[2/5] Refactor: make the fragment parsing helpers private - #435
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`parse_fragment`, `fill_in_indices` and `calculate_fragment_numbers` only serve `flatten_fragments`, and nothing in alphabase, alphadia or peptdeep calls them. A leading underscore states that, and frees their signatures for the refactoring that follows. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
GeorgWa
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mschwoer
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Sep 1, 2026
| number_of_fragment_types: int, | ||
| ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: | ||
| """ | ||
| Parse fragments to get fragment numbers, fragment positions and not top k excluded indices in one hit |
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"fragment numbers" is kinda ambigous.. is this counts? or enumeration? not sure if it should be renamed now (depends on the radius of this change), but at last a comment would help :-)
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PS: I'll be creating a PR soon to optimize the translation modules ( I think it will be better to reuse the much more optimized helpers here instead. |
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Pure refactor. Rename only, no functional change.
parse_fragment,fill_in_indicesandcalculate_fragment_numbersonly serveflatten_fragments, and nothing in alphabase, alphadia or peptdeep calls them. A leading underscore states that, and frees their signatures for the refactoring that follows.Stacked on #434. Splitting #429.
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