Dear Jalview developers,
Just a quick word to ask for a feature that would be greatly appreciated from the users of Jalview on the "Mobyle" portals (and maybe elsewhere?): we released officially a short time ago a feature that allows users to visualize data in applets like Jalview or Archaeopteryx, but also to bookmark them back to the server. This is apparently a popular feature, and had been asked for a long time.
Additionally, we wanted to enable users to take screenshots of the data as viewed in the applets, for publication purpose for instance. Thanks to Christian Zmasek, we have been able to add a method in the Archaeopteryx applet that returns the a screenshot of the edited phylogenetic tree in a chosen format, eg JPEG, and byte 64 encoded so that it can be retrieved as a string using javascript. Following this, the byte 64 encode string is sent to the server, where it is appropriately decoded and saved in the user workspace. This way users can take screenshots of their trees anytime during their work and save them for future use. First user trainings show that users like a lot this feature, but would like to get it as well in Jalview...
I know my technical explanations are probably not extremely clear, if you prefer to see the code, here is the forester revision where I included this feature in Archaeopteryx:
https://code.google.com/p/forester/source/detail?r=273.
Please let me know if something similar can be considered for Jalview.
Best,
Hervé Ménager
Hi Hervé! Nice to hear from you! 
elsewhere?): we released officially a short time ago a feature that
allows users to visualize data in applets like Jalview or Archaeopteryx,
but also to bookmark them back to the server. This is apparently a
popular feature, and had been asked for a long time.
This sounds very useful. I presume the bookmark is made to a URL on the mobyle server that launches the applets ?
Additionally, we wanted to enable users to take screenshots of the data
as viewed in the applets, for publication purpose for instance. Thanks
to Christian Zmasek, we have been able to add a method in the
Archaeopteryx applet that returns the a screenshot of the edited
phylogenetic tree in a chosen format, eg JPEG, and byte 64 encoded so
that it can be retrieved as a string using javascript. Following this,
the byte 64 encode string is sent to the server, where it is
appropriately decoded and saved in the user workspace. This way users
can take screenshots of their trees anytime during their work and save
them for future use. First user trainings show that users like a lot
this feature, but would like to get it as well in Jalview...
I took a look at the code. It would certainly be possible to add a method like this to the Jalview API, but there are a couple of subtle aspects which means I can't fit it in to the forthcoming release.
It's certainly something that could be looked at for the next but one - and will, in fact, be even easier to implement, since the jalview application includes all the machinery for figure generation, and the next few releases will bring the applet and application even closer together.
I've added a note on a rather old feature request about this solution - since a Javascript method (which we weren't really considering as a viable solution back in 2005) would neatly get around the difficulty of having an unsigned applet save an image to disk. A solution like the one Christian implemented would enable any javascript on the page to access images from the applet.
Jim.
···
On Thu Jun 7 21:40:12 2012, Hervé Ménager wrote:
Hi Jim,
Hi Hervé! Nice to hear from you!
elsewhere?): we released officially a short time ago a feature that
allows users to visualize data in applets like Jalview or Archaeopteryx,
but also to bookmark them back to the server. This is apparently a
popular feature, and had been asked for a long time.
This sounds very useful. I presume the bookmark is made to a URL on the
mobyle server that launches the applets ?
Yes, exactly.
Additionally, we wanted to enable users to take screenshots of the data
as viewed in the applets, for publication purpose for instance. Thanks
to Christian Zmasek, we have been able to add a method in the
Archaeopteryx applet that returns the a screenshot of the edited
phylogenetic tree in a chosen format, eg JPEG, and byte 64 encoded so
that it can be retrieved as a string using javascript. Following this,
the byte 64 encode string is sent to the server, where it is
appropriately decoded and saved in the user workspace. This way users
can take screenshots of their trees anytime during their work and save
them for future use. First user trainings show that users like a lot
this feature, but would like to get it as well in Jalview...
I took a look at the code. It would certainly be possible to add a
method like this to the Jalview API, but there are a couple of subtle
aspects which means I can't fit it in to the forthcoming release.
No worry about this, it is not an urgent matter, it is more in the "cool to have" category. Many of our users have to rely on programs like boxshade to print multiple alignments, but I think using a GUI like Jalview would be far easier for them, in a WYSIWYG approach.
It's certainly something that could be looked at for the next but one -
and will, in fact, be even easier to implement, since the jalview
application includes all the machinery for figure generation, and the
next few releases will bring the applet and application even closer
together.
I've added a note on a rather old feature request about this solution -
since a Javascript method (which we weren't really considering as a
viable solution back in 2005) would neatly get around the difficulty of
having an unsigned applet save an image to disk. A solution like the one
Christian implemented would enable any javascript on the page to access
images from the applet.
Exactly what I meant. Thanks a lot for accepting this feature request. If you need testing, just contact me, I'll be happy to help in any way.
Hervé
···
On 06/11/2012 08:58 AM, Jim Procter wrote:
On Thu Jun 7 21:40:12 2012, Hervé Ménager wrote:
Jim.
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Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Err, perhaps I have missed something, but if your users just need to print from Jalview, why not use the Jalview application? You can make the applet launch the application quite easily.
G.
···
On 11/06/2012 19:23, Hervé Ménager wrote:
Hi Jim,
On 06/11/2012 08:58 AM, Jim Procter wrote:
Hi Hervé! Nice to hear from you!
On Thu Jun 7 21:40:12 2012, Hervé Ménager wrote:
elsewhere?): we released officially a short time ago a feature that
allows users to visualize data in applets like Jalview or Archaeopteryx,
but also to bookmark them back to the server. This is apparently a
popular feature, and had been asked for a long time.
This sounds very useful. I presume the bookmark is made to a URL on the
mobyle server that launches the applets ?
Yes, exactly.
Additionally, we wanted to enable users to take screenshots of the data
as viewed in the applets, for publication purpose for instance. Thanks
to Christian Zmasek, we have been able to add a method in the
Archaeopteryx applet that returns the a screenshot of the edited
phylogenetic tree in a chosen format, eg JPEG, and byte 64 encoded so
that it can be retrieved as a string using javascript. Following this,
the byte 64 encode string is sent to the server, where it is
appropriately decoded and saved in the user workspace. This way users
can take screenshots of their trees anytime during their work and save
them for future use. First user trainings show that users like a lot
this feature, but would like to get it as well in Jalview...
I took a look at the code. It would certainly be possible to add a
method like this to the Jalview API, but there are a couple of subtle
aspects which means I can't fit it in to the forthcoming release.
No worry about this, it is not an urgent matter, it is more in the "cool
to have" category. Many of our users have to rely on programs like
boxshade to print multiple alignments, but I think using a GUI like
Jalview would be far easier for them, in a WYSIWYG approach.
It's certainly something that could be looked at for the next but one -
and will, in fact, be even easier to implement, since the jalview
application includes all the machinery for figure generation, and the
next few releases will bring the applet and application even closer
together.
I've added a note on a rather old feature request about this solution -
since a Javascript method (which we weren't really considering as a
viable solution back in 2005) would neatly get around the difficulty of
having an unsigned applet save an image to disk. A solution like the one
Christian implemented would enable any javascript on the page to access
images from the applet.
Exactly what I meant. Thanks a lot for accepting this feature request.
If you need testing, just contact me, I'll be happy to help in any way.
Hervé
Jim.
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
--
Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096
Hi,
Err, perhaps I have missed something, but if your users just need to
print from Jalview, why not use the Jalview application? You can make
the applet launch the application quite easily.
This is one of the things we will do. However, some of our users sometimes have issues with the configuration of Java which prevents them from using easily Java WebStart, and are not even authorized to modify themselves their configuration, hence the idea of allowing such a feature directly from the Applet. I know that it is not in any way Jalview developers' responsibility to workaround every badly configured os in the world, but it is still an attractive solution to me because it does not require important modifications (otherwise it is just not worth it).
Once again, this is only a suggestion, but from the reaction of our "test" users, it could be a nice addition.
In a more "future" perspective, base64 encoded pictures could be easily embedded in "HTML" notebooks available in web based environments such as Mobyle.
Hervé
···
On 06/11/2012 09:25 PM, Geoff Barton wrote:
G.
On 11/06/2012 19:23, Hervé Ménager wrote:
Hi Jim,
On 06/11/2012 08:58 AM, Jim Procter wrote:
Hi Hervé! Nice to hear from you!
On Thu Jun 7 21:40:12 2012, Hervé Ménager wrote:
elsewhere?): we released officially a short time ago a feature that
allows users to visualize data in applets like Jalview or
Archaeopteryx,
but also to bookmark them back to the server. This is apparently a
popular feature, and had been asked for a long time.
This sounds very useful. I presume the bookmark is made to a URL on the
mobyle server that launches the applets ?
Yes, exactly.
Additionally, we wanted to enable users to take screenshots of the data
as viewed in the applets, for publication purpose for instance. Thanks
to Christian Zmasek, we have been able to add a method in the
Archaeopteryx applet that returns the a screenshot of the edited
phylogenetic tree in a chosen format, eg JPEG, and byte 64 encoded so
that it can be retrieved as a string using javascript. Following this,
the byte 64 encode string is sent to the server, where it is
appropriately decoded and saved in the user workspace. This way users
can take screenshots of their trees anytime during their work and save
them for future use. First user trainings show that users like a lot
this feature, but would like to get it as well in Jalview...
I took a look at the code. It would certainly be possible to add a
method like this to the Jalview API, but there are a couple of subtle
aspects which means I can't fit it in to the forthcoming release.
No worry about this, it is not an urgent matter, it is more in the "cool
to have" category. Many of our users have to rely on programs like
boxshade to print multiple alignments, but I think using a GUI like
Jalview would be far easier for them, in a WYSIWYG approach.
It's certainly something that could be looked at for the next but one -
and will, in fact, be even easier to implement, since the jalview
application includes all the machinery for figure generation, and the
next few releases will bring the applet and application even closer
together.
I've added a note on a rather old feature request about this solution -
since a Javascript method (which we weren't really considering as a
viable solution back in 2005) would neatly get around the difficulty of
having an unsigned applet save an image to disk. A solution like the one
Christian implemented would enable any javascript on the page to access
images from the applet.
Exactly what I meant. Thanks a lot for accepting this feature request.
If you need testing, just contact me, I'll be happy to help in any way.
Hervé
Jim.
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss