public static class MolecularSequence.MolecularSequenceVariantComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
| Modifier and Type | Field and Description |
|---|---|
protected StringType |
cigar
Extended CIGAR string for aligning the sequence with reference bases.
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protected IntegerType |
end
End position of the variant on the reference sequence.
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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)).
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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)).
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protected IntegerType |
start
Start position of the variant on the reference sequence.
|
protected Reference |
variantPointer
A pointer to an Observation containing variant information.
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protected Observation |
variantPointerTarget
The actual object that is the target of the reference (A pointer to an Observation containing variant information.)
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modifierExtension| Constructor and Description |
|---|
MolecularSequenceVariantComponent()
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, removeExtension, setDisallowExtensions, setExtension, setId, setIdBase, setIdElementcastToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCanonical, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExpression, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMarketingStatus, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPopulation, 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, compareDeep, compareValues, compareValues, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, isResource, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINNclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddExtension, getExtension, hasExtensiongetFormatCommentsPost, getFormatCommentsPre, getUserData, hasFormatComment, setUserDataprotected IntegerType start
protected IntegerType end
protected StringType observedAllele
protected StringType referenceAllele
protected StringType cigar
protected Reference variantPointer
protected Observation variantPointerTarget
public MolecularSequenceVariantComponent()
public IntegerType getStartElement()
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 valuepublic boolean hasStartElement()
public boolean hasStart()
public MolecularSequence.MolecularSequenceVariantComponent setStartElement(IntegerType value)
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 valuepublic int getStart()
public MolecularSequence.MolecularSequenceVariantComponent setStart(int value)
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.public IntegerType getEndElement()
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 valuepublic boolean hasEndElement()
public boolean hasEnd()
public MolecularSequence.MolecularSequenceVariantComponent setEndElement(IntegerType value)
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 valuepublic int getEnd()
public MolecularSequence.MolecularSequenceVariantComponent setEnd(int value)
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.public StringType getObservedAlleleElement()
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 valuepublic boolean hasObservedAlleleElement()
public boolean hasObservedAllele()
public MolecularSequence.MolecularSequenceVariantComponent setObservedAlleleElement(StringType value)
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 valuepublic String getObservedAllele()
public MolecularSequence.MolecularSequenceVariantComponent setObservedAllele(String value)
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.public StringType getReferenceAlleleElement()
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 valuepublic boolean hasReferenceAlleleElement()
public boolean hasReferenceAllele()
public MolecularSequence.MolecularSequenceVariantComponent setReferenceAlleleElement(StringType value)
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 valuepublic String getReferenceAllele()
public MolecularSequence.MolecularSequenceVariantComponent setReferenceAllele(String value)
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.public StringType getCigarElement()
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 valuepublic boolean hasCigarElement()
public boolean hasCigar()
public MolecularSequence.MolecularSequenceVariantComponent setCigarElement(StringType value)
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 valuepublic String getCigar()
public MolecularSequence.MolecularSequenceVariantComponent setCigar(String value)
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).public Reference getVariantPointer()
variantPointer (A pointer to an Observation containing variant information.)public boolean hasVariantPointer()
public MolecularSequence.MolecularSequenceVariantComponent setVariantPointer(Reference value)
value - variantPointer (A pointer to an Observation containing variant information.)public Observation getVariantPointerTarget()
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.)public MolecularSequence.MolecularSequenceVariantComponent setVariantPointerTarget(Observation value)
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.)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 MolecularSequence.MolecularSequenceVariantComponent copy()
copy in class BackboneElementpublic void copyValues(MolecularSequence.MolecularSequenceVariantComponent dst)
public 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 interface org.hl7.fhir.instance.model.api.IBasefhirType in class BackboneElementCopyright © 2014–2021 Health Level 7. All rights reserved.