Package org.hl7.fhir.dstu3.model

Class Sequence.SequenceVariantComponent

java.lang.Object
org.hl7.fhir.dstu3.model.Base
org.hl7.fhir.dstu3.model.Element
org.hl7.fhir.dstu3.model.BackboneElement
org.hl7.fhir.dstu3.model.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:

  • 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 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).

    • variantPointer

      protected Reference variantPointer
      A pointer to an Observation containing variant information.

    • variantPointerTarget

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

  • Constructor Details

  • Method Details

    • 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

    • hasStartElement

      public boolean hasStartElement()

    • hasStart

      public boolean hasStart()

    • 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

    • hasEndElement

      public boolean hasEndElement()

    • 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

    • hasObservedAlleleElement

      public boolean hasObservedAlleleElement()

    • hasObservedAllele

      public boolean hasObservedAllele()

    • 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

    • hasReferenceAlleleElement

      public boolean hasReferenceAlleleElement()

    • hasReferenceAllele

      public boolean hasReferenceAllele()

    • 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

    • hasCigarElement

      public boolean hasCigarElement()

    • hasCigar

      public boolean hasCigar()

    • 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).

    • getVariantPointer

      public Reference getVariantPointer()
      Returns:
      variantPointer (A pointer to an Observation containing variant information.)

    • hasVariantPointer

      public boolean hasVariantPointer()

    • setVariantPointer

      public Sequence.SequenceVariantComponent setVariantPointer(Reference value)
      Parameters:
      value - variantPointer (A pointer to an Observation containing variant information.)

    • 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.)

    • setVariantPointerTarget

      public Sequence.SequenceVariantComponent setVariantPointerTarget(Observation value)
      Parameters:
      value - variantPointer The actual object that is the target of the reference. The reference library doesn't use these, but you can use it to hold the resource if you resolve it. (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

      public Sequence.SequenceVariantComponent copy()
      Specified by:
      copy in class BackboneElement

    • 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