org.molgenis.data.annotation.core.entity.impl.gavin

Class GavinThresholds

java.lang.Object

org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds

public abstract class GavinThresholds
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	MEAN_PATHOGENIC_CADD_SCORE
static String	MEAN_POPULATION_CADD_SCORE
static String	PATHO_MAF_THRESHOLD
static String	SENS_95TH_PER_CADD_THRESHOLD
static String	SPEC_95TH_PER_CADD_THRESHOLD

Constructor Summary

Constructors

Constructor and Description
GavinThresholds()

Method Summary

Modifier and Type	Method and Description
static GavinThresholds	create(Double pathoMAFThreshold, Double meanPathogenicCADDScore, Double meanPopulationCADDScore, Double spec95thPerCADDThreshold, Double sens95thPerCADDThreshold, Category category)
static GavinThresholds	fromEntity(Entity annotationSourceEntity)
abstract Category	getCategory()
abstract Double	getMeanPathogenicCADDScore()
abstract Double	getMeanPopulationCADDScore()
abstract Double	getPathoMAFThreshold()
abstract Double	getSens95thPerCADDThreshold()
abstract Double	getSpec95thPerCADDThreshold()
boolean	isAboveMeanPathogenicCADDScore(double caddScaled)
boolean	isAbovePathoMAFThreshold(Double exacMAF)
boolean	isAboveSpec95thPerCADDThreshold(double caddScaled)
boolean	isBelowMeanPopulationCADDScore(double caddScaled)
boolean	isBelowSens95PerCADDThreshold(double caddScaled)
GavinThresholds	withExtraSensitivity(int extraSensitivityFactor)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PATHO_MAF_THRESHOLD

public static final String PATHO_MAF_THRESHOLD

See Also:

Constant Field Values

MEAN_PATHOGENIC_CADD_SCORE

public static final String MEAN_PATHOGENIC_CADD_SCORE

See Also:

Constant Field Values

MEAN_POPULATION_CADD_SCORE

public static final String MEAN_POPULATION_CADD_SCORE

See Also:

Constant Field Values

SPEC_95TH_PER_CADD_THRESHOLD

public static final String SPEC_95TH_PER_CADD_THRESHOLD

See Also:

Constant Field Values

SENS_95TH_PER_CADD_THRESHOLD

public static final String SENS_95TH_PER_CADD_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

GavinThresholds

public GavinThresholds()

Method Detail

getPathoMAFThreshold

@Nullable
public abstract Double getPathoMAFThreshold()

getMeanPathogenicCADDScore

@Nullable
public abstract Double getMeanPathogenicCADDScore()

getMeanPopulationCADDScore

@Nullable
public abstract Double getMeanPopulationCADDScore()

getSpec95thPerCADDThreshold

@Nullable
public abstract Double getSpec95thPerCADDThreshold()

getSens95thPerCADDThreshold

@Nullable
public abstract Double getSens95thPerCADDThreshold()

getCategory

public abstract Category getCategory()

withExtraSensitivity

public GavinThresholds withExtraSensitivity(int extraSensitivityFactor)

create

public static GavinThresholds create(Double pathoMAFThreshold,
                                     Double meanPathogenicCADDScore,
                                     Double meanPopulationCADDScore,
                                     Double spec95thPerCADDThreshold,
                                     Double sens95thPerCADDThreshold,
                                     Category category)

fromEntity

public static GavinThresholds fromEntity(Entity annotationSourceEntity)

isAboveMeanPathogenicCADDScore

public boolean isAboveMeanPathogenicCADDScore(double caddScaled)

isBelowMeanPopulationCADDScore

public boolean isBelowMeanPopulationCADDScore(double caddScaled)

isAbovePathoMAFThreshold

public boolean isAbovePathoMAFThreshold(Double exacMAF)

isAboveSpec95thPerCADDThreshold

public boolean isAboveSpec95thPerCADDThreshold(double caddScaled)

isBelowSens95PerCADDThreshold

public boolean isBelowSens95PerCADDThreshold(double caddScaled)