Problems with alignment

Jalview Discussion
1

Hello Shanuki - it sounds like you are experiencing network problems -
either the Jalview Web services are not accessible from your local
network in York, or your computer's firewall is misconfigured.

Can you open these URLs in your web browser ?

http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS

This should have a simple HTML page returned.

http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS

A similar simple HTML page should be returned.

http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry?method=getServices

A page containing XML should be returned.

If all the above work with your web browser then you probably have
firewall issues - you will need to allow the Jalview application access
to the network (often this means adding the java executable to the list
of exceptions - programs that are allowed full access to the internet).
If you don't know how to do this then contact your local network
support, and show them this email.

All the best - happy Jalviewing!
Jim.

ish500@york.ac.uk wrote:

Hi, I'm running jaliview on commmand line(linux system)and trying to
align 320 protein se4quences. Since yesterday afternoon I have trying to
align my protein sequences using options the webservice menu(Muscle
Multiple Sequence alignment, MAFFT Multiple Sequence Alignment, ClustalW
Multiple Sequence Alignment).

Today morning I tried MAFFT Multiple

···

Sequence Alignment, ClustalW Multiple Sequence Alignment and keeps
giving the same error message.ON command lines it says : MAFFT Multiple
Sequence AlignmentClient: Failed to submit the sequences for alignment
(probably a server side problem) When contacting
Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS
java.net.ConnectException: Connection timed out

ClustalW Multiple Sequence AlignmentClient: Failed to submit the
sequences for a lignment (probably a server side problem) When
contacting
Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/Clusta lWS
java.net.ConnectException: Connection timed out

Is there any other way i could align my sequences on jaliview?
Thanking you,
Shanuki

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

2

Hello,
I am a biology teacher for secondary education in France and would like to use Jalview with my students. I was wondering if there is any plan for internationalization or if I should look into creating another Jalview version through a translation of the code ?
Thank-you,
Paul

3

Hello Paul.

Paul Pillot wrote:

I am a biology teacher for secondary education in France and would like
to use Jalview with my students. I was wondering if there is any plan
for internationalization or if I should look into creating another
Jalview version through a translation of the code ?

It would be best if the Jalview source did not fork into
internationalized and 'en-only' versions. However, we have not
explicitly planned for internationalization but it has been requested
quite frequently, and would obviously be of great benefit!

Now that Jalview development is slow, it may be a good time to think
about doing this, but the transformation of the user interface code will
have to be done by someone in their spare time. Are you familiar with
any automated tools for creating and maintaining internationalization
bundles ?

Jim.

···

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

4

Hi Jim,

A strategy for adding internationalization could be:

In Eclipse you can do "Externalize Strings" which can move String declarations into external properties files. These properties files can easily get translated into different languages (they are text only) and they then carry different file names depending on the language support they provide. This can then be used by Java automatically to switch to the correct translation based on the Locale.

An example in terms of source code, see below.

Hope that helps,
Cheers
Andreas

rather than doing

JButton button = new JButton("press here");

you would say

JButton button = new JButton (ResourceManager.getString("org.jalview.button"));

where the resourcemanager looks like below:

import java.util.ResourceBundle;
import java.util.MissingResourceException;
import java.util.logging.Logger;

public class ResourceManager {

     private static final String BUNDLE_NAME = "jalview";

     private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle(BUNDLE_NAME);

     public static Logger logger = Logger.getLogger(JalviewDefaults.LOGGER);

     private ResourceManager() {
     }

     public static String getString(String key) {

         try {
             return RESOURCE_BUNDLE.getString(key);
         } catch (MissingResourceException e) {
           logger.config(e.getMessage());
             return '!' + key + '!';
         }
     }
}

and the jalview.properties file contains

org.jalview.button = press here

and since I am a german speaker here goes the german translation:

jalview_de_DE.properties has the content

org.jalview.button = hier drücken

(eventually the ResourceManager needs a few more lines of code to check if the default locale is available as a translation and if not, fall back to en_GB, I could help out with that, if needed...)

Cheers,
Andreas

···

On 9 Jul 2008, at 09:37, James Procter wrote:

Hello Paul.

Paul Pillot wrote:

I am a biology teacher for secondary education in France and would like
to use Jalview with my students. I was wondering if there is any plan
for internationalization or if I should look into creating another
Jalview version through a translation of the code ?

It would be best if the Jalview source did not fork into
internationalized and 'en-only' versions. However, we have not
explicitly planned for internationalization but it has been requested
quite frequently, and would obviously be of great benefit!

Now that Jalview development is slow, it may be a good time to think
about doing this, but the transformation of the user interface code will
have to be done by someone in their spare time. Are you familiar with
any automated tools for creating and maintaining internationalization
bundles ?

Jim.

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
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Jalview-discuss mailing list
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Andreas Prlic Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

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5

G'day Andreas!

Andreas Prlic wrote:

A strategy for adding internationalization could be:

In Eclipse you can do "Externalize Strings" which can move String
declarations into external properties files. These properties files can
easily get translated into different languages (they are text only) and
they then carry different file names depending on the language support
they provide. This can then be used by Java automatically to switch to
the correct translation based on the Locale.

Trail: Internationalization (The Java™ Tutorials)

An example in terms of source code, see below.

Thanks very much! I was, indeed, planning to have a go at the source
with the Externalize strings function. It looks like the soruce code
transformation is very controllable, and relatively painless, but I
still need to work out the fine details of how the different Locale
bundles will be managed after the transformation is made (one issue is
source code documentation, of course!).

My cautiousness is because I've had experience in the past with programs
where the internationalization as gotten out of sync with the software
UI... which can lead to great user confusion ! Any help or advice on
how to manage this would be *greatly* appreciated.

Paul and I, and Geoff and I, have been discussing this off-list, and I
think it shouldn't take too long to transform Jalview. I'll post news on
the list concerning how we get on with this. I'll set up a a prototype
internationalized bundle for the applet and the application, and Paul
has already volunteered (thanks :wink: to help with a first translation of
the UI messages into French. However, no guarantees on how long it'll
be before we've done this!

Jim

···

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.