public class Sequence extends DomainResource
| Modifier and Type | Class and Description |
|---|---|
static class |
Sequence.SequenceQualityComponent |
static class |
Sequence.SequenceReferenceSeqComponent |
static class |
Sequence.SequenceRepositoryComponent |
static class |
Sequence.SequenceStructureVariationComponent |
static class |
Sequence.SequenceStructureVariationInnerComponent |
static class |
Sequence.SequenceStructureVariationOuterComponent |
static class |
Sequence.SequenceType |
static class |
Sequence.SequenceTypeEnumFactory |
static class |
Sequence.SequenceVariationComponent |
| Modifier and Type | Field and Description |
|---|---|
protected DecimalType |
allelicFrequency
Allele frequencies.
|
protected CodeableConcept |
allelicState
The level of occurrence of a single DNA Sequence Variation within a set of chromosomes.
|
static ca.uhn.fhir.rest.gclient.TokenClientParam |
CHROMOSOME
Fluent Client search parameter constant for chromosome
|
static ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> |
COORDINATE
Fluent Client search parameter constant for coordinate
|
protected CodeableConcept |
copyNumberEvent
Values: amplificaiton / deletion / LOH.
|
protected Reference |
device
The method for sequencing, for example, chip information.
|
protected Device |
deviceTarget
The actual object that is the target of the reference (The method for sequencing, for example, chip information.)
|
static ca.uhn.fhir.rest.gclient.NumberClientParam |
END
Fluent Client search parameter constant for end
|
static ca.uhn.fhir.model.api.Include |
INCLUDE_PATIENT
Constant for fluent queries to be used to add include statements.
|
protected Reference |
observation
Analysis of the sequence.
|
protected Observation |
observationTarget
The actual object that is the target of the reference (Analysis of the sequence.)
|
protected StringType |
observedSeq
Observed Sequence.
|
protected Reference |
patient
The patient, or group of patients whose sequencing results are described by this resource.
|
static ca.uhn.fhir.rest.gclient.ReferenceClientParam |
PATIENT
Fluent Client search parameter constant for patient
|
protected Patient |
patientTarget
The actual object that is the target of the reference (The patient, or group of patients whose sequencing results are described by this resource.)
|
protected List<Reference> |
pointer
Pointer to next atomic sequence which at most contains one variation.
|
protected List<Sequence> |
pointerTarget
The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variation.)
|
protected List<Sequence.SequenceQualityComponent> |
quality
Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.
|
protected Quantity |
quantity
Quantity of the sequence.
|
protected IntegerType |
readCoverage
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
|
protected List<Sequence.SequenceReferenceSeqComponent> |
referenceSeq
Reference Sequence.
|
protected List<Sequence.SequenceRepositoryComponent> |
repository
Configurations of the external repository.
|
static String |
SP_CHROMOSOME
Search parameter: chromosome
|
static String |
SP_COORDINATE
Search parameter: coordinate
|
static String |
SP_END
Search parameter: end
|
static String |
SP_PATIENT
Search parameter: patient
|
static String |
SP_SPECIES
Search parameter: species
|
static String |
SP_START
Search parameter: start
|
static String |
SP_TYPE
Search parameter: type
|
protected CodeableConcept |
species
The organism from which sample of the sequence was extracted.
|
static ca.uhn.fhir.rest.gclient.TokenClientParam |
SPECIES
Fluent Client search parameter constant for species
|
protected Reference |
specimen
Specimen used for sequencing.
|
protected Specimen |
specimenTarget
The actual object that is the target of the reference (Specimen used for sequencing.)
|
static ca.uhn.fhir.rest.gclient.NumberClientParam |
START
Fluent Client search parameter constant for start
|
protected Sequence.SequenceStructureVariationComponent |
structureVariation
Structural variant.
|
protected Enumeration<Sequence.SequenceType> |
type
Amino acid / cDNA transcript / RNA variation.
|
static ca.uhn.fhir.rest.gclient.TokenClientParam |
TYPE
Fluent Client search parameter constant for type
|
protected Sequence.SequenceVariationComponent |
variation
Variation info in this sequence.
|
contained, extension, modifierExtension, textid, implicitRules, language, meta| Constructor and Description |
|---|
Sequence()
Constructor
|
Sequence(Enumeration<Sequence.SequenceType> type)
Constructor
|
addContained, addExtension, addExtension, addModifierExtension, addModifierExtension, copyValues, getContained, getExtension, getExtensionsByUrl, getModifierExtension, getModifierExtensionsByUrl, getText, hasContained, hasExtension, hasModifierExtension, hasText, setTextcopyValues, getId, getIdElement, getImplicitRules, getImplicitRulesElement, getLanguage, getLanguageElement, getMeta, hasId, hasIdElement, hasImplicitRules, hasImplicitRulesElement, hasLanguage, hasLanguageElement, hasMeta, setId, setIdElement, setImplicitRules, setImplicitRulesElement, setLanguage, setLanguageElement, setMetagetStructureFhirVersionEnum, setIdcastToActionDefinition, castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactPoint, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToModuleMetadata, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToUnsignedInt, castToUri, children, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isMetadataBased, isPrimitive, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINNclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetId, getIdElement, getLanguageElement, getUserData, setId, setUserDataprotected Enumeration<Sequence.SequenceType> type
protected Reference patient
protected Patient patientTarget
protected Specimen specimenTarget
protected Device deviceTarget
protected CodeableConcept species
protected List<Sequence.SequenceReferenceSeqComponent> referenceSeq
protected Sequence.SequenceVariationComponent variation
protected List<Sequence.SequenceQualityComponent> quality
protected CodeableConcept allelicState
protected DecimalType allelicFrequency
protected CodeableConcept copyNumberEvent
protected IntegerType readCoverage
protected List<Sequence.SequenceRepositoryComponent> repository
protected List<Reference> pointer
protected List<Sequence> pointerTarget
protected StringType observedSeq
protected Reference observation
protected Observation observationTarget
protected Sequence.SequenceStructureVariationComponent structureVariation
public static final String SP_PATIENT
Description: The subject that the observation is about
Type: reference
Path: Sequence.patient
public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam PATIENT
Description: The subject that the observation is about
Type: reference
Path: Sequence.patient
public static final ca.uhn.fhir.model.api.Include INCLUDE_PATIENT
public static final String SP_SPECIES
Description: The organism from which sample of the sequence was extracted.
Type: token
Path: Sequence.species
public static final ca.uhn.fhir.rest.gclient.TokenClientParam SPECIES
Description: The organism from which sample of the sequence was extracted.
Type: token
Path: Sequence.species
public static final String SP_COORDINATE
Description: Genomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
Type: composite
Path:
public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,ca.uhn.fhir.rest.gclient.NumberClientParam> COORDINATE
Description: Genomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
Type: composite
Path:
public static final String SP_START
Description: Start position (0-based inclusive) of the sequence
Type: number
Path: Sequence.variation.start
public static final ca.uhn.fhir.rest.gclient.NumberClientParam START
Description: Start position (0-based inclusive) of the sequence
Type: number
Path: Sequence.variation.start
public static final String SP_TYPE
Description: The type of the variant: Amino acid / cDNA transcript / RNA variation.
Type: token
Path: Sequence.type
public static final ca.uhn.fhir.rest.gclient.TokenClientParam TYPE
Description: The type of the variant: Amino acid / cDNA transcript / RNA variation.
Type: token
Path: Sequence.type
public static final String SP_CHROMOSOME
Description: Chromosome of the sequence
Type: token
Path: Sequence.referenceSeq.chromosome
public static final ca.uhn.fhir.rest.gclient.TokenClientParam CHROMOSOME
Description: Chromosome of the sequence
Type: token
Path: Sequence.referenceSeq.chromosome
public static final String SP_END
Description: End position (0-based exclusive) of the sequence
Type: number
Path: Sequence.variation.end
public static final ca.uhn.fhir.rest.gclient.NumberClientParam END
Description: End position (0-based exclusive) of the sequence
Type: number
Path: Sequence.variation.end
public Sequence()
public Sequence(Enumeration<Sequence.SequenceType> type)
public Enumeration<Sequence.SequenceType> getTypeElement()
type (Amino acid / cDNA transcript / RNA variation.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the valuepublic boolean hasTypeElement()
public boolean hasType()
public Sequence setTypeElement(Enumeration<Sequence.SequenceType> value)
value - type (Amino acid / cDNA transcript / RNA variation.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the valuepublic Sequence.SequenceType getType()
public Sequence setType(Sequence.SequenceType value)
value - Amino acid / cDNA transcript / RNA variation.public Reference getPatient()
patient (The patient, or group of patients whose sequencing results are described by this resource.)public boolean hasPatient()
public Sequence setPatient(Reference value)
value - patient (The patient, or group of patients whose sequencing results are described by this resource.)public Patient getPatientTarget()
patient The actual object that is the target of the reference. The reference library doesn't populate this, but you can use it to hold the resource if you resolve it. (The patient, or group of patients whose sequencing results are described by this resource.)public Sequence setPatientTarget(Patient value)
value - patient The actual object that is the target of the reference. The reference library doesn't use these, but you can use it to hold the resource if you resolve it. (The patient, or group of patients whose sequencing results are described by this resource.)public Reference getSpecimen()
specimen (Specimen used for sequencing.)public boolean hasSpecimen()
public Sequence setSpecimen(Reference value)
value - specimen (Specimen used for sequencing.)public Specimen getSpecimenTarget()
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.)public Sequence setSpecimenTarget(Specimen value)
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.)public Reference getDevice()
device (The method for sequencing, for example, chip information.)public boolean hasDevice()
public Sequence setDevice(Reference value)
value - device (The method for sequencing, for example, chip information.)public Device getDeviceTarget()
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.)public Sequence setDeviceTarget(Device value)
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.)public Quantity getQuantity()
quantity (Quantity of the sequence.)public boolean hasQuantity()
public Sequence setQuantity(Quantity value)
value - quantity (Quantity of the sequence.)public CodeableConcept getSpecies()
species (The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.)public boolean hasSpecies()
public Sequence setSpecies(CodeableConcept value)
value - species (The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.)public List<Sequence.SequenceReferenceSeqComponent> getReferenceSeq()
referenceSeq (Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) .)public boolean hasReferenceSeq()
public Sequence.SequenceReferenceSeqComponent addReferenceSeq()
referenceSeq (Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) .)public Sequence addReferenceSeq(Sequence.SequenceReferenceSeqComponent t)
public Sequence.SequenceVariationComponent getVariation()
variation (Variation info in this sequence.)public boolean hasVariation()
public Sequence setVariation(Sequence.SequenceVariationComponent value)
value - variation (Variation info in this sequence.)public List<Sequence.SequenceQualityComponent> getQuality()
quality (Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.)public boolean hasQuality()
public Sequence.SequenceQualityComponent addQuality()
quality (Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.)public Sequence addQuality(Sequence.SequenceQualityComponent t)
public CodeableConcept getAllelicState()
allelicState (The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.)public boolean hasAllelicState()
public Sequence setAllelicState(CodeableConcept value)
value - allelicState (The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.)public DecimalType getAllelicFrequencyElement()
allelicFrequency (Allele frequencies.). This is the underlying object with id, value and extensions. The accessor "getAllelicFrequency" gives direct access to the valuepublic boolean hasAllelicFrequencyElement()
public boolean hasAllelicFrequency()
public Sequence setAllelicFrequencyElement(DecimalType value)
value - allelicFrequency (Allele frequencies.). This is the underlying object with id, value and extensions. The accessor "getAllelicFrequency" gives direct access to the valuepublic BigDecimal getAllelicFrequency()
public Sequence setAllelicFrequency(BigDecimal value)
value - Allele frequencies.public Sequence setAllelicFrequency(long value)
value - Allele frequencies.public Sequence setAllelicFrequency(double value)
value - Allele frequencies.public CodeableConcept getCopyNumberEvent()
copyNumberEvent (Values: amplificaiton / deletion / LOH.)public boolean hasCopyNumberEvent()
public Sequence setCopyNumberEvent(CodeableConcept value)
value - copyNumberEvent (Values: amplificaiton / deletion / LOH.)public IntegerType getReadCoverageElement()
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 valuepublic boolean hasReadCoverageElement()
public boolean hasReadCoverage()
public Sequence setReadCoverageElement(IntegerType value)
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 valuepublic int getReadCoverage()
public Sequence setReadCoverage(int value)
value - Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.public List<Sequence.SequenceRepositoryComponent> getRepository()
repository (Configurations of the external repository.)public boolean hasRepository()
public Sequence.SequenceRepositoryComponent addRepository()
repository (Configurations of the external repository.)public Sequence addRepository(Sequence.SequenceRepositoryComponent t)
public List<Reference> getPointer()
pointer (Pointer to next atomic sequence which at most contains one variation.)public boolean hasPointer()
public Reference addPointer()
pointer (Pointer to next atomic sequence which at most contains one variation.)public Sequence addPointer(Reference t)
public List<Sequence> getPointerTarget()
pointer (The actual objects that are the target of the reference. The reference library doesn't populate this, but you can use this to hold the resources if you resolvethemt. Pointer to next atomic sequence which at most contains one variation.)public Sequence addPointerTarget()
pointer (Add an actual object that is the target of the reference. The reference library doesn't use these, but you can use this to hold the resources if you resolvethemt. Pointer to next atomic sequence which at most contains one variation.)public StringType getObservedSeqElement()
observedSeq (Observed Sequence.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the valuepublic boolean hasObservedSeqElement()
public boolean hasObservedSeq()
public Sequence setObservedSeqElement(StringType value)
value - observedSeq (Observed Sequence.). This is the underlying object with id, value and extensions. The accessor "getObservedSeq" gives direct access to the valuepublic String getObservedSeq()
public Sequence setObservedSeq(String value)
value - Observed Sequence.public Reference getObservation()
observation (Analysis of the sequence.)public boolean hasObservation()
public Sequence setObservation(Reference value)
value - observation (Analysis of the sequence.)public Observation getObservationTarget()
observation The actual object that is the target of the reference. The reference library doesn't populate this, but you can use it to hold the resource if you resolve it. (Analysis of the sequence.)public Sequence setObservationTarget(Observation value)
value - observation The actual object that is the target of the reference. The reference library doesn't use these, but you can use it to hold the resource if you resolve it. (Analysis of the sequence.)public Sequence.SequenceStructureVariationComponent getStructureVariation()
structureVariation (Structural variant.)public boolean hasStructureVariation()
public Sequence setStructureVariation(Sequence.SequenceStructureVariationComponent value)
value - structureVariation (Structural variant.)protected void listChildren(List<Property> childrenList)
listChildren in class DomainResourcepublic Base[] getProperty(int hash, String name, boolean checkValid) throws org.hl7.fhir.exceptions.FHIRException
getProperty in class DomainResourceorg.hl7.fhir.exceptions.FHIRExceptionpublic void setProperty(int hash, String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
setProperty in class DomainResourceorg.hl7.fhir.exceptions.FHIRExceptionpublic void setProperty(String name, Base value) throws org.hl7.fhir.exceptions.FHIRException
setProperty in class DomainResourceorg.hl7.fhir.exceptions.FHIRExceptionpublic Base makeProperty(int hash, String name) throws org.hl7.fhir.exceptions.FHIRException
makeProperty in class DomainResourceorg.hl7.fhir.exceptions.FHIRExceptionpublic Base addChild(String name) throws org.hl7.fhir.exceptions.FHIRException
addChild in class DomainResourceorg.hl7.fhir.exceptions.FHIRExceptionpublic String fhirType()
fhirType in class DomainResourcepublic Sequence copy()
copy in class DomainResourcepublic boolean equalsDeep(Base other)
equalsDeep in class DomainResourcepublic boolean equalsShallow(Base other)
equalsShallow in class DomainResourcepublic boolean isEmpty()
isEmpty in interface org.hl7.fhir.instance.model.api.IBaseisEmpty in class DomainResourcepublic ResourceType getResourceType()
getResourceType in class ResourceCopyright © 2014–2018 University Health Network. All rights reserved.