Package org.hl7.fhir.r4.model

Class MolecularSequence.MolecularSequenceQualityComponent

java.lang.Object

org.hl7.fhir.r4.model.Base

org.hl7.fhir.r4.model.Element

org.hl7.fhir.r4.model.BackboneElement

org.hl7.fhir.r4.model.MolecularSequence.MolecularSequenceQualityComponent

All Implemented Interfaces:

ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseBackboneElement, org.hl7.fhir.instance.model.api.IBaseElement, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

Enclosing class:

MolecularSequence

public static class MolecularSequence.MolecularSequenceQualityComponent
extends BackboneElement
implements org.hl7.fhir.instance.model.api.IBaseBackboneElement

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected IntegerType	end	End position of the sequence.
protected DecimalType	fScore	Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
protected DecimalType	gtFP	The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e.
protected CodeableConcept	method	Which method is used to get sequence quality.
protected DecimalType	precision	QUERY.TP / (QUERY.TP + QUERY.FP).
protected DecimalType	queryFP	False positives, i.e.
protected DecimalType	queryTP	True positives, from the perspective of the query data, i.e.
protected DecimalType	recall	TRUTH.TP / (TRUTH.TP + TRUTH.FN).
protected MolecularSequence.MolecularSequenceQualityRocComponent	roc	Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
protected Quantity	score	The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
protected CodeableConcept	standardSequence	Gold standard sequence used for comparing against.
protected IntegerType	start	Start position of the sequence.
protected DecimalType	truthFN	False negatives, i.e.
protected DecimalType	truthTP	True positives, from the perspective of the truth data, i.e.
protected Enumeration<MolecularSequence.QualityType>	type	INDEL / SNP / Undefined variant.

Fields inherited from class org.hl7.fhir.r4.model.BackboneElement

modifierExtension

Fields inherited from class org.hl7.fhir.r4.model.Element

extension, id

Constructor Summary

Constructors

Constructor	Description
MolecularSequenceQualityComponent()	Constructor
MolecularSequenceQualityComponent(Enumeration<MolecularSequence.QualityType> type)	Constructor

Method Summary

Modifier and Type	Method	Description
Base	addChild(String name)
MolecularSequence.MolecularSequenceQualityComponent	copy()
void	copyValues(MolecularSequence.MolecularSequenceQualityComponent dst)
boolean	equalsDeep(Base other_)
boolean	equalsShallow(Base other_)
String	fhirType()
int	getEnd()
IntegerType	getEndElement()
BigDecimal	getFScore()
DecimalType	getFScoreElement()
BigDecimal	getGtFP()
DecimalType	getGtFPElement()
CodeableConcept	getMethod()
Property	getNamedProperty(int _hash, String _name, boolean _checkValid)
BigDecimal	getPrecision()
DecimalType	getPrecisionElement()
Base[]	getProperty(int hash, String name, boolean checkValid)
BigDecimal	getQueryFP()
DecimalType	getQueryFPElement()
BigDecimal	getQueryTP()
DecimalType	getQueryTPElement()
BigDecimal	getRecall()
DecimalType	getRecallElement()
MolecularSequence.MolecularSequenceQualityRocComponent	getRoc()
Quantity	getScore()
CodeableConcept	getStandardSequence()
int	getStart()
IntegerType	getStartElement()
BigDecimal	getTruthFN()
DecimalType	getTruthFNElement()
BigDecimal	getTruthTP()
DecimalType	getTruthTPElement()
MolecularSequence.QualityType	getType()
Enumeration<MolecularSequence.QualityType>	getTypeElement()
String[]	getTypesForProperty(int hash, String name)
boolean	hasEnd()
boolean	hasEndElement()
boolean	hasFScore()
boolean	hasFScoreElement()
boolean	hasGtFP()
boolean	hasGtFPElement()
boolean	hasMethod()
boolean	hasPrecision()
boolean	hasPrecisionElement()
boolean	hasQueryFP()
boolean	hasQueryFPElement()
boolean	hasQueryTP()
boolean	hasQueryTPElement()
boolean	hasRecall()
boolean	hasRecallElement()
boolean	hasRoc()
boolean	hasScore()
boolean	hasStandardSequence()
boolean	hasStart()
boolean	hasStartElement()
boolean	hasTruthFN()
boolean	hasTruthFNElement()
boolean	hasTruthTP()
boolean	hasTruthTPElement()
boolean	hasType()
boolean	hasTypeElement()
boolean	isEmpty()
protected void	listChildren(List<Property> children)
Base	makeProperty(int hash, String name)
void	removeChild(String name, Base value)
MolecularSequence.MolecularSequenceQualityComponent	setEnd(int value)
MolecularSequence.MolecularSequenceQualityComponent	setEndElement(IntegerType value)
MolecularSequence.MolecularSequenceQualityComponent	setFScore(double value)
MolecularSequence.MolecularSequenceQualityComponent	setFScore(long value)
MolecularSequence.MolecularSequenceQualityComponent	setFScore(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setFScoreElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setGtFP(double value)
MolecularSequence.MolecularSequenceQualityComponent	setGtFP(long value)
MolecularSequence.MolecularSequenceQualityComponent	setGtFP(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setGtFPElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setMethod(CodeableConcept value)
MolecularSequence.MolecularSequenceQualityComponent	setPrecision(double value)
MolecularSequence.MolecularSequenceQualityComponent	setPrecision(long value)
MolecularSequence.MolecularSequenceQualityComponent	setPrecision(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setPrecisionElement(DecimalType value)
Base	setProperty(int hash, String name, Base value)
Base	setProperty(String name, Base value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryFP(double value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryFP(long value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryFP(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryFPElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryTP(double value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryTP(long value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryTP(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setQueryTPElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setRecall(double value)
MolecularSequence.MolecularSequenceQualityComponent	setRecall(long value)
MolecularSequence.MolecularSequenceQualityComponent	setRecall(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setRecallElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setRoc(MolecularSequence.MolecularSequenceQualityRocComponent value)
MolecularSequence.MolecularSequenceQualityComponent	setScore(Quantity value)
MolecularSequence.MolecularSequenceQualityComponent	setStandardSequence(CodeableConcept value)
MolecularSequence.MolecularSequenceQualityComponent	setStart(int value)
MolecularSequence.MolecularSequenceQualityComponent	setStartElement(IntegerType value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthFN(double value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthFN(long value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthFN(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthFNElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthTP(double value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthTP(long value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthTP(BigDecimal value)
MolecularSequence.MolecularSequenceQualityComponent	setTruthTPElement(DecimalType value)
MolecularSequence.MolecularSequenceQualityComponent	setType(MolecularSequence.QualityType value)
MolecularSequence.MolecularSequenceQualityComponent	setTypeElement(Enumeration<MolecularSequence.QualityType> value)

Methods inherited from class org.hl7.fhir.r4.model.BackboneElement

addModifierExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyExtensions, copyNewExtensions, copyValues, getExtensionByUrl, getExtensionsByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionFirstRep, hasExtension, hasExtension, hasModifierExtension, removeExtension, setModifierExtension

Methods inherited from class org.hl7.fhir.r4.model.Element

addExtension, addExtension, addExtension, copyExtensions, copyNewExtensions, copyValues, getExtension, getExtensionFirstRep, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, setDisallowExtensions, setExtension, setId, setIdBase, setIdElement

Methods inherited from class org.hl7.fhir.r4.model.Base

castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCanonical, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExpression, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMarketingStatus, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPopulation, castToPositiveInt, castToProdCharacteristic, castToProductShelfLife, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToSubstanceAmount, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUrl, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, copyValues, dateTimeValue, equals, getChildByName, getChildValueByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, getXhtml, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, isResource, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase

getFormatCommentsPost, getFormatCommentsPre, getUserData, hasFormatComment, setUserData

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseElement

getUserData, setUserData

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasExtensions

addExtension, getExtension, hasExtension

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

addModifierExtension, getModifierExtension, hasModifierExtension

Field Details

type

protected Enumeration<MolecularSequence.QualityType> type

INDEL / SNP / Undefined variant.

standardSequence

protected CodeableConcept standardSequence

Gold standard sequence used for comparing against.

start

protected IntegerType start

Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

end

protected IntegerType end

End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

score

protected Quantity score

The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).

method

protected CodeableConcept method

Which method is used to get sequence quality.

truthTP

protected DecimalType truthTP

True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

queryTP

protected DecimalType queryTP

True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

truthFN

protected DecimalType truthFN

False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

queryFP

protected DecimalType queryFP

False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

gtFP

protected DecimalType gtFP

The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

precision

protected DecimalType precision

QUERY.TP / (QUERY.TP + QUERY.FP).

recall

protected DecimalType recall

TRUTH.TP / (TRUTH.TP + TRUTH.FN).

fScore

protected DecimalType fScore

Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

roc

protected MolecularSequence.MolecularSequenceQualityRocComponent roc

Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.

Constructor Details

MolecularSequenceQualityComponent

public MolecularSequenceQualityComponent()

Constructor

MolecularSequenceQualityComponent

public MolecularSequenceQualityComponent(Enumeration<MolecularSequence.QualityType> type)

Constructor

Method Details

getTypeElement

public Enumeration<MolecularSequence.QualityType> getTypeElement()

Returns:

type (INDEL / SNP / Undefined variant.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value

hasTypeElement

public boolean hasTypeElement()

hasType

public boolean hasType()

setTypeElement

public MolecularSequence.MolecularSequenceQualityComponent setTypeElement(Enumeration<MolecularSequence.QualityType> value)

Parameters:

value - type (INDEL / SNP / Undefined variant.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value

getType

public MolecularSequence.QualityType getType()

Returns:

INDEL / SNP / Undefined variant.

setType

public MolecularSequence.MolecularSequenceQualityComponent setType(MolecularSequence.QualityType value)

Parameters:

value - INDEL / SNP / Undefined variant.

getStandardSequence

public CodeableConcept getStandardSequence()

Returns:

standardSequence (Gold standard sequence used for comparing against.)

hasStandardSequence

public boolean hasStandardSequence()

setStandardSequence

public MolecularSequence.MolecularSequenceQualityComponent setStandardSequence(CodeableConcept value)

Parameters:

value - standardSequence (Gold standard sequence used for comparing against.)

getStartElement

public IntegerType getStartElement()

Returns:

start (Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value

hasStartElement

public boolean hasStartElement()

hasStart

public boolean hasStart()

setStartElement

public MolecularSequence.MolecularSequenceQualityComponent setStartElement(IntegerType value)

Parameters:

value - start (Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value

getStart

public int getStart()

Returns:

Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

setStart

public MolecularSequence.MolecularSequenceQualityComponent setStart(int value)

Parameters:

value - Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

getEndElement

public IntegerType getEndElement()

Returns:

end (End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value

hasEndElement

public boolean hasEndElement()

hasEnd

public boolean hasEnd()

setEndElement

public MolecularSequence.MolecularSequenceQualityComponent setEndElement(IntegerType value)

Parameters:

value - end (End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value

getEnd

public int getEnd()

Returns:

End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

setEnd

public MolecularSequence.MolecularSequenceQualityComponent setEnd(int value)

Parameters:

value - End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

getScore

public Quantity getScore()

Returns:

score (The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).)

hasScore

public boolean hasScore()

setScore

public MolecularSequence.MolecularSequenceQualityComponent setScore(Quantity value)

Parameters:

value - score (The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).)

getMethod

public CodeableConcept getMethod()

Returns:

method (Which method is used to get sequence quality.)

hasMethod

public boolean hasMethod()

setMethod

public MolecularSequence.MolecularSequenceQualityComponent setMethod(CodeableConcept value)

Parameters:

value - method (Which method is used to get sequence quality.)

getTruthTPElement

public DecimalType getTruthTPElement()

Returns:

truthTP (True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.). This is the underlying object with id, value and extensions. The accessor "getTruthTP" gives direct access to the value

hasTruthTPElement

public boolean hasTruthTPElement()

hasTruthTP

public boolean hasTruthTP()

setTruthTPElement

public MolecularSequence.MolecularSequenceQualityComponent setTruthTPElement(DecimalType value)

Parameters:

value - truthTP (True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.). This is the underlying object with id, value and extensions. The accessor "getTruthTP" gives direct access to the value

getTruthTP

public BigDecimal getTruthTP()

Returns:

True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setTruthTP

public MolecularSequence.MolecularSequenceQualityComponent setTruthTP(BigDecimal value)

Parameters:

value - True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setTruthTP

public MolecularSequence.MolecularSequenceQualityComponent setTruthTP(long value)

Parameters:

value - True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setTruthTP

public MolecularSequence.MolecularSequenceQualityComponent setTruthTP(double value)

Parameters:

value - True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

getQueryTPElement

public DecimalType getQueryTPElement()

Returns:

queryTP (True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.). This is the underlying object with id, value and extensions. The accessor "getQueryTP" gives direct access to the value

hasQueryTPElement

public boolean hasQueryTPElement()

hasQueryTP

public boolean hasQueryTP()

setQueryTPElement

public MolecularSequence.MolecularSequenceQualityComponent setQueryTPElement(DecimalType value)

Parameters:

value - queryTP (True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.). This is the underlying object with id, value and extensions. The accessor "getQueryTP" gives direct access to the value

getQueryTP

public BigDecimal getQueryTP()

Returns:

True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setQueryTP

public MolecularSequence.MolecularSequenceQualityComponent setQueryTP(BigDecimal value)

Parameters:

value - True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setQueryTP

public MolecularSequence.MolecularSequenceQualityComponent setQueryTP(long value)

Parameters:

value - True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

setQueryTP

public MolecularSequence.MolecularSequenceQualityComponent setQueryTP(double value)

Parameters:

value - True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

getTruthFNElement

public DecimalType getTruthFNElement()

Returns:

truthFN (False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.). This is the underlying object with id, value and extensions. The accessor "getTruthFN" gives direct access to the value

hasTruthFNElement

public boolean hasTruthFNElement()

hasTruthFN

public boolean hasTruthFN()

setTruthFNElement

public MolecularSequence.MolecularSequenceQualityComponent setTruthFNElement(DecimalType value)

Parameters:

value - truthFN (False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.). This is the underlying object with id, value and extensions. The accessor "getTruthFN" gives direct access to the value

getTruthFN

public BigDecimal getTruthFN()

Returns:

False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

setTruthFN

public MolecularSequence.MolecularSequenceQualityComponent setTruthFN(BigDecimal value)

Parameters:

value - False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

setTruthFN

public MolecularSequence.MolecularSequenceQualityComponent setTruthFN(long value)

Parameters:

value - False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

setTruthFN

public MolecularSequence.MolecularSequenceQualityComponent setTruthFN(double value)

Parameters:

value - False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

getQueryFPElement

public DecimalType getQueryFPElement()

Returns:

queryFP (False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.). This is the underlying object with id, value and extensions. The accessor "getQueryFP" gives direct access to the value

hasQueryFPElement

public boolean hasQueryFPElement()

hasQueryFP

public boolean hasQueryFP()

setQueryFPElement

public MolecularSequence.MolecularSequenceQualityComponent setQueryFPElement(DecimalType value)

Parameters:

value - queryFP (False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.). This is the underlying object with id, value and extensions. The accessor "getQueryFP" gives direct access to the value

getQueryFP

public BigDecimal getQueryFP()

Returns:

False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

setQueryFP

public MolecularSequence.MolecularSequenceQualityComponent setQueryFP(BigDecimal value)

Parameters:

value - False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

setQueryFP

public MolecularSequence.MolecularSequenceQualityComponent setQueryFP(long value)

Parameters:

value - False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

setQueryFP

public MolecularSequence.MolecularSequenceQualityComponent setQueryFP(double value)

Parameters:

value - False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

getGtFPElement

public DecimalType getGtFPElement()

Returns:

gtFP (The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).). This is the underlying object with id, value and extensions. The accessor "getGtFP" gives direct access to the value

hasGtFPElement

public boolean hasGtFPElement()

hasGtFP

public boolean hasGtFP()

setGtFPElement

public MolecularSequence.MolecularSequenceQualityComponent setGtFPElement(DecimalType value)

Parameters:

value - gtFP (The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).). This is the underlying object with id, value and extensions. The accessor "getGtFP" gives direct access to the value

getGtFP

public BigDecimal getGtFP()

Returns:

The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

setGtFP

public MolecularSequence.MolecularSequenceQualityComponent setGtFP(BigDecimal value)

Parameters:

value - The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

setGtFP

public MolecularSequence.MolecularSequenceQualityComponent setGtFP(long value)

Parameters:

value - The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

setGtFP

public MolecularSequence.MolecularSequenceQualityComponent setGtFP(double value)

Parameters:

value - The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

getPrecisionElement

public DecimalType getPrecisionElement()

Returns:

precision (QUERY.TP / (QUERY.TP + QUERY.FP).). This is the underlying object with id, value and extensions. The accessor "getPrecision" gives direct access to the value

hasPrecisionElement

public boolean hasPrecisionElement()

hasPrecision

public boolean hasPrecision()

setPrecisionElement

public MolecularSequence.MolecularSequenceQualityComponent setPrecisionElement(DecimalType value)

Parameters:

value - precision (QUERY.TP / (QUERY.TP + QUERY.FP).). This is the underlying object with id, value and extensions. The accessor "getPrecision" gives direct access to the value

getPrecision

public BigDecimal getPrecision()

Returns:

QUERY.TP / (QUERY.TP + QUERY.FP).

setPrecision

public MolecularSequence.MolecularSequenceQualityComponent setPrecision(BigDecimal value)

Parameters:

value - QUERY.TP / (QUERY.TP + QUERY.FP).

setPrecision

public MolecularSequence.MolecularSequenceQualityComponent setPrecision(long value)

Parameters:

value - QUERY.TP / (QUERY.TP + QUERY.FP).

setPrecision

public MolecularSequence.MolecularSequenceQualityComponent setPrecision(double value)

Parameters:

value - QUERY.TP / (QUERY.TP + QUERY.FP).

getRecallElement

public DecimalType getRecallElement()

Returns:

recall (TRUTH.TP / (TRUTH.TP + TRUTH.FN).). This is the underlying object with id, value and extensions. The accessor "getRecall" gives direct access to the value

hasRecallElement

public boolean hasRecallElement()

hasRecall

public boolean hasRecall()

setRecallElement

public MolecularSequence.MolecularSequenceQualityComponent setRecallElement(DecimalType value)

Parameters:

value - recall (TRUTH.TP / (TRUTH.TP + TRUTH.FN).). This is the underlying object with id, value and extensions. The accessor "getRecall" gives direct access to the value

getRecall

public BigDecimal getRecall()

Returns:

TRUTH.TP / (TRUTH.TP + TRUTH.FN).

setRecall

public MolecularSequence.MolecularSequenceQualityComponent setRecall(BigDecimal value)

Parameters:

value - TRUTH.TP / (TRUTH.TP + TRUTH.FN).

setRecall

public MolecularSequence.MolecularSequenceQualityComponent setRecall(long value)

Parameters:

value - TRUTH.TP / (TRUTH.TP + TRUTH.FN).

setRecall

public MolecularSequence.MolecularSequenceQualityComponent setRecall(double value)

Parameters:

value - TRUTH.TP / (TRUTH.TP + TRUTH.FN).

getFScoreElement

public DecimalType getFScoreElement()

Returns:

fScore (Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).). This is the underlying object with id, value and extensions. The accessor "getFScore" gives direct access to the value

hasFScoreElement

public boolean hasFScoreElement()

hasFScore

public boolean hasFScore()

setFScoreElement

public MolecularSequence.MolecularSequenceQualityComponent setFScoreElement(DecimalType value)

Parameters:

value - fScore (Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).). This is the underlying object with id, value and extensions. The accessor "getFScore" gives direct access to the value

getFScore

public BigDecimal getFScore()

Returns:

Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

setFScore

public MolecularSequence.MolecularSequenceQualityComponent setFScore(BigDecimal value)

Parameters:

value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

setFScore

public MolecularSequence.MolecularSequenceQualityComponent setFScore(long value)

Parameters:

value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

setFScore

public MolecularSequence.MolecularSequenceQualityComponent setFScore(double value)

Parameters:

value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

getRoc

public MolecularSequence.MolecularSequenceQualityRocComponent getRoc()

Returns:

roc (Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.)

hasRoc

public boolean hasRoc()

setRoc

public MolecularSequence.MolecularSequenceQualityComponent setRoc(MolecularSequence.MolecularSequenceQualityRocComponent value)

Parameters:

value - roc (Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.)

listChildren

protected void listChildren(List<Property> children)

Overrides:

listChildren in class BackboneElement

getNamedProperty

public Property getNamedProperty(int _hash,
 String _name,
 boolean _checkValid)
                          throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getNamedProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

getProperty

public Base[] getProperty(int hash,
 String name,
 boolean checkValid)
                   throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

setProperty

public Base setProperty(int hash,
 String name,
 Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

setProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

setProperty

public Base setProperty(String name,
 Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

setProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

removeChild

public void removeChild(String name,
 Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

removeChild in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

makeProperty

public Base makeProperty(int hash,
 String name)
                  throws org.hl7.fhir.exceptions.FHIRException

Overrides:

makeProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

getTypesForProperty

public String[] getTypesForProperty(int hash,
 String name)
                             throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getTypesForProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

addChild

public Base addChild(String name)
              throws org.hl7.fhir.exceptions.FHIRException

Overrides:

addChild in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

copy

public MolecularSequence.MolecularSequenceQualityComponent copy()

Specified by:

copy in class BackboneElement

copyValues

public void copyValues(MolecularSequence.MolecularSequenceQualityComponent dst)

equalsDeep

public boolean equalsDeep(Base other_)

Overrides:

equalsDeep in class BackboneElement

equalsShallow

public boolean equalsShallow(Base other_)

Overrides:

equalsShallow in class BackboneElement

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface org.hl7.fhir.instance.model.api.IBase

Overrides:

isEmpty in class BackboneElement

fhirType

public String fhirType()

Specified by:

fhirType in interface org.hl7.fhir.instance.model.api.IBase

Overrides:

fhirType in class BackboneElement