Problem:

I have an alignment file referenced into a container file. When I open the profile view of the referenced alignment, I do not see the alignment. I open the Level Display dialog and select the referenced alignment file. I notice that only the Default level is selected as turned on. None of my other Levels are turned on as seen below. How do I have them turn on without having to manually select them every time?

Answer:

There could be two things causing this.

1. Go to File > Settings > Configuration > Configuration Variables and set MS_REF_NEWLEVELDISPLAY to 1. When set to 1, the program will display newly created levels in the references. By default, the new levels are not displayed.
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2. If this variable is already set to 1, then it is being altered when you attach the reference. Go to the Reference Dialog and double click on the alignment file that is referenced. Make sure either Always is selected or Use MS_REF_NEWLEVELDISPLAY Configuration Variable is selected if it is set to value 1.
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