Integrate jalview in another application

Hello everybody

I’m new to Jalview list and this is my first question.

I’m developping a bioinformatics application using Netbeans IDE and would like to know if it is possible to use jalview inside my application to view multiple sequence alignments that I would like to viualize inside a JPanel.

Do anyone have an idea from where to start (if it is possible of course) ?

Regards

Rad

Hi Rad.

Hello everybody

I'm new to Jalview list and this is my first question.

I'm developping a bioinformatics application using Netbeans IDE and would like to know if it is possible to use jalview inside my application to view multiple sequence alignments that I would like to viualize inside a JPanel.

sounds like a great idea. However - you're quite right in working out that do this isn't easy to do at the moment. The easiest way to open an alignment view is to instantiate a jalview.gui.AlignFrame with an alignment, but that's a first class citizen on the desktop. This class is the owner of one or more alignPanels - and each of those holds an AlignViewport - which holds the view state data and the actual alignment being visualized. Unfortunately, AlignmentPanels and AlignFrames are tightly bound - and some refactoring will be necessary to extricate the cross-references.

If you just want to view an alignment, without any of the jalview menus then you should take a look at what Olja Sputh did to get Jalview into bioclipse : http://bioclipse.blogspot.com/2008/01/multiple-alignments-in-bioclipse.html
He actually used the classes in the jalview.appletgui package for this - because bioclipse uses SWT, and there's an AWT/SWT bridge.

So the choice is yours - I plan on refactoring the jalview.*gui packages in a couple of releases time to make this easier (this is part of the plan for jalview 3.0!), so if you want to try and hack the jalview.gui classes to get alignments displayed in a JPanel, I can use that as a guide when I do the refactoring later in the year.

Does that help ?
Jim.

ps. This is probably a conversation that should be moved to our development mailing list - jalview-dev@jalview.org (subscribe here: http://www.jalview.org/mailman/listinfo/jalview-dev ).

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On 14/05/2010 13:41, Radwen Aniba wrote: