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

[Thomas Juettemann]

Hello James,

thanks again for your advice. Your hint together with Sean Moore's
that a semicolon (= programming character) in the comment line is not
a good idea took care of that problem. The alignment file is later
used for MODELLER, it was easier to already include the P1; at that
stage.
I hope you will be able to help me with one last question: I tried to
embed Jalview in the webpage, using

<param name="embedded" value="true">

I get the message that it successfully loaded the file, but can't see
the alignment.

Thanks to everyone for their patience and help.

Cheers,
Thomas

On Wed, Aug 12, 2009 at 01:25, James Procter<jimp at compbio.dundee.ac.uk> wrote:
> 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.
>
> --
> -------------------------------------------------------------------
> 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.
>