Package org.linuxforhealth.fhir.model.resource

Class MolecularSequence.ReferenceSeq.Builder

    • Method Detail

      • id

        public MolecularSequence.ReferenceSeq.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.ReferenceSeq.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.ReferenceSeq.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.ReferenceSeq.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.ReferenceSeq.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

      • chromosome

        public MolecularSequence.ReferenceSeq.Builder chromosome​(CodeableConcept chromosome)
        Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology. org/browser/current_svn/term/SO:0000340)).
        Parameters:
        chromosome - Chromosome containing genetic finding
        Returns:
        A reference to this Builder instance

      • genomeBuild

        public MolecularSequence.ReferenceSeq.Builder genomeBuild​(String genomeBuild)
        The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
        Parameters:
        genomeBuild - The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
        Returns:
        A reference to this Builder instance

      • orientation

        public MolecularSequence.ReferenceSeq.Builder orientation​(OrientationType orientation)
        A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.
        Parameters:
        orientation - sense | antisense
        Returns:
        A reference to this Builder instance

      • referenceSeqId

        public MolecularSequence.ReferenceSeq.Builder referenceSeqId​(CodeableConcept referenceSeqId)
        Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.
        Parameters:
        referenceSeqId - Reference identifier
        Returns:
        A reference to this Builder instance

      • referenceSeqPointer

        public MolecularSequence.ReferenceSeq.Builder referenceSeqPointer​(Reference referenceSeqPointer)
        A pointer to another MolecularSequence entity as reference sequence.

        Allowed resource types for this reference:

        Parameters:
        referenceSeqPointer - A pointer to another MolecularSequence entity as reference sequence
        Returns:
        A reference to this Builder instance

      • referenceSeqString

        public MolecularSequence.ReferenceSeq.Builder referenceSeqString​(String referenceSeqString)
        A string like "ACGT".
        Parameters:
        referenceSeqString - A string to represent reference sequence
        Returns:
        A reference to this Builder instance

      • strand

        public MolecularSequence.ReferenceSeq.Builder strand​(StrandType strand)
        An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.
        Parameters:
        strand - watson | crick
        Returns:
        A reference to this Builder instance

      • windowStart

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

      • windowEnd

        public MolecularSequence.ReferenceSeq.Builder windowEnd​(Integer windowEnd)
        End position of the window 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:
        windowEnd - End position of the window on the reference sequence
        Returns:
        A reference to this Builder instance