Class SimpleOrthoPair

  • All Implemented Interfaces:
    OrthoPair

    public class SimpleOrthoPair
    extends java.lang.Object
    implements OrthoPair
    A no-frills implementation of the OrthoPair interface
    Author:
    David Huen
    • Constructor Detail

      • SimpleOrthoPair

        public SimpleOrthoPair​(Orthologue first,
                               Orthologue second,
                               SimilarityType type,
                               double percentIdentity)
        constructor for the computed form of an orthology relationship.
      • SimpleOrthoPair

        public SimpleOrthoPair​(Orthologue first,
                               Orthologue second,
                               java.lang.String ref)
        constructor for the curated form of an orthology relationship
    • Method Detail

      • getFirstOrthologue

        public Orthologue getFirstOrthologue()
        Description copied from interface: OrthoPair
        gets the first orthologue in the orthology relationship.

        I agree that this access route is somewhat sucky for a symmetric relationship but I'd hate returning a Set of orthologues more and all the fiddling would require.

        Specified by:
        getFirstOrthologue in interface OrthoPair
      • getSecondOrthologue

        public Orthologue getSecondOrthologue()
        Description copied from interface: OrthoPair
        gets the first orthologue in the orthology relationship. This will be the one with the lower TaxonID.
        Specified by:
        getSecondOrthologue in interface OrthoPair
      • getSimilarity

        public SimilarityType getSimilarity()
        Description copied from interface: OrthoPair
        gets the second orthologue in the orthology relationship. This will be the one with the higher TaxonID.
        Specified by:
        getSimilarity in interface OrthoPair
      • getPercentIdentity

        public double getPercentIdentity()
        Description copied from interface: OrthoPair
        get percentage identity.
        Specified by:
        getPercentIdentity in interface OrthoPair
      • getRef

        public java.lang.String getRef()
        Description copied from interface: OrthoPair
        get reference to evidence for orthology.
        Specified by:
        getRef in interface OrthoPair
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object