Sequence (HAPI FHIR Structures - FHIR R4 3.6.0 API)

java.lang.Object
- org.hl7.fhir.r4.model.Base
- - org.hl7.fhir.r4.model.BaseResource
  - - org.hl7.fhir.r4.model.Resource
    - - org.hl7.fhir.r4.model.DomainResource
      - org.hl7.fhir.r4.model.Sequence

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
```
public class Sequence
extends DomainResource
```
Raw data describing a biological sequence.

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`Sequence.OrientationType`
`static class`	`Sequence.OrientationTypeEnumFactory`
`static class`	`Sequence.QualityType`
`static class`	`Sequence.QualityTypeEnumFactory`
`static class`	`Sequence.RepositoryType`
`static class`	`Sequence.RepositoryTypeEnumFactory`
`static class`	`Sequence.SequenceQualityComponent`
`static class`	`Sequence.SequenceQualityRocComponent`
`static class`	`Sequence.SequenceReferenceSeqComponent`
`static class`	`Sequence.SequenceRepositoryComponent`
`static class`	`Sequence.SequenceStructureVariantComponent`
`static class`	`Sequence.SequenceStructureVariantInnerComponent`
`static class`	`Sequence.SequenceStructureVariantOuterComponent`
`static class`	`Sequence.SequenceType`
`static class`	`Sequence.SequenceTypeEnumFactory`
`static class`	`Sequence.SequenceVariantComponent`
`static class`	`Sequence.StrandType`
`static class`	`Sequence.StrandTypeEnumFactory`

Field Summary

Fields
Modifier and Type	Field and Description
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`CHROMOSOME` Fluent Client search parameter constant for chromosome
`static ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam>`	`COORDINATE` Fluent Client search parameter constant for coordinate
`protected IntegerType`	`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).
`protected Reference`	`device` The method for sequencing, for example, chip information.
`protected Device`	`deviceTarget` The actual object that is the target of the reference (The method for sequencing, for example, chip information.)
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`END` Fluent Client search parameter constant for end
`protected List<Identifier>`	`identifier` A unique identifier for this particular sequence instance.
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`IDENTIFIER` Fluent Client search parameter constant for identifier
`static ca.uhn.fhir.model.api.Include`	`INCLUDE_PATIENT` Constant for fluent queries to be used to add include statements.
`protected StringType`	`observedSeq` Sequence that was observed.
`protected Reference`	`patient` The patient whose sequencing results are described by this resource.
`static ca.uhn.fhir.rest.gclient.ReferenceClientParam`	`PATIENT` Fluent Client search parameter constant for patient
`protected Patient`	`patientTarget` The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.)
`protected Reference`	`performer` The organization or lab that should be responsible for this result.
`protected Organization`	`performerTarget` The actual object that is the target of the reference (The organization or lab that should be responsible for this result.)
`protected List<Reference>`	`pointer` Pointer to next atomic sequence which at most contains one variant.
`protected List<Sequence>`	`pointerTarget` The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.)
`protected List<Sequence.SequenceQualityComponent>`	`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)).
`protected Quantity`	`quantity` The number of copies of the seqeunce of interest.
`protected IntegerType`	`readCoverage` Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
`protected Sequence.SequenceReferenceSeqComponent`	`referenceSeq` A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
`protected List<Sequence.SequenceRepositoryComponent>`	`repository` Configurations of the external repository.
`static String`	`SP_CHROMOSOME` Search parameter: chromosome
`static String`	`SP_COORDINATE` Search parameter: coordinate
`static String`	`SP_END` Search parameter: end
`static String`	`SP_IDENTIFIER` Search parameter: identifier
`static String`	`SP_PATIENT` Search parameter: patient
`static String`	`SP_START` Search parameter: start
`static String`	`SP_TYPE` Search parameter: type
`protected Reference`	`specimen` Specimen used for sequencing.
`protected Specimen`	`specimenTarget` The actual object that is the target of the reference (Specimen used for sequencing.)
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`START` Fluent Client search parameter constant for start
`protected List<Sequence.SequenceStructureVariantComponent>`	`structureVariant` Information about chromosome structure variation.
`protected Enumeration<Sequence.SequenceType>`	`type` Amino Acid Sequence/ DNA Sequence / RNA Sequence.
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`TYPE` Fluent Client search parameter constant for type
`protected List<Sequence.SequenceVariantComponent>`	`variant` The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).

Fields 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, SP_RES_ID, SP_RES_LANGUAGE

Fields inherited from interface org.hl7.fhir.instance.model.api.IBaseResource
INCLUDE_ALL, WILDCARD_ALL_SET

Constructor Summary

Constructors
Constructor and Description

Sequence()
Constructor

Sequence(IntegerType coordinateSystem)
Constructor

Constructors
Constructor and Description
`Sequence()` Constructor
`Sequence(IntegerType coordinateSystem)` Constructor

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`Base`	`addChild(String name)`
`Identifier`	`addIdentifier()`
`Sequence`	`addIdentifier(Identifier t)`
`Reference`	`addPointer()`
`Sequence`	`addPointer(Reference t)`
`Sequence`	`addPointerTarget()` Deprecated. Use Reference#setResource(IBaseResource) instead
`Sequence.SequenceQualityComponent`	`addQuality()`
`Sequence`	`addQuality(Sequence.SequenceQualityComponent t)`
`Sequence.SequenceRepositoryComponent`	`addRepository()`
`Sequence`	`addRepository(Sequence.SequenceRepositoryComponent t)`
`Sequence.SequenceStructureVariantComponent`	`addStructureVariant()`
`Sequence`	`addStructureVariant(Sequence.SequenceStructureVariantComponent t)`
`Sequence.SequenceVariantComponent`	`addVariant()`
`Sequence`	`addVariant(Sequence.SequenceVariantComponent t)`
`Sequence`	`copy()`
`boolean`	`equalsDeep(Base other_)`
`boolean`	`equalsShallow(Base other_)`
`String`	`fhirType()`
`int`	`getCoordinateSystem()`
`IntegerType`	`getCoordinateSystemElement()`
`Reference`	`getDevice()`
`Device`	`getDeviceTarget()`
`List<Identifier>`	`getIdentifier()`
`Identifier`	`getIdentifierFirstRep()`
`Property`	`getNamedProperty(int _hash, String _name, boolean _checkValid)`
`String`	`getObservedSeq()`
`StringType`	`getObservedSeqElement()`
`Reference`	`getPatient()`
`Patient`	`getPatientTarget()`
`Reference`	`getPerformer()`
`Organization`	`getPerformerTarget()`
`List<Reference>`	`getPointer()`
`Reference`	`getPointerFirstRep()`
`List<Sequence>`	`getPointerTarget()` Deprecated. Use Reference#setResource(IBaseResource) instead
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`List<Sequence.SequenceQualityComponent>`	`getQuality()`
`Sequence.SequenceQualityComponent`	`getQualityFirstRep()`
`Quantity`	`getQuantity()`
`int`	`getReadCoverage()`
`IntegerType`	`getReadCoverageElement()`
`Sequence.SequenceReferenceSeqComponent`	`getReferenceSeq()`
`List<Sequence.SequenceRepositoryComponent>`	`getRepository()`
`Sequence.SequenceRepositoryComponent`	`getRepositoryFirstRep()`
`ResourceType`	`getResourceType()`
`Reference`	`getSpecimen()`
`Specimen`	`getSpecimenTarget()`
`List<Sequence.SequenceStructureVariantComponent>`	`getStructureVariant()`
`Sequence.SequenceStructureVariantComponent`	`getStructureVariantFirstRep()`
`Sequence.SequenceType`	`getType()`
`Enumeration<Sequence.SequenceType>`	`getTypeElement()`
`String[]`	`getTypesForProperty(int hash, String name)`
`List<Sequence.SequenceVariantComponent>`	`getVariant()`
`Sequence.SequenceVariantComponent`	`getVariantFirstRep()`
`boolean`	`hasCoordinateSystem()`
`boolean`	`hasCoordinateSystemElement()`
`boolean`	`hasDevice()`
`boolean`	`hasIdentifier()`
`boolean`	`hasObservedSeq()`
`boolean`	`hasObservedSeqElement()`
`boolean`	`hasPatient()`
`boolean`	`hasPerformer()`
`boolean`	`hasPointer()`
`boolean`	`hasQuality()`
`boolean`	`hasQuantity()`
`boolean`	`hasReadCoverage()`
`boolean`	`hasReadCoverageElement()`
`boolean`	`hasReferenceSeq()`
`boolean`	`hasRepository()`
`boolean`	`hasSpecimen()`
`boolean`	`hasStructureVariant()`
`boolean`	`hasType()`
`boolean`	`hasTypeElement()`
`boolean`	`hasVariant()`
`boolean`	`isEmpty()`
`protected void`	`listChildren(List<Property> children)`
`Base`	`makeProperty(int hash, String name)`
`Sequence`	`setCoordinateSystem(int value)`
`Sequence`	`setCoordinateSystemElement(IntegerType value)`
`Sequence`	`setDevice(Reference value)`
`Sequence`	`setDeviceTarget(Device value)`
`Sequence`	`setIdentifier(List<Identifier> theIdentifier)`
`Sequence`	`setObservedSeq(String value)`
`Sequence`	`setObservedSeqElement(StringType value)`
`Sequence`	`setPatient(Reference value)`
`Sequence`	`setPatientTarget(Patient value)`
`Sequence`	`setPerformer(Reference value)`
`Sequence`	`setPerformerTarget(Organization value)`
`Sequence`	`setPointer(List<Reference> thePointer)`
`Base`	`setProperty(int hash, String name, Base value)`
`Base`	`setProperty(String name, Base value)`
`Sequence`	`setQuality(List<Sequence.SequenceQualityComponent> theQuality)`
`Sequence`	`setQuantity(Quantity value)`
`Sequence`	`setReadCoverage(int value)`
`Sequence`	`setReadCoverageElement(IntegerType value)`
`Sequence`	`setReferenceSeq(Sequence.SequenceReferenceSeqComponent value)`
`Sequence`	`setRepository(List<Sequence.SequenceRepositoryComponent> theRepository)`
`Sequence`	`setSpecimen(Reference value)`
`Sequence`	`setSpecimenTarget(Specimen value)`
`Sequence`	`setStructureVariant(List<Sequence.SequenceStructureVariantComponent> theStructureVariant)`
`Sequence`	`setType(Sequence.SequenceType value)`
`Sequence`	`setTypeElement(Enumeration<Sequence.SequenceType> value)`
`Sequence`	`setVariant(List<Sequence.SequenceVariantComponent> theVariant)`
`protected Sequence`	`typedCopy()`

Methods inherited from class org.hl7.fhir.r4.model.DomainResource
addContained, addExtension, addExtension, addExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyValues, 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, 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, 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, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, 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.IBaseResource
getMeta, getStructureFhirVersionEnum, setId

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase
getFormatCommentsPost, getFormatCommentsPre, hasFormatComment

- Field Detail
  - identifier
```
protected List<Identifier> identifier
```
    A unique identifier for this particular sequence instance. This is a FHIR-defined id.
  - type
```
protected Enumeration<Sequence.SequenceType> type
```
    Amino Acid Sequence/ DNA Sequence / RNA Sequence.
  - coordinateSystem
```
protected IntegerType 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
```
protected Reference patient
```
    The patient whose sequencing results are described by this resource.
  - patientTarget
```
protected Patient patientTarget
```
    The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.)
  - specimen
```
protected Reference specimen
```
    Specimen used for sequencing.
  - specimenTarget
```
protected Specimen specimenTarget
```
    The actual object that is the target of the reference (Specimen used for sequencing.)
  - device
```
protected Reference device
```
    The method for sequencing, for example, chip information.
  - deviceTarget
```
protected Device deviceTarget
```
    The actual object that is the target of the reference (The method for sequencing, for example, chip information.)
  - performer
```
protected Reference performer
```
    The organization or lab that should be responsible for this result.
  - performerTarget
```
protected Organization performerTarget
```
    The actual object that is the target of the reference (The organization or lab that should be responsible for this result.)
  - quantity
```
protected Quantity quantity
```
    The number of copies of the seqeunce of interest. (RNASeq).
  - referenceSeq
```
protected Sequence.SequenceReferenceSeqComponent referenceSeq
```
    A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
  - variant
```
protected List<Sequence.SequenceVariantComponent> 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
```
protected StringType observedSeq
```
    Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - quality
```
protected List<Sequence.SequenceQualityComponent> 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
```
protected IntegerType readCoverage
```
    Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
  - repository
```
protected List<Sequence.SequenceRepositoryComponent> repository
```
    Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
  - pointer
```
protected List<Reference> pointer
```
    Pointer to next atomic sequence which at most contains one variant.
  - pointerTarget
```
protected List<Sequence> pointerTarget
```
    The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.)
  - structureVariant
```
protected List<Sequence.SequenceStructureVariantComponent> structureVariant
```
    Information about chromosome structure variation.
  - SP_IDENTIFIER
```
public static final String SP_IDENTIFIER
```
    Search parameter: identifier
    Description: The unique identity for a particular sequence
    Type: token
    Path: Sequence.identifier
    
    See Also:
    
    Constant Field Values
  - IDENTIFIER
```
public static final ca.uhn.fhir.rest.gclient.TokenClientParam IDENTIFIER
```
    Fluent Client search parameter constant for identifier
    Description: The unique identity for a particular sequence
    Type: token
    Path: Sequence.identifier
  - SP_COORDINATE
```
public static final String SP_COORDINATE
```
    Search parameter: coordinate
    Description: Search parameter for region of the reference DNA sequence string. 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 `coordinate=1$lt345$gt123`, this means it will search for the Sequence resource on chromosome 1 and with position >123 and <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:
    
    Constant Field Values
  - COORDINATE
```
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> COORDINATE
```
    Fluent Client search parameter constant for coordinate
    Description: Search parameter for region of the reference DNA sequence string. 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 `coordinate=1$lt345$gt123`, this means it will search for the Sequence resource on chromosome 1 and with position >123 and <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:
  - SP_PATIENT
```
public static final String SP_PATIENT
```
    Search parameter: patient
    Description: The subject that the observation is about
    Type: reference
    Path: Sequence.patient
    
    See Also:
    
    Constant Field Values
  - PATIENT
```
public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam PATIENT
```
    Fluent Client search parameter constant for patient
    Description: The subject that the observation is about
    Type: reference
    Path: Sequence.patient
  - INCLUDE_PATIENT
```
public static final ca.uhn.fhir.model.api.Include INCLUDE_PATIENT
```
    Constant for fluent queries to be used to add include statements. Specifies the path value of "Sequence:patient".
  - SP_CHROMOSOME
```
public static final String SP_CHROMOSOME
```
    Search parameter: chromosome
    Description: Chromosome number of the reference sequence
    Type: token
    Path: Sequence.referenceSeq.chromosome
    
    See Also:
    
    Constant Field Values
  - CHROMOSOME
```
public static final ca.uhn.fhir.rest.gclient.TokenClientParam CHROMOSOME
```
    Fluent Client search parameter constant for chromosome
    Description: Chromosome number of the reference sequence
    Type: token
    Path: Sequence.referenceSeq.chromosome
  - SP_START
```
public static final String SP_START
```
    Search parameter: start
    Description: 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: Sequence.referenceSeq.windowStart
    
    See Also:
    
    Constant Field Values
  - START
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam START
```
    Fluent Client search parameter constant for start
    Description: 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: Sequence.referenceSeq.windowStart
  - SP_END
```
public static final String SP_END
```
    Search parameter: end
    Description: 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: Sequence.referenceSeq.windowEnd
    
    See Also:
    
    Constant Field Values
  - END
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam END
```
    Fluent Client search parameter constant for end
    Description: 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: Sequence.referenceSeq.windowEnd
  - SP_TYPE
```
public static final String SP_TYPE
```
    Search parameter: type
    Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
    Type: token
    Path: Sequence.type
    
    See Also:
    
    Constant Field Values
  - TYPE
```
public static final ca.uhn.fhir.rest.gclient.TokenClientParam TYPE
```
    Fluent Client search parameter constant for type
    Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
    Type: token
    Path: Sequence.type
- Constructor Detail
  - Sequence
```
public Sequence()
```
    Constructor
  - Sequence
```
public Sequence(IntegerType coordinateSystem)
```
    Constructor
- Method Detail
  - getIdentifier
```
public List<Identifier> getIdentifier()
```
    Returns:
    
    identifier (A unique identifier for this particular sequence instance. This is a FHIR-defined id.)
  - setIdentifier
```
public Sequence setIdentifier(List<Identifier> theIdentifier)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasIdentifier
```
public boolean hasIdentifier()
```
  - addIdentifier
```
public Identifier addIdentifier()
```
  - addIdentifier
```
public Sequence addIdentifier(Identifier t)
```
  - getIdentifierFirstRep
```
public Identifier getIdentifierFirstRep()
```
    Returns:
    
    The first repetition of repeating field identifier, creating it if it does not already exist
  - getTypeElement
```
public Enumeration<Sequence.SequenceType> 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
  - hasTypeElement
```
public boolean hasTypeElement()
```
  - hasType
```
public boolean hasType()
```
  - setTypeElement
```
public Sequence setTypeElement(Enumeration<Sequence.SequenceType> value)
```
    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
  - getType
```
public Sequence.SequenceType getType()
```
    Returns:
    
    Amino Acid Sequence/ DNA Sequence / RNA Sequence.
  - setType
```
public Sequence setType(Sequence.SequenceType value)
```
    Parameters:
    
    value - Amino Acid Sequence/ DNA Sequence / RNA Sequence.
  - getCoordinateSystemElement
```
public IntegerType 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
  - hasCoordinateSystemElement
```
public boolean hasCoordinateSystemElement()
```
  - hasCoordinateSystem
```
public boolean hasCoordinateSystem()
```
  - setCoordinateSystemElement
```
public Sequence setCoordinateSystemElement(IntegerType value)
```
    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
  - getCoordinateSystem
```
public int 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).
  - setCoordinateSystem
```
public Sequence setCoordinateSystem(int value)
```
    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).
  - getPatient
```
public Reference getPatient()
```
    Returns:
    
    patient (The patient whose sequencing results are described by this resource.)
  - hasPatient
```
public boolean hasPatient()
```
  - setPatient
```
public Sequence setPatient(Reference value)
```
    Parameters:
    
    value - patient (The patient whose sequencing results are described by this resource.)
  - getPatientTarget
```
public Patient 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.)
  - setPatientTarget
```
public Sequence setPatientTarget(Patient value)
```
    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.)
  - getSpecimen
```
public Reference getSpecimen()
```
    Returns:
    
    specimen (Specimen used for sequencing.)
  - hasSpecimen
```
public boolean hasSpecimen()
```
  - setSpecimen
```
public Sequence setSpecimen(Reference value)
```
    Parameters:
    
    value - specimen (Specimen used for sequencing.)
  - getSpecimenTarget
```
public Specimen 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.)
  - setSpecimenTarget
```
public Sequence setSpecimenTarget(Specimen value)
```
    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.)
  - getDevice
```
public Reference getDevice()
```
    Returns:
    
    device (The method for sequencing, for example, chip information.)
  - hasDevice
```
public boolean hasDevice()
```
  - setDevice
```
public Sequence setDevice(Reference value)
```
    Parameters:
    
    value - device (The method for sequencing, for example, chip information.)
  - getDeviceTarget
```
public Device 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.)
  - setDeviceTarget
```
public Sequence setDeviceTarget(Device value)
```
    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
```
public Reference getPerformer()
```
    Returns:
    
    performer (The organization or lab that should be responsible for this result.)
  - hasPerformer
```
public boolean hasPerformer()
```
  - setPerformer
```
public Sequence setPerformer(Reference value)
```
    Parameters:
    
    value - performer (The organization or lab that should be responsible for this result.)
  - getPerformerTarget
```
public Organization 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
```
public Sequence setPerformerTarget(Organization value)
```
    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
```
public Quantity getQuantity()
```
    Returns:
    
    quantity (The number of copies of the seqeunce of interest. (RNASeq).)
  - hasQuantity
```
public boolean hasQuantity()
```
  - setQuantity
```
public Sequence setQuantity(Quantity value)
```
    Parameters:
    
    value - quantity (The number of copies of the seqeunce of interest. (RNASeq).)
  - getReferenceSeq
```
public Sequence.SequenceReferenceSeqComponent getReferenceSeq()
```
    Returns:
    
    referenceSeq (A sequence that is used as a reference to describe variants that are present in a sequence analyzed.)
  - hasReferenceSeq
```
public boolean hasReferenceSeq()
```
  - setReferenceSeq
```
public Sequence setReferenceSeq(Sequence.SequenceReferenceSeqComponent value)
```
    Parameters:
    
    value - referenceSeq (A sequence that is used as a reference to describe variants that are present in a sequence analyzed.)
  - getVariant
```
public List<Sequence.SequenceVariantComponent> 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 Sequence setVariant(List<Sequence.SequenceVariantComponent> theVariant)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasVariant
```
public boolean hasVariant()
```
  - addVariant
```
public Sequence.SequenceVariantComponent addVariant()
```
  - addVariant
```
public Sequence addVariant(Sequence.SequenceVariantComponent t)
```
  - getVariantFirstRep
```
public Sequence.SequenceVariantComponent getVariantFirstRep()
```
    Returns:
    
    The first repetition of repeating field variant, creating it if it does not already exist
  - getObservedSeqElement
```
public StringType getObservedSeqElement()
```
    Returns:
    
    observedSeq (Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts 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
```
public boolean hasObservedSeqElement()
```
  - hasObservedSeq
```
public boolean hasObservedSeq()
```
  - setObservedSeqElement
```
public Sequence setObservedSeqElement(StringType value)
```
    Parameters:
    
    value - observedSeq (Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts 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
```
public String getObservedSeq()
```
    Returns:
    
    Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - setObservedSeq
```
public Sequence setObservedSeq(String value)
```
    Parameters:
    
    value - Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - getQuality
```
public List<Sequence.SequenceQualityComponent> 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 Sequence setQuality(List<Sequence.SequenceQualityComponent> theQuality)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasQuality
```
public boolean hasQuality()
```
  - addQuality
```
public Sequence.SequenceQualityComponent addQuality()
```
  - addQuality
```
public Sequence addQuality(Sequence.SequenceQualityComponent t)
```
  - getQualityFirstRep
```
public Sequence.SequenceQualityComponent getQualityFirstRep()
```
    Returns:
    
    The first repetition of repeating field quality, creating it if it does not already exist
  - getReadCoverageElement
```
public IntegerType 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
```
public boolean hasReadCoverageElement()
```
  - hasReadCoverage
```
public boolean hasReadCoverage()
```
  - setReadCoverageElement
```
public Sequence setReadCoverageElement(IntegerType value)
```
    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
```
public int getReadCoverage()
```
    Returns:
    
    Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
  - setReadCoverage
```
public Sequence setReadCoverage(int value)
```
    Parameters:
    
    value - Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
  - getRepository
```
public List<Sequence.SequenceRepositoryComponent> getRepository()
```
    Returns:
    
    repository (Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.)
  - setRepository
```
public Sequence setRepository(List<Sequence.SequenceRepositoryComponent> theRepository)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasRepository
```
public boolean hasRepository()
```
  - addRepository
```
public Sequence.SequenceRepositoryComponent addRepository()
```
  - addRepository
```
public Sequence addRepository(Sequence.SequenceRepositoryComponent t)
```
  - getRepositoryFirstRep
```
public Sequence.SequenceRepositoryComponent getRepositoryFirstRep()
```
    Returns:
    
    The first repetition of repeating field repository, creating it if it does not already exist
  - getPointer
```
public List<Reference> getPointer()
```
    Returns:
    
    pointer (Pointer to next atomic sequence which at most contains one variant.)
  - setPointer
```
public Sequence setPointer(List<Reference> thePointer)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasPointer
```
public boolean hasPointer()
```
  - addPointer
```
public Reference addPointer()
```
  - addPointer
```
public Sequence addPointer(Reference t)
```
  - getPointerFirstRep
```
public Reference getPointerFirstRep()
```
    Returns:
    
    The first repetition of repeating field pointer, creating it if it does not already exist
  - getPointerTarget
```
@Deprecated
public List<Sequence> getPointerTarget()
```
    Deprecated. Use Reference#setResource(IBaseResource) instead
  - addPointerTarget
```
@Deprecated
public Sequence addPointerTarget()
```
    Deprecated. Use Reference#setResource(IBaseResource) instead
  - getStructureVariant
```
public List<Sequence.SequenceStructureVariantComponent> getStructureVariant()
```
    Returns:
    
    structureVariant (Information about chromosome structure variation.)
  - setStructureVariant
```
public Sequence setStructureVariant(List<Sequence.SequenceStructureVariantComponent> theStructureVariant)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasStructureVariant
```
public boolean hasStructureVariant()
```
  - addStructureVariant
```
public Sequence.SequenceStructureVariantComponent addStructureVariant()
```
  - addStructureVariant
```
public Sequence addStructureVariant(Sequence.SequenceStructureVariantComponent t)
```
  - getStructureVariantFirstRep
```
public Sequence.SequenceStructureVariantComponent getStructureVariantFirstRep()
```
    Returns:
    
    The first repetition of repeating field structureVariant, creating it if it does not already exist
  - listChildren
```
protected void listChildren(List<Property> children)
```
    Overrides:
    
    listChildren in class DomainResource
  - getNamedProperty
```
public Property getNamedProperty(int _hash,
                                 String _name,
                                 boolean _checkValid)
                          throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    getNamedProperty in class DomainResource
    
    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 class DomainResource
    
    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 class DomainResource
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - setProperty
```
public Base setProperty(String name,
                        Base value)
                 throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    setProperty in class DomainResource
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - makeProperty
```
public Base makeProperty(int hash,
                         String name)
                  throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    makeProperty in class DomainResource
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - getTypesForProperty
```
public String[] getTypesForProperty(int hash,
                                    String name)
                             throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    getTypesForProperty in class DomainResource
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - addChild
```
public Base addChild(String name)
              throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    addChild in class DomainResource
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - fhirType
```
public String fhirType()
```
    Overrides:
    
    fhirType in class DomainResource
  - copy
```
public Sequence copy()
```
    Specified by:
    
    copy in class DomainResource
  - typedCopy
```
protected Sequence typedCopy()
```
  - equalsDeep
```
public boolean equalsDeep(Base other_)
```
    Overrides:
    
    equalsDeep in class DomainResource
  - equalsShallow
```
public boolean equalsShallow(Base other_)
```
    Overrides:
    
    equalsShallow in class DomainResource
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface org.hl7.fhir.instance.model.api.IBase
    
    Overrides:
    
    isEmpty in class DomainResource
  - getResourceType
```
public ResourceType getResourceType()
```
    Specified by:
    
    getResourceType in class Resource

Class Sequence

Nested Class Summary

Field Summary

Fields inherited from class org.hl7.fhir.r4.model.DomainResource

Fields inherited from class org.hl7.fhir.r4.model.Resource

Fields inherited from interface org.hl7.fhir.instance.model.api.IAnyResource

Fields inherited from interface org.hl7.fhir.instance.model.api.IBaseResource

Constructor Summary

Method Summary

Methods inherited from class org.hl7.fhir.r4.model.DomainResource

Methods inherited from class org.hl7.fhir.r4.model.Resource

Methods inherited from class org.hl7.fhir.r4.model.BaseResource

Methods inherited from class org.hl7.fhir.r4.model.Base

Methods inherited from class java.lang.Object

Methods inherited from interface org.hl7.fhir.instance.model.api.IAnyResource

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseResource

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase

Field Detail

identifier

type

coordinateSystem

patient

patientTarget

specimen

specimenTarget

device

deviceTarget

performer

performerTarget

quantity

referenceSeq

variant

observedSeq

quality

readCoverage

repository

pointer

pointerTarget

structureVariant

SP_IDENTIFIER

IDENTIFIER

SP_COORDINATE

COORDINATE

SP_PATIENT

PATIENT

INCLUDE_PATIENT

SP_CHROMOSOME

CHROMOSOME

SP_START

START

SP_END

END

SP_TYPE

TYPE

Constructor Detail

Sequence

Sequence

Method Detail

getIdentifier

setIdentifier

hasIdentifier

addIdentifier

addIdentifier

getIdentifierFirstRep

getTypeElement

hasTypeElement

hasType

setTypeElement

getType

setType

getCoordinateSystemElement

hasCoordinateSystemElement

hasCoordinateSystem

setCoordinateSystemElement

getCoordinateSystem

setCoordinateSystem

getPatient

hasPatient

setPatient

getPatientTarget