varna library dependency

Jalview Developers
1

Hi Jan.

I Just noticed that you haven't actually committed and pushed the VARNAv3-3b.jar file to the jalview git repository.

Normally, a pre-compiled dependency like VARNA lives in the lib directory under the Jalview project. From the .classpath entry in the 2_5_1_rna_merge git branch, it looks like you have it in a directory called something like VARNAv3-3b - I'd suggest you simply use the refactor tool to relocate the jar file to the lib directory (which will also update its references in the Jalview project), and then commit it so I can pick up the dependency too.

Jim.

2

I fixed and committed it.
Maybe you can try if it works now.

Jan

···

On 06/23/11 14:41, Jim Procter wrote:

Hi Jan.

I Just noticed that you haven't actually committed and pushed the
VARNAv3-3b.jar file to the jalview git repository.

Normally, a pre-compiled dependency like VARNA lives in the lib
directory under the Jalview project. From the .classpath entry in the
2_5_1_rna_merge git branch, it looks like you have it in a directory
called something like VARNAv3-3b - I'd suggest you simply use the
refactor tool to relocate the jar file to the lib directory (which will
also update its references in the Jalview project), and then commit it
so I can pick up the dependency too.

Jim.

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3

It does :slight_smile:

I took a look at your code and think I know what the problem is regarding the VARNA frame appearing outside the Jalview desktop.

Basically, you have jalview.gui.AppVarnaBinding extending from JFrame, rather than the jalview.ext.VarnaBinding class. When your jalview.gui.AppVarna class creates a new varna binding, the JFrame appears outside of the Desktop window, regardless of anything you do to it.

Taking the Jmol viewer as an example, then the classes for embedding Varna should operate in the following way:

jalview.ext.varna.VarnaBinding : Abstract base class that holds references to a Varna display and any associated Jalview objects that the display is viewing. This class contains all the control logic for interfacing between Varna and Jalview's datamodel and events. It implements Jalview and Varna interfaces that enables it to pass events between the two systems, and holds any GUI independent functions useful for doing this.

Eventually, there might be many specific VarnaBinding classes - one for each Jalview GUI environment (currently, Swing, AWT, or when communicating to an external VARNA instance via javascript). Lets just focus on the Swing instance :

jalview.gui.VarnaBinding : extends from jalview.ext.varna.VarnaBinding. This is a concrete (non-abstract) class that contains additional control logic and references needed for interfacing between a Varna panel shown in the Jalview Desktop. In particular, it will probably implement abstract methods from jalview.ext.varna.VarnaBinding which contain code that interacts with a jalview.gui.AppVarna panel.

jalview.gui.AppVarna: the parent window for a VARNA frame in the Jalview desktop - should inherit from JInternalFrame (or a GUI skeleton class in jalview.jbgui). Constructors for this class are called by Jalview's Swing GUI code, and should handle any data-retrieval necessary prior to actually creating a VARNA view.

The reason for this complexity is because the ultimate aim is to minimise code duplication between jalview.appletgui and jalview.gui - so all non-gui related stuff sits in jalview.ext.varna. In practice, I suggest you just make sure the class hierarchy is correct, and then worry about refactoring the methods and data to the right place once you have actually got a fully working VARNA instance inside the desktop :slight_smile:

Hope this clears any confusion up. If it hasn't, then we can talk about it later today..
Jim.

···

On 27/06/2011 10:38, Jan Engelhardt wrote:

I fixed and committed it.
Maybe you can try if it works now.

4

Hi,

thanks for the window embedding mail. I need some time to parse your
long mails :slight_smile:

About the secondary structure: I failed to implement a method that gets
the secondary structure from the PopupMenu and I think thats because a
single sequence does not have a secondary structure but the alignment.
However I'm still not sure how can I implement an access to the
structure in an Alignment.
The last trace I found is that the structure is processed in
parseAnnotationRow() of StockholmFile but I'm not sure what happends
with the returned AlignmentAnnotation-object and in which way I can
access it later.
Could you give me a hint what happens after that?

Maybe we can have a talk tomorrow in the evening?
Jan