Bugfix for numbering reference between model and receptor

[rvhonorato]

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Before the alignment was just taking sections that overlap, now it should correctly use the numbering reference, also improved a bit the readability of the sequence alignment function and updated the tests.

[codecov-commenter]

Codecov Report

Merging #404 (af0c2fa) into main (c80475f) will increase coverage by 0.01%.
The diff coverage is 96.55%.

@@            Coverage Diff             @@
##             main     #404      +/-   ##
==========================================
+ Coverage   62.53%   62.54%   +0.01%     
==========================================
  Files          70       70              
  Lines        4449     4451       +2     
==========================================
+ Hits         2782     2784       +2     
  Misses       1667     1667              

Impacted Files	Coverage Δ
src/haddock/modules/analysis/caprieval/capri.py	82.59% <96.42%> (+0.05%)	⬆️
tests/test_module_caprieval.py	100.00% <100.00%> (ø)

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[mgiulini]

Very nice, I think there's also a major improvement in the overall code readability.