JAL-2704: Gap colour should not be affected by PID or Conservation shading
A User Defined colour scheme can specify a colour other than white for gaps. Currently, this colour gets faded if Colour by Conservation is applied, and is always white where conservation score is zero. If Colour Above Identity Threshold is applied, gaps are always white, as they do not match the consensus residue. A bespoke gap colour should be left unchanged in these scenarios.
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