[Jalview-discuss] applet doesn't load fasta file

[James Procter]

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.