Jal-1420

Jalview Developers
1

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

···

On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

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Jalview-dev@jalview.org
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On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

2

I’m not seeing any error in the console either.

m

···

On Mon, Sep 29, 2014 at 12:01 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

El 29/09/2014 10:26, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hello David,

JAL-1420 - I’m not succeeding in reproducing the error before trying the patch.
I seem to be able to apply / OK / save a colour scheme with no colours selected, without error.
Any tips for reproducing the error?

Thanks

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

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Jalview-dev@jalview.org
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On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

3

Mungo,

These are the steps I’ve followed (see http://issues.jalview.org/browse/JAL-1420 comments).

  1. Load an alignment (I’m attaching the clustal omega file)
  2. Colour → User defined…
  3. Press OK/Apply button

If the patch is not applied, you’ll find an stacktrace similar to
Exception in thread “AWT-EventQueue-2” java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Vector.java:470)
at jalview.gui.UserDefinedColours.getSchemeFromButtons(UserDefinedColours.java:464)
…

If the patch is applied, a warning message is shown to the user until he/she makes a colour selection for the scheme (see Captura.PNG at the jira).

I’m testing under Release_2_8_2_Branch.

Cheers,

David

clustalo-I20140809-085435-0437-45098911-pg.clustal (30.5 KB)

···

2014-09-29 13:52 GMT+02:00 Mungo Carstairs <gmungoc@gmail.com>:

I’m not seeing any error in the console either.

m

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Mon, Sep 29, 2014 at 12:01 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

El 29/09/2014 10:26, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hello David,

JAL-1420 - I’m not succeeding in reproducing the error before trying the patch.
I seem to be able to apply / OK / save a colour scheme with no colours selected, without error.
Any tips for reproducing the error?

Thanks

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

4

Nope, no error for me with that file and steps either.
It looks as though UserDefinedColours.resetButtonPanel() should populate the upperCaseButtons Vector.
I can’t see how to break this!

mungo

···

On Mon, Sep 29, 2014 at 1:06 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Mungo,

These are the steps I’ve followed (see http://issues.jalview.org/browse/JAL-1420 comments).

  1. Load an alignment (I’m attaching the clustal omega file)
  2. Colour → User defined…
  3. Press OK/Apply button

If the patch is not applied, you’ll find an stacktrace similar to
Exception in thread “AWT-EventQueue-2” java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Vector.java:470)
at jalview.gui.UserDefinedColours.getSchemeFromButtons(UserDefinedColours.java:464)
…

If the patch is applied, a warning message is shown to the user until he/she makes a colour selection for the scheme (see Captura.PNG at the jira).

I’m testing under Release_2_8_2_Branch.

Cheers,

David

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

2014-09-29 13:52 GMT+02:00 Mungo Carstairs <gmungoc@gmail.com>:

I’m not seeing any error in the console either.

m

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Mon, Sep 29, 2014 at 12:01 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

El 29/09/2014 10:26, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hello David,

JAL-1420 - I’m not succeeding in reproducing the error before trying the patch.
I seem to be able to apply / OK / save a colour scheme with no colours selected, without error.
Any tips for reproducing the error?

Thanks

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

5

ups. then I suggest to close the ticket as non reproducible or apply the original patch that prevents for potential NPE.
What do you think about that?

···

On Mon, Sep 29, 2014 at 1:06 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Mungo,

These are the steps I’ve followed (see http://issues.jalview.org/browse/JAL-1420 comments).

  1. Load an alignment (I’m attaching the clustal omega file)
  2. Colour → User defined…
  3. Press OK/Apply button

If the patch is not applied, you’ll find an stacktrace similar to
Exception in thread “AWT-EventQueue-2” java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Vector.java:470)
at jalview.gui.UserDefinedColours.getSchemeFromButtons(UserDefinedColours.java:464)
…

If the patch is applied, a warning message is shown to the user until he/she makes a colour selection for the scheme (see Captura.PNG at the jira).

I’m testing under Release_2_8_2_Branch.

Cheers,

David

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

2014-09-29 13:52 GMT+02:00 Mungo Carstairs <gmungoc@gmail.com>:

I’m not seeing any error in the console either.

m

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Mon, Sep 29, 2014 at 12:01 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

El 29/09/2014 10:26, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hello David,

JAL-1420 - I’m not succeeding in reproducing the error before trying the patch.
I seem to be able to apply / OK / save a colour scheme with no colours selected, without error.
Any tips for reproducing the error?

Thanks

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

6

Hi David,

I would always (wherever possible) want to reproduce any problem before applying a fix. That way you can find out the root cause (which may need a different fix), and ideally add unit tests to expose the problem and verify the fix.

I’ll check with Jim to see if he can suggest a route to cause this error, if not maybe close as not reproducible.

Are you able to commit updates to Messages_es.properties to match the latest code changes?

e.g.

label.new_sequence_fetcher​

etc

You said you were waiting for something from Ipek? What is Ipek?

Thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of David Roldán Martínez darolmar@gmail.com
Sent: 29 September 2014 16:25
To: Jalview Development List
Subject: Re: [Jalview-dev] Jal-1420

ups. then I suggest to close the ticket as non reproducible or apply the original patch that prevents for potential NPE.
What do you think about that?

El 29/09/2014 14:44, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Nope, no error for me with that file and steps either.
It looks as though UserDefinedColours.resetButtonPanel() should populate the upperCaseButtons Vector.
I can’t see how to break this!

mungo

On Mon, Sep 29, 2014 at 1:06 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Mungo,

These are the steps I’ve followed (see http://issues.jalview.org/browse/JAL-1420 comments).

  1. Load an alignment (I’m attaching the clustal omega file)
  2. Colour → User defined…
  3. Press OK/Apply button

If the patch is not applied, you’ll find an stacktrace similar to
Exception in thread “AWT-EventQueue-2” java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Vector.java:470)
at jalview.gui.UserDefinedColours.getSchemeFromButtons(UserDefinedColours.java:464)
…

If the patch is applied, a warning message is shown to the user until he/she makes a colour selection for the scheme (see Captura.PNG at the jira).

I’m testing under Release_2_8_2_Branch.

Cheers,

David

2014-09-29 13:52 GMT+02:00 Mungo Carstairs <gmungoc@gmail.com>:

I’m not seeing any error in the console either.

m

On Mon, Sep 29, 2014 at 12:01 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

Hi Mungo,
No apparent error at the gui but an exception appears at the console.
Cheers,
David

El 29/09/2014 10:26, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hello David,

JAL-1420 - I’m not succeeding in reproducing the error before trying the patch.
I seem to be able to apply / OK / save a colour scheme with no colours selected, without error.
Any tips for reproducing the error?

Thanks

Mungo

On Fri, Sep 26, 2014 at 7:53 PM, David Roldán Martínez <darolmar@gmail.com> wrote:

ok. I’ll try to take a look tomorrow. Thanks!

El 26/09/2014 14:13, “Mungo Carstairs” <gmungoc@gmail.com> escribió:

Hi David,

95% ok but some things to tidy up!

I’ve dumped all my findings as a comment to JAL-1428.
Please have a look some time and let me know if anything isn’t clear or you disagree.

Thanks!

Mungo

On Thu, Sep 25, 2014 at 1:52 PM, Mungo Carstairs <g.m.carstairs@dundee.ac.uk> wrote:

Hi David,

I’ll have a go with your branch and let you know if I spot anything *algo que falta.*​

Thanks,

Mungo

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of David Roldán Martínez <darolmar@gmail.com>
Sent: 23 September 2014 17:32
To: Jalview Development List
Subject: [Jalview-dev] i18n review for 2.8.2

Hi all,

I’ve just fixed all the i18n bugs I’ve found for 2.8.2. They’re commited at Release_2_8_2_Branch_i18n (http://source.jalview.org/gitweb/?p=jalview.git;a=shortlog;h=refs/heads/Release_2_8_2_Branch_i18n).

Although I’ve made some basic tests before to commit, I’m not an advanced Jalview user and thus I would appreciate if anybody checkouts branch code and make further tests. If, additionally, these tests are documented at wiki, for future releases I’l be able to do them on my own. :slight_smile:

Now I’m going to work with translations. Let’s see Jalview speaking more languages!!!

Cheers,

David

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

Jalview-dev mailing list
Jalview-dev@jalview.org
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Jalview-dev mailing list
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