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Consolidate branch length methods to new Dataset subclass #55

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willdumm opened this issue Sep 11, 2024 · 1 comment · Fixed by #89
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Consolidate branch length methods to new Dataset subclass #55

willdumm opened this issue Sep 11, 2024 · 1 comment · Fixed by #89
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Many Dataset subclasses have duplicated methods like export_branch_lengths, and the branch lengths setter. These should be moved to something called BranchLengthDataset, which can be subclassed by all the classes that currently independently implement these methods.

Originally posted by @willdumm in #50 (comment)
@willdumm willdumm mentioned this issue Sep 11, 2024
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@willdumm willdumm self-assigned this Sep 11, 2024
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use 55-consolidate-dataset-methods

@willdumm willdumm mentioned this issue Nov 22, 2024
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willdumm added a commit that referenced this issue Nov 26, 2024
@willdumm
New Dataset superclass (#89)
469420e 
* Addressing #55, I consolidating some branch lengths-related code into a new superclass BranchLengthDataset.
* addressed #22 by moving some methods and functions around. All pre-existing functions and methods should work as they did before. Now, a DXSM crepe can be called on sequences to get selection factors. Previously, this required calling the method `selection_factors_of_aa_str` on a DXSM model.
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New Dataset superclass matsengrp/netam
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