Update the alignment figure

[alyst]

Update the alignment figure in the documentation

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📋 Additional detail

As a follow-up to #61, I have updated the figure. Now it combines both the pairwise alignment (which before was a verbatim text) and sequence of anchors (before it was Julia code, now it's a table in a SVG file). I think it makes the idea of the anchors more clear.

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[codecov]

Codecov Report

Merging #62 (2d3be18) into master (ed08737) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #62   +/-   ##
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  Coverage   87.95%   87.95%           
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  Files          16       16           
  Lines        1121     1121           
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  Hits          986      986           
  Misses        135      135           

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[CiaranOMara]

Firstly, a belated thank you for putting together this PR.

I like the idea of an image because it can more comfortably display positions in the tens, something text images cannot do well. Including an image like the one you've constructed would be nice.

I appreciate that you may have moved to other things after all this time. If that's the case, please let us know so that someone else can step in and revive your PR.

[CiaranOMara]

I have got a few points regarding the image that I hope are trivial to address:

• I think it is important for the dashes and dots in the alignment row to align with the query and reference.
• Also, some of the position pointers/indicators appear between symbols. But, I think the symbols occupy the relative position/index, so I'd want these pointers to point to the middle of a symbol - please feel free to correct me.
• I'm unconvinced that the enumeration in the circles adds information. So instead of enumerating the operations/anchors in the alignment row, could the aln position be shown instead?

[alyst]

• I think it is important for the dashes and dots in the alignment row to align with the query and reference.

I think it was the font problem. Now I have switched SVG to the embedded fonts, so the alignment should be ok. Let me know if some alignment issues still remain.

• I'm unconvinced that the enumeration in the circles adds information. So instead of enumerating the operations/anchors in the alignment row, could the aln position be shown instead?

The numbers refer to the exact row in the table. If replaced by the alignment position (also then the alignment position should be moved to the right side of the block), matching operations on the diagram and in the table becomes less straightforward. So I would rather keep it as it is.