public static class Sequence.SequenceReferenceSeqComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
| Modifier and Type | Field and Description |
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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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protected StringType |
genomeBuild
The Genome Build used for reference, following GRCh build versions e.g.
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protected Enumeration<Sequence.OrientationType> |
orientation
A relative reference to a DNA strand based on gene orientation.
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protected CodeableConcept |
referenceSeqId
Reference identifier of reference sequence submitted to NCBI.
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protected Reference |
referenceSeqPointer
A Pointer to another Sequence entity as reference sequence.
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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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protected StringType |
referenceSeqString
A string like "ACGT".
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protected Enumeration<Sequence.StrandType> |
strand
An absolute reference to a strand.
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protected IntegerType |
windowEnd
End position of the window on the reference sequence.
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protected IntegerType |
windowStart
Start position of the window on the reference sequence.
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modifierExtension| Constructor and Description |
|---|
SequenceReferenceSeqComponent()
Constructor
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SequenceReferenceSeqComponent(IntegerType windowStart,
IntegerType windowEnd)
Constructor
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addModifierExtension, addModifierExtension, checkNoModifiers, copyValues, getModifierExtension, getModifierExtensionFirstRep, hasModifierExtension, setModifierExtensionaddExtension, addExtension, addExtension, copyValues, getExtension, getExtensionByUrl, getExtensionFirstRep, getExtensionsByUrl, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, setDisallowExtensions, setExtension, setId, setIdBase, setIdElementcastToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCanonical, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMarketingStatus, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToProdCharacteristic, castToProductShelfLife, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToSubstanceAmount, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUrl, 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, setUserDataINNclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormatCommentsPost, getFormatCommentsPre, hasFormatCommentprotected CodeableConcept chromosome
protected StringType genomeBuild
protected Enumeration<Sequence.OrientationType> orientation
protected CodeableConcept referenceSeqId
protected Reference referenceSeqPointer
protected Sequence referenceSeqPointerTarget
protected StringType referenceSeqString
protected Enumeration<Sequence.StrandType> strand
protected IntegerType windowStart
protected IntegerType windowEnd
public SequenceReferenceSeqComponent()
public SequenceReferenceSeqComponent(IntegerType windowStart, IntegerType windowEnd)
public CodeableConcept getChromosome()
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)).)public boolean hasChromosome()
public Sequence.SequenceReferenceSeqComponent setChromosome(CodeableConcept value)
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)).)public StringType getGenomeBuildElement()
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 valuepublic boolean hasGenomeBuildElement()
public boolean hasGenomeBuild()
public Sequence.SequenceReferenceSeqComponent setGenomeBuildElement(StringType value)
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 valuepublic String getGenomeBuild()
public Sequence.SequenceReferenceSeqComponent setGenomeBuild(String value)
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.public Enumeration<Sequence.OrientationType> getOrientationElement()
orientation (A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.). This is the underlying object with id, value and extensions. The accessor "getOrientation" gives direct access to the valuepublic boolean hasOrientationElement()
public boolean hasOrientation()
public Sequence.SequenceReferenceSeqComponent setOrientationElement(Enumeration<Sequence.OrientationType> value)
value - orientation (A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.). This is the underlying object with id, value and extensions. The accessor "getOrientation" gives direct access to the valuepublic Sequence.OrientationType getOrientation()
public Sequence.SequenceReferenceSeqComponent setOrientation(Sequence.OrientationType value)
value - A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.public CodeableConcept getReferenceSeqId()
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.)public boolean hasReferenceSeqId()
public Sequence.SequenceReferenceSeqComponent setReferenceSeqId(CodeableConcept value)
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.)public Reference getReferenceSeqPointer()
referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)public boolean hasReferenceSeqPointer()
public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointer(Reference value)
value - referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)public Sequence getReferenceSeqPointerTarget()
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.)public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointerTarget(Sequence value)
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.)public StringType getReferenceSeqStringElement()
referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the valuepublic boolean hasReferenceSeqStringElement()
public boolean hasReferenceSeqString()
public Sequence.SequenceReferenceSeqComponent setReferenceSeqStringElement(StringType value)
value - referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the valuepublic String getReferenceSeqString()
public Sequence.SequenceReferenceSeqComponent setReferenceSeqString(String value)
value - A string like "ACGT".public Enumeration<Sequence.StrandType> getStrandElement()
strand (An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the valuepublic boolean hasStrandElement()
public boolean hasStrand()
public Sequence.SequenceReferenceSeqComponent setStrandElement(Enumeration<Sequence.StrandType> value)
value - strand (An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the valuepublic Sequence.StrandType getStrand()
public Sequence.SequenceReferenceSeqComponent setStrand(Sequence.StrandType value)
value - An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.public IntegerType getWindowStartElement()
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 valuepublic boolean hasWindowStartElement()
public boolean hasWindowStart()
public Sequence.SequenceReferenceSeqComponent setWindowStartElement(IntegerType value)
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 valuepublic int getWindowStart()
public Sequence.SequenceReferenceSeqComponent setWindowStart(int value)
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.public IntegerType getWindowEndElement()
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 valuepublic boolean hasWindowEndElement()
public boolean hasWindowEnd()
public Sequence.SequenceReferenceSeqComponent setWindowEndElement(IntegerType value)
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 valuepublic int getWindowEnd()
public Sequence.SequenceReferenceSeqComponent setWindowEnd(int value)
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.protected void listChildren(List<Property> children)
listChildren in class BackboneElementpublic Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws org.hl7.fhir.exceptions.FHIRException
getNamedProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Base[] getProperty(int hash, String name, boolean checkValid) throws org.hl7.fhir.exceptions.FHIRException
getProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Base setProperty(int hash, String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
setProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Base setProperty(String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
setProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Base makeProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
makeProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic String[] getTypesForProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
getTypesForProperty in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Base addChild(String name) throws org.hl7.fhir.exceptions.FHIRException
addChild in class BackboneElementorg.hl7.fhir.exceptions.FHIRExceptionpublic Sequence.SequenceReferenceSeqComponent copy()
copy in class BackboneElementpublic boolean equalsDeep(Base other_)
equalsDeep in class BackboneElementpublic boolean equalsShallow(Base other_)
equalsShallow in class BackboneElementpublic boolean isEmpty()
isEmpty in interface org.hl7.fhir.instance.model.api.IBaseisEmpty in class BackboneElementpublic String fhirType()
fhirType in class BackboneElementCopyright © 2014–2018 University Health Network. All rights reserved.