Package org.linuxforhealth.fhir.model.resource

Class MolecularSequence.Quality.Builder

    • Method Detail

      • id

        public MolecularSequence.Quality.Builder id​(java.lang.String id)
        Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
        Overrides:
        id in class BackboneElement.Builder
        Parameters:
        id - Unique id for inter-element referencing
        Returns:
        A reference to this Builder instance

      • extension

        public MolecularSequence.Quality.Builder extension​(Extension... extension)
        May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Overrides:
        extension in class BackboneElement.Builder
        Parameters:
        extension - Additional content defined by implementations
        Returns:
        A reference to this Builder instance

      • extension

        public MolecularSequence.Quality.Builder extension​(java.util.Collection<Extension> extension)
        May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Overrides:
        extension in class BackboneElement.Builder
        Parameters:
        extension - Additional content defined by implementations
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • modifierExtension

        public MolecularSequence.Quality.Builder modifierExtension​(Extension... modifierExtension)
        May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

        Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Overrides:
        modifierExtension in class BackboneElement.Builder
        Parameters:
        modifierExtension - Extensions that cannot be ignored even if unrecognized
        Returns:
        A reference to this Builder instance

      • modifierExtension

        public MolecularSequence.Quality.Builder modifierExtension​(java.util.Collection<Extension> modifierExtension)
        May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

        Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Overrides:
        modifierExtension in class BackboneElement.Builder
        Parameters:
        modifierExtension - Extensions that cannot be ignored even if unrecognized
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • type

        public MolecularSequence.Quality.Builder type​(QualityType type)
        INDEL / SNP / Undefined variant.

        This element is required.

        Parameters:
        type - indel | snp | unknown
        Returns:
        A reference to this Builder instance

      • standardSequence

        public MolecularSequence.Quality.Builder standardSequence​(CodeableConcept standardSequence)
        Gold standard sequence used for comparing against.
        Parameters:
        standardSequence - Standard sequence for comparison
        Returns:
        A reference to this Builder instance

      • start

        public MolecularSequence.Quality.Builder start​(Integer start)
        Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
        Parameters:
        start - Start position of the sequence
        Returns:
        A reference to this Builder instance

      • end

        public MolecularSequence.Quality.Builder end​(Integer 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.
        Parameters:
        end - End position of the sequence
        Returns:
        A reference to this Builder instance

      • score

        public MolecularSequence.Quality.Builder score​(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)).
        Parameters:
        score - Quality score for the comparison
        Returns:
        A reference to this Builder instance

      • truthTP

        public MolecularSequence.Quality.Builder truthTP​(Decimal 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.
        Parameters:
        truthTP - True positives from the perspective of the truth data
        Returns:
        A reference to this Builder instance

      • queryTP

        public MolecularSequence.Quality.Builder queryTP​(Decimal 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.
        Parameters:
        queryTP - True positives from the perspective of the query data
        Returns:
        A reference to this Builder instance

      • truthFN

        public MolecularSequence.Quality.Builder truthFN​(Decimal 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.
        Parameters:
        truthFN - False negatives
        Returns:
        A reference to this Builder instance

      • queryFP

        public MolecularSequence.Quality.Builder queryFP​(Decimal 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.
        Parameters:
        queryFP - False positives
        Returns:
        A reference to this Builder instance

      • gtFP

        public MolecularSequence.Quality.Builder gtFP​(Decimal 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).
        Parameters:
        gtFP - False positives where the non-REF alleles in the Truth and Query Call Sets match
        Returns:
        A reference to this Builder instance

      • precision

        public MolecularSequence.Quality.Builder precision​(Decimal precision)
        QUERY.TP / (QUERY.TP + QUERY.FP).
        Parameters:
        precision - Precision of comparison
        Returns:
        A reference to this Builder instance

      • recall

        public MolecularSequence.Quality.Builder recall​(Decimal recall)
        TRUTH.TP / (TRUTH.TP + TRUTH.FN).
        Parameters:
        recall - Recall of comparison
        Returns:
        A reference to this Builder instance

      • fScore

        public MolecularSequence.Quality.Builder fScore​(Decimal fScore)
        Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
        Parameters:
        fScore - F-score
        Returns:
        A reference to this Builder instance