Package org.hl7.fhir.dstu3.model

Class Sequence.SequenceReferenceSeqComponent

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.SequenceReferenceSeqComponent
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.SequenceReferenceSeqComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
See Also:

  • Field Details

    • chromosome

      protected 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)).

    • genomeBuild

      protected StringType 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.

    • referenceSeqId

      protected CodeableConcept referenceSeqId
      Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, ?NG_? identifies reference sequence for genes, ?NM_? for messenger RNA transcripts, and ?NP_? for amino acid sequences.

    • referenceSeqPointer

      protected Reference referenceSeqPointer
      A Pointer to another Sequence entity as reference sequence.

    • referenceSeqPointerTarget

      protected Sequence referenceSeqPointerTarget
      The actual object that is the target of the reference (A Pointer to another Sequence entity as reference sequence.)

    • referenceSeqString

      protected StringType referenceSeqString
      A string like "ACGT".

    • strand

      protected IntegerType strand
      Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.

    • windowStart

      protected IntegerType 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.

    • windowEnd

      protected IntegerType windowEnd
      End position of the window 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.

  • Constructor Details

  • Method Details

    • getChromosome

      public CodeableConcept getChromosome()
      Returns:
      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)).)

    • hasChromosome

      public boolean hasChromosome()

    • setChromosome

      public Sequence.SequenceReferenceSeqComponent setChromosome(CodeableConcept value)
      Parameters:
      value - 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)).)

    • getGenomeBuildElement

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

    • hasGenomeBuildElement

      public boolean hasGenomeBuildElement()

    • hasGenomeBuild

      public boolean hasGenomeBuild()

    • setGenomeBuildElement

      public Sequence.SequenceReferenceSeqComponent setGenomeBuildElement(StringType value)
      Parameters:
      value - 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.). This is the underlying object with id, value and extensions. The accessor "getGenomeBuild" gives direct access to the value

    • getGenomeBuild

      public String getGenomeBuild()
      Returns:
      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.

    • setGenomeBuild

      public Sequence.SequenceReferenceSeqComponent setGenomeBuild(String value)
      Parameters:
      value - 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.

    • getReferenceSeqId

      public CodeableConcept getReferenceSeqId()
      Returns:
      referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, ?NG_? identifies reference sequence for genes, ?NM_? for messenger RNA transcripts, and ?NP_? for amino acid sequences.)

    • hasReferenceSeqId

      public boolean hasReferenceSeqId()

    • setReferenceSeqId

      public Sequence.SequenceReferenceSeqComponent setReferenceSeqId(CodeableConcept value)
      Parameters:
      value - referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, ?NG_? identifies reference sequence for genes, ?NM_? for messenger RNA transcripts, and ?NP_? for amino acid sequences.)

    • getReferenceSeqPointer

      public Reference getReferenceSeqPointer()
      Returns:
      referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)

    • hasReferenceSeqPointer

      public boolean hasReferenceSeqPointer()

    • setReferenceSeqPointer

      public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointer(Reference value)
      Parameters:
      value - referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)

    • getReferenceSeqPointerTarget

      public Sequence getReferenceSeqPointerTarget()
      Returns:
      referenceSeqPointer 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 another Sequence entity as reference sequence.)

    • setReferenceSeqPointerTarget

      public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointerTarget(Sequence value)
      Parameters:
      value - referenceSeqPointer 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 another Sequence entity as reference sequence.)

    • getReferenceSeqStringElement

      public StringType getReferenceSeqStringElement()
      Returns:
      referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the value

    • hasReferenceSeqStringElement

      public boolean hasReferenceSeqStringElement()

    • hasReferenceSeqString

      public boolean hasReferenceSeqString()

    • setReferenceSeqStringElement

      public Sequence.SequenceReferenceSeqComponent setReferenceSeqStringElement(StringType value)
      Parameters:
      value - referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the value

    • getReferenceSeqString

      public String getReferenceSeqString()
      Returns:
      A string like "ACGT".

    • setReferenceSeqString

      public Sequence.SequenceReferenceSeqComponent setReferenceSeqString(String value)
      Parameters:
      value - A string like "ACGT".

    • getStrandElement

      public IntegerType getStrandElement()
      Returns:
      strand (Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the value

    • hasStrandElement

      public boolean hasStrandElement()

    • hasStrand

      public boolean hasStrand()

    • setStrandElement

      public Sequence.SequenceReferenceSeqComponent setStrandElement(IntegerType value)
      Parameters:
      value - strand (Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the value

    • getStrand

      public int getStrand()
      Returns:
      Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.

    • setStrand

      public Sequence.SequenceReferenceSeqComponent setStrand(int value)
      Parameters:
      value - Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.

    • getWindowStartElement

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

    • hasWindowStartElement

      public boolean hasWindowStartElement()

    • hasWindowStart

      public boolean hasWindowStart()

    • setWindowStartElement

      public Sequence.SequenceReferenceSeqComponent setWindowStartElement(IntegerType value)
      Parameters:
      value - 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.). This is the underlying object with id, value and extensions. The accessor "getWindowStart" gives direct access to the value

    • getWindowStart

      public int getWindowStart()
      Returns:
      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.

    • setWindowStart

      public Sequence.SequenceReferenceSeqComponent setWindowStart(int value)
      Parameters:
      value - 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.

    • getWindowEndElement

      public IntegerType getWindowEndElement()
      Returns:
      windowEnd (End position of the window 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 "getWindowEnd" gives direct access to the value

    • hasWindowEndElement

      public boolean hasWindowEndElement()

    • hasWindowEnd

      public boolean hasWindowEnd()

    • setWindowEndElement

      public Sequence.SequenceReferenceSeqComponent setWindowEndElement(IntegerType value)
      Parameters:
      value - windowEnd (End position of the window 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 "getWindowEnd" gives direct access to the value

    • getWindowEnd

      public int getWindowEnd()
      Returns:
      End position of the window 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.

    • setWindowEnd

      public Sequence.SequenceReferenceSeqComponent setWindowEnd(int value)
      Parameters:
      value - End position of the window 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.

    • 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.SequenceReferenceSeqComponent 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