Here are the points covered in our GSOC project teleconference today:
* Varna source
-> Work on 3.8b version : contact Yann to check on whether he can be on hand to fix up bugs/code quickly
-> aim to include 3.8(b) with the version of Jalview that integrates varna.
==> Either wait on Yann to inform us of a release date - or include a copy of the beta's source with Jalview's source distribution until v3.8 of VARNA is available on the web.
-> developing/identifying varna API : Jan + Yann - invite Yann to Jalview-dev.
-> follow example shown on demo page - interactive update of secondary structure diagram when contacts are edited, and interactive feedback if secondary structure brackets do not match up correctly
* Data model - probably ok for the moment - Jan examined the VARNA datamodel (which uses a list of pairs indexed by sequence position - so less space efficient, but more time efficient), and also checked out if there were any scaling issues (with number of sequences) with jalview's existing one, and didn't find anything serious. However, he's prepared to have to modify the strategy in the future.
* Annotation undo
- Jan's put in a new bug regarding undoing annotation edits
- Jim said Jan will also need to create a new jalview.commands.<annotation edit> set of classes that allows jalview to do/undo an annotation edit after it is made.
* Annotation IO - jalview.io.AnnotationFile
- Jan: bug hunt/test case: He needs to ensure that the RNA secondary structure parsing routines are called when annotation is imported: ie. export ss annotation, import on to new bare alignment, ensure that the new annotation is processed as RNA pair annotation corectly.
Jan is unavailable at the normal time next week, so we will postpone our weekly meeting until the following week. However, he should still make his report to the NESCEnt list. We'll communicate via email for the intervening time.
Thanks for joining - it was a good talk, despite the connectivity problems