On Thu Jun 28 17:37:49 2012, Wei Jen wrote:
> Thanks Jim,
>
> We did sign the jar file, and it doesn't work for us.
> We are trying to figure out a way, so user can get the consense
> sequence without moving to the full version (which kind of leave our
> site where we have some javascript code to interact with jalview).

You've two options - both involve patching the jalviewlite code.
1. Provide an additional method to get at the consensus sequence via 
javascript, and add a new button to your web page that gets the current 
jalview's consensus sequence and puts it into the system clipboard.

2. Change the copy consensus sequence action so that it also opens a 
text box showing the sequence.  The user will then be able to copy and 
paste that sequence.

both are reasonably easy to accomplish. I'm not sure what you might 
prefer.
Jim.
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