Class MolecularSequence
- All Implemented Interfaces:
ca.uhn.fhir.model.api.IElement
,Serializable
,org.hl7.fhir.instance.model.api.IAnyResource
,org.hl7.fhir.instance.model.api.IBase
,org.hl7.fhir.instance.model.api.IBaseHasExtensions
,org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions
,org.hl7.fhir.instance.model.api.IBaseResource
,org.hl7.fhir.instance.model.api.IDomainResource
- See Also:
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Nested Class Summary
Modifier and TypeClassDescriptionstatic class
static class
static class
static class
static class
static class
static class
static class
static enum
static class
static enum
static class
static enum
static class
static enum
static class
static enum
static class
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Field Summary
Modifier and TypeFieldDescriptionstatic final ca.uhn.fhir.rest.gclient.TokenClientParam
Fluent Client search parameter constant for chromosomestatic final ca.uhn.fhir.rest.gclient.CompositeClientParam
<ca.uhn.fhir.rest.gclient.TokenClientParam, ca.uhn.fhir.rest.gclient.NumberClientParam> Fluent Client search parameter constant for chromosome-variant-coordinatestatic final ca.uhn.fhir.rest.gclient.CompositeClientParam
<ca.uhn.fhir.rest.gclient.TokenClientParam, ca.uhn.fhir.rest.gclient.NumberClientParam> Fluent Client search parameter constant for chromosome-window-coordinateprotected IntegerType
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).protected Reference
The method for sequencing, for example, chip information.protected Device
The actual object that is the target of the reference (The method for sequencing, for example, chip information.)protected List
<Identifier> A unique identifier for this particular sequence instance.static final ca.uhn.fhir.rest.gclient.TokenClientParam
Fluent Client search parameter constant for identifierstatic final ca.uhn.fhir.model.api.Include
Constant for fluent queries to be used to add include statements.protected StringType
Sequence that was observed.protected Reference
The patient whose sequencing results are described by this resource.static final ca.uhn.fhir.rest.gclient.ReferenceClientParam
Fluent Client search parameter constant for patientprotected Patient
The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.)protected Reference
The organization or lab that should be responsible for this result.protected Organization
The actual object that is the target of the reference (The organization or lab that should be responsible for this result.)Pointer to next atomic sequence which at most contains one variant.protected List
<MolecularSequence> The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.)An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).protected Quantity
The number of copies of the sequence of interest.protected IntegerType
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.A sequence that is used as a reference to describe variants that are present in a sequence analyzed.static final ca.uhn.fhir.rest.gclient.TokenClientParam
Fluent Client search parameter constant for referenceseqidstatic final ca.uhn.fhir.rest.gclient.CompositeClientParam
<ca.uhn.fhir.rest.gclient.TokenClientParam, ca.uhn.fhir.rest.gclient.NumberClientParam> Fluent Client search parameter constant for referenceseqid-variant-coordinatestatic final ca.uhn.fhir.rest.gclient.CompositeClientParam
<ca.uhn.fhir.rest.gclient.TokenClientParam, ca.uhn.fhir.rest.gclient.NumberClientParam> Fluent Client search parameter constant for referenceseqid-window-coordinateConfigurations of the external repository.static final String
Search parameter: chromosomestatic final String
Search parameter: chromosome-variant-coordinatestatic final String
Search parameter: chromosome-window-coordinatestatic final String
Search parameter: identifierstatic final String
Search parameter: patientstatic final String
Search parameter: referenceseqidstatic final String
Search parameter: referenceseqid-variant-coordinatestatic final String
Search parameter: referenceseqid-window-coordinatestatic final String
Search parameter: typestatic final String
Search parameter: variant-endstatic final String
Search parameter: variant-startstatic final String
Search parameter: window-endstatic final String
Search parameter: window-startprotected Reference
Specimen used for sequencing.protected Specimen
The actual object that is the target of the reference (Specimen used for sequencing.)Information about chromosome structure variation.protected Enumeration
<MolecularSequence.SequenceType> Amino Acid Sequence/ DNA Sequence / RNA Sequence.static final ca.uhn.fhir.rest.gclient.TokenClientParam
Fluent Client search parameter constant for typeThe definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).static final ca.uhn.fhir.rest.gclient.NumberClientParam
Fluent Client search parameter constant for variant-endstatic final ca.uhn.fhir.rest.gclient.NumberClientParam
Fluent Client search parameter constant for variant-startstatic final ca.uhn.fhir.rest.gclient.NumberClientParam
Fluent Client search parameter constant for window-endstatic final ca.uhn.fhir.rest.gclient.NumberClientParam
Fluent Client search parameter constant for window-startFields inherited from class org.hl7.fhir.r4.model.DomainResource
contained, extension, modifierExtension, text
Fields inherited from class org.hl7.fhir.r4.model.Resource
id, implicitRules, language, meta
Fields inherited from interface org.hl7.fhir.instance.model.api.IAnyResource
RES_ID, RES_LAST_UPDATED, RES_PROFILE, RES_SECURITY, RES_TAG, SP_RES_ID, SP_RES_LAST_UPDATED, SP_RES_PROFILE, SP_RES_SECURITY, SP_RES_TAG
Fields inherited from interface org.hl7.fhir.instance.model.api.IBaseResource
INCLUDE_ALL, WILDCARD_ALL_SET
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionDeprecated.Use Reference#setResource(IBaseResource) insteadcopy()
void
boolean
equalsDeep
(Base other_) boolean
equalsShallow
(Base other_) fhirType()
int
getNamedProperty
(int _hash, String _name, boolean _checkValid) Deprecated.Use Reference#setResource(IBaseResource) insteadBase[]
getProperty
(int hash, String name, boolean checkValid) int
getType()
String[]
getTypesForProperty
(int hash, String name) boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
hasType()
boolean
boolean
boolean
isEmpty()
protected void
listChildren
(List<Property> children) makeProperty
(int hash, String name) void
removeChild
(String name, Base value) setCoordinateSystem
(int value) setDeviceTarget
(Device value) setIdentifier
(List<Identifier> theIdentifier) setObservedSeq
(String value) setObservedSeqElement
(StringType value) setPatient
(Reference value) setPatientTarget
(Patient value) setPerformer
(Reference value) setPerformerTarget
(Organization value) setPointer
(List<Reference> thePointer) setProperty
(int hash, String name, Base value) setProperty
(String name, Base value) setQuantity
(Quantity value) setReadCoverage
(int value) setRepository
(List<MolecularSequence.MolecularSequenceRepositoryComponent> theRepository) setSpecimen
(Reference value) setSpecimenTarget
(Specimen value) setStructureVariant
(List<MolecularSequence.MolecularSequenceStructureVariantComponent> theStructureVariant) protected MolecularSequence
Methods inherited from class org.hl7.fhir.r4.model.DomainResource
addContained, addExtension, addExtension, addExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyValues, getContained, getContained, getExtension, getExtensionByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionsByUrl, getText, hasContained, hasExtension, hasExtension, hasModifierExtension, hasText, setContained, setExtension, setModifierExtension, setText
Methods inherited from class org.hl7.fhir.r4.model.Resource
copyValues, getId, getIdBase, getIdElement, getIdPart, getImplicitRules, getImplicitRulesElement, getLanguage, getLanguage, getLanguageElement, getMeta, hasId, hasIdElement, hasImplicitRules, hasImplicitRulesElement, hasLanguage, hasLanguageElement, hasMeta, setId, setIdBase, setIdElement, setImplicitRules, setImplicitRulesElement, setLanguage, setLanguageElement, setMeta
Methods inherited from class org.hl7.fhir.r4.model.BaseResource
getStructureFhirVersionEnum, isResource, setId
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, 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.IAnyResource
getId, getIdElement, getLanguageElement, getUserData, setId, setUserData
Methods inherited from interface org.hl7.fhir.instance.model.api.IBase
getFormatCommentsPost, getFormatCommentsPre, hasFormatComment
Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseResource
getMeta, getStructureFhirVersionEnum, isDeleted, setId
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Field Details
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identifier
A unique identifier for this particular sequence instance. This is a FHIR-defined id. -
type
Amino Acid Sequence/ DNA Sequence / RNA Sequence. -
coordinateSystem
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end). -
patient
The patient whose sequencing results are described by this resource. -
patientTarget
The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.) -
specimen
Specimen used for sequencing. -
specimenTarget
The actual object that is the target of the reference (Specimen used for sequencing.) -
device
The method for sequencing, for example, chip information. -
deviceTarget
The actual object that is the target of the reference (The method for sequencing, for example, chip information.) -
performer
The organization or lab that should be responsible for this result. -
performerTarget
The actual object that is the target of the reference (The organization or lab that should be responsible for this result.) -
quantity
The number of copies of the sequence of interest. (RNASeq). -
referenceSeq
A sequence that is used as a reference to describe variants that are present in a sequence analyzed. -
variant
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string. -
observedSeq
Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd. -
quality
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)). -
readCoverage
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. -
repository
Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq. -
pointer
Pointer to next atomic sequence which at most contains one variant. -
pointerTarget
The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.) -
structureVariant
Information about chromosome structure variation. -
SP_IDENTIFIER
Search parameter: identifierDescription: The unique identity for a particular sequence
Type: token
Path: MolecularSequence.identifier
- See Also:
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IDENTIFIER
Fluent Client search parameter constant for identifierDescription: The unique identity for a particular sequence
Type: token
Path: MolecularSequence.identifier
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SP_REFERENCESEQID_VARIANT_COORDINATE
Search parameter: referenceseqid-variant-coordinateDescription: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
- See Also:
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REFERENCESEQID_VARIANT_COORDINATE
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_VARIANT_COORDINATEFluent Client search parameter constant for referenceseqid-variant-coordinateDescription: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
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SP_CHROMOSOME
Search parameter: chromosomeDescription: Chromosome number of the reference sequence
Type: token
Path: MolecularSequence.referenceSeq.chromosome
- See Also:
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CHROMOSOME
Fluent Client search parameter constant for chromosomeDescription: Chromosome number of the reference sequence
Type: token
Path: MolecularSequence.referenceSeq.chromosome
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SP_WINDOW_END
Search parameter: window-endDescription: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.
Type: number
Path: MolecularSequence.referenceSeq.windowEnd
- See Also:
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WINDOW_END
Fluent Client search parameter constant for window-endDescription: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.
Type: number
Path: MolecularSequence.referenceSeq.windowEnd
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SP_TYPE
Search parameter: typeDescription: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: MolecularSequence.type
- See Also:
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TYPE
Fluent Client search parameter constant for typeDescription: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: MolecularSequence.type
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SP_WINDOW_START
Search parameter: window-startDescription: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.
Type: number
Path: MolecularSequence.referenceSeq.windowStart
- See Also:
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WINDOW_START
Fluent Client search parameter constant for window-startDescription: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.
Type: number
Path: MolecularSequence.referenceSeq.windowStart
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SP_VARIANT_END
Search parameter: variant-endDescription: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.
Type: number
Path: MolecularSequence.variant.end
- See Also:
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VARIANT_END
Fluent Client search parameter constant for variant-endDescription: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.
Type: number
Path: MolecularSequence.variant.end
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SP_CHROMOSOME_VARIANT_COORDINATE
Search parameter: chromosome-variant-coordinateDescription: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
- See Also:
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CHROMOSOME_VARIANT_COORDINATE
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_VARIANT_COORDINATEFluent Client search parameter constant for chromosome-variant-coordinateDescription: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
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SP_PATIENT
Search parameter: patientDescription: The subject that the observation is about
Type: reference
Path: MolecularSequence.patient
- See Also:
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PATIENT
Fluent Client search parameter constant for patientDescription: The subject that the observation is about
Type: reference
Path: MolecularSequence.patient
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INCLUDE_PATIENT
Constant for fluent queries to be used to add include statements. Specifies the path value of "MolecularSequence:patient". -
SP_VARIANT_START
Search parameter: variant-startDescription: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
Type: number
Path: MolecularSequence.variant.start
- See Also:
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VARIANT_START
Fluent Client search parameter constant for variant-startDescription: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
Type: number
Path: MolecularSequence.variant.start
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SP_CHROMOSOME_WINDOW_COORDINATE
Search parameter: chromosome-window-coordinateDescription: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
- See Also:
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CHROMOSOME_WINDOW_COORDINATE
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_WINDOW_COORDINATEFluent Client search parameter constant for chromosome-window-coordinateDescription: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
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SP_REFERENCESEQID_WINDOW_COORDINATE
Search parameter: referenceseqid-window-coordinateDescription: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
- See Also:
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REFERENCESEQID_WINDOW_COORDINATE
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_WINDOW_COORDINATEFluent Client search parameter constant for referenceseqid-window-coordinateDescription: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and invalid input: '<'345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
Type: composite
Path:
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SP_REFERENCESEQID
Search parameter: referenceseqidDescription: Reference Sequence of the sequence
Type: token
Path: MolecularSequence.referenceSeq.referenceSeqId
- See Also:
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REFERENCESEQID
Fluent Client search parameter constant for referenceseqidDescription: Reference Sequence of the sequence
Type: token
Path: MolecularSequence.referenceSeq.referenceSeqId
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Constructor Details
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MolecularSequence
public MolecularSequence()Constructor -
MolecularSequence
Constructor
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Method Details
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getIdentifier
- Returns:
identifier
(A unique identifier for this particular sequence instance. This is a FHIR-defined id.)
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setIdentifier
- Returns:
- Returns a reference to
this
for easy method chaining
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hasIdentifier
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addIdentifier
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addIdentifier
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getIdentifierFirstRep
- Returns:
- The first repetition of repeating field
identifier
, creating it if it does not already exist
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getTypeElement
- Returns:
type
(Amino Acid Sequence/ DNA Sequence / RNA Sequence.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value
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hasTypeElement
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hasType
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setTypeElement
- Parameters:
value
-type
(Amino Acid Sequence/ DNA Sequence / RNA Sequence.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value
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getType
- Returns:
- Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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setType
- Parameters:
value
- Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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getCoordinateSystemElement
- Returns:
coordinateSystem
(Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).). This is the underlying object with id, value and extensions. The accessor "getCoordinateSystem" gives direct access to the value
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hasCoordinateSystemElement
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hasCoordinateSystem
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setCoordinateSystemElement
- Parameters:
value
-coordinateSystem
(Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).). This is the underlying object with id, value and extensions. The accessor "getCoordinateSystem" gives direct access to the value
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getCoordinateSystem
- Returns:
- Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
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setCoordinateSystem
- Parameters:
value
- Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
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getPatient
- Returns:
patient
(The patient whose sequencing results are described by this resource.)
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hasPatient
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setPatient
- Parameters:
value
-patient
(The patient whose sequencing results are described by this resource.)
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getPatientTarget
- Returns:
patient
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. (The patient whose sequencing results are described by this resource.)
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setPatientTarget
- Parameters:
value
-patient
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. (The patient whose sequencing results are described by this resource.)
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getSpecimen
- Returns:
specimen
(Specimen used for sequencing.)
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hasSpecimen
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setSpecimen
- Parameters:
value
-specimen
(Specimen used for sequencing.)
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getSpecimenTarget
- Returns:
specimen
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. (Specimen used for sequencing.)
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setSpecimenTarget
- Parameters:
value
-specimen
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. (Specimen used for sequencing.)
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getDevice
- Returns:
device
(The method for sequencing, for example, chip information.)
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hasDevice
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setDevice
- Parameters:
value
-device
(The method for sequencing, for example, chip information.)
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getDeviceTarget
- Returns:
device
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. (The method for sequencing, for example, chip information.)
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setDeviceTarget
- Parameters:
value
-device
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. (The method for sequencing, for example, chip information.)
-
getPerformer
- Returns:
performer
(The organization or lab that should be responsible for this result.)
-
hasPerformer
-
setPerformer
- Parameters:
value
-performer
(The organization or lab that should be responsible for this result.)
-
getPerformerTarget
- Returns:
performer
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. (The organization or lab that should be responsible for this result.)
-
setPerformerTarget
- Parameters:
value
-performer
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. (The organization or lab that should be responsible for this result.)
-
getQuantity
- Returns:
quantity
(The number of copies of the sequence of interest. (RNASeq).)
-
hasQuantity
-
setQuantity
- Parameters:
value
-quantity
(The number of copies of the sequence of interest. (RNASeq).)
-
getReferenceSeq
- Returns:
referenceSeq
(A sequence that is used as a reference to describe variants that are present in a sequence analyzed.)
-
hasReferenceSeq
-
setReferenceSeq
public MolecularSequence setReferenceSeq(MolecularSequence.MolecularSequenceReferenceSeqComponent value) - Parameters:
value
-referenceSeq
(A sequence that is used as a reference to describe variants that are present in a sequence analyzed.)
-
getVariant
- Returns:
variant
(The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.)
-
setVariant
public MolecularSequence setVariant(List<MolecularSequence.MolecularSequenceVariantComponent> theVariant) - Returns:
- Returns a reference to
this
for easy method chaining
-
hasVariant
-
addVariant
-
addVariant
-
getVariantFirstRep
- Returns:
- The first repetition of repeating field
variant
, creating it if it does not already exist
-
getObservedSeqElement
- Returns:
observedSeq
(Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the value
-
hasObservedSeqElement
-
hasObservedSeq
-
setObservedSeqElement
- Parameters:
value
-observedSeq
(Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the value
-
getObservedSeq
- Returns:
- Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
-
setObservedSeq
- Parameters:
value
- Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
-
getQuality
- Returns:
quality
(An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).)
-
setQuality
public MolecularSequence setQuality(List<MolecularSequence.MolecularSequenceQualityComponent> theQuality) - Returns:
- Returns a reference to
this
for easy method chaining
-
hasQuality
-
addQuality
-
addQuality
-
getQualityFirstRep
- Returns:
- The first repetition of repeating field
quality
, creating it if it does not already exist
-
getReadCoverageElement
- Returns:
readCoverage
(Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.). This is the underlying object with id, value and extensions. The accessor "getReadCoverage" gives direct access to the value
-
hasReadCoverageElement
-
hasReadCoverage
-
setReadCoverageElement
- Parameters:
value
-readCoverage
(Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.). This is the underlying object with id, value and extensions. The accessor "getReadCoverage" gives direct access to the value
-
getReadCoverage
- Returns:
- Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
-
setReadCoverage
- Parameters:
value
- Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
-
getRepository
- Returns:
repository
(Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.)
-
setRepository
public MolecularSequence setRepository(List<MolecularSequence.MolecularSequenceRepositoryComponent> theRepository) - Returns:
- Returns a reference to
this
for easy method chaining
-
hasRepository
-
addRepository
-
addRepository
-
getRepositoryFirstRep
- Returns:
- The first repetition of repeating field
repository
, creating it if it does not already exist
-
getPointer
- Returns:
pointer
(Pointer to next atomic sequence which at most contains one variant.)
-
setPointer
- Returns:
- Returns a reference to
this
for easy method chaining
-
hasPointer
-
addPointer
-
addPointer
-
getPointerFirstRep
- Returns:
- The first repetition of repeating field
pointer
, creating it if it does not already exist
-
getPointerTarget
Deprecated.Use Reference#setResource(IBaseResource) instead -
addPointerTarget
Deprecated.Use Reference#setResource(IBaseResource) instead -
getStructureVariant
- Returns:
structureVariant
(Information about chromosome structure variation.)
-
setStructureVariant
public MolecularSequence setStructureVariant(List<MolecularSequence.MolecularSequenceStructureVariantComponent> theStructureVariant) - Returns:
- Returns a reference to
this
for easy method chaining
-
hasStructureVariant
-
addStructureVariant
-
addStructureVariant
-
getStructureVariantFirstRep
- Returns:
- The first repetition of repeating field
structureVariant
, creating it if it does not already exist
-
listChildren
- Overrides:
listChildren
in classDomainResource
-
getNamedProperty
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws org.hl7.fhir.exceptions.FHIRException - Overrides:
getNamedProperty
in classDomainResource
- 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 classDomainResource
- 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 classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
setProperty
- Overrides:
setProperty
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
removeChild
- Overrides:
removeChild
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
makeProperty
- Overrides:
makeProperty
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
getTypesForProperty
public String[] getTypesForProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException - Overrides:
getTypesForProperty
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
addChild
- Overrides:
addChild
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
fhirType
- Specified by:
fhirType
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
fhirType
in classDomainResource
-
copy
- Specified by:
copy
in classDomainResource
-
copyValues
-
typedCopy
-
equalsDeep
- Overrides:
equalsDeep
in classDomainResource
-
equalsShallow
- Overrides:
equalsShallow
in classDomainResource
-
isEmpty
- Specified by:
isEmpty
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
isEmpty
in classDomainResource
-
getResourceType
- Specified by:
getResourceType
in classResource
-