Package org.hl7.fhir.r4.model
Class MolecularSequence.MolecularSequenceVariantComponent
java.lang.Object
org.hl7.fhir.r4.model.Base
org.hl7.fhir.r4.model.Element
org.hl7.fhir.r4.model.BackboneElement
org.hl7.fhir.r4.model.MolecularSequence.MolecularSequenceVariantComponent
- 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:
MolecularSequence
public static class MolecularSequence.MolecularSequenceVariantComponent
extends BackboneElement
implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
- See Also:
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Field Summary
Modifier and TypeFieldDescriptionprotected StringType
Extended CIGAR string for aligning the sequence with reference bases.protected IntegerType
End position of the variant on the reference sequence.protected StringType
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)).protected StringType
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)).protected IntegerType
Start position of the variant on the reference sequence.protected Reference
A pointer to an Observation containing variant information.protected Observation
The actual object that is the target of the reference (A pointer to an Observation containing variant information.)Fields inherited from class org.hl7.fhir.r4.model.BackboneElement
modifierExtension
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptioncopy()
void
boolean
equalsDeep
(Base other_) boolean
equalsShallow
(Base other_) fhirType()
getCigar()
int
getEnd()
getNamedProperty
(int _hash, String _name, boolean _checkValid) Base[]
getProperty
(int hash, String name, boolean checkValid) int
getStart()
String[]
getTypesForProperty
(int hash, String name) boolean
hasCigar()
boolean
boolean
hasEnd()
boolean
boolean
boolean
boolean
boolean
boolean
hasStart()
boolean
boolean
boolean
isEmpty()
protected void
listChildren
(List<Property> children) makeProperty
(int hash, String name) void
removeChild
(String name, Base value) setCigarElement
(StringType value) setEnd
(int value) setEndElement
(IntegerType value) setObservedAllele
(String value) setProperty
(int hash, String name, Base value) setProperty
(String name, Base value) setReferenceAllele
(String value) setStart
(int value) setStartElement
(IntegerType value) setVariantPointer
(Reference value) Methods inherited from class org.hl7.fhir.r4.model.BackboneElement
addModifierExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyExtensions, copyNewExtensions, copyValues, getExtensionByUrl, getExtensionsByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionFirstRep, hasExtension, hasExtension, hasModifierExtension, removeExtension, setModifierExtension
Methods inherited from class org.hl7.fhir.r4.model.Element
addExtension, addExtension, addExtension, copyExtensions, copyNewExtensions, copyValues, getExtension, getExtensionFirstRep, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, setDisallowExtensions, setExtension, setId, setIdBase, setIdElement
Methods inherited from class org.hl7.fhir.r4.model.Base
castToAddress, 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, copyValues, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, getXhtml, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, isResource, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.hl7.fhir.instance.model.api.IBase
getFormatCommentsPost, getFormatCommentsPre, getUserData, hasFormatComment, setUserData
Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseElement
getUserData, setUserData
Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasExtensions
addExtension, getExtension, hasExtension
Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions
addModifierExtension, getModifierExtension, hasModifierExtension
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Field Details
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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
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. -
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
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
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
A pointer to an Observation containing variant information. -
variantPointerTarget
The actual object that is the target of the reference (A pointer to an Observation containing variant information.)
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Constructor Details
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MolecularSequenceVariantComponent
public MolecularSequenceVariantComponent()Constructor
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Method Details
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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
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hasStartElement
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hasStart
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setStartElement
- 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
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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.
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setStart
- 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.
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getEndElement
- Returns:
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 value
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hasEndElement
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hasEnd
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setEndElement
- Parameters:
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 value
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getEnd
- Returns:
- 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.
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setEnd
- Parameters:
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.
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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
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hasObservedAlleleElement
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hasObservedAllele
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setObservedAlleleElement
public MolecularSequence.MolecularSequenceVariantComponent 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
- 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.
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setObservedAllele
- 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.
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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
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hasReferenceAlleleElement
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hasReferenceAllele
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setReferenceAlleleElement
public MolecularSequence.MolecularSequenceVariantComponent 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
- 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
- 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.
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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
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hasCigarElement
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hasCigar
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setCigarElement
- 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
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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).
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setCigar
- 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).
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getVariantPointer
- Returns:
variantPointer
(A pointer to an Observation containing variant information.)
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hasVariantPointer
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setVariantPointer
- Parameters:
value
-variantPointer
(A pointer to an Observation containing variant information.)
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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.)
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setVariantPointerTarget
public MolecularSequence.MolecularSequenceVariantComponent 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.)
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listChildren
- 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
-
setProperty
- Overrides:
setProperty
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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removeChild
- Overrides:
removeChild
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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makeProperty
- 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
- Overrides:
addChild
in classBackboneElement
- Throws:
org.hl7.fhir.exceptions.FHIRException
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copy
- Specified by:
copy
in classBackboneElement
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copyValues
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equalsDeep
- Overrides:
equalsDeep
in classBackboneElement
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equalsShallow
- Overrides:
equalsShallow
in classBackboneElement
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isEmpty
- Specified by:
isEmpty
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
isEmpty
in classBackboneElement
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fhirType
- Specified by:
fhirType
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
fhirType
in classBackboneElement
-