Class Sequence.SequenceVariantComponent

  • 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.SequenceVariantComponent
    extends BackboneElement
    implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
    See Also:
    Serialized Form
    • Field Detail

      • start

        protected IntegerType 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.
      • end

        protected IntegerType end
        End position of the variant on the reference 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.
      • observedAllele

        protected StringType 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.
      • referenceAllele

        protected StringType 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.
      • cigar

        protected StringType 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).
      • variantPointerTarget

        protected Observation variantPointerTarget
        The actual object that is the target of the reference (A pointer to an Observation containing variant information.)
    • Method Detail

      • getStartElement

        public IntegerType getStartElement()
        Returns:
        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.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value
      • setStartElement

        public Sequence.SequenceVariantComponent setStartElement​(IntegerType value)
        Parameters:
        value - 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.). 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 variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.
      • setStart

        public Sequence.SequenceVariantComponent setStart​(int value)
        Parameters:
        value - 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.
      • getEndElement

        public IntegerType getEndElement()
        Returns:
        end (End position of the variant on the reference 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.SequenceVariantComponent setEndElement​(IntegerType value)
        Parameters:
        value - end (End position of the variant on the reference 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 variant on the reference 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.SequenceVariantComponent setEnd​(int value)
        Parameters:
        value - End position of the variant on the reference 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.
      • getObservedAlleleElement

        public StringType getObservedAlleleElement()
        Returns:
        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.). This is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value
      • setObservedAlleleElement

        public Sequence.SequenceVariantComponent setObservedAlleleElement​(StringType value)
        Parameters:
        value - 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.). This is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value
      • getObservedAllele

        public String getObservedAllele()
        Returns:
        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.
      • setObservedAllele

        public Sequence.SequenceVariantComponent setObservedAllele​(String value)
        Parameters:
        value - 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.
      • getReferenceAlleleElement

        public StringType getReferenceAlleleElement()
        Returns:
        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.). This is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value
      • setReferenceAlleleElement

        public Sequence.SequenceVariantComponent setReferenceAlleleElement​(StringType value)
        Parameters:
        value - 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.). This is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value
      • getReferenceAllele

        public String getReferenceAllele()
        Returns:
        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.
      • setReferenceAllele

        public Sequence.SequenceVariantComponent setReferenceAllele​(String value)
        Parameters:
        value - 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.
      • getCigarElement

        public StringType getCigarElement()
        Returns:
        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).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value
      • setCigarElement

        public Sequence.SequenceVariantComponent setCigarElement​(StringType value)
        Parameters:
        value - 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).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value
      • getCigar

        public String getCigar()
        Returns:
        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).
      • setCigar

        public Sequence.SequenceVariantComponent setCigar​(String value)
        Parameters:
        value - 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).
      • getVariantPointerTarget

        public Observation getVariantPointerTarget()
        Returns:
        variantPointer The actual object that is the target of the reference. The reference library doesn't populate this, but you can use it to hold the resource if you resolve it. (A pointer to an Observation containing variant information.)
      • isEmpty

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