still be good to have a Java version with the 
flexibility of the applet to build customized user interfaces.


I am wondering how much effort it would be to extend the applet by a 
HTML/CSS rendering and Javascript engine like it is provided by systems 
like 'JavaFX - WebView Component 
(https://docs.oracle.com/javase/8/javafx/api/toc.htm 
https://stackoverflow.com/questions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane), 
Oracle Nashorn 
(http://www.oracle.com/technetwork/articles/java/jf14-nashorn-2126515.html), 
and HtmlUnit (http://htmlunit.sourceforge.net/).


I woud guess one of the critical points would be how much of the 
Javascript/Applet communication would still be possible in such application.


Regards,
Rolf

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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Eric Martz]

Hi, Henry,

In addition to Internet Explorer 11* (still included in Windows 10 as 
far as I know), several minor browsers that still supported Java when 
last I checked in March 2017 are listed here:


http://proteopedia.org/w/Installing_and_enabling_Java#Browsers_That_Support_Java

* See

http://proteopedia.org/w/Installing_and_enabling_Java#Accessing_Internet_Explorer_in_Windows_10

-Eric

On 6/8/17 6:29 AM, Rzepa, Henry S wrote:

I have had a look at Safari preview 32.  In the preferences/security tab, the 
current production safari has settings for

1. Allow WebGL
2. Allow Internet Plugins,  and in this latter one can configure to allow  Java.

In Safari 32, both of these are now gone.   With  High Sierra developer preview 
about to be released into  beta, may bring confirmation that  Safari too has 
now not merely been deprecated but disallowed.

If correct, this means that Jmol.jar can only now run in application mode, and 
not as a browser plugin.

Still,  Apple promise that the new Safari will be  “faster”, although  I 
suspect it has some way to go to be as fast as compiled Java.


I wonder what the missing  WebGL means? It never really took off did it!

Henry


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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

09/29/2005  08:18 AM 1,813,012 ch3cl-density.cub
09/17/2006  07:47 AM   600,830 ch3cl-density.cub.gz
06/08/2017  08:39 AM 4,631 ch3cl-density.jvxl
06/08/2017  08:40 AM 2,928 ch3cl-density.jvxl.gz

So that is 390:1 with just the JVXL, or 619:1 compression using JVXL+GZ.

(There is never a need to use GZ for web-based files; they almost certainly
will be automatically gzipped by the server anyway.)

So I can't say I'm super impressed. If it's truly full volume data, that
would be impressive.

Bob


On Thu, Jun 8, 2017 at 7:48 AM, Rzepa, Henry S 
wrote:

>
> > On 8 Jun 2017, at 13:45, Robert Hanson  wrote:
> >
> > ps -- neither of the VMD images at http://www.ch.imperial.ac.uk/
> rzepa/blog/?p=18365#comment-243964 are volume rendering, by the way. They
> are just surfaces, one with reflection; one just a mesh. Right?
>
> Yes.  The  reduction in cube size of  ~500 is impressive, but then  JVXL
> manages ~100 (and perhaps more if compressed?)
>
> Contact  Brian Skinner for the inside story.  bsk...@alum.mit.edu
>
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rzepa, Henry S]

> On 8 Jun 2017, at 13:45, Robert Hanson  wrote:
> 
> ps -- neither of the VMD images at 
> http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 are volume 
> rendering, by the way. They are just surfaces, one with reflection; one just 
> a mesh. Right?

Yes.  The  reduction in cube size of  ~500 is impressive, but then  JVXL 
manages ~100 (and perhaps more if compressed?)

Contact  Brian Skinner for the inside story.  bsk...@alum.mit.edu

> 
> On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson  wrote:
> RIP,  Java applets.
> 
> On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S  wrote:
> I have had a look at Safari preview 32.  In the preferences/security tab, the 
> current production safari has settings for
> 
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow  
> Java.
> 
> In Safari 32, both of these are now gone.   With  High Sierra developer 
> preview about to be released into  beta, may bring confirmation that  Safari 
> too has now not merely been deprecated but disallowed.
> 
> If correct, this means that Jmol.jar can only now run in application mode, 
> and not as a browser plugin.
> 
> Still,  Apple promise that the new Safari will be  “faster”, although  I 
> suspect it has some way to go to be as fast as compiled Java.
> 
> 
> I wonder what the missing  WebGL means? It never really took off did it!
> 
> ?? WebGL is fantastic. Everyone is using it, including JSmol if you use that 
> option. See this note relative to WebGPU, though: 
> https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/
> 
> Is curious, though. I can't seem to find any reference to WebGL at the 
> preview site. Where do you see that, Henry?
> 
> 
> Bob
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> 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
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! 
> http://sdm.link/slashdot___
> Jmol-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users



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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

ps -- neither of the VMD images at
http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 are volume
rendering, by the way. They are just surfaces, one with reflection; one
just a mesh. Right?

On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson  wrote:

> RIP,  Java applets.
>
> On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S 
> wrote:
>
>> I have had a look at Safari preview 32.  In the preferences/security tab,
>> the current production safari has settings for
>>
>> 1. Allow WebGL
>> 2. Allow Internet Plugins,  and in this latter one can configure to
>> allow  Java.
>>
>> In Safari 32, both of these are now gone.   With  High Sierra developer
>> preview about to be released into  beta, may bring confirmation that
>> Safari too has now not merely been deprecated but disallowed.
>>
>> If correct, this means that Jmol.jar can only now run in application
>> mode, and not as a browser plugin.
>>
>> Still,  Apple promise that the new Safari will be  “faster”, although  I
>> suspect it has some way to go to be as fast as compiled Java.
>>
>>
>> I wonder what the missing  WebGL means? It never really took off did it!
>>
>
> ?? WebGL is fantastic. Everyone is using it, including JSmol if you use
> that option. See this note relative to WebGPU, though:
> https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/
>
> Is curious, though. I can't seem to find any reference to WebGL at the
> preview site. Where do you see that, Henry?
>
>
> Bob
>
>


-- 
Robert M. Hanson
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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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

RIP,  Java applets.

On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S 
wrote:

> I have had a look at Safari preview 32.  In the preferences/security tab,
> the current production safari has settings for
>
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow
> Java.
>
> In Safari 32, both of these are now gone.   With  High Sierra developer
> preview about to be released into  beta, may bring confirmation that
> Safari too has now not merely been deprecated but disallowed.
>
> If correct, this means that Jmol.jar can only now run in application mode,
> and not as a browser plugin.
>
> Still,  Apple promise that the new Safari will be  “faster”, although  I
> suspect it has some way to go to be as fast as compiled Java.
>
>
> I wonder what the missing  WebGL means? It never really took off did it!
>

?? WebGL is fantastic. Everyone is using it, including JSmol if you use
that option. See this note relative to WebGPU, though:
https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/

Is curious, though. I can't seem to find any reference to WebGL at the
preview site. Where do you see that, Henry?


Bob
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