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Lc/minimal improvements suggestions - #48

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leokim-l wants to merge 5 commits into
bboqafrom
lc/minimal_improvements_suggestions
Open

Lc/minimal improvements suggestions#48
leokim-l wants to merge 5 commits into
bboqafrom
lc/minimal_improvements_suggestions

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@leokim-l

@leokim-l leokim-l commented Aug 5, 2026

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@pnrobinson this PR is simply a way of showing some minor edits that are open to debate and that do not go beyond - in design terms - than what you have done. Bigger design choices, as we said, we can discuss in person. Given our discussion today, I hope this is OK, if not, please let's discuss what to change. I pretty much:

  1. moved fromObservedHpoTermList to the implementing class DefaultPatientData and out of the interface DiseaseData, isn't that more appropriate?
  2. added getPrimaryTermId also in DefaultPatientData, in order to avoid errors when old HPO IDs are used. We don't expect this from Exomiser, I suppose...
  3. removed redundant check in algorithm parameters
  4. removed redundant disease id and label from BoqaCounts, since we don't need it anymore, our bookkeeping is now done differently and classes such as TargetDisease or DiseaseComponent already contain id and label.
  5. removed duplicate TargetDisease class
  6. In the sealed interface sometimes methods were explicitly overridden, sometimes not. I personally find it more understandable if they are either all overridden, or none is (among those that are trivially returning values).
  7. We might want to keep a BlendedCounter or not, in any case, I made sure it does exactly what BoqaSetCounter. This was a source of bugs in the past.

This compiles without tests, mainly because of the change in signature of BoqaCounts. Before investing too much time into fixing it, I thought I'd run these suggestions by you.

leokim-l and others added 5 commits August 5, 2026 17:19
… term filtering and mapping to primary term id
…ntains a TargetDisease and a BoqaCounts. Since the refactoring introduces these, maybe it's time to remove id and label from BoqaCounts
Added a method to create PatientData from a list of observed HPO terms.
Removed the fromObservedHpoTermList method that converts a list of HPO identifiers to PatientData.
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