
Class Sequence
- java.lang.Object
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- org.hl7.fhir.dstu3.model.Base
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- org.hl7.fhir.dstu3.model.BaseResource
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- org.hl7.fhir.dstu3.model.Resource
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- org.hl7.fhir.dstu3.model.DomainResource
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- org.hl7.fhir.dstu3.model.Sequence
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Sequence.QualityType
static class
Sequence.QualityTypeEnumFactory
static class
Sequence.RepositoryType
static class
Sequence.RepositoryTypeEnumFactory
static class
Sequence.SequenceQualityComponent
static class
Sequence.SequenceReferenceSeqComponent
static class
Sequence.SequenceRepositoryComponent
static class
Sequence.SequenceType
static class
Sequence.SequenceTypeEnumFactory
static class
Sequence.SequenceVariantComponent
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Field Summary
Fields Modifier and Type Field Description static ca.uhn.fhir.rest.gclient.TokenClientParam
CHROMOSOME
Fluent Client search parameter constant for chromosomestatic 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 coordinateprotected 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 endprotected 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 identifierstatic 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 patientprotected 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: chromosomestatic String
SP_COORDINATE
Search parameter: coordinatestatic String
SP_END
Search parameter: endstatic String
SP_IDENTIFIER
Search parameter: identifierstatic String
SP_PATIENT
Search parameter: patientstatic String
SP_START
Search parameter: startstatic String
SP_TYPE
Search parameter: typeprotected 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 startprotected 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 typeprotected 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.dstu3.model.DomainResource
contained, extension, modifierExtension, text
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Fields inherited from class org.hl7.fhir.dstu3.model.Resource
id, implicitRules, language, meta
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Constructor Summary
Constructors Constructor Description Sequence()
ConstructorSequence(IntegerType coordinateSystem)
Constructor
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Method Summary
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Methods inherited from class org.hl7.fhir.dstu3.model.DomainResource
addContained, addExtension, addExtension, addModifierExtension, addModifierExtension, copyValues, getContained, getExtension, getExtensionsByUrl, getModifierExtension, getModifierExtensionsByUrl, getText, hasContained, hasExtension, hasModifierExtension, hasText, setContained, setExtension, setModifierExtension, setText
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Methods inherited from class org.hl7.fhir.dstu3.model.Resource
copyValues, getId, getIdBase, getIdElement, getImplicitRules, getImplicitRulesElement, getLanguage, getLanguageElement, getMeta, hasId, hasIdElement, hasImplicitRules, hasImplicitRulesElement, hasLanguage, hasLanguageElement, hasMeta, setId, setIdBase, setIdElement, setImplicitRules, setImplicitRulesElement, setLanguage, setLanguageElement, setMeta
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Methods inherited from class org.hl7.fhir.dstu3.model.BaseResource
getStructureFhirVersionEnum, isResource, setId
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Methods inherited from class org.hl7.fhir.dstu3.model.Base
castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, 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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.hl7.fhir.instance.model.api.IAnyResource
getId, getIdElement, getLanguageElement, getUserData, setId, setUserData
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Field Detail
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identifier
protected List<Identifier> identifier
A unique identifier for this particular sequence instance. This is a FHIR-defined id.
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type
protected Enumeration<Sequence.SequenceType> type
Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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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).
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patient
protected Reference patient
The patient whose sequencing results are described by this resource.
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patientTarget
protected Patient patientTarget
The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.)
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specimenTarget
protected Specimen specimenTarget
The actual object that is the target of the reference (Specimen used for sequencing.)
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deviceTarget
protected Device deviceTarget
The actual object that is the target of the reference (The method for sequencing, for example, chip information.)
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performer
protected Reference performer
The organization or lab that should be responsible for this result.
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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.)
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referenceSeq
protected Sequence.SequenceReferenceSeqComponent referenceSeq
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
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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.
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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.
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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)).
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readCoverage
protected IntegerType readCoverage
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
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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.
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pointer
protected List<Reference> pointer
Pointer to next atomic sequence which at most contains one variant.
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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.)
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SP_IDENTIFIER
public static final String SP_IDENTIFIER
Search parameter: identifierDescription: The unique identity for a particular sequence
Type: token
Path: Sequence.identifier
- See Also:
- Constant Field Values
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IDENTIFIER
public static final ca.uhn.fhir.rest.gclient.TokenClientParam IDENTIFIER
Fluent Client search parameter constant for identifierDescription: The unique identity for a particular sequence
Type: token
Path: Sequence.identifier
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SP_COORDINATE
public static final String SP_COORDINATE
Search parameter: coordinateDescription: 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
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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 coordinateDescription: 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:
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SP_PATIENT
public static final String SP_PATIENT
Search parameter: patientDescription: The subject that the observation is about
Type: reference
Path: Sequence.patient
- See Also:
- Constant Field Values
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PATIENT
public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam PATIENT
Fluent Client search parameter constant for patientDescription: The subject that the observation is about
Type: reference
Path: Sequence.patient
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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".
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SP_CHROMOSOME
public static final String SP_CHROMOSOME
Search parameter: chromosomeDescription: Chromosome number of the reference sequence
Type: token
Path: Sequence.referenceSeq.chromosome
- See Also:
- Constant Field Values
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CHROMOSOME
public static final ca.uhn.fhir.rest.gclient.TokenClientParam CHROMOSOME
Fluent Client search parameter constant for chromosomeDescription: Chromosome number of the reference sequence
Type: token
Path: Sequence.referenceSeq.chromosome
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SP_START
public static final String SP_START
Search parameter: 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: Sequence.referenceSeq.windowStart
- See Also:
- Constant Field Values
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START
public static final ca.uhn.fhir.rest.gclient.NumberClientParam START
Fluent Client search parameter constant for 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: Sequence.referenceSeq.windowStart
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SP_END
public static final String SP_END
Search parameter: 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: Sequence.referenceSeq.windowEnd
- See Also:
- Constant Field Values
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END
public static final ca.uhn.fhir.rest.gclient.NumberClientParam END
Fluent Client search parameter constant for 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: Sequence.referenceSeq.windowEnd
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SP_TYPE
public static final String SP_TYPE
Search parameter: typeDescription: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: Sequence.type
- See Also:
- Constant Field Values
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TYPE
public static final ca.uhn.fhir.rest.gclient.TokenClientParam TYPE
Fluent Client search parameter constant for typeDescription: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: Sequence.type
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Constructor Detail
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Sequence
public Sequence()
Constructor
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Sequence
public Sequence(IntegerType coordinateSystem)
Constructor
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Method Detail
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getIdentifier
public List<Identifier> getIdentifier()
- Returns:
identifier
(A unique identifier for this particular sequence instance. This is a FHIR-defined id.)
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setIdentifier
public Sequence setIdentifier(List<Identifier> theIdentifier)
- Returns:
- Returns a reference to
this
for easy method chaining
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hasIdentifier
public boolean hasIdentifier()
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addIdentifier
public Identifier addIdentifier()
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addIdentifier
public Sequence addIdentifier(Identifier t)
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getIdentifierFirstRep
public Identifier getIdentifierFirstRep()
- Returns:
- The first repetition of repeating field
identifier
, creating it if it does not already exist
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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
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hasTypeElement
public boolean hasTypeElement()
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hasType
public boolean hasType()
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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
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getType
public Sequence.SequenceType getType()
- Returns:
- Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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setType
public Sequence setType(Sequence.SequenceType value)
- Parameters:
value
- Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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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
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hasCoordinateSystemElement
public boolean hasCoordinateSystemElement()
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hasCoordinateSystem
public boolean hasCoordinateSystem()
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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
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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).
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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).
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getPatient
public Reference getPatient()
- Returns:
patient
(The patient whose sequencing results are described by this resource.)
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hasPatient
public boolean hasPatient()
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setPatient
public Sequence setPatient(Reference value)
- Parameters:
value
-patient
(The patient whose sequencing results are described by this resource.)
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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.)
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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.)
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getSpecimen
public Reference getSpecimen()
- Returns:
specimen
(Specimen used for sequencing.)
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hasSpecimen
public boolean hasSpecimen()
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setSpecimen
public Sequence setSpecimen(Reference value)
- Parameters:
value
-specimen
(Specimen used for sequencing.)
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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.)
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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.)
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getDevice
public Reference getDevice()
- Returns:
device
(The method for sequencing, for example, chip information.)
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hasDevice
public boolean hasDevice()
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setDevice
public Sequence setDevice(Reference value)
- Parameters:
value
-device
(The method for sequencing, for example, chip information.)
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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.)
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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.)
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getPerformer
public Reference getPerformer()
- Returns:
performer
(The organization or lab that should be responsible for this result.)
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hasPerformer
public boolean hasPerformer()
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setPerformer
public Sequence setPerformer(Reference value)
- Parameters:
value
-performer
(The organization or lab that should be responsible for this result.)
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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.)
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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.)
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getQuantity
public Quantity getQuantity()
- Returns:
quantity
(The number of copies of the seqeunce of interest. (RNASeq).)
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hasQuantity
public boolean hasQuantity()
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setQuantity
public Sequence setQuantity(Quantity value)
- Parameters:
value
-quantity
(The number of copies of the seqeunce of interest. (RNASeq).)
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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.)
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hasReferenceSeq
public boolean hasReferenceSeq()
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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.)
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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.)
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setVariant
public Sequence setVariant(List<Sequence.SequenceVariantComponent> theVariant)
- Returns:
- Returns a reference to
this
for easy method chaining
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hasVariant
public boolean hasVariant()
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addVariant
public Sequence.SequenceVariantComponent addVariant()
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addVariant
public Sequence addVariant(Sequence.SequenceVariantComponent t)
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getVariantFirstRep
public Sequence.SequenceVariantComponent getVariantFirstRep()
- Returns:
- The first repetition of repeating field
variant
, creating it if it does not already exist
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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
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hasObservedSeqElement
public boolean hasObservedSeqElement()
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hasObservedSeq
public boolean hasObservedSeq()
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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
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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.
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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.
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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)).)
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setQuality
public Sequence setQuality(List<Sequence.SequenceQualityComponent> theQuality)
- Returns:
- Returns a reference to
this
for easy method chaining
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hasQuality
public boolean hasQuality()
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addQuality
public Sequence.SequenceQualityComponent addQuality()
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addQuality
public Sequence addQuality(Sequence.SequenceQualityComponent t)
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getQualityFirstRep
public Sequence.SequenceQualityComponent getQualityFirstRep()
- Returns:
- The first repetition of repeating field
quality
, creating it if it does not already exist
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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
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hasReadCoverageElement
public boolean hasReadCoverageElement()
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hasReadCoverage
public boolean hasReadCoverage()
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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
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getReadCoverage
public int getReadCoverage()
- Returns:
- Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
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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.
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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.)
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setRepository
public Sequence setRepository(List<Sequence.SequenceRepositoryComponent> theRepository)
- Returns:
- Returns a reference to
this
for easy method chaining
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hasRepository
public boolean hasRepository()
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addRepository
public Sequence.SequenceRepositoryComponent addRepository()
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addRepository
public Sequence addRepository(Sequence.SequenceRepositoryComponent t)
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getRepositoryFirstRep
public Sequence.SequenceRepositoryComponent getRepositoryFirstRep()
- Returns:
- The first repetition of repeating field
repository
, creating it if it does not already exist
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getPointer
public List<Reference> getPointer()
- Returns:
pointer
(Pointer to next atomic sequence which at most contains one variant.)
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setPointer
public Sequence setPointer(List<Reference> thePointer)
- Returns:
- Returns a reference to
this
for easy method chaining
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hasPointer
public boolean hasPointer()
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addPointer
public Reference addPointer()
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addPointer
public Sequence addPointer(Reference t)
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getPointerFirstRep
public Reference getPointerFirstRep()
- Returns:
- The first repetition of repeating field
pointer
, creating it if it does not already exist
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getPointerTarget
@Deprecated public List<Sequence> getPointerTarget()
Deprecated.Use Reference#setResource(IBaseResource) instead
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addPointerTarget
@Deprecated public Sequence addPointerTarget()
Deprecated.Use Reference#setResource(IBaseResource) instead
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listChildren
protected void listChildren(List<Property> children)
- Overrides:
listChildren
in classDomainResource
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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
public Base setProperty(String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
setProperty
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
makeProperty
public Base makeProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
- 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
public Base addChild(String name) throws org.hl7.fhir.exceptions.FHIRException
- Overrides:
addChild
in classDomainResource
- Throws:
org.hl7.fhir.exceptions.FHIRException
-
fhirType
public String fhirType()
- Specified by:
fhirType
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
fhirType
in classDomainResource
-
copy
public Sequence copy()
- Specified by:
copy
in classDomainResource
-
equalsDeep
public boolean equalsDeep(Base other_)
- Overrides:
equalsDeep
in classDomainResource
-
equalsShallow
public boolean equalsShallow(Base other_)
- Overrides:
equalsShallow
in classDomainResource
-
isEmpty
public boolean isEmpty()
- Specified by:
isEmpty
in interfaceorg.hl7.fhir.instance.model.api.IBase
- Overrides:
isEmpty
in classDomainResource
-
getResourceType
public ResourceType getResourceType()
- Specified by:
getResourceType
in classResource
-
-