TermId

[pnrobinson]

We should not represent the HPO Term identifiers as Strings, we should use TermId. The input should be transformed to TermIds when we first ingest the data. This allows better quality control and also obviates the need for transforming them later on

  public void initQueryLayer(Set<String> queryTerms){
        // TODO should this live in phenol?
        Set<TermId> queryTermIDs = queryTerms.stream()
                .map(TermId::of)
                .collect(Collectors.toSet());
        this.queryLayerInitialized = initLayer(queryTermIDs);
    }

[leokim-l]

Todo: after merging what is already in draft mode, startrefactor branch to make Strings into TermIds and included to observed. @pnrobinson if you see other refactoring necessary you can comment here, I will reference this issue when working on that.

[leokim-l]

Apparently Exomiser does not use TermIds (yet) so we can stick to Strings for now. We have a bit of a mix of Strings/TermIds at the current stage. I would leave this as is as long as it works and worry about refactoring when working on the Exomiser interface part of the project