[Jalview-discuss] jalview.ButtonAlignApplet

[Jim Procter]

Hello Daron.

Daron Standley wrote:
> 1. I can't seem to find "jalview.ButtonAlignApplet" in 
> the jalviewApplet.jar file, although this 
> code seems to be used in many of the examples I find on the web. 
>
You can be almost 100% certain that all these examples are using the old 
version of Jalview, which had a package structure like 
jalview.<classname> for many of the classes. Jalview 2 has a class 
structure like jalview.<mainpackage>.<class> for nearly all of its 
source code.
> 2. I can find and use "jalview/bin/JalviewLite.class".
That is most definitely the one to use. You'll find examples of the 
applet being launched here:
http://www.jalview.org/examples/applet.html
http://www.jalview.org/examples/appletParameters.html

> However, I wonder if this will allow me to display
> alignments in the form: 
>
> <PARAM name="numseqs" value=3>
> <PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR">
> <PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR">
> <PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR">
These parameters are wrong. The format for passing an alignment as 
applet parameters is given on the appletParameters link above. Firstly - 
you don't need numseqs at all, and secondly, jalview searches for 
parameters called 'sequence<i>' - where <i> is 1,2,3,.... The value of 
each sequence<i> parameter is the i'th line of the alignment file. For 
example:
<param name="sequence1" value="s1  a-cde">
<param name="sequence2" value="s2  apcde">
<param name="sequence3" value="s3  a--de">

Each line specifies a sequence name and alignment row in PFAM format.
> I can not get this to work using the jalviewLite class.  I get  an 
> error where the button should be
> saying Jalview can't open "NO FILE".
this is the generic error that the applet gives when the formats or 
parameters are incorrect. Always check on the browser's Java console for 
more information about what has caused  the error.

> 3. Assuming I eventually figure out how to do #2 (above) I am 
> wondering if I can then display a single sequence
> along with some properties (conservation, secondary structure, 
> functional residues, etc.)  I am hoping this
> will be a nice way to present such properties at the Protein Data Bank 
> Japan (currently we only show a the 
> FASTA sequence in a text window).
all possible. Have a look at the current development version of the 
applet's parameters and (rudimentary) API. Secondary structure 
annotation is passed into Jalview via it's own alignment annotations 
file format, and sequence features (ie DAS style sequence annotation) 
can be read from GFF or via a Jalview Features file. You don't need to 
create these files statically - the location of a servlet that generates 
the appropriate annotation file is all that's necessary.

> Thanks in advance, and sorry if my question is not clear. I am not 
> very familiar with java.
no problem. Now if only it were possible to eliminate all incorrect 
documentation ;)

hope it helps..
Jim

-- 
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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.