When alphabet of a sequence, added to a multiple alignment, differs from alphabet of the alignment, the alignment alphabet may be modified. This use case is not currently taken into account by "Color" and "Highlighting" items on the options panel.
For example, to reproduce the issue:
- Open "data/samples/CLUSTALW/COI.aln".
- Add an addition sequence from a file, e.g. amino acid sequence "_common_data/fasta/amino_ext.fa".
- Open "Highlighting" option panel tab.
items in the "Color" and "Highlighting" combo boxes correspond to the obsolete alphabet.
- Alphabet of the alignment was updated (to "Standard amino acid" alphabet in this case).
- Items in the "Color" and "Highlighting" combo boxes correspond to the values of the new alphabet.
- The values of the combo boxes are set to default for the current alphabet.
- Close the Alignment Editor.
- Open the view again.
- Open the "Highlighting" tab.
: "Color" and "Highlighting" combo boxes are empty.
Values of the combo boxes are the same as on step 3.
Fix the issue for possible modifications of an alignment alphabet (Standard DNA > Standard amino acid, Standard RNA > Raw, etc.).