Package org.linuxforhealth.fhir.model.resource

Class MolecularSequence.Variant.Builder

    • Method Detail

      • id

        public MolecularSequence.Variant.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.Variant.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.Variant.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.Variant.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.Variant.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

      • start

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

      • end

        public MolecularSequence.Variant.Builder end​(Integer end)
        End position of the variant on the reference 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 variant on the reference sequence
        Returns:
        A reference to this Builder instance

      • observedAllele

        public MolecularSequence.Variant.Builder observedAllele​(String observedAllele)
        An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology. org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
        Parameters:
        observedAllele - Allele that was observed
        Returns:
        A reference to this Builder instance

      • referenceAllele

        public MolecularSequence.Variant.Builder referenceAllele​(String referenceAllele)
        An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology. org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
        Parameters:
        referenceAllele - Allele in the reference sequence
        Returns:
        A reference to this Builder instance

      • cigar

        public MolecularSequence.Variant.Builder cigar​(String cigar)
        Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support. illumina. com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat. htm).
        Parameters:
        cigar - Extended CIGAR string for aligning the sequence with reference bases
        Returns:
        A reference to this Builder instance

      • variantPointer

        public MolecularSequence.Variant.Builder variantPointer​(Reference variantPointer)
        A pointer to an Observation containing variant information.

        Allowed resource types for this reference:

        Parameters:
        variantPointer - Pointer to observed variant information
        Returns:
        A reference to this Builder instance