[Jalview-discuss] jalview.ButtonAlignApplet

[Daron Standley]

Hi Jim,

Thanks so much.  Your advice cleared up all my problems, and I now  
understand why things weren't working.

One minor point: I could access the link:

http://www.jalview.org/examples/appletParameters.html

but not:

  http://www.jalview.org/examples/applet.html

Don't know if thats significant or not.

Thanks again. As soon as I can get a prototype working I can hand  
this off to the java experts, and they will make it beautiful.
Hopefully we will have jalview running here shortly.

-Daron


On Apr 3, 2008, at 5:28 PM, Jim Procter wrote:

> 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
>
> -- 
> -------------------------------------------------------------------
> 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.
>
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