Package org.linuxforhealth.fhir.model.resource

Class MolecularSequence.Quality

  • All Implemented Interfaces:
    Visitable
    Enclosing class:
    MolecularSequence
    public static class MolecularSequence.Quality
extends BackboneElement
    An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).

    • Method Detail

      • getType

        public QualityType getType()
        INDEL / SNP / Undefined variant.
        Returns:
        An immutable object of type QualityType that is non-null.

      • getStandardSequence

        public CodeableConcept getStandardSequence()
        Gold standard sequence used for comparing against.
        Returns:
        An immutable object of type CodeableConcept that may be null.

      • getStart

        public Integer getStart()
        Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
        Returns:
        An immutable object of type Integer that may be null.

      • getEnd

        public Integer getEnd()
        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.
        Returns:
        An immutable object of type Integer that may be null.

      • getScore

        public Quantity getScore()
        The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology. org/browser/current_svn/term/SO:0001685)).
        Returns:
        An immutable object of type Quantity that may be null.

      • getMethod

        public CodeableConcept getMethod()
        Which method is used to get sequence quality.
        Returns:
        An immutable object of type CodeableConcept that may be null.

      • getTruthTP

        public Decimal getTruthTP()
        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.
        Returns:
        An immutable object of type Decimal that may be null.

      • getQueryTP

        public Decimal getQueryTP()
        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.
        Returns:
        An immutable object of type Decimal that may be null.

      • getTruthFN

        public Decimal getTruthFN()
        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.
        Returns:
        An immutable object of type Decimal that may be null.

      • getQueryFP

        public Decimal getQueryFP()
        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.
        Returns:
        An immutable object of type Decimal that may be null.

      • getGtFP

        public Decimal getGtFP()
        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).
        Returns:
        An immutable object of type Decimal that may be null.

      • getPrecision

        public Decimal getPrecision()
        QUERY.TP / (QUERY.TP + QUERY.FP).
        Returns:
        An immutable object of type Decimal that may be null.

      • getRecall

        public Decimal getRecall()
        TRUTH.TP / (TRUTH.TP + TRUTH.FN).
        Returns:
        An immutable object of type Decimal that may be null.

      • getFScore

        public Decimal getFScore()
        Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
        Returns:
        An immutable object of type Decimal that may be null.

      • accept

        public void accept​(java.lang.String elementName,
                   int elementIndex,
                   Visitor visitor)
        Description copied from interface: Visitable
        Accept a Visitor and invoke the appropriate visit methods. A typical implementation would look like this: 
         if (visitor.preVisit(this)) {
     visitor.visitStart(elementName, elementIndex, this);
     if (visitor.visit(elementName, elementIndex, this)) {
         // visit children
     }
     visitor.visitEnd(elementName, elementIndex, this);
     visitor.postVisit(this);
 }
        Specified by:
        accept in interface Visitable
        Specified by:
        accept in class AbstractVisitable
        Parameters:
        elementName - the name of the element in the context of this visit
        elementIndex - the index of the element in a list or -1 if it is not contained within a List
        visitor - the visitor to use

      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object