It looks like rendering with transparency stopped working after 774962a
This is most likely a runtime issue - @benzoid did some careful testing with JalviewJS, stepping through all subsequent commits after 774962a to see what broke (https://issues.jalview.org/browse/JAL-4025?focusedCommentId=25553&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-25553):
774962a - last fully working commit
272041b - rendering of different coloured transparent rectangles on top of each other stops working (ie only see colour for last rendered transparent rectangle).
1f2922e - rendering an image with transparency on top of an existing image stops working (ie only see transparent image).
It looks like rendering with transparency stopped working after 774962a
This is most likely a runtime issue - @benzoid did some careful testing with JalviewJS, stepping through all subsequent commits after 774962a to see what broke (https://issues.jalview.org/browse/JAL-4025?focusedCommentId=25553&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-25553):
774962a - last fully working commit
272041b - rendering of different coloured transparent rectangles on top of each other stops working (ie only see colour for last rendered transparent rectangle).
1f2922e - rendering an image with transparency on top of an existing image stops working (ie only see transparent image).