Lc/minimal improvements suggestions - #48
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… 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
…e in BoqaSetCounter
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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@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:
fromObservedHpoTermListto the implementing classDefaultPatientDataand out of the interfaceDiseaseData, isn't that more appropriate?getPrimaryTermIdalso inDefaultPatientData, in order to avoid errors when old HPO IDs are used. We don't expect this from Exomiser, I suppose...BoqaCounts, since we don't need it anymore, our bookkeeping is now done differently and classes such asTargetDiseaseorDiseaseComponentalready contain id and label.TargetDiseaseclassBlendedCounteror not, in any case, I made sure it does exactly whatBoqaSetCounter. 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.