Yesterday I updated java and jalview installAnywhere to the latest. Now when I select Above Identity Threshold and set that to 1, as I normally do, all the characters lose their color. I installed the jre with jalview also and tried that and same result. I get the same problem with my previous version of jalview. It seems the jalview jre and the current java are both 1.8. I think I might have had java 1.7 before.
Related to the "Above identity Threshold", it would very helpful if there was a setting in preferences that allowed you to automatically start jalview with "Above identity Threshold" active and set to some specified value. On another note, installing jalview was problematic, both with and without the jre included. I ended up having to uninstall java to get jalview to install. I would get an error like: "windows error 2 occurred while loading the java vm jalview".
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