Hi,
I've got a multiple sequence alignment with an annotation file. For some residues, I want to link to a another page on my site.
However, when I put something like this in the annotations file:
<html><a href="/mutations/acm1_rat/K136">K136</a></html> ACM1_RAT -1 136 136 mutation
I can right-click on those residues in the msa and the link menu appears, but when I click on it nothing happens...
Regards,
Bas
Hello Bas.
Bas Vroling wrote:
I've got a multiple sequence alignment with an annotation file. For some
residues, I want to link to a another page on my site.
However, when I put something like this in the annotations file:<html><a href="/mutations/acm1_rat/K136">K136</a></html> ACM1_RAT
-1 136 136 mutationI can right-click on those residues in the msa and the link menu
appears, but when I click on it nothing happens...
Can you check in your browser that the applet examples page works ?
http://www.jalview.org/examples/applets.html
Open the 'Displays a features file on the alignment' jalview appet, and
try to open a link from the PFAM annotation.
A problem that we have noticed recently is that popup-blockers
(specifically, on windows vista) do not inform you when they block the
'showURL' call that an applet makes when it tries to open a URL in the
browser. So check the popup-blocker settings for your site.
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.
Hi Jim,
The applet version on the jalview site works great. Might it have something to do with the links being relative instead of absolute?
Bas
On 4 Sep, at 11:59, James Procter wrote:
Hello Bas.
Bas Vroling wrote:
I've got a multiple sequence alignment with an annotation file. For some
residues, I want to link to a another page on my site.
However, when I put something like this in the annotations file:<html><a href="/mutations/acm1_rat/K136">K136</a></html> ACM1_RAT
-1 136 136 mutationI can right-click on those residues in the msa and the link menu
appears, but when I click on it nothing happens...Can you check in your browser that the applet examples page works ?
http://www.jalview.org/examples/applets.html
Open the 'Displays a features file on the alignment' jalview appet, and
try to open a link from the PFAM annotation.A problem that we have noticed recently is that popup-blockers
(specifically, on windows vista) do not inform you when they block the
'showURL' call that an applet makes when it tries to open a URL in the
browser. So check the popup-blocker settings for your site.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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Bas Vroling wrote:
Hi Jim,
The applet version on the jalview site works great. Might it have
something to do with the links being relative instead of absolute?
ah. maybe. yes!
<html><a href="/mutations/acm1_rat/K136">K136</a></html> ACM1_RAT
-1 136 136 mutation
Have you tried opening the console window ? there should be an 'open
url: ...' message output when jalview tries to open the URL.
When I tried using a bare href string like the one above, it failed with
a 'malformedURLException'. So - the applet does not try to append the
codebase to the URL before it opens it. I've put a TODO and a quick
check for this in the jalview applet code, and this should propagate to
the latest CVS release build shortly. However, it will need testing.
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.
Wow, thanks for the quick response. I got the error too, so I'll try to checkout the cvs release and start testing 
Regards,
Bas
On 4 Sep, at 15:01, James Procter wrote:
Bas Vroling wrote:
Hi Jim,
The applet version on the jalview site works great. Might it have
something to do with the links being relative instead of absolute?ah. maybe. yes!
<html><a href="/mutations/acm1_rat/K136">K136</a></html> ACM1_RAT
-1 136 136 mutationHave you tried opening the console window ? there should be an 'open
url: ...' message output when jalview tries to open the URL.When I tried using a bare href string like the one above, it failed with
a 'malformedURLException'. So - the applet does not try to append the
codebase to the URL before it opens it. I've put a TODO and a quick
check for this in the jalview applet code, and this should propagate to
the latest CVS release build shortly. However, it will need testing.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.