MolecularSequence (org.hl7.fhir.r4 5.4.0 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.MolecularSequence

All Implemented Interfaces:

ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IAnyResource, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions, org.hl7.fhir.instance.model.api.IBaseResource, org.hl7.fhir.instance.model.api.IDomainResource
```
public class MolecularSequence
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`	`MolecularSequence.MolecularSequenceQualityComponent`
`static class`	`MolecularSequence.MolecularSequenceQualityRocComponent`
`static class`	`MolecularSequence.MolecularSequenceReferenceSeqComponent`
`static class`	`MolecularSequence.MolecularSequenceRepositoryComponent`
`static class`	`MolecularSequence.MolecularSequenceStructureVariantComponent`
`static class`	`MolecularSequence.MolecularSequenceStructureVariantInnerComponent`
`static class`	`MolecularSequence.MolecularSequenceStructureVariantOuterComponent`
`static class`	`MolecularSequence.MolecularSequenceVariantComponent`
`static class`	`MolecularSequence.OrientationType`
`static class`	`MolecularSequence.OrientationTypeEnumFactory`
`static class`	`MolecularSequence.QualityType`
`static class`	`MolecularSequence.QualityTypeEnumFactory`
`static class`	`MolecularSequence.RepositoryType`
`static class`	`MolecularSequence.RepositoryTypeEnumFactory`
`static class`	`MolecularSequence.SequenceType`
`static class`	`MolecularSequence.SequenceTypeEnumFactory`
`static class`	`MolecularSequence.StrandType`
`static class`	`MolecularSequence.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>`	`CHROMOSOME_VARIANT_COORDINATE` Fluent Client search parameter constant for chromosome-variant-coordinate
`static ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam>`	`CHROMOSOME_WINDOW_COORDINATE` Fluent Client search parameter constant for chromosome-window-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.)
`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<MolecularSequence>`	`pointerTarget` The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.)
`protected List<MolecularSequence.MolecularSequenceQualityComponent>`	`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 sequence 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 MolecularSequence.MolecularSequenceReferenceSeqComponent`	`referenceSeq` A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
`static ca.uhn.fhir.rest.gclient.TokenClientParam`	`REFERENCESEQID` Fluent Client search parameter constant for referenceseqid
`static ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam>`	`REFERENCESEQID_VARIANT_COORDINATE` Fluent Client search parameter constant for referenceseqid-variant-coordinate
`static ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam>`	`REFERENCESEQID_WINDOW_COORDINATE` Fluent Client search parameter constant for referenceseqid-window-coordinate
`protected List<MolecularSequence.MolecularSequenceRepositoryComponent>`	`repository` Configurations of the external repository.
`static String`	`SP_CHROMOSOME` Search parameter: chromosome
`static String`	`SP_CHROMOSOME_VARIANT_COORDINATE` Search parameter: chromosome-variant-coordinate
`static String`	`SP_CHROMOSOME_WINDOW_COORDINATE` Search parameter: chromosome-window-coordinate
`static String`	`SP_IDENTIFIER` Search parameter: identifier
`static String`	`SP_PATIENT` Search parameter: patient
`static String`	`SP_REFERENCESEQID` Search parameter: referenceseqid
`static String`	`SP_REFERENCESEQID_VARIANT_COORDINATE` Search parameter: referenceseqid-variant-coordinate
`static String`	`SP_REFERENCESEQID_WINDOW_COORDINATE` Search parameter: referenceseqid-window-coordinate
`static String`	`SP_TYPE` Search parameter: type
`static String`	`SP_VARIANT_END` Search parameter: variant-end
`static String`	`SP_VARIANT_START` Search parameter: variant-start
`static String`	`SP_WINDOW_END` Search parameter: window-end
`static String`	`SP_WINDOW_START` Search parameter: window-start
`protected Reference`	`specimen` Specimen used for sequencing.
`protected Specimen`	`specimenTarget` The actual object that is the target of the reference (Specimen used for sequencing.)
`protected List<MolecularSequence.MolecularSequenceStructureVariantComponent>`	`structureVariant` Information about chromosome structure variation.
`protected Enumeration<MolecularSequence.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<MolecularSequence.MolecularSequenceVariantComponent>`	`variant` The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`VARIANT_END` Fluent Client search parameter constant for variant-end
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`VARIANT_START` Fluent Client search parameter constant for variant-start
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`WINDOW_END` Fluent Client search parameter constant for window-end
`static ca.uhn.fhir.rest.gclient.NumberClientParam`	`WINDOW_START` Fluent Client search parameter constant for window-start

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

MolecularSequence()
Constructor

MolecularSequence(IntegerType coordinateSystem)
Constructor

Constructors
Constructor and Description
`MolecularSequence()` Constructor
`MolecularSequence(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()`
`MolecularSequence`	`addIdentifier(Identifier t)`
`Reference`	`addPointer()`
`MolecularSequence`	`addPointer(Reference t)`
`MolecularSequence`	`addPointerTarget()` Deprecated. Use Reference#setResource(IBaseResource) instead
`MolecularSequence.MolecularSequenceQualityComponent`	`addQuality()`
`MolecularSequence`	`addQuality(MolecularSequence.MolecularSequenceQualityComponent t)`
`MolecularSequence.MolecularSequenceRepositoryComponent`	`addRepository()`
`MolecularSequence`	`addRepository(MolecularSequence.MolecularSequenceRepositoryComponent t)`
`MolecularSequence.MolecularSequenceStructureVariantComponent`	`addStructureVariant()`
`MolecularSequence`	`addStructureVariant(MolecularSequence.MolecularSequenceStructureVariantComponent t)`
`MolecularSequence.MolecularSequenceVariantComponent`	`addVariant()`
`MolecularSequence`	`addVariant(MolecularSequence.MolecularSequenceVariantComponent t)`
`MolecularSequence`	`copy()`
`void`	`copyValues(MolecularSequence dst)`
`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<MolecularSequence>`	`getPointerTarget()` Deprecated. Use Reference#setResource(IBaseResource) instead
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`List<MolecularSequence.MolecularSequenceQualityComponent>`	`getQuality()`
`MolecularSequence.MolecularSequenceQualityComponent`	`getQualityFirstRep()`
`Quantity`	`getQuantity()`
`int`	`getReadCoverage()`
`IntegerType`	`getReadCoverageElement()`
`MolecularSequence.MolecularSequenceReferenceSeqComponent`	`getReferenceSeq()`
`List<MolecularSequence.MolecularSequenceRepositoryComponent>`	`getRepository()`
`MolecularSequence.MolecularSequenceRepositoryComponent`	`getRepositoryFirstRep()`
`ResourceType`	`getResourceType()`
`Reference`	`getSpecimen()`
`Specimen`	`getSpecimenTarget()`
`List<MolecularSequence.MolecularSequenceStructureVariantComponent>`	`getStructureVariant()`
`MolecularSequence.MolecularSequenceStructureVariantComponent`	`getStructureVariantFirstRep()`
`MolecularSequence.SequenceType`	`getType()`
`Enumeration<MolecularSequence.SequenceType>`	`getTypeElement()`
`String[]`	`getTypesForProperty(int hash, String name)`
`List<MolecularSequence.MolecularSequenceVariantComponent>`	`getVariant()`
`MolecularSequence.MolecularSequenceVariantComponent`	`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)`
`MolecularSequence`	`setCoordinateSystem(int value)`
`MolecularSequence`	`setCoordinateSystemElement(IntegerType value)`
`MolecularSequence`	`setDevice(Reference value)`
`MolecularSequence`	`setDeviceTarget(Device value)`
`MolecularSequence`	`setIdentifier(List<Identifier> theIdentifier)`
`MolecularSequence`	`setObservedSeq(String value)`
`MolecularSequence`	`setObservedSeqElement(StringType value)`
`MolecularSequence`	`setPatient(Reference value)`
`MolecularSequence`	`setPatientTarget(Patient value)`
`MolecularSequence`	`setPerformer(Reference value)`
`MolecularSequence`	`setPerformerTarget(Organization value)`
`MolecularSequence`	`setPointer(List<Reference> thePointer)`
`Base`	`setProperty(int hash, String name, Base value)`
`Base`	`setProperty(String name, Base value)`
`MolecularSequence`	`setQuality(List<MolecularSequence.MolecularSequenceQualityComponent> theQuality)`
`MolecularSequence`	`setQuantity(Quantity value)`
`MolecularSequence`	`setReadCoverage(int value)`
`MolecularSequence`	`setReadCoverageElement(IntegerType value)`
`MolecularSequence`	`setReferenceSeq(MolecularSequence.MolecularSequenceReferenceSeqComponent value)`
`MolecularSequence`	`setRepository(List<MolecularSequence.MolecularSequenceRepositoryComponent> theRepository)`
`MolecularSequence`	`setSpecimen(Reference value)`
`MolecularSequence`	`setSpecimenTarget(Specimen value)`
`MolecularSequence`	`setStructureVariant(List<MolecularSequence.MolecularSequenceStructureVariantComponent> theStructureVariant)`
`MolecularSequence`	`setType(MolecularSequence.SequenceType value)`
`MolecularSequence`	`setTypeElement(Enumeration<MolecularSequence.SequenceType> value)`
`MolecularSequence`	`setVariant(List<MolecularSequence.MolecularSequenceVariantComponent> theVariant)`
`protected MolecularSequence`	`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, castToPopulation, castToPositiveInt, castToProdCharacteristic, castToProductShelfLife, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToSubstanceAmount, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUrl, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.hl7.fhir.instance.model.api.IAnyResource
getId, getIdElement, getLanguageElement, getUserData, setId, setUserData

Methods inherited from interface org.hl7.fhir.instance.model.api.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<MolecularSequence.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 sequence of interest. (RNASeq).
  - referenceSeq
```
protected MolecularSequence.MolecularSequenceReferenceSeqComponent referenceSeq
```
    A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
  - variant
```
protected List<MolecularSequence.MolecularSequenceVariantComponent> 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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - quality
```
protected List<MolecularSequence.MolecularSequenceQualityComponent> 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<MolecularSequence.MolecularSequenceRepositoryComponent> 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<MolecularSequence> 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<MolecularSequence.MolecularSequenceStructureVariantComponent> 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: MolecularSequence.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: MolecularSequence.identifier
  - SP_REFERENCESEQID_VARIANT_COORDINATE
```
public static final String SP_REFERENCESEQID_VARIANT_COORDINATE
```
    Search parameter: referenceseqid-variant-coordinate
    Description: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
    Type: composite
    Path:
    
    See Also:
    
    Constant Field Values
  - REFERENCESEQID_VARIANT_COORDINATE
```
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_VARIANT_COORDINATE
```
    Fluent Client search parameter constant for referenceseqid-variant-coordinate
    Description: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
    Type: composite
    Path:
  - SP_CHROMOSOME
```
public static final String SP_CHROMOSOME
```
    Search parameter: chromosome
    Description: Chromosome number of the reference sequence
    Type: token
    Path: MolecularSequence.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: MolecularSequence.referenceSeq.chromosome
  - SP_WINDOW_END
```
public static final String SP_WINDOW_END
```
    Search parameter: window-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: MolecularSequence.referenceSeq.windowEnd
    
    See Also:
    
    Constant Field Values
  - WINDOW_END
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam WINDOW_END
```
    Fluent Client search parameter constant for window-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: MolecularSequence.referenceSeq.windowEnd
  - SP_TYPE
```
public static final String SP_TYPE
```
    Search parameter: type
    Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
    Type: token
    Path: MolecularSequence.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: MolecularSequence.type
  - SP_WINDOW_START
```
public static final String SP_WINDOW_START
```
    Search parameter: window-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: MolecularSequence.referenceSeq.windowStart
    
    See Also:
    
    Constant Field Values
  - WINDOW_START
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam WINDOW_START
```
    Fluent Client search parameter constant for window-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: MolecularSequence.referenceSeq.windowStart
  - SP_VARIANT_END
```
public static final String SP_VARIANT_END
```
    Search parameter: variant-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 variant.
    Type: number
    Path: MolecularSequence.variant.end
    
    See Also:
    
    Constant Field Values
  - VARIANT_END
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam VARIANT_END
```
    Fluent Client search parameter constant for variant-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 variant.
    Type: number
    Path: MolecularSequence.variant.end
  - SP_CHROMOSOME_VARIANT_COORDINATE
```
public static final String SP_CHROMOSOME_VARIANT_COORDINATE
```
    Search parameter: chromosome-variant-coordinate
    Description: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <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
  - CHROMOSOME_VARIANT_COORDINATE
```
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_VARIANT_COORDINATE
```
    Fluent Client search parameter constant for chromosome-variant-coordinate
    Description: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <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: MolecularSequence.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: MolecularSequence.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 "MolecularSequence:patient".
  - SP_VARIANT_START
```
public static final String SP_VARIANT_START
```
    Search parameter: variant-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 variant.
    Type: number
    Path: MolecularSequence.variant.start
    
    See Also:
    
    Constant Field Values
  - VARIANT_START
```
public static final ca.uhn.fhir.rest.gclient.NumberClientParam VARIANT_START
```
    Fluent Client search parameter constant for variant-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 variant.
    Type: number
    Path: MolecularSequence.variant.start
  - SP_CHROMOSOME_WINDOW_COORDINATE
```
public static final String SP_CHROMOSOME_WINDOW_COORDINATE
```
    Search parameter: chromosome-window-coordinate
    Description: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <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
  - CHROMOSOME_WINDOW_COORDINATE
```
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_WINDOW_COORDINATE
```
    Fluent Client search parameter constant for chromosome-window-coordinate
    Description: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <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_REFERENCESEQID_WINDOW_COORDINATE
```
public static final String SP_REFERENCESEQID_WINDOW_COORDINATE
```
    Search parameter: referenceseqid-window-coordinate
    Description: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
    Type: composite
    Path:
    
    See Also:
    
    Constant Field Values
  - REFERENCESEQID_WINDOW_COORDINATE
```
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_WINDOW_COORDINATE
```
    Fluent Client search parameter constant for referenceseqid-window-coordinate
    Description: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
    Type: composite
    Path:
  - SP_REFERENCESEQID
```
public static final String SP_REFERENCESEQID
```
    Search parameter: referenceseqid
    Description: Reference Sequence of the sequence
    Type: token
    Path: MolecularSequence.referenceSeq.referenceSeqId
    
    See Also:
    
    Constant Field Values
  - REFERENCESEQID
```
public static final ca.uhn.fhir.rest.gclient.TokenClientParam REFERENCESEQID
```
    Fluent Client search parameter constant for referenceseqid
    Description: Reference Sequence of the sequence
    Type: token
    Path: MolecularSequence.referenceSeq.referenceSeqId
- Constructor Detail
  - MolecularSequence
```
public MolecularSequence()
```
    Constructor
  - MolecularSequence
```
public MolecularSequence(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 MolecularSequence setIdentifier(List<Identifier> theIdentifier)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasIdentifier
```
public boolean hasIdentifier()
```
  - addIdentifier
```
public Identifier addIdentifier()
```
  - addIdentifier
```
public MolecularSequence 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<MolecularSequence.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 MolecularSequence setTypeElement(Enumeration<MolecularSequence.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 MolecularSequence.SequenceType getType()
```
    Returns:
    
    Amino Acid Sequence/ DNA Sequence / RNA Sequence.
  - setType
```
public MolecularSequence setType(MolecularSequence.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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 MolecularSequence 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 sequence of interest. (RNASeq).)
  - hasQuantity
```
public boolean hasQuantity()
```
  - setQuantity
```
public MolecularSequence setQuantity(Quantity value)
```
    Parameters:
    
    value - quantity (The number of copies of the sequence of interest. (RNASeq).)
  - getReferenceSeq
```
public MolecularSequence.MolecularSequenceReferenceSeqComponent 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 MolecularSequence setReferenceSeq(MolecularSequence.MolecularSequenceReferenceSeqComponent value)
```
    Parameters:
    
    value - referenceSeq (A sequence that is used as a reference to describe variants that are present in a sequence analyzed.)
  - getVariant
```
public List<MolecularSequence.MolecularSequenceVariantComponent> getVariant()
```
    Returns:
    
    variant (The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.)
  - setVariant
```
public MolecularSequence setVariant(List<MolecularSequence.MolecularSequenceVariantComponent> theVariant)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasVariant
```
public boolean hasVariant()
```
  - addVariant
```
public MolecularSequence.MolecularSequenceVariantComponent addVariant()
```
  - addVariant
```
public MolecularSequence addVariant(MolecularSequence.MolecularSequenceVariantComponent t)
```
  - getVariantFirstRep
```
public MolecularSequence.MolecularSequenceVariantComponent 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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the value
  - hasObservedSeqElement
```
public boolean hasObservedSeqElement()
```
  - hasObservedSeq
```
public boolean hasObservedSeq()
```
  - setObservedSeqElement
```
public MolecularSequence 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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the value
  - getObservedSeq
```
public String getObservedSeq()
```
    Returns:
    
    Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - setObservedSeq
```
public MolecularSequence setObservedSeq(String value)
```
    Parameters:
    
    value - Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
  - getQuality
```
public List<MolecularSequence.MolecularSequenceQualityComponent> getQuality()
```
    Returns:
    
    quality (An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).)
  - setQuality
```
public MolecularSequence setQuality(List<MolecularSequence.MolecularSequenceQualityComponent> theQuality)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasQuality
```
public boolean hasQuality()
```
  - addQuality
```
public MolecularSequence.MolecularSequenceQualityComponent addQuality()
```
  - addQuality
```
public MolecularSequence addQuality(MolecularSequence.MolecularSequenceQualityComponent t)
```
  - getQualityFirstRep
```
public MolecularSequence.MolecularSequenceQualityComponent 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 MolecularSequence 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 MolecularSequence 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<MolecularSequence.MolecularSequenceRepositoryComponent> getRepository()
```
    Returns:
    
    repository (Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.)
  - setRepository
```
public MolecularSequence setRepository(List<MolecularSequence.MolecularSequenceRepositoryComponent> theRepository)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasRepository
```
public boolean hasRepository()
```
  - addRepository
```
public MolecularSequence.MolecularSequenceRepositoryComponent addRepository()
```
  - addRepository
```
public MolecularSequence addRepository(MolecularSequence.MolecularSequenceRepositoryComponent t)
```
  - getRepositoryFirstRep
```
public MolecularSequence.MolecularSequenceRepositoryComponent 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 MolecularSequence setPointer(List<Reference> thePointer)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasPointer
```
public boolean hasPointer()
```
  - addPointer
```
public Reference addPointer()
```
  - addPointer
```
public MolecularSequence 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<MolecularSequence> getPointerTarget()
```
    Deprecated. Use Reference#setResource(IBaseResource) instead
  - addPointerTarget
```
@Deprecated
public MolecularSequence addPointerTarget()
```
    Deprecated. Use Reference#setResource(IBaseResource) instead
  - getStructureVariant
```
public List<MolecularSequence.MolecularSequenceStructureVariantComponent> getStructureVariant()
```
    Returns:
    
    structureVariant (Information about chromosome structure variation.)
  - setStructureVariant
```
public MolecularSequence setStructureVariant(List<MolecularSequence.MolecularSequenceStructureVariantComponent> theStructureVariant)
```
    Returns:
    
    Returns a reference to this for easy method chaining
  - hasStructureVariant
```
public boolean hasStructureVariant()
```
  - addStructureVariant
```
public MolecularSequence.MolecularSequenceStructureVariantComponent addStructureVariant()
```
  - addStructureVariant
```
public MolecularSequence addStructureVariant(MolecularSequence.MolecularSequenceStructureVariantComponent t)
```
  - getStructureVariantFirstRep
```
public MolecularSequence.MolecularSequenceStructureVariantComponent 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()
```
    Specified by:
    
    fhirType in interface org.hl7.fhir.instance.model.api.IBase
    
    Overrides:
    
    fhirType in class DomainResource
  - copy
```
public MolecularSequence copy()
```
    Specified by:
    
    copy in class DomainResource
  - copyValues
```
public void copyValues(MolecularSequence dst)
```
  - typedCopy
```
protected MolecularSequence 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 MolecularSequence

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_REFERENCESEQID_VARIANT_COORDINATE

REFERENCESEQID_VARIANT_COORDINATE

SP_CHROMOSOME

CHROMOSOME

SP_WINDOW_END

WINDOW_END

SP_TYPE

TYPE

SP_WINDOW_START

WINDOW_START

SP_VARIANT_END

VARIANT_END

SP_CHROMOSOME_VARIANT_COORDINATE

CHROMOSOME_VARIANT_COORDINATE

SP_PATIENT

PATIENT

INCLUDE_PATIENT

SP_VARIANT_START

VARIANT_START

SP_CHROMOSOME_WINDOW_COORDINATE

CHROMOSOME_WINDOW_COORDINATE

SP_REFERENCESEQID_WINDOW_COORDINATE

REFERENCESEQID_WINDOW_COORDINATE

SP_REFERENCESEQID

REFERENCESEQID

Constructor Detail

MolecularSequence

MolecularSequence

Method Detail

getIdentifier

setIdentifier

hasIdentifier

addIdentifier

addIdentifier

getIdentifierFirstRep

getTypeElement

hasTypeElement

hasType

setTypeElement