New DisGeNET data retrieval and additional features/adjustments (such as HPO retrieval using ontology). #2
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…s specific URI based on HPO/DisGeNET dataset). Allows for reduced number of database requests if HPO parent/child retrieval is separated from DisGeNET database.
…Entity creation (prefix not optional anymore).
…tic final variable.
…ith a collection of phenotypes connected to it).
…single Phenotype.
…rk, bug fix regarding same Phenotype being crossed with different distances, generalisation input phenotypes requirement).
…HPOs are retrieved BEFORE querying).
…fic retrieval from a collection of PhenotypeNetworks.
…one both inside a class and before adding to the respective class).
… for benchmarking.
… traverse manually).
…hen adding Phenotypes was removed to allow for more algorithm flexibility when adding new Phenotypes. Due to this, internal List was replaced by a Map.
…ver at higher values.
…her maxDistance even if the same number of phenotypes were returned (now validates for both determining which phenotypes to visit next and for adding to the network instead of only the latter).
…s still need to implement a static method to support this, though can also be used outside enums themselves as long as enum implemented the interface).
…efiner external usage).
…w optional using different RunMode, et cetera).
…parators (also added a convenience method for file closing).
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Rewritten the DisGeNET data retrieval, added phenotype retrieval using HPO ontology, further implemented output file writing, some adjustments for better looking code, adjustments/added unit-tests.