Annotation panel and "About Cytoscape"

[michael.ri...@gmail.com]

I'm running Cytoscape 3.7.0 with Java 1.8.0_191 on Mac OS 10.14.1. 

I'm running into a number of behaviors that seem likely to be bugs. Some of them can be fixed by closing and reopening Cytoscape.

1) I created an annotation in my network, but it doesn't appear anywhere in the annotation panel panel for either "Foreground" or "Background". I can close Cytoscape and reopen it and the annotation is still on the canvas but not on the annotation panel.

EDIT: I was able to resolve #1 as follows. There was another network in the networks panel that had been created from a JSON file and probably processed through an earlier version of Cytoscape. When I deleted that other network, the annotations appeared in the annotations panels.

2) I just opened "About Cytoscape" from the Cytoscape menu. The popup appears over the canvas but there doesn't seem to be anyway to make it go away. It is blocking my view of the canvas.

3) Usually, changing the node shape mapping affects node shapes on the canvas immediately, but occasionally I need to close and reopen Cytoscape before they appear.

I appreciate any help you can offer.

-Michael

[Scooter Morris]

Hi Michael,

On Monday, December 17, 2018 at 7:12:07 PM UTC-8, michael.ri...@gmail.com wrote:

I'm running Cytoscape 3.7.0 with Java 1.8.0_191 on Mac OS 10.14.1. 

I'm running into a number of behaviors that seem likely to be bugs. Some of them can be fixed by closing and reopening Cytoscape.

1) I created an annotation in my network, but it doesn't appear anywhere in the annotation panel panel for either "Foreground" or "Background". I can close Cytoscape and reopen it and the annotation is still on the canvas but not on the annotation panel.

EDIT: I was able to resolve #1 as follows. There was another network in the networks panel that had been created from a JSON file and probably processed through an earlier version of Cytoscape. When I deleted that other network, the annotations appeared in the annotations panels.

Ah, OK.  That still shouldn't happen.  If you have the session file from before you deleted the offending network, it would be useful to have to help us debug this behavior.

2) I just opened "About Cytoscape" from the Cytoscape menu. The popup appears over the canvas but there doesn't seem to be anyway to make it go away. It is blocking my view of the canvas.

You should be able to just click on the panel and it should disappear.

3) Usually, changing the node shape mapping affects node shapes on the canvas immediately, but occasionally I need to close and reopen Cytoscape before they appear.

Can you say a little more about the circumstances when it doesn't work?  Is it on large networks? 

I appreciate any help you can offer.

-Michael

 

-- scooter