Hello Denis - Thanks for the email - I've also posted my reply to the jalview-discuss list so it gets into our archives.
Denis Reshetov wrote:
I have a problem with a creating of a new annotation for a selected
alignment column. If some sequences have gaps on the column,
and I chose a color for the annotation, the sequences with gaps
will be colored unless they don't have a nucleotide in the column.
Well spotted! This is a tiny bug that I thought I'd fixed, but it seems only in a parallel universe. Duly noted and will be addressed in the next release.
Jim.
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