[Wg-phyloinformatics] Jalview Progress report #4

Thanks for the update Jan. I look forward to playing with Varna in Jalview once I get back to the UK :slight_smile:


J. B. Procter Jalview/enfin Barton group


-----Original Message-----
From: Jan Engelhardt <engelhardt87@googlemail.com>
To: wg-phyloinformatics@nescent.org
Sent: Tue, 21 Jun 2011 11:42
Subject: [Wg-phyloinformatics] Jalview Progress report #4


here is my newest progress report.

This week:
Goal 4: A VARNA window is embedded in the Jalview Swing interface.
Necessary menu items are included in the Jalview alignment window. Test:
The embedded window will be evaluated manually using Rfam alignments.
Achievements: Created classes were adopted for Varna;
AppVarnaBinding.java was adopted according to
fr.orsay.lri.varna.applications.VARNAGUI.java; VARNA gui can be called
from within Jalview; 鈥榁iew RNA structure鈥-method added via PopupMenu.java;
ToDo: The embedding is still a bit basic and has to be further improved.

Next week:
Goal 5: Add functionality for editing secondary structures and fix
issues from last years code with that.
Minor Goals: VARNA classes could be more structured;
Test: Edit the structure in the alignment and see if it works.


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