Class MolecularSequence.MolecularSequenceVariantComponent

java.lang.Object
org.hl7.fhir.r5.model.Base
org.hl7.fhir.r5.model.Element
org.hl7.fhir.r5.model.BackboneElement
org.hl7.fhir.r5.model.MolecularSequence.MolecularSequenceVariantComponent
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:
MolecularSequence

public static class MolecularSequence.MolecularSequenceVariantComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
See Also:
  • Field Details

    • 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 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

      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

      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).
    • variantPointer

      A pointer to an Observation containing variant information.
  • Constructor Details

  • Method Details

    • 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
    • hasStartElement

      public boolean hasStartElement()
    • hasStart

      public boolean hasStart()
    • setStartElement

      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

      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

      Returns:
      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.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value
    • hasEndElement

      public boolean hasEndElement()
    • hasEnd

      public boolean hasEnd()
    • setEndElement

      Parameters:
      value - 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.). 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 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

      Parameters:
      value - 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.
    • 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
    • hasObservedAlleleElement

      public boolean hasObservedAlleleElement()
    • hasObservedAllele

      public boolean hasObservedAllele()
    • setObservedAlleleElement

      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

      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

      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

      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
    • hasReferenceAlleleElement

      public boolean hasReferenceAlleleElement()
    • hasReferenceAllele

      public boolean hasReferenceAllele()
    • setReferenceAlleleElement

      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

      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

      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

      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
    • hasCigarElement

      public boolean hasCigarElement()
    • hasCigar

      public boolean hasCigar()
    • setCigarElement

      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

      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).
    • getVariantPointer

      Returns:
      variantPointer (A pointer to an Observation containing variant information.)
    • hasVariantPointer

      public boolean hasVariantPointer()
    • setVariantPointer

      Parameters:
      value - variantPointer (A pointer to an Observation containing variant information.)
    • listChildren

      protected void listChildren(List<Property> children)
      Overrides:
      listChildren in class BackboneElement
    • getNamedProperty

      public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      getNamedProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • getProperty

      public Base[] getProperty(int hash, String name, boolean checkValid) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      getProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • setProperty

      public Base setProperty(int hash, String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      setProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • setProperty

      public Base setProperty(String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      setProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • makeProperty

      public Base makeProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      makeProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • getTypesForProperty

      public String[] getTypesForProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      getTypesForProperty in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • addChild

      public Base addChild(String name) throws org.hl7.fhir.exceptions.FHIRException
      Overrides:
      addChild in class BackboneElement
      Throws:
      org.hl7.fhir.exceptions.FHIRException
    • copy

      Specified by:
      copy in class BackboneElement
    • copyValues

    • equalsDeep

      public boolean equalsDeep(Base other_)
      Overrides:
      equalsDeep in class BackboneElement
    • equalsShallow

      public boolean equalsShallow(Base other_)
      Overrides:
      equalsShallow in class BackboneElement
    • isEmpty

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

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