ca.uhn.fhir.model.dstu.resource.GeneExpression Maven / Gradle / Ivy
package ca.uhn.fhir.model.dstu.resource;
import java.util.*;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.annotation.*;
import ca.uhn.fhir.rest.gclient.*;
import ca.uhn.fhir.model.dstu.composite.AddressDt;
import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
import ca.uhn.fhir.model.dstu.valueset.AdmitSourceEnum;
import ca.uhn.fhir.model.dstu.resource.AdverseReaction;
import ca.uhn.fhir.model.dstu.valueset.AggregationModeEnum;
import ca.uhn.fhir.model.dstu.valueset.AlertStatusEnum;
import ca.uhn.fhir.model.dstu.resource.AllergyIntolerance;
import ca.uhn.fhir.model.dstu.valueset.AnimalSpeciesEnum;
import ca.uhn.fhir.model.dstu.resource.Appointment;
import ca.uhn.fhir.model.dstu.composite.AttachmentDt;
import ca.uhn.fhir.model.dstu.resource.Availability;
import ca.uhn.fhir.model.dstu.valueset.BindingConformanceEnum;
import ca.uhn.fhir.model.dstu.resource.CarePlan;
import ca.uhn.fhir.model.dstu.valueset.CarePlanActivityCategoryEnum;
import ca.uhn.fhir.model.dstu.valueset.CarePlanActivityStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.CarePlanGoalStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.CarePlanStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.CausalityExpectationEnum;
import ca.uhn.fhir.model.dstu.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu.composite.CodingDt;
import ca.uhn.fhir.model.dstu.valueset.CompositionAttestationModeEnum;
import ca.uhn.fhir.model.dstu.valueset.CompositionStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.ConceptMapEquivalenceEnum;
import ca.uhn.fhir.model.dstu.resource.Condition;
import ca.uhn.fhir.model.dstu.valueset.ConditionRelationshipTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ConditionStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.ConformanceEventModeEnum;
import ca.uhn.fhir.model.dstu.valueset.ConformanceStatementStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.ConstraintSeverityEnum;
import ca.uhn.fhir.model.dstu.composite.ContactDt;
import ca.uhn.fhir.model.dstu.valueset.ContactUseEnum;
import ca.uhn.fhir.model.dstu.valueset.CriticalityEnum;
import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
import ca.uhn.fhir.model.dstu.resource.Device;
import ca.uhn.fhir.model.dstu.resource.DeviceObservationReport;
import ca.uhn.fhir.model.dstu.resource.DiagnosticOrder;
import ca.uhn.fhir.model.dstu.valueset.DiagnosticOrderPriorityEnum;
import ca.uhn.fhir.model.dstu.valueset.DiagnosticOrderStatusEnum;
import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu.valueset.DiagnosticReportStatusEnum;
import ca.uhn.fhir.model.dstu.resource.DocumentManifest;
import ca.uhn.fhir.model.dstu.valueset.DocumentModeEnum;
import ca.uhn.fhir.model.dstu.resource.DocumentReference;
import ca.uhn.fhir.model.dstu.valueset.DocumentReferenceStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.DocumentRelationshipTypeEnum;
import ca.uhn.fhir.model.dstu.resource.Encounter;
import ca.uhn.fhir.model.dstu.valueset.EncounterClassEnum;
import ca.uhn.fhir.model.dstu.valueset.EncounterStateEnum;
import ca.uhn.fhir.model.dstu.valueset.EncounterTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ExposureTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ExtensionContextEnum;
import ca.uhn.fhir.model.dstu.valueset.FHIRDefinedTypeEnum;
import ca.uhn.fhir.model.dstu.resource.FamilyHistory;
import ca.uhn.fhir.model.dstu.valueset.FilterOperatorEnum;
import ca.uhn.fhir.model.dstu.resource.GVFMeta;
import ca.uhn.fhir.model.dstu.resource.Group;
import ca.uhn.fhir.model.dstu.valueset.GroupTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.HierarchicalRelationshipTypeEnum;
import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
import ca.uhn.fhir.model.dstu.valueset.ImagingModalityEnum;
import ca.uhn.fhir.model.dstu.resource.ImagingStudy;
import ca.uhn.fhir.model.dstu.resource.Immunization;
import ca.uhn.fhir.model.dstu.valueset.ImmunizationReasonCodesEnum;
import ca.uhn.fhir.model.dstu.resource.ImmunizationRecommendation;
import ca.uhn.fhir.model.dstu.valueset.ImmunizationRecommendationDateCriterionCodesEnum;
import ca.uhn.fhir.model.dstu.valueset.ImmunizationRecommendationStatusCodesEnum;
import ca.uhn.fhir.model.dstu.valueset.ImmunizationRouteCodesEnum;
import ca.uhn.fhir.model.dstu.valueset.InstanceAvailabilityEnum;
import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.dstu.valueset.IssueTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.LinkTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ListModeEnum;
import ca.uhn.fhir.model.dstu.resource.Location;
import ca.uhn.fhir.model.dstu.valueset.LocationModeEnum;
import ca.uhn.fhir.model.dstu.valueset.LocationStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.LocationTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.MaritalStatusCodesEnum;
import ca.uhn.fhir.model.dstu.resource.Media;
import ca.uhn.fhir.model.dstu.valueset.MediaTypeEnum;
import ca.uhn.fhir.model.dstu.resource.Medication;
import ca.uhn.fhir.model.dstu.resource.MedicationAdministration;
import ca.uhn.fhir.model.dstu.valueset.MedicationAdministrationStatusEnum;
import ca.uhn.fhir.model.dstu.resource.MedicationDispense;
import ca.uhn.fhir.model.dstu.valueset.MedicationDispenseStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.MedicationKindEnum;
import ca.uhn.fhir.model.dstu.resource.MedicationPrescription;
import ca.uhn.fhir.model.dstu.valueset.MedicationPrescriptionStatusEnum;
import ca.uhn.fhir.model.dstu.resource.MedicationStatement;
import ca.uhn.fhir.model.dstu.valueset.MessageEventEnum;
import ca.uhn.fhir.model.dstu.valueset.MessageSignificanceCategoryEnum;
import ca.uhn.fhir.model.dstu.valueset.MessageTransportEnum;
import ca.uhn.fhir.model.dstu.resource.Microarray;
import ca.uhn.fhir.model.dstu.valueset.ModalityEnum;
import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.valueset.ObservationRelationshipTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ObservationReliabilityEnum;
import ca.uhn.fhir.model.dstu.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu.resource.Order;
import ca.uhn.fhir.model.dstu.valueset.OrderOutcomeStatusEnum;
import ca.uhn.fhir.model.dstu.resource.Organization;
import ca.uhn.fhir.model.dstu.valueset.OrganizationTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ParticipantTypeEnum;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu.composite.PeriodDt;
import ca.uhn.fhir.model.dstu.resource.Practitioner;
import ca.uhn.fhir.model.dstu.valueset.PractitionerRoleEnum;
import ca.uhn.fhir.model.dstu.valueset.PractitionerSpecialtyEnum;
import ca.uhn.fhir.model.dstu.resource.Procedure;
import ca.uhn.fhir.model.dstu.valueset.ProcedureRelationshipTypeEnum;
import ca.uhn.fhir.model.dstu.resource.Profile;
import ca.uhn.fhir.model.dstu.valueset.PropertyRepresentationEnum;
import ca.uhn.fhir.model.dstu.valueset.ProvenanceEntityRoleEnum;
import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.valueset.QueryOutcomeEnum;
import ca.uhn.fhir.model.dstu.valueset.QuestionnaireGroupNameEnum;
import ca.uhn.fhir.model.dstu.valueset.QuestionnaireNameEnum;
import ca.uhn.fhir.model.dstu.valueset.QuestionnaireStatusEnum;
import ca.uhn.fhir.model.dstu.composite.RangeDt;
import ca.uhn.fhir.model.dstu.composite.RatioDt;
import ca.uhn.fhir.model.dstu.valueset.ReactionSeverityEnum;
import ca.uhn.fhir.model.dstu.resource.RelatedPerson;
import ca.uhn.fhir.model.dstu.valueset.ResourceProfileStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.ResourceTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.ResponseTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.RestfulConformanceModeEnum;
import ca.uhn.fhir.model.dstu.valueset.RestfulOperationSystemEnum;
import ca.uhn.fhir.model.dstu.valueset.RestfulOperationTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.RestfulSecurityServiceEnum;
import ca.uhn.fhir.model.dstu.composite.SampledDataDt;
import ca.uhn.fhir.model.dstu.composite.ScheduleDt;
import ca.uhn.fhir.model.dstu.valueset.SearchParamTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventActionEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventObjectLifecycleEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventObjectRoleEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventObjectTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventOutcomeEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventParticipantNetworkTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.SecurityEventSourceTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.SensitivityStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.SensitivityTypeEnum;
import ca.uhn.fhir.model.dstu.resource.SequencingAnalysis;
import ca.uhn.fhir.model.dstu.resource.SequencingLab;
import ca.uhn.fhir.model.dstu.valueset.SlicingRulesEnum;
import ca.uhn.fhir.model.dstu.resource.Slot;
import ca.uhn.fhir.model.dstu.resource.Specimen;
import ca.uhn.fhir.model.dstu.valueset.SpecimenCollectionMethodEnum;
import ca.uhn.fhir.model.dstu.resource.Substance;
import ca.uhn.fhir.model.dstu.valueset.SupplyDispenseStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.SupplyItemTypeEnum;
import ca.uhn.fhir.model.dstu.valueset.SupplyStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.SupplyTypeEnum;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.dstu.resource.ValueSet;
import ca.uhn.fhir.model.dstu.valueset.ValueSetStatusEnum;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.composite.AgeDt;
import ca.uhn.fhir.model.dstu.composite.DurationDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.Binary;
import ca.uhn.fhir.model.primitive.Base64BinaryDt;
import ca.uhn.fhir.model.primitive.BooleanDt;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.model.primitive.BoundCodeableConceptDt;
import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.IdrefDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.OidDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
/**
* HAPI/FHIR GeneExpression Resource
* (Resource that records the patient's expression of a gene)
*
*
* Definition:
* Resource that records the patient's expression of a gene
*
*
*
* Requirements:
*
*
*
*
* Profile Definition:
* http://hl7.org/fhir/profiles/GeneExpression
*
*
*/
@ResourceDef(name="GeneExpression", profile="http://hl7.org/fhir/profiles/GeneExpression", id="geneexpression")
public class GeneExpression extends ca.uhn.fhir.model.dstu.resource.BaseResource
implements IResource {
/**
* Search parameter constant for subject
*
* Description: subject being described by the resource
* Type: reference
* Path: GeneExpression.subject
*
*/
@SearchParamDefinition(name="subject", path="GeneExpression.subject", description="subject being described by the resource", type="reference" )
public static final String SP_SUBJECT = "subject";
/**
* Fluent Client search parameter constant for subject
*
* Description: subject being described by the resource
* Type: reference
* Path: GeneExpression.subject
*
*/
public static final ReferenceClientParam SUBJECT = new ReferenceClientParam(SP_SUBJECT);
/**
* Constant for fluent queries to be used to add include statements. Specifies
* the path value of "GeneExpression.subject".
*/
public static final Include INCLUDE_SUBJECT = new Include("GeneExpression.subject");
/**
* Search parameter constant for gene
*
* Description: Id of the gene
* Type: string
* Path: GeneExpression.gene.identifier
*
*/
@SearchParamDefinition(name="gene", path="GeneExpression.gene.identifier", description="Id of the gene", type="string" )
public static final String SP_GENE = "gene";
/**
* Fluent Client search parameter constant for gene
*
* Description: Id of the gene
* Type: string
* Path: GeneExpression.gene.identifier
*
*/
public static final StringClientParam GENE = new StringClientParam(SP_GENE);
/**
* Search parameter constant for coordinate
*
* Description: Coordinate of the gene
* Type: string
* Path: GeneExpression.gene.coordinate
*
*/
@SearchParamDefinition(name="coordinate", path="GeneExpression.gene.coordinate", description="Coordinate of the gene", type="string" )
public static final String SP_COORDINATE = "coordinate";
/**
* Fluent Client search parameter constant for coordinate
*
* Description: Coordinate of the gene
* Type: string
* Path: GeneExpression.gene.coordinate
*
*/
public static final StringClientParam COORDINATE = new StringClientParam(SP_COORDINATE);
@Child(name="subject", order=0, min=0, max=1, summary=false, modifier=false, type={
ca.uhn.fhir.model.dstu.resource.Patient.class })
@Description(
shortDefinition="Subject described by the resource",
formalDefinition="Subject described by the resource"
)
private ResourceReferenceDt mySubject;
@Child(name="gene", order=1, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Gene of study",
formalDefinition="Gene of study"
)
private Gene myGene;
@Child(name="microarray", order=2, min=0, max=Child.MAX_UNLIMITED, summary=false, modifier=false, type={
ca.uhn.fhir.model.dstu.resource.Microarray.class })
@Description(
shortDefinition="Microarray that studies the gene",
formalDefinition="Microarray that studies the gene"
)
private java.util.List myMicroarray;
@Child(name="rnaSeq", order=3, min=0, max=Child.MAX_UNLIMITED, summary=false, modifier=false)
@Description(
shortDefinition="RNA-Seq that studies the gene",
formalDefinition="RNA-Seq that studies the gene"
)
private java.util.List myRnaSeq;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( mySubject, myGene, myMicroarray, myRnaSeq);
}
@Override
public List getAllPopulatedChildElementsOfType(Class theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, mySubject, myGene, myMicroarray, myRnaSeq);
}
/**
* Gets the value(s) for subject (Subject described by the resource).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Subject described by the resource
*
*/
public ResourceReferenceDt getSubject() {
if (mySubject == null) {
mySubject = new ResourceReferenceDt();
}
return mySubject;
}
/**
* Gets the value(s) for subject (Subject described by the resource).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Subject described by the resource
*
*/
public ResourceReferenceDt getSubjectElement() {
if (mySubject == null) {
mySubject = new ResourceReferenceDt();
}
return mySubject;
}
/**
* Sets the value(s) for subject (Subject described by the resource)
*
*
* Definition:
* Subject described by the resource
*
*/
public GeneExpression setSubject(ResourceReferenceDt theValue) {
mySubject = theValue;
return this;
}
/**
* Gets the value(s) for gene (Gene of study).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Gene of study
*
*/
public Gene getGene() {
if (myGene == null) {
myGene = new Gene();
}
return myGene;
}
/**
* Gets the value(s) for gene (Gene of study).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Gene of study
*
*/
public Gene getGeneElement() {
if (myGene == null) {
myGene = new Gene();
}
return myGene;
}
/**
* Sets the value(s) for gene (Gene of study)
*
*
* Definition:
* Gene of study
*
*/
public GeneExpression setGene(Gene theValue) {
myGene = theValue;
return this;
}
/**
* Gets the value(s) for microarray (Microarray that studies the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Microarray that studies the gene
*
*/
public java.util.List getMicroarray() {
if (myMicroarray == null) {
myMicroarray = new java.util.ArrayList();
}
return myMicroarray;
}
/**
* Gets the value(s) for microarray (Microarray that studies the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Microarray that studies the gene
*
*/
public java.util.List getMicroarrayElement() {
if (myMicroarray == null) {
myMicroarray = new java.util.ArrayList();
}
return myMicroarray;
}
/**
* Sets the value(s) for microarray (Microarray that studies the gene)
*
*
* Definition:
* Microarray that studies the gene
*
*/
public GeneExpression setMicroarray(java.util.List theValue) {
myMicroarray = theValue;
return this;
}
/**
* Adds and returns a new value for microarray (Microarray that studies the gene)
*
*
* Definition:
* Microarray that studies the gene
*
*/
public ResourceReferenceDt addMicroarray() {
ResourceReferenceDt newType = new ResourceReferenceDt();
getMicroarray().add(newType);
return newType;
}
/**
* Gets the value(s) for rnaSeq (RNA-Seq that studies the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
public java.util.List getRnaSeq() {
if (myRnaSeq == null) {
myRnaSeq = new java.util.ArrayList();
}
return myRnaSeq;
}
/**
* Gets the value(s) for rnaSeq (RNA-Seq that studies the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
public java.util.List getRnaSeqElement() {
if (myRnaSeq == null) {
myRnaSeq = new java.util.ArrayList();
}
return myRnaSeq;
}
/**
* Sets the value(s) for rnaSeq (RNA-Seq that studies the gene)
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
public GeneExpression setRnaSeq(java.util.List theValue) {
myRnaSeq = theValue;
return this;
}
/**
* Adds and returns a new value for rnaSeq (RNA-Seq that studies the gene)
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
public RnaSeq addRnaSeq() {
RnaSeq newType = new RnaSeq();
getRnaSeq().add(newType);
return newType;
}
/**
* Gets the first repetition for rnaSeq (RNA-Seq that studies the gene),
* creating it if it does not already exist.
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
public RnaSeq getRnaSeqFirstRep() {
if (getRnaSeq().isEmpty()) {
return addRnaSeq();
}
return getRnaSeq().get(0);
}
/**
* Block class for child element: GeneExpression.gene (Gene of study)
*
*
* Definition:
* Gene of study
*
*/
@Block()
public static class Gene
extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="identifier", type=StringDt.class, order=0, min=0, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Identifier of the gene",
formalDefinition="Identifier of the gene"
)
private StringDt myIdentifier;
@Child(name="coordinate", order=1, min=0, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Coordinate of the gene",
formalDefinition="Coordinate of the gene"
)
private GeneCoordinate myCoordinate;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myIdentifier, myCoordinate);
}
@Override
public List getAllPopulatedChildElementsOfType(Class theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myIdentifier, myCoordinate);
}
/**
* Gets the value(s) for identifier (Identifier of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Identifier of the gene
*
*/
public StringDt getIdentifier() {
if (myIdentifier == null) {
myIdentifier = new StringDt();
}
return myIdentifier;
}
/**
* Gets the value(s) for identifier (Identifier of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Identifier of the gene
*
*/
public StringDt getIdentifierElement() {
if (myIdentifier == null) {
myIdentifier = new StringDt();
}
return myIdentifier;
}
/**
* Sets the value(s) for identifier (Identifier of the gene)
*
*
* Definition:
* Identifier of the gene
*
*/
public Gene setIdentifier(StringDt theValue) {
myIdentifier = theValue;
return this;
}
/**
* Sets the value for identifier (Identifier of the gene)
*
*
* Definition:
* Identifier of the gene
*
*/
public Gene setIdentifier( String theString) {
myIdentifier = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for coordinate (Coordinate of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Coordinate of the gene
*
*/
public GeneCoordinate getCoordinate() {
if (myCoordinate == null) {
myCoordinate = new GeneCoordinate();
}
return myCoordinate;
}
/**
* Gets the value(s) for coordinate (Coordinate of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Coordinate of the gene
*
*/
public GeneCoordinate getCoordinateElement() {
if (myCoordinate == null) {
myCoordinate = new GeneCoordinate();
}
return myCoordinate;
}
/**
* Sets the value(s) for coordinate (Coordinate of the gene)
*
*
* Definition:
* Coordinate of the gene
*
*/
public Gene setCoordinate(GeneCoordinate theValue) {
myCoordinate = theValue;
return this;
}
}
/**
* Block class for child element: GeneExpression.gene.coordinate (Coordinate of the gene)
*
*
* Definition:
* Coordinate of the gene
*
*/
@Block()
public static class GeneCoordinate
extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="chromosome", type=StringDt.class, order=0, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Chromosome",
formalDefinition="Chromosome"
)
private StringDt myChromosome;
@Child(name="start", type=IntegerDt.class, order=1, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Start position",
formalDefinition="Start position"
)
private IntegerDt myStart;
@Child(name="end", type=IntegerDt.class, order=2, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="End position",
formalDefinition="End position"
)
private IntegerDt myEnd;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myChromosome, myStart, myEnd);
}
@Override
public List getAllPopulatedChildElementsOfType(Class theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myChromosome, myStart, myEnd);
}
/**
* Gets the value(s) for chromosome (Chromosome).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Chromosome
*
*/
public StringDt getChromosome() {
if (myChromosome == null) {
myChromosome = new StringDt();
}
return myChromosome;
}
/**
* Gets the value(s) for chromosome (Chromosome).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Chromosome
*
*/
public StringDt getChromosomeElement() {
if (myChromosome == null) {
myChromosome = new StringDt();
}
return myChromosome;
}
/**
* Sets the value(s) for chromosome (Chromosome)
*
*
* Definition:
* Chromosome
*
*/
public GeneCoordinate setChromosome(StringDt theValue) {
myChromosome = theValue;
return this;
}
/**
* Sets the value for chromosome (Chromosome)
*
*
* Definition:
* Chromosome
*
*/
public GeneCoordinate setChromosome( String theString) {
myChromosome = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for start (Start position).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Start position
*
*/
public IntegerDt getStart() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Gets the value(s) for start (Start position).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Start position
*
*/
public IntegerDt getStartElement() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Sets the value(s) for start (Start position)
*
*
* Definition:
* Start position
*
*/
public GeneCoordinate setStart(IntegerDt theValue) {
myStart = theValue;
return this;
}
/**
* Sets the value for start (Start position)
*
*
* Definition:
* Start position
*
*/
public GeneCoordinate setStart( int theInteger) {
myStart = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for end (End position).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* End position
*
*/
public IntegerDt getEnd() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Gets the value(s) for end (End position).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* End position
*
*/
public IntegerDt getEndElement() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Sets the value(s) for end (End position)
*
*
* Definition:
* End position
*
*/
public GeneCoordinate setEnd(IntegerDt theValue) {
myEnd = theValue;
return this;
}
/**
* Sets the value for end (End position)
*
*
* Definition:
* End position
*
*/
public GeneCoordinate setEnd( int theInteger) {
myEnd = new IntegerDt(theInteger);
return this;
}
}
/**
* Block class for child element: GeneExpression.rnaSeq (RNA-Seq that studies the gene)
*
*
* Definition:
* RNA-Seq that studies the gene
*
*/
@Block()
public static class RnaSeq
extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="inputLab", order=0, min=0, max=1, summary=false, modifier=false, type={
ca.uhn.fhir.model.dstu.resource.SequencingLab.class })
@Description(
shortDefinition="Input lab for the RNA-Seq",
formalDefinition="Input lab for the RNA-Seq"
)
private ResourceReferenceDt myInputLab;
@Child(name="inputAnalysis", order=1, min=0, max=1, summary=false, modifier=false, type={
ca.uhn.fhir.model.dstu.resource.SequencingAnalysis.class })
@Description(
shortDefinition="Input analysis for the RNA-Seq",
formalDefinition="Input analysis for the RNA-Seq"
)
private ResourceReferenceDt myInputAnalysis;
@Child(name="expression", type=DecimalDt.class, order=2, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Expression level of the gene in RPKM",
formalDefinition="Expression level of the gene in RPKM"
)
private DecimalDt myExpression;
@Child(name="isoform", order=3, min=0, max=Child.MAX_UNLIMITED, summary=false, modifier=false)
@Description(
shortDefinition="Isoform of the gene",
formalDefinition="Isoform of the gene"
)
private java.util.List myIsoform;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myInputLab, myInputAnalysis, myExpression, myIsoform);
}
@Override
public List getAllPopulatedChildElementsOfType(Class theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myInputLab, myInputAnalysis, myExpression, myIsoform);
}
/**
* Gets the value(s) for inputLab (Input lab for the RNA-Seq).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Input lab for the RNA-Seq
*
*/
public ResourceReferenceDt getInputLab() {
if (myInputLab == null) {
myInputLab = new ResourceReferenceDt();
}
return myInputLab;
}
/**
* Gets the value(s) for inputLab (Input lab for the RNA-Seq).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Input lab for the RNA-Seq
*
*/
public ResourceReferenceDt getInputLabElement() {
if (myInputLab == null) {
myInputLab = new ResourceReferenceDt();
}
return myInputLab;
}
/**
* Sets the value(s) for inputLab (Input lab for the RNA-Seq)
*
*
* Definition:
* Input lab for the RNA-Seq
*
*/
public RnaSeq setInputLab(ResourceReferenceDt theValue) {
myInputLab = theValue;
return this;
}
/**
* Gets the value(s) for inputAnalysis (Input analysis for the RNA-Seq).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Input analysis for the RNA-Seq
*
*/
public ResourceReferenceDt getInputAnalysis() {
if (myInputAnalysis == null) {
myInputAnalysis = new ResourceReferenceDt();
}
return myInputAnalysis;
}
/**
* Gets the value(s) for inputAnalysis (Input analysis for the RNA-Seq).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Input analysis for the RNA-Seq
*
*/
public ResourceReferenceDt getInputAnalysisElement() {
if (myInputAnalysis == null) {
myInputAnalysis = new ResourceReferenceDt();
}
return myInputAnalysis;
}
/**
* Sets the value(s) for inputAnalysis (Input analysis for the RNA-Seq)
*
*
* Definition:
* Input analysis for the RNA-Seq
*
*/
public RnaSeq setInputAnalysis(ResourceReferenceDt theValue) {
myInputAnalysis = theValue;
return this;
}
/**
* Gets the value(s) for expression (Expression level of the gene in RPKM).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public DecimalDt getExpression() {
if (myExpression == null) {
myExpression = new DecimalDt();
}
return myExpression;
}
/**
* Gets the value(s) for expression (Expression level of the gene in RPKM).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public DecimalDt getExpressionElement() {
if (myExpression == null) {
myExpression = new DecimalDt();
}
return myExpression;
}
/**
* Sets the value(s) for expression (Expression level of the gene in RPKM)
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public RnaSeq setExpression(DecimalDt theValue) {
myExpression = theValue;
return this;
}
/**
* Sets the value for expression (Expression level of the gene in RPKM)
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public RnaSeq setExpression( long theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
/**
* Sets the value for expression (Expression level of the gene in RPKM)
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public RnaSeq setExpression( double theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
/**
* Sets the value for expression (Expression level of the gene in RPKM)
*
*
* Definition:
* Expression level of the gene in RPKM
*
*/
public RnaSeq setExpression( java.math.BigDecimal theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
/**
* Gets the value(s) for isoform (Isoform of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Isoform of the gene
*
*/
public java.util.List getIsoform() {
if (myIsoform == null) {
myIsoform = new java.util.ArrayList();
}
return myIsoform;
}
/**
* Gets the value(s) for isoform (Isoform of the gene).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Isoform of the gene
*
*/
public java.util.List getIsoformElement() {
if (myIsoform == null) {
myIsoform = new java.util.ArrayList();
}
return myIsoform;
}
/**
* Sets the value(s) for isoform (Isoform of the gene)
*
*
* Definition:
* Isoform of the gene
*
*/
public RnaSeq setIsoform(java.util.List theValue) {
myIsoform = theValue;
return this;
}
/**
* Adds and returns a new value for isoform (Isoform of the gene)
*
*
* Definition:
* Isoform of the gene
*
*/
public RnaSeqIsoform addIsoform() {
RnaSeqIsoform newType = new RnaSeqIsoform();
getIsoform().add(newType);
return newType;
}
/**
* Gets the first repetition for isoform (Isoform of the gene),
* creating it if it does not already exist.
*
*
* Definition:
* Isoform of the gene
*
*/
public RnaSeqIsoform getIsoformFirstRep() {
if (getIsoform().isEmpty()) {
return addIsoform();
}
return getIsoform().get(0);
}
}
/**
* Block class for child element: GeneExpression.rnaSeq.isoform (Isoform of the gene)
*
*
* Definition:
* Isoform of the gene
*
*/
@Block()
public static class RnaSeqIsoform
extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="identity", type=StringDt.class, order=0, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Identifier of the isoform",
formalDefinition="Identifier of the isoform"
)
private StringDt myIdentity;
@Child(name="expression", type=DecimalDt.class, order=1, min=1, max=1, summary=false, modifier=false)
@Description(
shortDefinition="Expression level of the isoform in RPKM",
formalDefinition="Expression level of the isoform in RPKM"
)
private DecimalDt myExpression;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myIdentity, myExpression);
}
@Override
public List getAllPopulatedChildElementsOfType(Class theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myIdentity, myExpression);
}
/**
* Gets the value(s) for identity (Identifier of the isoform).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Identifier of the isoform
*
*/
public StringDt getIdentity() {
if (myIdentity == null) {
myIdentity = new StringDt();
}
return myIdentity;
}
/**
* Gets the value(s) for identity (Identifier of the isoform).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Identifier of the isoform
*
*/
public StringDt getIdentityElement() {
if (myIdentity == null) {
myIdentity = new StringDt();
}
return myIdentity;
}
/**
* Sets the value(s) for identity (Identifier of the isoform)
*
*
* Definition:
* Identifier of the isoform
*
*/
public RnaSeqIsoform setIdentity(StringDt theValue) {
myIdentity = theValue;
return this;
}
/**
* Sets the value for identity (Identifier of the isoform)
*
*
* Definition:
* Identifier of the isoform
*
*/
public RnaSeqIsoform setIdentity( String theString) {
myIdentity = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for expression (Expression level of the isoform in RPKM).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public DecimalDt getExpression() {
if (myExpression == null) {
myExpression = new DecimalDt();
}
return myExpression;
}
/**
* Gets the value(s) for expression (Expression level of the isoform in RPKM).
* creating it if it does
* not exist. Will not return null.
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public DecimalDt getExpressionElement() {
if (myExpression == null) {
myExpression = new DecimalDt();
}
return myExpression;
}
/**
* Sets the value(s) for expression (Expression level of the isoform in RPKM)
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public RnaSeqIsoform setExpression(DecimalDt theValue) {
myExpression = theValue;
return this;
}
/**
* Sets the value for expression (Expression level of the isoform in RPKM)
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public RnaSeqIsoform setExpression( long theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
/**
* Sets the value for expression (Expression level of the isoform in RPKM)
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public RnaSeqIsoform setExpression( double theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
/**
* Sets the value for expression (Expression level of the isoform in RPKM)
*
*
* Definition:
* Expression level of the isoform in RPKM
*
*/
public RnaSeqIsoform setExpression( java.math.BigDecimal theValue) {
myExpression = new DecimalDt(theValue);
return this;
}
}
@Override
public String getResourceName() {
return "GeneExpression";
}
public ca.uhn.fhir.context.FhirVersionEnum getStructureFhirVersionEnum() {
return ca.uhn.fhir.context.FhirVersionEnum.DSTU1;
}
}
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