Details
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Type:
Improvement
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: 2.11.5.0
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Component/s: analysis, annotation, gui, Properties and Preferences
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Labels:None
Description
Although 2.11.5.0 introduced support for secondary structure consensus rows, it is not enabled by default in preferences, and there is in fact no way of enabling its display for an alignment! (although Group Secondary Structure Consensus can be enabled).
This is more than little problematic for demonstrating the new consensus track since one has to adjust preferences before creating a new view/importing. Perhaps a 'Show SS Consensus' option could be added ?
It is also a more general problem that we simply never got around to prioritising: View specific controls for toggling visibility of automatic calculations like Consensus, Occupancy and Conservation, etc. Whilst they can be individually hidden, they have a habit of coming back - which is a little painful.
Basically, we need a toggle option under Annotations (or is it Calculations ;) ) to show/hide all of the different autocalculated rows. These need to be covered with tests that also verify the calculations are properly intialised when they are enabled if user preferences did not have then enabled at construction time, and that they can be disabled/re-enabled.
Also checks are needed to make sure that calculation dependent colourschemes behave correctly - PID and Clustal schemes depend on the consensus calculation, and conservation shading is only possible if the conservation track is visible.
This is more than little problematic for demonstrating the new consensus track since one has to adjust preferences before creating a new view/importing. Perhaps a 'Show SS Consensus' option could be added ?
It is also a more general problem that we simply never got around to prioritising: View specific controls for toggling visibility of automatic calculations like Consensus, Occupancy and Conservation, etc. Whilst they can be individually hidden, they have a habit of coming back - which is a little painful.
Basically, we need a toggle option under Annotations (or is it Calculations ;) ) to show/hide all of the different autocalculated rows. These need to be covered with tests that also verify the calculations are properly intialised when they are enabled if user preferences did not have then enabled at construction time, and that they can be disabled/re-enabled.
Also checks are needed to make sure that calculation dependent colourschemes behave correctly - PID and Clustal schemes depend on the consensus calculation, and conservation shading is only possible if the conservation track is visible.