Read mutation data insertions, deletions, stop codons, and multi-residue mutants

[Tom Goddard]

Currently the ChimeraX mutation .csv reader ignores deletions, insertions, stop codons and multi-residue variants and only read non-synonymous and synonymous mutations. Would like to read all these types of variants and be able to visualize them in at least limited ways.

[Tom Goddard]

Done.

Introduced a new Variant class that uses HGVS notation strings and accepts any protein HGVS descriptor. Made the mutation visualization code able to show deletions, insertions, and stop codons in heatmaps and in coloring structures. Scatterplots and histograms currently do not show those sequence variants. None of the visualization methods currently work with multi-residue variants except for consecutive deletions or multi-residue insertions at a single site. In both those cases the heatmap and structure coloring display the scores for those variants using the first deleted residue or the residue immediately preceding the insertion.

I added documentation on the new capabilities to the User Guide.

It would be interesting to develop at least some rudimentary capabilities to show multi-site mutations.