Package org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity

Class PathogenicityData

java.lang.Object
org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
public class PathogenicityData extends Object
Container for Pathogenicity data about a variant.
Since:
3.0.0
Author:
Jules Jacobsen <jules.jacobsen@sanger.ac.uk>

  • Method Details

    • of

      public static PathogenicityData of(PathogenicityScore pathScore)

    • of

      public static PathogenicityData of(PathogenicityScore... pathScore)

    • of

      public static PathogenicityData of(Collection<PathogenicityScore> pathScores)

    • of

      public static PathogenicityData of(ClinVarData clinVarData, PathogenicityScore pathScore)
      Since:
      10.1.0

    • of

      public static PathogenicityData of(ClinVarData clinVarData, PathogenicityScore... pathScore)
      Since:
      10.1.0

    • of

      public static PathogenicityData of(ClinVarData clinVarData, Collection<PathogenicityScore> pathScores)
      Since:
      10.1.0

    • empty

      public static PathogenicityData empty()

    • clinVarData

      public ClinVarData clinVarData()
      Returns a ClinVarData object. It is highly likely that this field will contain a ClinVarData.empty() object. For this reason the companion method hasClinVarData() can be used to check whether there is any real data. Alternatively clinVarData.isEmpty() can be called on the object returned from this method.
      Returns:
      a ClinVarData object
      Since:
      10.1.0

    • hasClinVarData

      public boolean hasClinVarData()
      Method used to check whether there is any real ClinVar data associated with this object.
      Returns:
      true if there is any associated ClinVar data, otherwise returns false.
      Since:
      10.1.0

    • pathogenicityScores

      public List<PathogenicityScore> pathogenicityScores()

    • isEmpty

      public boolean isEmpty()

    • hasPredictedScore

      public boolean hasPredictedScore()

    • hasPredictedScore

      public boolean hasPredictedScore(PathogenicitySource pathogenicitySource)

    • pathogenicityScore

      public PathogenicityScore pathogenicityScore(PathogenicitySource pathogenicitySource)
      Returns the PathogenicityScore from the requested source, or null if not present.
      Parameters:
      pathogenicitySource -
      Returns:

    • pathogenicityScore

      public float pathogenicityScore()
      Returns:
      the predicted pathogenicity score for this data set. The score is ranked from 0 (non-pathogenic) to 1 (highly pathogenic)

    • mostPathogenicScore

      @Nullable public PathogenicityScore mostPathogenicScore()
      Returns:
      The most pathogenic score or null if there are no predicted scores

    • equals

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

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object