MolecularSequence.MolecularSequenceQualityComponent (org.hl7.fhir.r4 5.4.0 API)

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 and 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 and Description

MolecularSequenceQualityComponent()
Constructor

MolecularSequenceQualityComponent(Enumeration<MolecularSequence.QualityType> type)
Constructor

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setEnd(int value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setEndElement(IntegerType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setFScore(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setFScore(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setFScore(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setFScoreElement(DecimalType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setGtFP(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setGtFP(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setGtFP(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setGtFPElement(DecimalType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setMethod(CodeableConcept value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setPrecision(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setPrecision(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setPrecision(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setPrecisionElement(DecimalType value)`
`Base`	`setProperty(int hash, String name, Base value)`
`Base`	`setProperty(String name, Base value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryFP(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryFP(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryFP(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryFPElement(DecimalType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryTP(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryTP(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryTP(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setQueryTPElement(DecimalType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setRecall(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setRecall(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setRecall(long 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(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthFN(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthFN(long value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthFNElement(DecimalType value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthTP(BigDecimal value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthTP(double value)`
`MolecularSequence.MolecularSequenceQualityComponent`	`setTruthTP(long 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, checkNoModifiers, copyValues, getModifierExtension, getModifierExtensionFirstRep, hasModifierExtension, setModifierExtension

Methods inherited from class org.hl7.fhir.r4.model.Element
addExtension, addExtension, addExtension, copyValues, getExtension, getExtensionByUrl, getExtensionFirstRep, getExtensionsByUrl, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, removeExtension, 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, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, 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.IBaseHasExtensions
addExtension, getExtension, hasExtension

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.IBaseHasModifierExtensions
addModifierExtension, getModifierExtension, hasModifierExtension

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

- Field Detail
  - 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 Detail
  - MolecularSequenceQualityComponent
```
public MolecularSequenceQualityComponent()
```
    Constructor
  - MolecularSequenceQualityComponent
```
public MolecularSequenceQualityComponent(Enumeration<MolecularSequence.QualityType> type)
```
    Constructor
- Method Detail
  - 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
  - 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

Class MolecularSequence.MolecularSequenceQualityComponent

Field Summary

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

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

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

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

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

Field Detail

type

standardSequence

start

end

score

method

truthTP

queryTP

truthFN

queryFP

gtFP

precision

recall

fScore

roc

Constructor Detail

MolecularSequenceQualityComponent

MolecularSequenceQualityComponent

Method Detail

getTypeElement

hasTypeElement

hasType

setTypeElement

getType

setType

getStandardSequence

hasStandardSequence

setStandardSequence

getStartElement

hasStartElement

hasStart

setStartElement

getStart

setStart

getEndElement

hasEndElement

hasEnd

setEndElement

getEnd

setEnd

getScore

hasScore

setScore

getMethod

hasMethod

setMethod

getTruthTPElement

hasTruthTPElement

hasTruthTP

setTruthTPElement

getTruthTP

setTruthTP

setTruthTP

setTruthTP

getQueryTPElement

hasQueryTPElement

hasQueryTP

setQueryTPElement

getQueryTP

setQueryTP

setQueryTP

setQueryTP

getTruthFNElement

hasTruthFNElement

hasTruthFN