applet doesn't load fasta file

Jalview Discussion
1

Hi-

I have a fasta-formatted alignment:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/MS16560/mafftash_msa.txt

which doesn’t seem to load from the applet launcher:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/MS16560/launch_jalview.html

I don’t see any errors in the error console either.

So, I tried to load it in jalview stand alone. Strangely, only the sequence titles appeared,
so it seemed like something was wrong with my file. But after I updated to the latest version
of Jalview, it loaded fine in the stand-alone version. However, it still doesn’t load in the applet,
even when I use the latest version. Since the title are rather long, I tried chopping them but
it made no difference…

Just wondering if there is an obvious fix for this.

Best wishes,

Daron

Daron M. Standley, Ph.D.
Systems Immunology Laboratory
Immunology Frontier Research Center
Osaka University
Tel: +81-(0)6-6879-4311
FAX: +81-(0)6-6879-8636

2

Hi Daron.

Daron Standley wrote:

I have a fasta-formatted alignment:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/MS16560/mafftash_msa.txt

which doesn't seem to load from the applet launcher:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/MS16560/launch_jalview.html

I don't see any errors in the error console either.

When I tried this, I get this exception in the java console:
Exception in thread "AWT-EventQueue-2" java.lang.OutOfMemoryError: Java
heap space
  at java.awt.image.DataBufferInt.<init>(Unknown Source)
<snip>
  at jalview.appletgui.IdCanvas.paint(IdCanvas.java:157)
  at sun.awt.RepaintArea.paintComponent(Unknown Source)
<snip>

So, I tried to load it in jalview stand alone. Strangely, only the
sequence titles appeared,
so it seemed like something was wrong with my file.

... confirmed.
What's happening is that the sequence ID of the first sequence is so
long, that the subwindow displaying the sequence ID is made wider than
the window containing it. In the embedded applet, this results in an
exception (although when I tried it here:
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/applet/spacefasta.html
I could just drag the ID panel back by clicking on the top right of the
alignment display area and dragging to the left, at which point the
exceptions stop).

Just wondering if there is an obvious fix for this.

erm. not sure. This is actually a known issue, but I hadn't realised it
could cause semi-fatal exceptions. Can you try the latest development
build to see if it behaves any better ? I can then put in some checks
to make sure the width doesn't go beyond some proportion of the
alignment display area...

Jim.