Package org.hl7.fhir.dstu3.model

Class Sequence.SequenceQualityComponent

java.lang.Object
org.hl7.fhir.dstu3.model.Base
org.hl7.fhir.dstu3.model.Element
org.hl7.fhir.dstu3.model.BackboneElement
org.hl7.fhir.dstu3.model.Sequence.SequenceQualityComponent
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:
Sequence
public static class Sequence.SequenceQualityComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
See Also:

  • Field Details

    • type

      protected Enumeration<Sequence.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 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).

  • Constructor Details

  • Method Details

    • getTypeElement

      public Enumeration<Sequence.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 Sequence.SequenceQualityComponent setTypeElement(Enumeration<Sequence.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 Sequence.QualityType getType()
      Returns:
      INDEL / SNP / Undefined variant.

    • setType

      public Sequence.SequenceQualityComponent setType(Sequence.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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 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 Sequence.SequenceQualityComponent setEndElement(IntegerType value)
      Parameters:
      value - end (End position of the sequence.If the coordinate system is 0-based then end is 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 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 Sequence.SequenceQualityComponent setEnd(int value)
      Parameters:
      value - End position of the sequence.If the coordinate system is 0-based then end is 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent setPrecision(BigDecimal value)
      Parameters:
      value - QUERY.TP / (QUERY.TP + QUERY.FP).

    • setPrecision

      public Sequence.SequenceQualityComponent setPrecision(long value)
      Parameters:
      value - QUERY.TP / (QUERY.TP + QUERY.FP).

    • setPrecision

      public Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent setRecall(BigDecimal value)
      Parameters:
      value - TRUTH.TP / (TRUTH.TP + TRUTH.FN).

    • setRecall

      public Sequence.SequenceQualityComponent setRecall(long value)
      Parameters:
      value - TRUTH.TP / (TRUTH.TP + TRUTH.FN).

    • setRecall

      public Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent 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 Sequence.SequenceQualityComponent setFScore(BigDecimal value)
      Parameters:
      value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

    • setFScore

      public Sequence.SequenceQualityComponent setFScore(long value)
      Parameters:
      value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

    • setFScore

      public Sequence.SequenceQualityComponent setFScore(double value)
      Parameters:
      value - Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

    • 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 Sequence.SequenceQualityComponent copy()
      Specified by:
      copy in class BackboneElement

    • 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