Package org.monarchinitiative.lirical.core.service

Class VariantPathogenicity

java.lang.Object
org.monarchinitiative.lirical.core.service.VariantPathogenicity
public class VariantPathogenicity extends Object
Class to represent pathogenicity data available for a genomic variant. The pathogenicity data usually represents the highest value of algorithms (i.e. PolyPhen2, Mutation Taster).

The empty() variant pathogenicity should be used when the pathogenicity data is not available (i.e. the database is not available during runtime). This is in contrast with case when database is available and pathogenicity score for a variant is missing. The score is set to zero in this case.

  • Method Details

    • empty

      public static VariantPathogenicity empty()

    • of

      public static VariantPathogenicity of(float pathogenicity, ClinvarClnSig clinvarClnSig)

    • isEmpty

      public boolean isEmpty()
      Returns:
      true if the pathogenicity data was not available, and we cannot say if the variant is or is not pathogenic.

    • clinvarClnSig

      public Optional<ClinvarClnSig> clinvarClnSig()

    • pathogenicity

      public float pathogenicity()

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object