[Jalview-discuss] jalview.ButtonAlignApplet

[Daron Standley]

Hi-

I am just getting started using the latest jalview, and I am confused  
on a few points:

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.

2. I can find and use "jalview/bin/JalviewLite.class". 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">

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".

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).

Thanks in advance, and sorry if my question is not clear. I am not  
very familiar with java.

Best regards,

Daron
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