[Jalview-discuss] Newbie: Exception: java.lang.ClassNotFoundException: jalview.bin.JalviewLite

[James Procter]

G'day, Thomas.

Thomas Juettemann wrote:
> many thanks for your reply. I have the applet working now, but it is
well done!
> not displaying the alignment, it concatenates all sequences.
:(
> The input file can found here:
> 
>  http://bisc.cse.ucsc.edu/models/BiscHet/P15303-P20606/P15303-1M2O_A.muscle.out.fasta
I think the problem is that Jalview is confusing the >P1; lines as the 
beginning of a PIR file, rather than a FASTA file - and trying to parse 
it with the PIR parser - since this expects a '*' terminator, the whole 
alignment is appended to the first sequence.

The quick fix would be to remove 'P1;' from the file. There's no way to 
force jalview to use a certain parser (although there is one very 
strident supporter of this), but I'll add this as a bug and it will 
probably be fixed for the next release.

Jim.

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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