Yesterday I updated java and jalview installAnywhere to the latest. Now when I select Above Identity Threshold and set that to 1, as I normally do, all the characters lose their color. I installed the jre with jalview also and tried that and same result. I get the same problem with my previous version of jalview. It seems the jalview jre and the current java are both 1.8. I think I might have had java 1.7 before.
Related to the “Above identity Threshold”, it would very helpful if there was a setting in preferences that allowed you to automatically start jalview with “Above identity Threshold” active and set to some specified value.
On another note, installing jalview was problematic, both with and without the jre included. I ended up having to uninstall java to get jalview to install. I would get an error like: “windows error 2 occurred while loading the java vm jalview”.
I have not managed to reproduce your problem with the colouring (having tried Java 7 and Java 8).
Could you retry with (Tools | Show Java Console) enabled, and copy and paste for us what is shown there?
That will pin down the version of Java, Jalview and O/S (and any exceptions that might be logged).
Are you able to email a copy of your alignment data (by personal email if you prefer)?
Thanks,
Mungo
···
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk
Yesterday I updated java and jalview installAnywhere to the latest. Now when I select Above Identity Threshold and set that to 1, as I normally do, all the characters lose their color. I installed the jre with jalview also and tried that and same result. I get the same problem with my previous version of jalview. It seems the jalview jre and the current java are both 1.8. I think I might have had java 1.7 before.
Related to the “Above identity Threshold”, it would very helpful if there was a setting in preferences that allowed you to automatically start jalview with “Above identity Threshold” active and set to some specified value.
On another note, installing jalview was problematic, both with and without the jre included. I ended up having to uninstall java to get jalview to install. I would get an error like: “windows error 2 occurred while loading the java vm jalview”.
The University of Dundee is a registered Scottish Charity, No: SC015096
I noticed that "Above Identity Treshold" or "Percent Identity" which
probably runs along similar lines, not always work after opening an
alignment. I always use these colour-modes in combination with getting a
consensus-logo. To see what I want, I have to make sure that 'show
annotations' is set and - for 'Autocalculated Annotation'- have
'Show Consensus Logo' set and then tick, untick, tick (until it happens)
the box 'AutoCalculate Consensus' under 'Calculate'. Yes a bit
cumbersome, but it generates the images I am after...
HTH.
Rob
···
On Sun, 25 Sep 2016 12:32:49 -0400 Danny Rice <dnaslave@gmail.com> wrote:
Yesterday I updated java and jalview installAnywhere to the latest.
Now when I select Above Identity Threshold and set that to 1, as I
normally do, all the characters lose their color. I installed the
jre with jalview also and tried that and same result. I get the same
problem with my previous version of jalview. It seems the jalview
jre and the current java are both 1.8. I think I might have had java
1.7 before.
Related to the "Above identity Threshold", it would very helpful if
there was a setting in preferences that allowed you to automatically
start jalview with "Above identity Threshold" active and set to some
specified value.
On another note, installing jalview was problematic, both with and
without the jre included. I ended up having to uninstall java to get
jalview to install. I would get an error like: "windows error 2
occurred while loading the java vm jalview".
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.8.0_101
x86 Windows 10 10.0
Jalview Version: 2.9.0b2
Jalview Installation: installAnywhere git-commit:c19d2a9 [Release_2_9_0b1_Branch]
Build Date: 16 October 2015
Java version: 1.8.0_101
x86 Windows 10 10.0
“Above identity Threshold” removes all color. It does not seem to depend on the alignment but attached is an example alignment.
I do not see any additional stdout or stderr when I adjust the identity setting. Attached are stdout and stderr for the new version.
Thanks for adding “Above identity Threshold” startup preferences to issues. In general, it would be very nice if all options/settings were configurable from the command line.
I noticed that “Above Identity Treshold” or “Percent Identity” which
probably runs along similar lines, not always work after opening an
alignment. I always use these colour-modes in combination with getting a
consensus-logo. To see what I want, I have to make sure that ‘show
annotations’ is set and - for ‘Autocalculated Annotation’- have
‘Show Consensus Logo’ set and then tick, untick, tick (until it happens)
the box ‘AutoCalculate Consensus’ under ‘Calculate’. Yes a bit
cumbersome, but it generates the images I am after…
HTH.
Rob
On Sun, 25 Sep 2016 12:32:49 -0400
Danny Rice <dnaslave@gmail.com> wrote:
Yesterday I updated java and jalview installAnywhere to the latest.
Now when I select Above Identity Threshold and set that to 1, as I
normally do, all the characters lose their color. I installed the
jre with jalview also and tried that and same result. I get the same
problem with my previous version of jalview. It seems the jalview
jre and the current java are both 1.8. I think I might have had java
1.7 before.
Related to the “Above identity Threshold”, it would very helpful if
there was a setting in preferences that allowed you to automatically
start jalview with “Above identity Threshold” active and set to some
specified value.
On another note, installing jalview was problematic, both with and
without the jre included. I ended up having to uninstall java to get
jalview to install. I would get an error like: “windows error 2
occurred while loading the java vm jalview”.
–
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
I am on java 1.8 and jalview 2.9.0b2; Java errors normally appear when
the program more or less crashes (and then you'll find an
automatically generated error-log somewhere in your home folder), which
is rarely the case.
Did you try to use the autocalculate consensus route I
described? If not please do; it might show what you want.
···
On Mon, 26 Sep 2016 13:54:08 -0400 Danny Rice <dnaslave@gmail.com> wrote:
Same result with old and new versions
Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.8.0_101
x86 Windows 10 10.0
Jalview Version: 2.9.0b2
Jalview Installation: installAnywhere git-commit:c19d2a9
[Release_2_9_0b1_Branch]
Build Date: 16 October 2015
Java version: 1.8.0_101
x86 Windows 10 10.0
"Above identity Threshold" removes all color. It does not seem to
depend on the alignment but attached is an example alignment.
I do not see any additional stdout or stderr when I adjust the
identity setting. Attached are stdout and stderr for the new version.
Thanks for adding "Above identity Threshold" startup preferences to
issues. In general, it would be very nice if all options/settings
were configurable from the command line.
On Mon, Sep 26, 2016 at 5:59 AM, rob van nues <rob.van-nues@ed.ac.uk> > wrote:
> Hi Danny,
>
> I noticed that "Above Identity Treshold" or "Percent Identity" which
> probably runs along similar lines, not always work after opening an
> alignment. I always use these colour-modes in combination with
> getting a consensus-logo. To see what I want, I have to make sure
> that 'show annotations' is set and - for 'Autocalculated
> Annotation'- have 'Show Consensus Logo' set and then tick, untick,
> tick (until it happens) the box 'AutoCalculate Consensus' under
> 'Calculate'. Yes a bit cumbersome, but it generates the images I am
> after...
>
> HTH.
>
> Rob
>
> On Sun, 25 Sep 2016 12:32:49 -0400 > > Danny Rice <dnaslave@gmail.com> wrote:
>
> > Yesterday I updated java and jalview installAnywhere to the
> > latest. Now when I select Above Identity Threshold and set that
> > to 1, as I normally do, all the characters lose their color. I
> > installed the jre with jalview also and tried that and same
> > result. I get the same problem with my previous version of
> > jalview. It seems the jalview jre and the current java are both
> > 1.8. I think I might have had java 1.7 before.
> >
> > Related to the "Above identity Threshold", it would very helpful
> > if there was a setting in preferences that allowed you to
> > automatically start jalview with "Above identity Threshold"
> > active and set to some specified value.
> >
> > On another note, installing jalview was problematic, both with and
> > without the jre included. I ended up having to uninstall java to
> > get jalview to install. I would get an error like: "windows error
> > 2 occurred while loading the java vm jalview".
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Thanks Rob. Yes setting “autocalculate consensus” in preferences fixes the problem. I normally have that set but disabled it around the time I updated Jalview/Java. So this particular issue is probably not due to updating java.
I am on java 1.8 and jalview 2.9.0b2; Java errors normally appear when
the program more or less crashes (and then you’ll find an
automatically generated error-log somewhere in your home folder), which
is rarely the case.
Did you try to use the autocalculate consensus route I
described? If not please do; it might show what you want.
Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.8.0_101
x86 Windows 10 10.0
Jalview Version: 2.9.0b2
Jalview Installation: installAnywhere git-commit:c19d2a9
[Release_2_9_0b1_Branch]
Build Date: 16 October 2015
Java version: 1.8.0_101
x86 Windows 10 10.0
“Above identity Threshold” removes all color. It does not seem to
depend on the alignment but attached is an example alignment.
I do not see any additional stdout or stderr when I adjust the
identity setting. Attached are stdout and stderr for the new version.
Thanks for adding “Above identity Threshold” startup preferences to
issues. In general, it would be very nice if all options/settings
were configurable from the command line.
I noticed that “Above Identity Treshold” or “Percent Identity” which
probably runs along similar lines, not always work after opening an
alignment. I always use these colour-modes in combination with
getting a consensus-logo. To see what I want, I have to make sure
that ‘show annotations’ is set and - for ‘Autocalculated
Annotation’- have ‘Show Consensus Logo’ set and then tick, untick,
tick (until it happens) the box ‘AutoCalculate Consensus’ under
‘Calculate’. Yes a bit cumbersome, but it generates the images I am
after…
HTH.
Rob
On Sun, 25 Sep 2016 12:32:49 -0400
Danny Rice <dnaslave@gmail.com> wrote:
Yesterday I updated java and jalview installAnywhere to the
latest. Now when I select Above Identity Threshold and set that
to 1, as I normally do, all the characters lose their color. I
installed the jre with jalview also and tried that and same
result. I get the same problem with my previous version of
jalview. It seems the jalview jre and the current java are both
1.8. I think I might have had java 1.7 before.
Related to the “Above identity Threshold”, it would very helpful
if there was a setting in preferences that allowed you to
automatically start jalview with “Above identity Threshold”
active and set to some specified value.
On another note, installing jalview was problematic, both with and
without the jre included. I ended up having to uninstall java to
get jalview to install. I would get an error like: “windows error
2 occurred while loading the java vm jalview”.
–
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
–
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.