Class 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:
    Serialized Form
    • Field Detail

      • 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)).
      • 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).
      • fScore

        protected DecimalType fScore
        Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
    • Method Detail

      • hasType

        public boolean hasType()
      • 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
      • 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
      • 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)).)
      • 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
      • 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
      • 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
      • 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
      • 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
      • 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
      • 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
      • 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
      • 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).
      • isEmpty

        public boolean isEmpty()
        Specified by:
        isEmpty in interface org.hl7.fhir.instance.model.api.IBase
        Overrides:
        isEmpty in class BackboneElement