java.lang.Object
- org.hl7.fhir.dstu2016may.model.Base
- - org.hl7.fhir.dstu2016may.model.BaseResource
  - - org.hl7.fhir.dstu2016may.model.Resource
    - - org.hl7.fhir.dstu2016may.model.DomainResource
      - org.hl7.fhir.dstu2016may.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
```
Variation and Sequence data.

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`Sequence.SequenceQualityComponent`
`static class`	`Sequence.SequenceReferenceSeqComponent`
`static class`	`Sequence.SequenceRepositoryComponent`
`static class`	`Sequence.SequenceStructureVariationComponent`
`static class`	`Sequence.SequenceStructureVariationInnerComponent`
`static class`	`Sequence.SequenceStructureVariationOuterComponent`
`static class`	`Sequence.SequenceType`
`static class`	`Sequence.SequenceTypeEnumFactory`
`static class`	`Sequence.SequenceVariationComponent`

Field Summary

Fields
Modifier and Type	Field	Description
`protected DecimalType`	`allelicFrequency`	Allele frequencies.
`protected CodeableConcept`	`allelicState`	The level of occurrence of a single DNA Sequence Variation within a set of chromosomes.
`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 CodeableConcept`	`copyNumberEvent`	Values: amplificaiton / deletion / LOH.
`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
`static ca.uhn.fhir.model.api.Include`	`INCLUDE_PATIENT`	Constant for fluent queries to be used to add include statements.
`protected Reference`	`observation`	Analysis of the sequence.
`protected Observation`	`observationTarget`	The actual object that is the target of the reference (Analysis of the sequence.)
`protected StringType`	`observedSeq`	Observed Sequence.
`protected Reference`	`patient`	The patient, or group of patients 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, or group of patients whose sequencing results are described by this resource.)
`protected List<Reference>`	`pointer`	Pointer to next atomic sequence which at most contains one variation.
`protected List<Sequence>`	`pointerTarget`	The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variation.)
`protected List<Sequence.SequenceQualityComponent>`	`quality`	Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.
`protected Quantity`	`quantity`	Quantity of the sequence.
`protected IntegerType`	`readCoverage`	Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
`protected List<Sequence.SequenceReferenceSeqComponent>`	`referenceSeq`	Reference Sequence.
`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_PATIENT`	Search parameter: patient
`static String`	`SP_SPECIES`	Search parameter: species
`static String`	`SP_START`	Search parameter: start
`static String`	`SP_TYPE`	Search parameter: type
`protected CodeableConcept`	`species`	The organism from which sample of the sequence was extracted.
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`SPECIES`	Fluent Client search parameter constant for species
`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 Sequence.SequenceStructureVariationComponent`	`structureVariation`	Structural variant.
`protected Enumeration<Sequence.SequenceType>`	`type`	Amino acid / cDNA transcript / RNA variation.
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`TYPE`	Fluent Client search parameter constant for type
`protected Sequence.SequenceVariationComponent`	`variation`	Variation info in this sequence.

Fields inherited from class org.hl7.fhir.dstu2016may.model.DomainResource
contained, extension, modifierExtension, text

Fields inherited from class org.hl7.fhir.dstu2016may.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 Description

Sequence()
Constructor

Sequence(Enumeration<Sequence.SequenceType> type)
Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Base`	`addChild(String name)`
`Reference`	`addPointer()`
`Sequence`	`addPointer(Reference t)`
`Sequence`	`addPointerTarget()`
`Sequence.SequenceQualityComponent`	`addQuality()`
`Sequence`	`addQuality(Sequence.SequenceQualityComponent t)`
`Sequence.SequenceReferenceSeqComponent`	`addReferenceSeq()`
`Sequence`	`addReferenceSeq(Sequence.SequenceReferenceSeqComponent t)`
`Sequence.SequenceRepositoryComponent`	`addRepository()`
`Sequence`	`addRepository(Sequence.SequenceRepositoryComponent t)`
`Sequence`	`copy()`
`boolean`	`equalsDeep(Base other)`
`boolean`	`equalsShallow(Base other)`
`String`	`fhirType()`
`BigDecimal`	`getAllelicFrequency()`
`DecimalType`	`getAllelicFrequencyElement()`
`CodeableConcept`	`getAllelicState()`
`CodeableConcept`	`getCopyNumberEvent()`
`Reference`	`getDevice()`
`Device`	`getDeviceTarget()`
`Reference`	`getObservation()`
`Observation`	`getObservationTarget()`
`String`	`getObservedSeq()`
`StringType`	`getObservedSeqElement()`
`Reference`	`getPatient()`
`Patient`	`getPatientTarget()`
`List<Reference>`	`getPointer()`
`List<Sequence>`	`getPointerTarget()`
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`List<Sequence.SequenceQualityComponent>`	`getQuality()`
`Quantity`	`getQuantity()`
`int`	`getReadCoverage()`
`IntegerType`	`getReadCoverageElement()`
`List<Sequence.SequenceReferenceSeqComponent>`	`getReferenceSeq()`
`List<Sequence.SequenceRepositoryComponent>`	`getRepository()`
`ResourceType`	`getResourceType()`
`CodeableConcept`	`getSpecies()`
`Reference`	`getSpecimen()`
`Specimen`	`getSpecimenTarget()`
`Sequence.SequenceStructureVariationComponent`	`getStructureVariation()`
`Sequence.SequenceType`	`getType()`
`Enumeration<Sequence.SequenceType>`	`getTypeElement()`
`Sequence.SequenceVariationComponent`	`getVariation()`
`boolean`	`hasAllelicFrequency()`
`boolean`	`hasAllelicFrequencyElement()`
`boolean`	`hasAllelicState()`
`boolean`	`hasCopyNumberEvent()`
`boolean`	`hasDevice()`
`boolean`	`hasObservation()`
`boolean`	`hasObservedSeq()`
`boolean`	`hasObservedSeqElement()`
`boolean`	`hasPatient()`
`boolean`	`hasPointer()`
`boolean`	`hasQuality()`
`boolean`	`hasQuantity()`
`boolean`	`hasReadCoverage()`
`boolean`	`hasReadCoverageElement()`
`boolean`	`hasReferenceSeq()`
`boolean`	`hasRepository()`
`boolean`	`hasSpecies()`
`boolean`	`hasSpecimen()`
`boolean`	`hasStructureVariation()`
`boolean`	`hasType()`
`boolean`	`hasTypeElement()`
`boolean`	`hasVariation()`
`boolean`	`isEmpty()`
`protected void`	`listChildren(List<Property> childrenList)`
`Base`	`makeProperty(int hash, String name)`	make an instance of a property.
`Sequence`	`setAllelicFrequency(double value)`
`Sequence`	`setAllelicFrequency(long value)`
`Sequence`	`setAllelicFrequency(BigDecimal value)`
`Sequence`	`setAllelicFrequencyElement(DecimalType value)`
`Sequence`	`setAllelicState(CodeableConcept value)`
`Sequence`	`setCopyNumberEvent(CodeableConcept value)`
`Sequence`	`setDevice(Reference value)`
`Sequence`	`setDeviceTarget(Device value)`
`Sequence`	`setObservation(Reference value)`
`Sequence`	`setObservationTarget(Observation value)`
`Sequence`	`setObservedSeq(String value)`
`Sequence`	`setObservedSeqElement(StringType value)`
`Sequence`	`setPatient(Reference value)`
`Sequence`	`setPatientTarget(Patient value)`
`void`	`setProperty(int hash, String name, Base value)`
`void`	`setProperty(String name, Base value)`
`Sequence`	`setQuantity(Quantity value)`
`Sequence`	`setReadCoverage(int value)`
`Sequence`	`setReadCoverageElement(IntegerType value)`
`Sequence`	`setSpecies(CodeableConcept value)`
`Sequence`	`setSpecimen(Reference value)`
`Sequence`	`setSpecimenTarget(Specimen value)`
`Sequence`	`setStructureVariation(Sequence.SequenceStructureVariationComponent value)`
`Sequence`	`setType(Sequence.SequenceType value)`
`Sequence`	`setTypeElement(Enumeration<Sequence.SequenceType> value)`
`Sequence`	`setVariation(Sequence.SequenceVariationComponent value)`
`protected Sequence`	`typedCopy()`

Methods inherited from class org.hl7.fhir.dstu2016may.model.DomainResource
addContained, addExtension, addExtension, addModifierExtension, addModifierExtension, copyValues, getContained, getExtension, getExtensionsByUrl, getModifierExtension, getModifierExtensionsByUrl, getText, hasContained, hasExtension, hasModifierExtension, hasText, setText

Methods inherited from class org.hl7.fhir.dstu2016may.model.Resource
copyValues, getId, getIdElement, getImplicitRules, getImplicitRulesElement, getLanguage, getLanguageElement, getMeta, hasId, hasIdElement, hasImplicitRules, hasImplicitRulesElement, hasLanguage, hasLanguageElement, hasMeta, setId, setIdElement, setImplicitRules, setImplicitRulesElement, setLanguage, setLanguageElement, setMeta

Methods inherited from class org.hl7.fhir.dstu2016may.model.BaseResource
getStructureFhirVersionEnum, setId

Methods inherited from class org.hl7.fhir.dstu2016may.model.Base
castToActionDefinition, castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactPoint, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToModuleMetadata, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToUnsignedInt, castToUri, children, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, 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, setId

- Field Detail
  - type
```
protected Enumeration<Sequence.SequenceType> type
```
    Amino acid / cDNA transcript / RNA variation.
  - patient
```
protected Reference patient
```
    The patient, or group of patients whose sequencing results are described by this resource.
  - patientTarget
```
protected Patient patientTarget
```
    The actual object that is the target of the reference (The patient, or group of patients 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.)
  - quantity
```
protected Quantity quantity
```
    Quantity of the sequence.
  - species
```
protected CodeableConcept species
```
    The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.
  - referenceSeq
```
protected List<Sequence.SequenceReferenceSeqComponent> referenceSeq
```
    Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) .
  - variation
```
protected Sequence.SequenceVariationComponent variation
```
    Variation info in this sequence.
  - quality
```
protected List<Sequence.SequenceQualityComponent> quality
```
    Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.
  - allelicState
```
protected CodeableConcept allelicState
```
    The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.
  - allelicFrequency
```
protected DecimalType allelicFrequency
```
    Allele frequencies.
  - copyNumberEvent
```
protected CodeableConcept copyNumberEvent
```
    Values: amplificaiton / deletion / LOH.
  - 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.
  - pointer
```
protected List<Reference> pointer
```
    Pointer to next atomic sequence which at most contains one variation.
  - 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 variation.)
  - observedSeq
```
protected StringType observedSeq
```
    Observed Sequence.
  - observation
```
protected Reference observation
```
    Analysis of the sequence.
  - observationTarget
```
protected Observation observationTarget
```
    The actual object that is the target of the reference (Analysis of the sequence.)
  - structureVariation
```
protected Sequence.SequenceStructureVariationComponent structureVariation
```
    Structural variant.
  - 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_SPECIES
```
public static final String SP_SPECIES
```
    Search parameter: species
    Description: The organism from which sample of the sequence was extracted.
    Type: token
    Path: Sequence.species
    
    See Also:
    
    Constant Field Values
  - SPECIES
```
public static final ca.uhn.fhir.rest.gclient.TokenClientParam SPECIES
```
    Fluent Client search parameter constant for species
    Description: The organism from which sample of the sequence was extracted.
    Type: token
    Path: Sequence.species
  - SP_COORDINATE
```
public static final String SP_COORDINATE
```
    Search parameter: coordinate
    Description: Genomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
    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: Genomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
    Type: composite
    Path:
  - SP_START
```
public static final String SP_START
```
    Search parameter: start
    Description: Start position (0-based inclusive) of the sequence
    Type: number
    Path: Sequence.variation.start
    
    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) of the sequence
    Type: number
    Path: Sequence.variation.start
  - SP_TYPE
```
public static final String SP_TYPE
```
    Search parameter: type
    Description: The type of the variant: Amino acid / cDNA transcript / RNA variation.
    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: The type of the variant: Amino acid / cDNA transcript / RNA variation.
    Type: token
    Path: Sequence.type
  - SP_CHROMOSOME
```
public static final String SP_CHROMOSOME
```
    Search parameter: chromosome
    Description: Chromosome of the 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 of the sequence
    Type: token
    Path: Sequence.referenceSeq.chromosome
  - SP_END
```
public static final String SP_END
```
    Search parameter: end
    Description: End position (0-based exclusive) of the sequence
    Type: number
    Path: Sequence.variation.end
    
    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) of the sequence
    Type: number
    Path: Sequence.variation.end
- Constructor Detail
  - Sequence
```
public Sequence()
```
    Constructor
  - Sequence
```
public Sequence(Enumeration<Sequence.SequenceType> type)
```
    Constructor
- Method Detail
  - getTypeElement
```
public Enumeration<Sequence.SequenceType> getTypeElement()
```
    Returns:
    
    type (Amino acid / cDNA transcript / RNA variation.). 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 / cDNA transcript / RNA variation.). 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 / cDNA transcript / RNA variation.
  - setType
```
public Sequence setType(Sequence.SequenceType value)
```
    Parameters:
    
    value - Amino acid / cDNA transcript / RNA variation.
  - getPatient
```
public Reference getPatient()
```
    Returns:
    
    patient (The patient, or group of patients whose sequencing results are described by this resource.)
  - hasPatient
```
public boolean hasPatient()
```
  - setPatient
```
public Sequence setPatient(Reference value)
```
    Parameters:
    
    value - patient (The patient, or group of patients 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, or group of patients 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, or group of patients 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.)
  - getQuantity
```
public Quantity getQuantity()
```
    Returns:
    
    quantity (Quantity of the sequence.)
  - hasQuantity
```
public boolean hasQuantity()
```
  - setQuantity
```
public Sequence setQuantity(Quantity value)
```
    Parameters:
    
    value - quantity (Quantity of the sequence.)
  - getSpecies
```
public CodeableConcept getSpecies()
```
    Returns:
    
    species (The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.)
  - hasSpecies
```
public boolean hasSpecies()
```
  - setSpecies
```
public Sequence setSpecies(CodeableConcept value)
```
    Parameters:
    
    value - species (The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.)
  - getReferenceSeq
```
public List<Sequence.SequenceReferenceSeqComponent> getReferenceSeq()
```
    Returns:
    
    referenceSeq (Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) .)
  - hasReferenceSeq
```
public boolean hasReferenceSeq()
```
  - addReferenceSeq
```
public Sequence.SequenceReferenceSeqComponent addReferenceSeq()
```
    Returns:
    
    referenceSeq (Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) .)
  - addReferenceSeq
```
public Sequence addReferenceSeq(Sequence.SequenceReferenceSeqComponent t)
```
  - getVariation
```
public Sequence.SequenceVariationComponent getVariation()
```
    Returns:
    
    variation (Variation info in this sequence.)
  - hasVariation
```
public boolean hasVariation()
```
  - setVariation
```
public Sequence setVariation(Sequence.SequenceVariationComponent value)
```
    Parameters:
    
    value - variation (Variation info in this sequence.)
  - getQuality
```
public List<Sequence.SequenceQualityComponent> getQuality()
```
    Returns:
    
    quality (Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.)
  - hasQuality
```
public boolean hasQuality()
```
  - addQuality
```
public Sequence.SequenceQualityComponent addQuality()
```
    Returns:
    
    quality (Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.)
  - addQuality
```
public Sequence addQuality(Sequence.SequenceQualityComponent t)
```
  - getAllelicState
```
public CodeableConcept getAllelicState()
```
    Returns:
    
    allelicState (The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.)
  - hasAllelicState
```
public boolean hasAllelicState()
```
  - setAllelicState
```
public Sequence setAllelicState(CodeableConcept value)
```
    Parameters:
    
    value - allelicState (The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.)
  - getAllelicFrequencyElement
```
public DecimalType getAllelicFrequencyElement()
```
    Returns:
    
    allelicFrequency (Allele frequencies.). This is the underlying object with id, value and extensions. The accessor "getAllelicFrequency" gives direct access to the value
  - hasAllelicFrequencyElement
```
public boolean hasAllelicFrequencyElement()
```
  - hasAllelicFrequency
```
public boolean hasAllelicFrequency()
```
  - setAllelicFrequencyElement
```
public Sequence setAllelicFrequencyElement(DecimalType value)
```
    Parameters:
    
    value - allelicFrequency (Allele frequencies.). This is the underlying object with id, value and extensions. The accessor "getAllelicFrequency" gives direct access to the value
  - getAllelicFrequency
```
public BigDecimal getAllelicFrequency()
```
    Returns:
    
    Allele frequencies.
  - setAllelicFrequency
```
public Sequence setAllelicFrequency(BigDecimal value)
```
    Parameters:
    
    value - Allele frequencies.
  - setAllelicFrequency
```
public Sequence setAllelicFrequency(long value)
```
    Parameters:
    
    value - Allele frequencies.
  - setAllelicFrequency
```
public Sequence setAllelicFrequency(double value)
```
    Parameters:
    
    value - Allele frequencies.
  - getCopyNumberEvent
```
public CodeableConcept getCopyNumberEvent()
```
    Returns:
    
    copyNumberEvent (Values: amplificaiton / deletion / LOH.)
  - hasCopyNumberEvent
```
public boolean hasCopyNumberEvent()
```
  - setCopyNumberEvent
```
public Sequence setCopyNumberEvent(CodeableConcept value)
```
    Parameters:
    
    value - copyNumberEvent (Values: amplificaiton / deletion / LOH.)
  - 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.)
  - hasRepository
```
public boolean hasRepository()
```
  - addRepository
```
public Sequence.SequenceRepositoryComponent addRepository()
```
    Returns:
    
    repository (Configurations of the external repository.)
  - addRepository
```
public Sequence addRepository(Sequence.SequenceRepositoryComponent t)
```
  - getPointer
```
public List<Reference> getPointer()
```
    Returns:
    
    pointer (Pointer to next atomic sequence which at most contains one variation.)
  - hasPointer
```
public boolean hasPointer()
```
  - addPointer
```
public Reference addPointer()
```
    Returns:
    
    pointer (Pointer to next atomic sequence which at most contains one variation.)
  - addPointer
```
public Sequence addPointer(Reference t)
```
  - getPointerTarget
```
public List<Sequence> getPointerTarget()
```
    Returns:
    
    pointer (The actual objects that are the target of the reference. The reference library doesn't populate this, but you can use this to hold the resources if you resolvethemt. Pointer to next atomic sequence which at most contains one variation.)
  - addPointerTarget
```
public Sequence addPointerTarget()
```
    Returns:
    
    pointer (Add an actual object that is the target of the reference. The reference library doesn't use these, but you can use this to hold the resources if you resolvethemt. Pointer to next atomic sequence which at most contains one variation.)
  - getObservedSeqElement
```
public StringType getObservedSeqElement()
```
    Returns:
    
    observedSeq (Observed Sequence.). 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 (Observed Sequence.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the value
  - getObservedSeq
```
public String getObservedSeq()
```
    Returns:
    
    Observed Sequence.
  - setObservedSeq
```
public Sequence setObservedSeq(String value)
```
    Parameters:
    
    value - Observed Sequence.
  - getObservation
```
public Reference getObservation()
```
    Returns:
    
    observation (Analysis of the sequence.)
  - hasObservation
```
public boolean hasObservation()
```
  - setObservation
```
public Sequence setObservation(Reference value)
```
    Parameters:
    
    value - observation (Analysis of the sequence.)
  - getObservationTarget
```
public Observation getObservationTarget()
```
    Returns:
    
    observation 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. (Analysis of the sequence.)
  - setObservationTarget
```
public Sequence setObservationTarget(Observation value)
```
    Parameters:
    
    value - observation 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. (Analysis of the sequence.)
  - getStructureVariation
```
public Sequence.SequenceStructureVariationComponent getStructureVariation()
```
    Returns:
    
    structureVariation (Structural variant.)
  - hasStructureVariation
```
public boolean hasStructureVariation()
```
  - setStructureVariation
```
public Sequence setStructureVariation(Sequence.SequenceStructureVariationComponent value)
```
    Parameters:
    
    value - structureVariation (Structural variant.)
  - listChildren
```
protected void listChildren(List<Property> childrenList)
```
    Overrides:
    
    listChildren in class DomainResource
  - 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 void 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 void 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
```
    Description copied from class: Base
    
    make an instance of a property. If the property is a repeating property, make a new instance. if the property is not repeating, return the property
    
    Overrides:
    
    makeProperty in class DomainResource
    
    Returns:
    
    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()
```
    Specified by:
    
    fhirType in interface org.hl7.fhir.instance.model.api.IBase
    
    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

Constructor	Description
`Sequence()`	Constructor
`Sequence(Enumeration<Sequence.SequenceType> type)`	Constructor

Class Sequence

Nested Class Summary

Field Summary

Fields inherited from class org.hl7.fhir.dstu2016may.model.DomainResource

Fields inherited from class org.hl7.fhir.dstu2016may.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.dstu2016may.model.DomainResource

Methods inherited from class org.hl7.fhir.dstu2016may.model.Resource

Methods inherited from class org.hl7.fhir.dstu2016may.model.BaseResource

Methods inherited from class org.hl7.fhir.dstu2016may.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.IBase

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

Field Detail

type

patient

patientTarget

specimen

specimenTarget

device

deviceTarget

quantity

species

referenceSeq

variation

quality

allelicState

allelicFrequency

copyNumberEvent

readCoverage

repository

pointer

pointerTarget

observedSeq

observation

observationTarget

structureVariation

SP_PATIENT

PATIENT

INCLUDE_PATIENT

SP_SPECIES

SPECIES

SP_COORDINATE

COORDINATE

SP_START

START

SP_TYPE

TYPE

SP_CHROMOSOME

CHROMOSOME

SP_END

END

Constructor Detail

Sequence

Sequence

Method Detail

getTypeElement

hasTypeElement

hasType

setTypeElement

getType

setType

getPatient

hasPatient

setPatient

getPatientTarget

setPatientTarget

getSpecimen

hasSpecimen

setSpecimen

getSpecimenTarget

setSpecimenTarget

getDevice

hasDevice

setDevice

getDeviceTarget