
Package org.hl7.fhir.dstu3.model
Class Sequence.SequenceReferenceSeqComponent
- java.lang.Object
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- org.hl7.fhir.dstu3.model.Base
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- org.hl7.fhir.dstu3.model.Element
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- org.hl7.fhir.dstu3.model.BackboneElement
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- org.hl7.fhir.dstu3.model.Sequence.SequenceReferenceSeqComponent
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- 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:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description 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)).protected StringType
genomeBuild
The Genome Build used for reference, following GRCh build versions e.g.protected CodeableConcept
referenceSeqId
Reference identifier of reference sequence submitted to NCBI.protected Reference
referenceSeqPointer
A Pointer to another Sequence entity as reference sequence.protected Sequence
referenceSeqPointerTarget
The actual object that is the target of the reference (A Pointer to another Sequence entity as reference sequence.)protected StringType
referenceSeqString
A string like "ACGT".protected IntegerType
strand
Directionality of DNA sequence.protected IntegerType
windowEnd
End position of the window on the reference sequence.protected IntegerType
windowStart
Start position of the window on the reference sequence.-
Fields inherited from class org.hl7.fhir.dstu3.model.BackboneElement
modifierExtension
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Constructor Summary
Constructors Constructor Description SequenceReferenceSeqComponent()
ConstructorSequenceReferenceSeqComponent(IntegerType windowStart, IntegerType windowEnd)
Constructor
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Method Summary
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Methods inherited from class org.hl7.fhir.dstu3.model.BackboneElement
addModifierExtension, addModifierExtension, copyValues, getModifierExtension, getModifierExtensionFirstRep, hasModifierExtension, setModifierExtension
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Methods inherited from class org.hl7.fhir.dstu3.model.Element
addExtension, addExtension, addExtension, copyValues, getExtension, getExtensionFirstRep, getExtensionsByUrl, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, setExtension, setId, setIdBase, setIdElement
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Methods inherited from class org.hl7.fhir.dstu3.model.Base
castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isMetadataBased, isPrimitive, isResource, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.hl7.fhir.instance.model.api.IBase
getFormatCommentsPost, getFormatCommentsPre, getUserData, hasFormatComment, setUserData
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Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseElement
getUserData, setUserData
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Field Detail
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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)).
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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.
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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.
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referenceSeqPointer
protected Reference referenceSeqPointer
A Pointer to another Sequence entity as reference sequence.
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referenceSeqPointerTarget
protected Sequence referenceSeqPointerTarget
The actual object that is the target of the reference (A Pointer to another Sequence entity as reference sequence.)
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referenceSeqString
protected StringType referenceSeqString
A string like "ACGT".
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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.
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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.
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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.
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Constructor Detail
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SequenceReferenceSeqComponent
public SequenceReferenceSeqComponent()
Constructor
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SequenceReferenceSeqComponent
public SequenceReferenceSeqComponent(IntegerType windowStart, IntegerType windowEnd)
Constructor
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Method Detail
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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)).)
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hasChromosome
public boolean hasChromosome()
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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)).)
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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
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hasGenomeBuildElement
public boolean hasGenomeBuildElement()
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hasGenomeBuild
public boolean hasGenomeBuild()
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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
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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.
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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.
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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.)
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hasReferenceSeqId
public boolean hasReferenceSeqId()
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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.)
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getReferenceSeqPointer
public Reference getReferenceSeqPointer()
- Returns:
referenceSeqPointer
(A Pointer to another Sequence entity as reference sequence.)
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hasReferenceSeqPointer
public boolean hasReferenceSeqPointer()
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setReferenceSeqPointer
public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointer(Reference value)
- Parameters:
value
-referenceSeqPointer
(A Pointer to another Sequence entity as reference sequence.)
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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.)
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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.)
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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
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hasReferenceSeqStringElement
public boolean hasReferenceSeqStringElement()
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hasReferenceSeqString
public boolean hasReferenceSeqString()
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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
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getReferenceSeqString
public String getReferenceSeqString()
- Returns:
- A string like "ACGT".
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setReferenceSeqString
public Sequence.SequenceReferenceSeqComponent setReferenceSeqString(String value)
- Parameters:
value
- A string like "ACGT".
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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
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hasStrandElement
public boolean hasStrandElement()
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hasStrand
public boolean hasStrand()
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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
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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.
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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.
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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
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hasWindowStartElement
public boolean hasWindowStartElement()
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hasWindowStart
public boolean hasWindowStart()
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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
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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.
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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.
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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
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hasWindowEndElement
public boolean hasWindowEndElement()
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hasWindowEnd
public boolean hasWindowEnd()
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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
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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.
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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.
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listChildren
protected void listChildren(List<Property> children)
- Overrides:
listChildren
in classBackboneElement
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getNamedProperty
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
getNamedProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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getProperty
public Base[] getProperty(int hash, String name, boolean checkValid) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
getProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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setProperty
public Base setProperty(int hash, String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
setProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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setProperty
public Base setProperty(String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
setProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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makeProperty
public Base makeProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
makeProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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getTypesForProperty
public String[] getTypesForProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
getTypesForProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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addChild
public Base addChild(String name) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
addChild
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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copy
public Sequence.SequenceReferenceSeqComponent copy()
- Specified by:
copy
in classBackboneElement
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equalsDeep
public boolean equalsDeep(Base other_)
- Overrides:
equalsDeep
in classBackboneElement
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equalsShallow
public boolean equalsShallow(Base other_)
- Overrides:
equalsShallow
in classBackboneElement
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isEmpty
public boolean isEmpty()
- Specified by:
isEmpty
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
isEmpty
in classBackboneElement
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fhirType
public String fhirType()
- Specified by:
fhirType
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
fhirType
in classBackboneElement
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