Support highlighting of alignments in raw alphabet

Sometimes users prefer to use characters, such as '?', '!', and others, when analyzing an alignment. This characters are not included into the amino acid alphabet, i.e. the alignment alphabet becomes "Raw".

Currently, the highlighting modes are not supported for alignments with "Raw" alphabet, so the alignments becomes white.

Instead, the highlighting mode can be supported partially - characters of the amino acid alphabet are highlighted in their colors, other characters are highlighted e.g. in gray.

Also, consider to support highlighting of extended alphabet, when custom coloring schemes are used.