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Tangletree genotype colouring #1785

Merged
merged 6 commits into from
Jun 10, 2024
Merged

Tangletree genotype colouring #1785

merged 6 commits into from
Jun 10, 2024

Commits on Jun 10, 2024

  1. [tangletrees] check if genome maps are identical 

    This property will be used in upcoming work to show genotype colourings
on both trees
    @jameshadfield
    jameshadfield committed Jun 10, 2024
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  2. [tangletrees] recompute data when loading via UI 

    This particular method of loading a second tree is (I believe) rarely
used and rarely developed -- see both the TODOs in the surrounding code
and the (dev-only) redux immutability errors fixed in this commit.
Still, we should support it!
    @jameshadfield
    jameshadfield committed Jun 10, 2024
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  3. [tangletrees] store root-sequence of second tree 

    In preparation for showing genotype colorings across multiple trees

We don't (yet) consider root-sequences which are defined via
sidecar files (i.e. not inline in the main JSON)

We could improve memory efficiency if we compared the nuc/aa sequences
for equality and used references to the main tree's root-sequence data,
but as we're here only considering inlined root-sequences (i.e. small
ones!) this implementation is simpler.
    @jameshadfield
    jameshadfield committed Jun 10, 2024
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  4. [tangletrees] show genotype coloring on both trees 

    Includes some (overly!) strict conditionals. This functionality is
particularly useful when comparing trees using the same (or very
similar) sequences / sets of sequences to aid in understanding the
different tree structures.

Closes #1773
    @jameshadfield
    jameshadfield committed Jun 10, 2024
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  5. [bugfix] typo in tree visibility property 

    Oh how TypeScript would have helped!

This bug was found while debugging the ability to show genotype
colorings on both trees (added in the parent commit) where the
visibility of the second tree was `undefined` upon loading, leading to
`createVisibleLegendValues` not considering the second tree and thus
removing legend items which were only observed in the second tree.

Bug introduced ~4 years ago via 391bca4
although its effect was minor (and probably never noticed?)
    @jameshadfield
    jameshadfield committed Jun 10, 2024
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  6. changelog

    @jameshadfield
    jameshadfield committed Jun 10, 2024
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