Demonstration of embedded JalviewJS components
This simple page illustrates how one can embed the JalviewJS desktop into a web page. The basic idea is that we have something interesting to say — some sort of scientific context — something we want to get across to our visitors with more than just text and images. The idea is to have a dynamic page that will involve user interaction.

We start with a Jalview desktop. You can't see it, because I have placed it in a div tag with style width:0px;height:0px just after the period that ends this sentence.

The idea is NOT to teach visitors how to use Jalview. The idea is to seamlessly integrate components of Jalview that can be used to enrich a discussion. Like JSmol in Proteopedia. For example, in the space to the right, after a few seconds, you will see an alignment frame. This alignment is for 15 genes that code for one of the domains in the ferredoxin family (NIR_SIR_ferr (PF03460)).

What you see initially is just the first few residues. Doesn't look like much of an alignment, does it? But scroll to the right. See the big block of red color? That's the Ferredoxin folddomain.

The alignment frame will appear here momentarily. When it does, you can go ahead and manipulate the alignment with your mouse.
Select a few alignments by left-dragging across a few rows of the alignment to make a selection box. Then click one of the buttons below to see more information about your selected subset of the alignment.


One more thing. Let's take a look at the 3D structure of one these proteins. Ferredoxins are important, because they have iron-sulfur clusters that can accept and deliver electrons in metabolic processes. Let's see if we can find it.
This is System.out. clear it
Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files
get _j2sClassList.txt