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

Method Summary

Modifier and Type	Method	Description
static PathogenicityData	empty()
boolean	equals(Object o)
ClinVarData	getClinVarData()	Returns a ClinVarData object.
PathogenicityScore	getMostPathogenicScore()
List<PathogenicityScore>	getPredictedPathogenicityScores()
PathogenicityScore	getPredictedScore(PathogenicitySource pathogenicitySource)	Returns the PathogenicityScore from the requested source, or null if not present.
float	getScore()
boolean	hasClinVarData()	Method used to check whether there is any real ClinVar data associated with this object.
int	hashCode()
boolean	hasPredictedScore()
boolean	hasPredictedScore(PathogenicitySource pathogenicitySource)
boolean	isEmpty()
static PathogenicityData	of(Collection<PathogenicityScore> pathScores)
static PathogenicityData	of(ClinVarData clinVarData, Collection<PathogenicityScore> pathScores)
static PathogenicityData	of(ClinVarData clinVarData, PathogenicityScore pathScore)
static PathogenicityData	of(ClinVarData clinVarData, PathogenicityScore... pathScore)
static PathogenicityData	of(PathogenicityScore pathScore)
static PathogenicityData	of(PathogenicityScore... pathScore)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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()

getClinVarData

public ClinVarData getClinVarData()

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

getPredictedPathogenicityScores

public List<PathogenicityScore> getPredictedPathogenicityScores()

isEmpty

public boolean isEmpty()

hasPredictedScore

public boolean hasPredictedScore()

hasPredictedScore

public boolean hasPredictedScore(PathogenicitySource pathogenicitySource)

getPredictedScore

public PathogenicityScore getPredictedScore(PathogenicitySource pathogenicitySource)

Returns the PathogenicityScore from the requested source, or null if not present.

Parameters:

pathogenicitySource -

Returns:

getScore

public float getScore()

Returns:

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

getMostPathogenicScore

public PathogenicityScore getMostPathogenicScore()

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