package ca.uhn.fhir.model.dstu.resource;
/*
* #%L
* HAPI FHIR Library
* %%
* Copyright (C) 2014 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import ca.uhn.fhir.model.api.BaseIdentifiableElement;
import ca.uhn.fhir.model.api.BaseResource;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.IResourceBlock;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.Block;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
import ca.uhn.fhir.model.dstu.composite.AttachmentDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.gclient.ReferenceParam;
import ca.uhn.fhir.rest.gclient.StringParam;
/**
* HAPI/FHIR <b>GVFVariant</b> Resource
* (GVF Variant)
*
* <p>
* <b>Definition:</b>
* A segment of a GVF file
* </p>
*
* <p>
* <b>Requirements:</b>
*
* </p>
*
* <p>
* <b>Profile Definition:</b>
* <a href="http://hl7.org/fhir/profiles/GVFVariant">http://hl7.org/fhir/profiles/GVFVariant</a>
* </p>
*
*/
@ResourceDef(name="GVFVariant", profile="http://hl7.org/fhir/profiles/GVFVariant", id="gvfvariant")
public class GVFVariant extends BaseResource implements IResource {
/**
* Search parameter constant for <b>patient</b>
* <p>
* Description: <b>Patient being described </b><br/>
* Type: <b>reference</b><br/>
* Path: <b>GVFVariant.subject.patient</b><br/>
* </p>
*/
@SearchParamDefinition(name="patient", path="GVFVariant.subject.patient", description="Patient being described ", type="reference")
public static final String SP_PATIENT = "patient";
/**
* <b>Fluent Client</b> search parameter constant for <b>patient</b>
* <p>
* Description: <b>Patient being described </b><br/>
* Type: <b>reference</b><br/>
* Path: <b>GVFVariant.subject.patient</b><br/>
* </p>
*/
public static final ReferenceParam PATIENT = new ReferenceParam(SP_PATIENT);
/**
* Constant for fluent queries to be used to add include statements. Specifies
* the path value of "<b>GVFVariant.subject.patient</b>".
*/
public static final Include INCLUDE_SUBJECT_PATIENT = new Include("GVFVariant.subject.patient");
/**
* Search parameter constant for <b>coordinate</b>
* <p>
* Description: <b>Coordinate of the variant being studied</b><br/>
* Type: <b>string</b><br/>
* Path: <b></b><br/>
* </p>
*/
@SearchParamDefinition(name="coordinate", path="", description="Coordinate of the variant being studied", type="string")
public static final String SP_COORDINATE = "coordinate";
/**
* <b>Fluent Client</b> search parameter constant for <b>coordinate</b>
* <p>
* Description: <b>Coordinate of the variant being studied</b><br/>
* Type: <b>string</b><br/>
* Path: <b></b><br/>
* </p>
*/
public static final StringParam COORDINATE = new StringParam(SP_COORDINATE);
@Child(name="subject", order=0, min=0, max=1)
@Description(
shortDefinition="Subject described by this segment of GVF file",
formalDefinition="Subject described by this segment of GVF file"
)
private Subject mySubject;
@Child(name="meta", order=1, min=0, max=1, type={
ca.uhn.fhir.model.dstu.resource.GVFMeta.class })
@Description(
shortDefinition="GVF Meta",
formalDefinition="Meta information of a GVF file"
)
private ResourceReferenceDt myMeta;
@Child(name="sourceFile", type=AttachmentDt.class, order=2, min=0, max=1)
@Description(
shortDefinition="Source file",
formalDefinition="Source GVF file"
)
private AttachmentDt mySourceFile;
@Child(name="seqid", type=StringDt.class, order=3, min=1, max=1)
@Description(
shortDefinition="Sequence Id",
formalDefinition="Id the sequence being described"
)
private StringDt mySeqid;
@Child(name="source", type=StringDt.class, order=4, min=1, max=1)
@Description(
shortDefinition="Data source",
formalDefinition="Algorithm or software used to generate the data"
)
private StringDt mySource;
@Child(name="type", type=CodeDt.class, order=5, min=1, max=1)
@Description(
shortDefinition="Feature type",
formalDefinition="Type of the feature being described"
)
private CodeDt myType;
@Child(name="start", type=IntegerDt.class, order=6, min=1, max=1)
@Description(
shortDefinition="Start position",
formalDefinition="Start position"
)
private IntegerDt myStart;
@Child(name="end", type=IntegerDt.class, order=7, min=1, max=1)
@Description(
shortDefinition="End position",
formalDefinition="End position"
)
private IntegerDt myEnd;
@Child(name="score", type=IntegerDt.class, order=8, min=1, max=1)
@Description(
shortDefinition="Sequence score",
formalDefinition="Phred scaled score of the sequence"
)
private IntegerDt myScore;
@Child(name="strand", type=CodeDt.class, order=9, min=1, max=1)
@Description(
shortDefinition="Strand",
formalDefinition="Direction of the strand"
)
private CodeDt myStrand;
@Child(name="featureId", type=StringDt.class, order=10, min=1, max=1)
@Description(
shortDefinition="Id of the feature",
formalDefinition="Id of the attribute, unique to other segments in the same source file"
)
private StringDt myFeatureId;
@Child(name="alias", type=StringDt.class, order=11, min=0, max=1)
@Description(
shortDefinition="Alias of the feature",
formalDefinition="Alias of the feature being described"
)
private StringDt myAlias;
@Child(name="dbxref", order=12, min=0, max=1)
@Description(
shortDefinition="Reference of the feature in a database",
formalDefinition="Reference of the feature in a database"
)
private Dbxref myDbxref;
@Child(name="variantSeq", type=StringDt.class, order=13, min=1, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Sequence presents in the variant",
formalDefinition="Sequence presents in the variant"
)
private java.util.List<StringDt> myVariantSeq;
@Child(name="referenceSeq", type=StringDt.class, order=14, min=0, max=1)
@Description(
shortDefinition="Reference sequence",
formalDefinition="Reference sequence"
)
private StringDt myReferenceSeq;
@Child(name="variantFreq", type=DecimalDt.class, order=15, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Variant frequency",
formalDefinition="Frequency of the variant"
)
private java.util.List<DecimalDt> myVariantFreq;
@Child(name="variantEffect", order=16, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Variant effect",
formalDefinition="Effect of the variant"
)
private java.util.List<VariantEffect> myVariantEffect;
@Child(name="startRange", order=17, min=0, max=1)
@Description(
shortDefinition="Start range",
formalDefinition="Attribute describing ambiguity of the start position of the feature"
)
private StartRange myStartRange;
@Child(name="endRange", order=18, min=0, max=1)
@Description(
shortDefinition="End range",
formalDefinition="Attribute describing ambiguity of the end position of the feature"
)
private EndRange myEndRange;
@Child(name="variantCodon", type=StringDt.class, order=19, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Codons that overlap with feature being described",
formalDefinition="Codons that overlap with the feature being described"
)
private java.util.List<StringDt> myVariantCodon;
@Child(name="referenceCodon", type=StringDt.class, order=20, min=0, max=1)
@Description(
shortDefinition="Codon that overlap with the reference sequence",
formalDefinition="Codon that overlap with the reference sequence"
)
private StringDt myReferenceCodon;
@Child(name="variantAA", type=StringDt.class, order=21, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Amino acids that overlap with the features being described",
formalDefinition="Amino acids that overlap with the features being described"
)
private java.util.List<StringDt> myVariantAA;
@Child(name="referenceAA", type=StringDt.class, order=22, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Amino acids that overlaps with the reference sequence",
formalDefinition="Amino acids that overlaps with the reference sequence"
)
private java.util.List<StringDt> myReferenceAA;
@Child(name="breakpointDetail", order=23, min=0, max=1)
@Description(
shortDefinition="Coordinate of a variant with zero length",
formalDefinition="Coordinate of a variant with zero length"
)
private BreakpointDetail myBreakpointDetail;
@Child(name="sequenceContext", order=24, min=0, max=1)
@Description(
shortDefinition="Context of features being described",
formalDefinition="Sequences adjacent to the feature"
)
private SequenceContext mySequenceContext;
@Child(name="individual", type=StringDt.class, order=25, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Individuals being described",
formalDefinition="Individuals for whom the feature is described"
)
private java.util.List<StringDt> myIndividual;
@Child(name="sample", order=26, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Individual genotypic information",
formalDefinition="Individual genotypic information"
)
private java.util.List<Sample> mySample;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( mySubject, myMeta, mySourceFile, mySeqid, mySource, myType, myStart, myEnd, myScore, myStrand, myFeatureId, myAlias, myDbxref, myVariantSeq, myReferenceSeq, myVariantFreq, myVariantEffect, myStartRange, myEndRange, myVariantCodon, myReferenceCodon, myVariantAA, myReferenceAA, myBreakpointDetail, mySequenceContext, myIndividual, mySample);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, mySubject, myMeta, mySourceFile, mySeqid, mySource, myType, myStart, myEnd, myScore, myStrand, myFeatureId, myAlias, myDbxref, myVariantSeq, myReferenceSeq, myVariantFreq, myVariantEffect, myStartRange, myEndRange, myVariantCodon, myReferenceCodon, myVariantAA, myReferenceAA, myBreakpointDetail, mySequenceContext, myIndividual, mySample);
}
/**
* Gets the value(s) for <b>subject</b> (Subject described by this segment of GVF file).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Subject described by this segment of GVF file
* </p>
*/
public Subject getSubject() {
if (mySubject == null) {
mySubject = new Subject();
}
return mySubject;
}
/**
* Sets the value(s) for <b>subject</b> (Subject described by this segment of GVF file)
*
* <p>
* <b>Definition:</b>
* Subject described by this segment of GVF file
* </p>
*/
public GVFVariant setSubject(Subject theValue) {
mySubject = theValue;
return this;
}
/**
* Gets the value(s) for <b>meta</b> (GVF Meta).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Meta information of a GVF file
* </p>
*/
public ResourceReferenceDt getMeta() {
if (myMeta == null) {
myMeta = new ResourceReferenceDt();
}
return myMeta;
}
/**
* Sets the value(s) for <b>meta</b> (GVF Meta)
*
* <p>
* <b>Definition:</b>
* Meta information of a GVF file
* </p>
*/
public GVFVariant setMeta(ResourceReferenceDt theValue) {
myMeta = theValue;
return this;
}
/**
* Gets the value(s) for <b>sourceFile</b> (Source file).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Source GVF file
* </p>
*/
public AttachmentDt getSourceFile() {
if (mySourceFile == null) {
mySourceFile = new AttachmentDt();
}
return mySourceFile;
}
/**
* Sets the value(s) for <b>sourceFile</b> (Source file)
*
* <p>
* <b>Definition:</b>
* Source GVF file
* </p>
*/
public GVFVariant setSourceFile(AttachmentDt theValue) {
mySourceFile = theValue;
return this;
}
/**
* Gets the value(s) for <b>seqid</b> (Sequence Id).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Id the sequence being described
* </p>
*/
public StringDt getSeqid() {
if (mySeqid == null) {
mySeqid = new StringDt();
}
return mySeqid;
}
/**
* Sets the value(s) for <b>seqid</b> (Sequence Id)
*
* <p>
* <b>Definition:</b>
* Id the sequence being described
* </p>
*/
public GVFVariant setSeqid(StringDt theValue) {
mySeqid = theValue;
return this;
}
/**
* Sets the value for <b>seqid</b> (Sequence Id)
*
* <p>
* <b>Definition:</b>
* Id the sequence being described
* </p>
*/
public GVFVariant setSeqid( String theString) {
mySeqid = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>source</b> (Data source).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Algorithm or software used to generate the data
* </p>
*/
public StringDt getSource() {
if (mySource == null) {
mySource = new StringDt();
}
return mySource;
}
/**
* Sets the value(s) for <b>source</b> (Data source)
*
* <p>
* <b>Definition:</b>
* Algorithm or software used to generate the data
* </p>
*/
public GVFVariant setSource(StringDt theValue) {
mySource = theValue;
return this;
}
/**
* Sets the value for <b>source</b> (Data source)
*
* <p>
* <b>Definition:</b>
* Algorithm or software used to generate the data
* </p>
*/
public GVFVariant setSource( String theString) {
mySource = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>type</b> (Feature type).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public CodeDt getType() {
if (myType == null) {
myType = new CodeDt();
}
return myType;
}
/**
* Sets the value(s) for <b>type</b> (Feature type)
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public GVFVariant setType(CodeDt theValue) {
myType = theValue;
return this;
}
/**
* Sets the value for <b>type</b> (Feature type)
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public GVFVariant setType( String theCode) {
myType = new CodeDt(theCode);
return this;
}
/**
* Gets the value(s) for <b>start</b> (Start position).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public IntegerDt getStart() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Sets the value(s) for <b>start</b> (Start position)
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public GVFVariant setStart(IntegerDt theValue) {
myStart = theValue;
return this;
}
/**
* Sets the value for <b>start</b> (Start position)
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public GVFVariant setStart( int theInteger) {
myStart = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>end</b> (End position).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public IntegerDt getEnd() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Sets the value(s) for <b>end</b> (End position)
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public GVFVariant setEnd(IntegerDt theValue) {
myEnd = theValue;
return this;
}
/**
* Sets the value for <b>end</b> (End position)
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public GVFVariant setEnd( int theInteger) {
myEnd = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>score</b> (Sequence score).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Phred scaled score of the sequence
* </p>
*/
public IntegerDt getScore() {
if (myScore == null) {
myScore = new IntegerDt();
}
return myScore;
}
/**
* Sets the value(s) for <b>score</b> (Sequence score)
*
* <p>
* <b>Definition:</b>
* Phred scaled score of the sequence
* </p>
*/
public GVFVariant setScore(IntegerDt theValue) {
myScore = theValue;
return this;
}
/**
* Sets the value for <b>score</b> (Sequence score)
*
* <p>
* <b>Definition:</b>
* Phred scaled score of the sequence
* </p>
*/
public GVFVariant setScore( int theInteger) {
myScore = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>strand</b> (Strand).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Direction of the strand
* </p>
*/
public CodeDt getStrand() {
if (myStrand == null) {
myStrand = new CodeDt();
}
return myStrand;
}
/**
* Sets the value(s) for <b>strand</b> (Strand)
*
* <p>
* <b>Definition:</b>
* Direction of the strand
* </p>
*/
public GVFVariant setStrand(CodeDt theValue) {
myStrand = theValue;
return this;
}
/**
* Sets the value for <b>strand</b> (Strand)
*
* <p>
* <b>Definition:</b>
* Direction of the strand
* </p>
*/
public GVFVariant setStrand( String theCode) {
myStrand = new CodeDt(theCode);
return this;
}
/**
* Gets the value(s) for <b>featureId</b> (Id of the feature).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Id of the attribute, unique to other segments in the same source file
* </p>
*/
public StringDt getFeatureId() {
if (myFeatureId == null) {
myFeatureId = new StringDt();
}
return myFeatureId;
}
/**
* Sets the value(s) for <b>featureId</b> (Id of the feature)
*
* <p>
* <b>Definition:</b>
* Id of the attribute, unique to other segments in the same source file
* </p>
*/
public GVFVariant setFeatureId(StringDt theValue) {
myFeatureId = theValue;
return this;
}
/**
* Sets the value for <b>featureId</b> (Id of the feature)
*
* <p>
* <b>Definition:</b>
* Id of the attribute, unique to other segments in the same source file
* </p>
*/
public GVFVariant setFeatureId( String theString) {
myFeatureId = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>alias</b> (Alias of the feature).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Alias of the feature being described
* </p>
*/
public StringDt getAlias() {
if (myAlias == null) {
myAlias = new StringDt();
}
return myAlias;
}
/**
* Sets the value(s) for <b>alias</b> (Alias of the feature)
*
* <p>
* <b>Definition:</b>
* Alias of the feature being described
* </p>
*/
public GVFVariant setAlias(StringDt theValue) {
myAlias = theValue;
return this;
}
/**
* Sets the value for <b>alias</b> (Alias of the feature)
*
* <p>
* <b>Definition:</b>
* Alias of the feature being described
* </p>
*/
public GVFVariant setAlias( String theString) {
myAlias = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>dbxref</b> (Reference of the feature in a database).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Reference of the feature in a database
* </p>
*/
public Dbxref getDbxref() {
if (myDbxref == null) {
myDbxref = new Dbxref();
}
return myDbxref;
}
/**
* Sets the value(s) for <b>dbxref</b> (Reference of the feature in a database)
*
* <p>
* <b>Definition:</b>
* Reference of the feature in a database
* </p>
*/
public GVFVariant setDbxref(Dbxref theValue) {
myDbxref = theValue;
return this;
}
/**
* Gets the value(s) for <b>variantSeq</b> (Sequence presents in the variant).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Sequence presents in the variant
* </p>
*/
public java.util.List<StringDt> getVariantSeq() {
if (myVariantSeq == null) {
myVariantSeq = new java.util.ArrayList<StringDt>();
}
return myVariantSeq;
}
/**
* Sets the value(s) for <b>variantSeq</b> (Sequence presents in the variant)
*
* <p>
* <b>Definition:</b>
* Sequence presents in the variant
* </p>
*/
public GVFVariant setVariantSeq(java.util.List<StringDt> theValue) {
myVariantSeq = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantSeq</b> (Sequence presents in the variant)
*
* <p>
* <b>Definition:</b>
* Sequence presents in the variant
* </p>
*/
public StringDt addVariantSeq() {
StringDt newType = new StringDt();
getVariantSeq().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantSeq</b> (Sequence presents in the variant),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Sequence presents in the variant
* </p>
*/
public StringDt getVariantSeqFirstRep() {
if (getVariantSeq().isEmpty()) {
return addVariantSeq();
}
return getVariantSeq().get(0);
}
/**
* Adds a new value for <b>variantSeq</b> (Sequence presents in the variant)
*
* <p>
* <b>Definition:</b>
* Sequence presents in the variant
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantSeq( String theString) {
if (myVariantSeq == null) {
myVariantSeq = new java.util.ArrayList<StringDt>();
}
myVariantSeq.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>referenceSeq</b> (Reference sequence).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Reference sequence
* </p>
*/
public StringDt getReferenceSeq() {
if (myReferenceSeq == null) {
myReferenceSeq = new StringDt();
}
return myReferenceSeq;
}
/**
* Sets the value(s) for <b>referenceSeq</b> (Reference sequence)
*
* <p>
* <b>Definition:</b>
* Reference sequence
* </p>
*/
public GVFVariant setReferenceSeq(StringDt theValue) {
myReferenceSeq = theValue;
return this;
}
/**
* Sets the value for <b>referenceSeq</b> (Reference sequence)
*
* <p>
* <b>Definition:</b>
* Reference sequence
* </p>
*/
public GVFVariant setReferenceSeq( String theString) {
myReferenceSeq = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>variantFreq</b> (Variant frequency).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*/
public java.util.List<DecimalDt> getVariantFreq() {
if (myVariantFreq == null) {
myVariantFreq = new java.util.ArrayList<DecimalDt>();
}
return myVariantFreq;
}
/**
* Sets the value(s) for <b>variantFreq</b> (Variant frequency)
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*/
public GVFVariant setVariantFreq(java.util.List<DecimalDt> theValue) {
myVariantFreq = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantFreq</b> (Variant frequency)
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*/
public DecimalDt addVariantFreq() {
DecimalDt newType = new DecimalDt();
getVariantFreq().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantFreq</b> (Variant frequency),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*/
public DecimalDt getVariantFreqFirstRep() {
if (getVariantFreq().isEmpty()) {
return addVariantFreq();
}
return getVariantFreq().get(0);
}
/**
* Adds a new value for <b>variantFreq</b> (Variant frequency)
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantFreq( long theValue) {
if (myVariantFreq == null) {
myVariantFreq = new java.util.ArrayList<DecimalDt>();
}
myVariantFreq.add(new DecimalDt(theValue));
return this;
}
/**
* Adds a new value for <b>variantFreq</b> (Variant frequency)
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantFreq( double theValue) {
if (myVariantFreq == null) {
myVariantFreq = new java.util.ArrayList<DecimalDt>();
}
myVariantFreq.add(new DecimalDt(theValue));
return this;
}
/**
* Adds a new value for <b>variantFreq</b> (Variant frequency)
*
* <p>
* <b>Definition:</b>
* Frequency of the variant
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantFreq( java.math.BigDecimal theValue) {
if (myVariantFreq == null) {
myVariantFreq = new java.util.ArrayList<DecimalDt>();
}
myVariantFreq.add(new DecimalDt(theValue));
return this;
}
/**
* Gets the value(s) for <b>variantEffect</b> (Variant effect).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public java.util.List<VariantEffect> getVariantEffect() {
if (myVariantEffect == null) {
myVariantEffect = new java.util.ArrayList<VariantEffect>();
}
return myVariantEffect;
}
/**
* Sets the value(s) for <b>variantEffect</b> (Variant effect)
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public GVFVariant setVariantEffect(java.util.List<VariantEffect> theValue) {
myVariantEffect = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantEffect</b> (Variant effect)
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public VariantEffect addVariantEffect() {
VariantEffect newType = new VariantEffect();
getVariantEffect().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantEffect</b> (Variant effect),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public VariantEffect getVariantEffectFirstRep() {
if (getVariantEffect().isEmpty()) {
return addVariantEffect();
}
return getVariantEffect().get(0);
}
/**
* Gets the value(s) for <b>startRange</b> (Start range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the start position of the feature
* </p>
*/
public StartRange getStartRange() {
if (myStartRange == null) {
myStartRange = new StartRange();
}
return myStartRange;
}
/**
* Sets the value(s) for <b>startRange</b> (Start range)
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the start position of the feature
* </p>
*/
public GVFVariant setStartRange(StartRange theValue) {
myStartRange = theValue;
return this;
}
/**
* Gets the value(s) for <b>endRange</b> (End range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the end position of the feature
* </p>
*/
public EndRange getEndRange() {
if (myEndRange == null) {
myEndRange = new EndRange();
}
return myEndRange;
}
/**
* Sets the value(s) for <b>endRange</b> (End range)
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the end position of the feature
* </p>
*/
public GVFVariant setEndRange(EndRange theValue) {
myEndRange = theValue;
return this;
}
/**
* Gets the value(s) for <b>variantCodon</b> (Codons that overlap with feature being described).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Codons that overlap with the feature being described
* </p>
*/
public java.util.List<StringDt> getVariantCodon() {
if (myVariantCodon == null) {
myVariantCodon = new java.util.ArrayList<StringDt>();
}
return myVariantCodon;
}
/**
* Sets the value(s) for <b>variantCodon</b> (Codons that overlap with feature being described)
*
* <p>
* <b>Definition:</b>
* Codons that overlap with the feature being described
* </p>
*/
public GVFVariant setVariantCodon(java.util.List<StringDt> theValue) {
myVariantCodon = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantCodon</b> (Codons that overlap with feature being described)
*
* <p>
* <b>Definition:</b>
* Codons that overlap with the feature being described
* </p>
*/
public StringDt addVariantCodon() {
StringDt newType = new StringDt();
getVariantCodon().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantCodon</b> (Codons that overlap with feature being described),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Codons that overlap with the feature being described
* </p>
*/
public StringDt getVariantCodonFirstRep() {
if (getVariantCodon().isEmpty()) {
return addVariantCodon();
}
return getVariantCodon().get(0);
}
/**
* Adds a new value for <b>variantCodon</b> (Codons that overlap with feature being described)
*
* <p>
* <b>Definition:</b>
* Codons that overlap with the feature being described
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantCodon( String theString) {
if (myVariantCodon == null) {
myVariantCodon = new java.util.ArrayList<StringDt>();
}
myVariantCodon.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>referenceCodon</b> (Codon that overlap with the reference sequence).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Codon that overlap with the reference sequence
* </p>
*/
public StringDt getReferenceCodon() {
if (myReferenceCodon == null) {
myReferenceCodon = new StringDt();
}
return myReferenceCodon;
}
/**
* Sets the value(s) for <b>referenceCodon</b> (Codon that overlap with the reference sequence)
*
* <p>
* <b>Definition:</b>
* Codon that overlap with the reference sequence
* </p>
*/
public GVFVariant setReferenceCodon(StringDt theValue) {
myReferenceCodon = theValue;
return this;
}
/**
* Sets the value for <b>referenceCodon</b> (Codon that overlap with the reference sequence)
*
* <p>
* <b>Definition:</b>
* Codon that overlap with the reference sequence
* </p>
*/
public GVFVariant setReferenceCodon( String theString) {
myReferenceCodon = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>variantAA</b> (Amino acids that overlap with the features being described).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Amino acids that overlap with the features being described
* </p>
*/
public java.util.List<StringDt> getVariantAA() {
if (myVariantAA == null) {
myVariantAA = new java.util.ArrayList<StringDt>();
}
return myVariantAA;
}
/**
* Sets the value(s) for <b>variantAA</b> (Amino acids that overlap with the features being described)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlap with the features being described
* </p>
*/
public GVFVariant setVariantAA(java.util.List<StringDt> theValue) {
myVariantAA = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantAA</b> (Amino acids that overlap with the features being described)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlap with the features being described
* </p>
*/
public StringDt addVariantAA() {
StringDt newType = new StringDt();
getVariantAA().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantAA</b> (Amino acids that overlap with the features being described),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Amino acids that overlap with the features being described
* </p>
*/
public StringDt getVariantAAFirstRep() {
if (getVariantAA().isEmpty()) {
return addVariantAA();
}
return getVariantAA().get(0);
}
/**
* Adds a new value for <b>variantAA</b> (Amino acids that overlap with the features being described)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlap with the features being described
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addVariantAA( String theString) {
if (myVariantAA == null) {
myVariantAA = new java.util.ArrayList<StringDt>();
}
myVariantAA.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>referenceAA</b> (Amino acids that overlaps with the reference sequence).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Amino acids that overlaps with the reference sequence
* </p>
*/
public java.util.List<StringDt> getReferenceAA() {
if (myReferenceAA == null) {
myReferenceAA = new java.util.ArrayList<StringDt>();
}
return myReferenceAA;
}
/**
* Sets the value(s) for <b>referenceAA</b> (Amino acids that overlaps with the reference sequence)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlaps with the reference sequence
* </p>
*/
public GVFVariant setReferenceAA(java.util.List<StringDt> theValue) {
myReferenceAA = theValue;
return this;
}
/**
* Adds and returns a new value for <b>referenceAA</b> (Amino acids that overlaps with the reference sequence)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlaps with the reference sequence
* </p>
*/
public StringDt addReferenceAA() {
StringDt newType = new StringDt();
getReferenceAA().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>referenceAA</b> (Amino acids that overlaps with the reference sequence),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Amino acids that overlaps with the reference sequence
* </p>
*/
public StringDt getReferenceAAFirstRep() {
if (getReferenceAA().isEmpty()) {
return addReferenceAA();
}
return getReferenceAA().get(0);
}
/**
* Adds a new value for <b>referenceAA</b> (Amino acids that overlaps with the reference sequence)
*
* <p>
* <b>Definition:</b>
* Amino acids that overlaps with the reference sequence
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addReferenceAA( String theString) {
if (myReferenceAA == null) {
myReferenceAA = new java.util.ArrayList<StringDt>();
}
myReferenceAA.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>breakpointDetail</b> (Coordinate of a variant with zero length).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Coordinate of a variant with zero length
* </p>
*/
public BreakpointDetail getBreakpointDetail() {
if (myBreakpointDetail == null) {
myBreakpointDetail = new BreakpointDetail();
}
return myBreakpointDetail;
}
/**
* Sets the value(s) for <b>breakpointDetail</b> (Coordinate of a variant with zero length)
*
* <p>
* <b>Definition:</b>
* Coordinate of a variant with zero length
* </p>
*/
public GVFVariant setBreakpointDetail(BreakpointDetail theValue) {
myBreakpointDetail = theValue;
return this;
}
/**
* Gets the value(s) for <b>sequenceContext</b> (Context of features being described).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Sequences adjacent to the feature
* </p>
*/
public SequenceContext getSequenceContext() {
if (mySequenceContext == null) {
mySequenceContext = new SequenceContext();
}
return mySequenceContext;
}
/**
* Sets the value(s) for <b>sequenceContext</b> (Context of features being described)
*
* <p>
* <b>Definition:</b>
* Sequences adjacent to the feature
* </p>
*/
public GVFVariant setSequenceContext(SequenceContext theValue) {
mySequenceContext = theValue;
return this;
}
/**
* Gets the value(s) for <b>individual</b> (Individuals being described).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Individuals for whom the feature is described
* </p>
*/
public java.util.List<StringDt> getIndividual() {
if (myIndividual == null) {
myIndividual = new java.util.ArrayList<StringDt>();
}
return myIndividual;
}
/**
* Sets the value(s) for <b>individual</b> (Individuals being described)
*
* <p>
* <b>Definition:</b>
* Individuals for whom the feature is described
* </p>
*/
public GVFVariant setIndividual(java.util.List<StringDt> theValue) {
myIndividual = theValue;
return this;
}
/**
* Adds and returns a new value for <b>individual</b> (Individuals being described)
*
* <p>
* <b>Definition:</b>
* Individuals for whom the feature is described
* </p>
*/
public StringDt addIndividual() {
StringDt newType = new StringDt();
getIndividual().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>individual</b> (Individuals being described),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Individuals for whom the feature is described
* </p>
*/
public StringDt getIndividualFirstRep() {
if (getIndividual().isEmpty()) {
return addIndividual();
}
return getIndividual().get(0);
}
/**
* Adds a new value for <b>individual</b> (Individuals being described)
*
* <p>
* <b>Definition:</b>
* Individuals for whom the feature is described
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public GVFVariant addIndividual( String theString) {
if (myIndividual == null) {
myIndividual = new java.util.ArrayList<StringDt>();
}
myIndividual.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>sample</b> (Individual genotypic information).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Individual genotypic information
* </p>
*/
public java.util.List<Sample> getSample() {
if (mySample == null) {
mySample = new java.util.ArrayList<Sample>();
}
return mySample;
}
/**
* Sets the value(s) for <b>sample</b> (Individual genotypic information)
*
* <p>
* <b>Definition:</b>
* Individual genotypic information
* </p>
*/
public GVFVariant setSample(java.util.List<Sample> theValue) {
mySample = theValue;
return this;
}
/**
* Adds and returns a new value for <b>sample</b> (Individual genotypic information)
*
* <p>
* <b>Definition:</b>
* Individual genotypic information
* </p>
*/
public Sample addSample() {
Sample newType = new Sample();
getSample().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>sample</b> (Individual genotypic information),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Individual genotypic information
* </p>
*/
public Sample getSampleFirstRep() {
if (getSample().isEmpty()) {
return addSample();
}
return getSample().get(0);
}
/**
* Block class for child element: <b>GVFVariant.subject</b> (Subject described by this segment of GVF file)
*
* <p>
* <b>Definition:</b>
* Subject described by this segment of GVF file
* </p>
*/
@Block()
public static class Subject extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="patient", order=0, min=1, max=1, type={
ca.uhn.fhir.model.dstu.resource.Patient.class })
@Description(
shortDefinition="Subject",
formalDefinition="Patient resource that stores information of the subejct"
)
private ResourceReferenceDt myPatient;
@Child(name="fileId", type=StringDt.class, order=1, min=0, max=1)
@Description(
shortDefinition="Individual Id",
formalDefinition="Id of individual in GVF file that corresponds to the subject (only mandatory if the file is a multi-individual one"
)
private StringDt myFileId;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myPatient, myFileId);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myPatient, myFileId);
}
/**
* Gets the value(s) for <b>patient</b> (Subject).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Patient resource that stores information of the subejct
* </p>
*/
public ResourceReferenceDt getPatient() {
if (myPatient == null) {
myPatient = new ResourceReferenceDt();
}
return myPatient;
}
/**
* Sets the value(s) for <b>patient</b> (Subject)
*
* <p>
* <b>Definition:</b>
* Patient resource that stores information of the subejct
* </p>
*/
public Subject setPatient(ResourceReferenceDt theValue) {
myPatient = theValue;
return this;
}
/**
* Gets the value(s) for <b>fileId</b> (Individual Id).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Id of individual in GVF file that corresponds to the subject (only mandatory if the file is a multi-individual one
* </p>
*/
public StringDt getFileId() {
if (myFileId == null) {
myFileId = new StringDt();
}
return myFileId;
}
/**
* Sets the value(s) for <b>fileId</b> (Individual Id)
*
* <p>
* <b>Definition:</b>
* Id of individual in GVF file that corresponds to the subject (only mandatory if the file is a multi-individual one
* </p>
*/
public Subject setFileId(StringDt theValue) {
myFileId = theValue;
return this;
}
/**
* Sets the value for <b>fileId</b> (Individual Id)
*
* <p>
* <b>Definition:</b>
* Id of individual in GVF file that corresponds to the subject (only mandatory if the file is a multi-individual one
* </p>
*/
public Subject setFileId( String theString) {
myFileId = new StringDt(theString);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.dbxref</b> (Reference of the feature in a database)
*
* <p>
* <b>Definition:</b>
* Reference of the feature in a database
* </p>
*/
@Block()
public static class Dbxref extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="database", type=CodeDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="Name of the database",
formalDefinition="Name of the database"
)
private CodeDt myDatabase;
@Child(name="identity", type=StringDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="Id of the feature within the database",
formalDefinition="Id of the feature within the database"
)
private StringDt myIdentity;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myDatabase, myIdentity);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myDatabase, myIdentity);
}
/**
* Gets the value(s) for <b>database</b> (Name of the database).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Name of the database
* </p>
*/
public CodeDt getDatabase() {
if (myDatabase == null) {
myDatabase = new CodeDt();
}
return myDatabase;
}
/**
* Sets the value(s) for <b>database</b> (Name of the database)
*
* <p>
* <b>Definition:</b>
* Name of the database
* </p>
*/
public Dbxref setDatabase(CodeDt theValue) {
myDatabase = theValue;
return this;
}
/**
* Sets the value for <b>database</b> (Name of the database)
*
* <p>
* <b>Definition:</b>
* Name of the database
* </p>
*/
public Dbxref setDatabase( String theCode) {
myDatabase = new CodeDt(theCode);
return this;
}
/**
* Gets the value(s) for <b>identity</b> (Id of the feature within the database).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Id of the feature within the database
* </p>
*/
public StringDt getIdentity() {
if (myIdentity == null) {
myIdentity = new StringDt();
}
return myIdentity;
}
/**
* Sets the value(s) for <b>identity</b> (Id of the feature within the database)
*
* <p>
* <b>Definition:</b>
* Id of the feature within the database
* </p>
*/
public Dbxref setIdentity(StringDt theValue) {
myIdentity = theValue;
return this;
}
/**
* Sets the value for <b>identity</b> (Id of the feature within the database)
*
* <p>
* <b>Definition:</b>
* Id of the feature within the database
* </p>
*/
public Dbxref setIdentity( String theString) {
myIdentity = new StringDt(theString);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.variantEffect</b> (Variant effect)
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
@Block()
public static class VariantEffect extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="sequenceVariant", type=CodeDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="Effect of the variant",
formalDefinition="Effect of the variant"
)
private CodeDt mySequenceVariant;
@Child(name="index", type=IntegerDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="Index of variant being discussed",
formalDefinition="Zero-based index that tells the variant being discussed"
)
private IntegerDt myIndex;
@Child(name="featureType", type=CodeDt.class, order=2, min=1, max=1)
@Description(
shortDefinition="Feature type",
formalDefinition="Type of the feature being described"
)
private CodeDt myFeatureType;
@Child(name="featureId", type=StringDt.class, order=3, min=1, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Feature Id",
formalDefinition="Id of features being affected by the variant"
)
private java.util.List<StringDt> myFeatureId;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( mySequenceVariant, myIndex, myFeatureType, myFeatureId);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, mySequenceVariant, myIndex, myFeatureType, myFeatureId);
}
/**
* Gets the value(s) for <b>sequenceVariant</b> (Effect of the variant).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public CodeDt getSequenceVariant() {
if (mySequenceVariant == null) {
mySequenceVariant = new CodeDt();
}
return mySequenceVariant;
}
/**
* Sets the value(s) for <b>sequenceVariant</b> (Effect of the variant)
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public VariantEffect setSequenceVariant(CodeDt theValue) {
mySequenceVariant = theValue;
return this;
}
/**
* Sets the value for <b>sequenceVariant</b> (Effect of the variant)
*
* <p>
* <b>Definition:</b>
* Effect of the variant
* </p>
*/
public VariantEffect setSequenceVariant( String theCode) {
mySequenceVariant = new CodeDt(theCode);
return this;
}
/**
* Gets the value(s) for <b>index</b> (Index of variant being discussed).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Zero-based index that tells the variant being discussed
* </p>
*/
public IntegerDt getIndex() {
if (myIndex == null) {
myIndex = new IntegerDt();
}
return myIndex;
}
/**
* Sets the value(s) for <b>index</b> (Index of variant being discussed)
*
* <p>
* <b>Definition:</b>
* Zero-based index that tells the variant being discussed
* </p>
*/
public VariantEffect setIndex(IntegerDt theValue) {
myIndex = theValue;
return this;
}
/**
* Sets the value for <b>index</b> (Index of variant being discussed)
*
* <p>
* <b>Definition:</b>
* Zero-based index that tells the variant being discussed
* </p>
*/
public VariantEffect setIndex( int theInteger) {
myIndex = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>featureType</b> (Feature type).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public CodeDt getFeatureType() {
if (myFeatureType == null) {
myFeatureType = new CodeDt();
}
return myFeatureType;
}
/**
* Sets the value(s) for <b>featureType</b> (Feature type)
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public VariantEffect setFeatureType(CodeDt theValue) {
myFeatureType = theValue;
return this;
}
/**
* Sets the value for <b>featureType</b> (Feature type)
*
* <p>
* <b>Definition:</b>
* Type of the feature being described
* </p>
*/
public VariantEffect setFeatureType( String theCode) {
myFeatureType = new CodeDt(theCode);
return this;
}
/**
* Gets the value(s) for <b>featureId</b> (Feature Id).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Id of features being affected by the variant
* </p>
*/
public java.util.List<StringDt> getFeatureId() {
if (myFeatureId == null) {
myFeatureId = new java.util.ArrayList<StringDt>();
}
return myFeatureId;
}
/**
* Sets the value(s) for <b>featureId</b> (Feature Id)
*
* <p>
* <b>Definition:</b>
* Id of features being affected by the variant
* </p>
*/
public VariantEffect setFeatureId(java.util.List<StringDt> theValue) {
myFeatureId = theValue;
return this;
}
/**
* Adds and returns a new value for <b>featureId</b> (Feature Id)
*
* <p>
* <b>Definition:</b>
* Id of features being affected by the variant
* </p>
*/
public StringDt addFeatureId() {
StringDt newType = new StringDt();
getFeatureId().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>featureId</b> (Feature Id),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Id of features being affected by the variant
* </p>
*/
public StringDt getFeatureIdFirstRep() {
if (getFeatureId().isEmpty()) {
return addFeatureId();
}
return getFeatureId().get(0);
}
/**
* Adds a new value for <b>featureId</b> (Feature Id)
*
* <p>
* <b>Definition:</b>
* Id of features being affected by the variant
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public VariantEffect addFeatureId( String theString) {
if (myFeatureId == null) {
myFeatureId = new java.util.ArrayList<StringDt>();
}
myFeatureId.add(new StringDt(theString));
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.startRange</b> (Start range)
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the start position of the feature
* </p>
*/
@Block()
public static class StartRange extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="start", type=IntegerDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="Start of the start range",
formalDefinition="Start of the start range"
)
private IntegerDt myStart;
@Child(name="end", type=IntegerDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="End of the start range",
formalDefinition="End of the start range"
)
private IntegerDt myEnd;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myStart, myEnd);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myStart, myEnd);
}
/**
* Gets the value(s) for <b>start</b> (Start of the start range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Start of the start range
* </p>
*/
public IntegerDt getStart() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Sets the value(s) for <b>start</b> (Start of the start range)
*
* <p>
* <b>Definition:</b>
* Start of the start range
* </p>
*/
public StartRange setStart(IntegerDt theValue) {
myStart = theValue;
return this;
}
/**
* Sets the value for <b>start</b> (Start of the start range)
*
* <p>
* <b>Definition:</b>
* Start of the start range
* </p>
*/
public StartRange setStart( int theInteger) {
myStart = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>end</b> (End of the start range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* End of the start range
* </p>
*/
public IntegerDt getEnd() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Sets the value(s) for <b>end</b> (End of the start range)
*
* <p>
* <b>Definition:</b>
* End of the start range
* </p>
*/
public StartRange setEnd(IntegerDt theValue) {
myEnd = theValue;
return this;
}
/**
* Sets the value for <b>end</b> (End of the start range)
*
* <p>
* <b>Definition:</b>
* End of the start range
* </p>
*/
public StartRange setEnd( int theInteger) {
myEnd = new IntegerDt(theInteger);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.endRange</b> (End range)
*
* <p>
* <b>Definition:</b>
* Attribute describing ambiguity of the end position of the feature
* </p>
*/
@Block()
public static class EndRange extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="start", type=IntegerDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="Start of the end range",
formalDefinition="Start of the end range"
)
private IntegerDt myStart;
@Child(name="end", type=IntegerDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="End of the end range",
formalDefinition="End of the end range"
)
private IntegerDt myEnd;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myStart, myEnd);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myStart, myEnd);
}
/**
* Gets the value(s) for <b>start</b> (Start of the end range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Start of the end range
* </p>
*/
public IntegerDt getStart() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Sets the value(s) for <b>start</b> (Start of the end range)
*
* <p>
* <b>Definition:</b>
* Start of the end range
* </p>
*/
public EndRange setStart(IntegerDt theValue) {
myStart = theValue;
return this;
}
/**
* Sets the value for <b>start</b> (Start of the end range)
*
* <p>
* <b>Definition:</b>
* Start of the end range
* </p>
*/
public EndRange setStart( int theInteger) {
myStart = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>end</b> (End of the end range).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* End of the end range
* </p>
*/
public IntegerDt getEnd() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Sets the value(s) for <b>end</b> (End of the end range)
*
* <p>
* <b>Definition:</b>
* End of the end range
* </p>
*/
public EndRange setEnd(IntegerDt theValue) {
myEnd = theValue;
return this;
}
/**
* Sets the value for <b>end</b> (End of the end range)
*
* <p>
* <b>Definition:</b>
* End of the end range
* </p>
*/
public EndRange setEnd( int theInteger) {
myEnd = new IntegerDt(theInteger);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.breakpointDetail</b> (Coordinate of a variant with zero length)
*
* <p>
* <b>Definition:</b>
* Coordinate of a variant with zero length
* </p>
*/
@Block()
public static class BreakpointDetail extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="seqid", type=StringDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="Sequence Id of the variant",
formalDefinition="Sequence Id of the variant"
)
private StringDt mySeqid;
@Child(name="start", type=IntegerDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="Start position",
formalDefinition="Start position"
)
private IntegerDt myStart;
@Child(name="end", type=IntegerDt.class, order=2, min=1, max=1)
@Description(
shortDefinition="End position",
formalDefinition="End position"
)
private IntegerDt myEnd;
@Child(name="strand", type=CodeDt.class, order=3, min=1, max=1)
@Description(
shortDefinition="Strand",
formalDefinition="Direction of strand"
)
private CodeDt myStrand;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( mySeqid, myStart, myEnd, myStrand);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, mySeqid, myStart, myEnd, myStrand);
}
/**
* Gets the value(s) for <b>seqid</b> (Sequence Id of the variant).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Sequence Id of the variant
* </p>
*/
public StringDt getSeqid() {
if (mySeqid == null) {
mySeqid = new StringDt();
}
return mySeqid;
}
/**
* Sets the value(s) for <b>seqid</b> (Sequence Id of the variant)
*
* <p>
* <b>Definition:</b>
* Sequence Id of the variant
* </p>
*/
public BreakpointDetail setSeqid(StringDt theValue) {
mySeqid = theValue;
return this;
}
/**
* Sets the value for <b>seqid</b> (Sequence Id of the variant)
*
* <p>
* <b>Definition:</b>
* Sequence Id of the variant
* </p>
*/
public BreakpointDetail setSeqid( String theString) {
mySeqid = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>start</b> (Start position).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public IntegerDt getStart() {
if (myStart == null) {
myStart = new IntegerDt();
}
return myStart;
}
/**
* Sets the value(s) for <b>start</b> (Start position)
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public BreakpointDetail setStart(IntegerDt theValue) {
myStart = theValue;
return this;
}
/**
* Sets the value for <b>start</b> (Start position)
*
* <p>
* <b>Definition:</b>
* Start position
* </p>
*/
public BreakpointDetail setStart( int theInteger) {
myStart = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>end</b> (End position).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public IntegerDt getEnd() {
if (myEnd == null) {
myEnd = new IntegerDt();
}
return myEnd;
}
/**
* Sets the value(s) for <b>end</b> (End position)
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public BreakpointDetail setEnd(IntegerDt theValue) {
myEnd = theValue;
return this;
}
/**
* Sets the value for <b>end</b> (End position)
*
* <p>
* <b>Definition:</b>
* End position
* </p>
*/
public BreakpointDetail setEnd( int theInteger) {
myEnd = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>strand</b> (Strand).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Direction of strand
* </p>
*/
public CodeDt getStrand() {
if (myStrand == null) {
myStrand = new CodeDt();
}
return myStrand;
}
/**
* Sets the value(s) for <b>strand</b> (Strand)
*
* <p>
* <b>Definition:</b>
* Direction of strand
* </p>
*/
public BreakpointDetail setStrand(CodeDt theValue) {
myStrand = theValue;
return this;
}
/**
* Sets the value for <b>strand</b> (Strand)
*
* <p>
* <b>Definition:</b>
* Direction of strand
* </p>
*/
public BreakpointDetail setStrand( String theCode) {
myStrand = new CodeDt(theCode);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.sequenceContext</b> (Context of features being described)
*
* <p>
* <b>Definition:</b>
* Sequences adjacent to the feature
* </p>
*/
@Block()
public static class SequenceContext extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="fivePrime", type=StringDt.class, order=0, min=1, max=1)
@Description(
shortDefinition="5 prime of the context",
formalDefinition="Sequence adjacent to the feature at its 5 prime"
)
private StringDt myFivePrime;
@Child(name="threePrime", type=StringDt.class, order=1, min=1, max=1)
@Description(
shortDefinition="3 prime of the context",
formalDefinition="Sequence adjacent to the feature at its 3 prime"
)
private StringDt myThreePrime;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myFivePrime, myThreePrime);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myFivePrime, myThreePrime);
}
/**
* Gets the value(s) for <b>fivePrime</b> (5 prime of the context).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 5 prime
* </p>
*/
public StringDt getFivePrime() {
if (myFivePrime == null) {
myFivePrime = new StringDt();
}
return myFivePrime;
}
/**
* Sets the value(s) for <b>fivePrime</b> (5 prime of the context)
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 5 prime
* </p>
*/
public SequenceContext setFivePrime(StringDt theValue) {
myFivePrime = theValue;
return this;
}
/**
* Sets the value for <b>fivePrime</b> (5 prime of the context)
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 5 prime
* </p>
*/
public SequenceContext setFivePrime( String theString) {
myFivePrime = new StringDt(theString);
return this;
}
/**
* Gets the value(s) for <b>threePrime</b> (3 prime of the context).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 3 prime
* </p>
*/
public StringDt getThreePrime() {
if (myThreePrime == null) {
myThreePrime = new StringDt();
}
return myThreePrime;
}
/**
* Sets the value(s) for <b>threePrime</b> (3 prime of the context)
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 3 prime
* </p>
*/
public SequenceContext setThreePrime(StringDt theValue) {
myThreePrime = theValue;
return this;
}
/**
* Sets the value for <b>threePrime</b> (3 prime of the context)
*
* <p>
* <b>Definition:</b>
* Sequence adjacent to the feature at its 3 prime
* </p>
*/
public SequenceContext setThreePrime( String theString) {
myThreePrime = new StringDt(theString);
return this;
}
}
/**
* Block class for child element: <b>GVFVariant.sample</b> (Individual genotypic information)
*
* <p>
* <b>Definition:</b>
* Individual genotypic information
* </p>
*/
@Block()
public static class Sample extends BaseIdentifiableElement implements IResourceBlock {
@Child(name="phased", type=StringDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Phase status of the sequence",
formalDefinition="Attribute describing the phasing of a sequence"
)
private java.util.List<StringDt> myPhased;
@Child(name="genotype", type=StringDt.class, order=1, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Genotype of individuals",
formalDefinition="Genotypes of the individual"
)
private java.util.List<StringDt> myGenotype;
@Child(name="variantReads", type=IntegerDt.class, order=2, min=0, max=Child.MAX_UNLIMITED)
@Description(
shortDefinition="Read number of the sequence",
formalDefinition="Renumber of the sequence"
)
private java.util.List<IntegerDt> myVariantReads;
@Child(name="totalReads", type=IntegerDt.class, order=3, min=0, max=1)
@Description(
shortDefinition="Total reads",
formalDefinition="Total reads of all sequence present in the sample"
)
private IntegerDt myTotalReads;
@Child(name="zygosity", type=CodeDt.class, order=4, min=0, max=1)
@Description(
shortDefinition="Zygosity",
formalDefinition="Zygosity of the sequences"
)
private CodeDt myZygosity;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myPhased, myGenotype, myVariantReads, myTotalReads, myZygosity);
}
@Override
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements(theType, myPhased, myGenotype, myVariantReads, myTotalReads, myZygosity);
}
/**
* Gets the value(s) for <b>phased</b> (Phase status of the sequence).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Attribute describing the phasing of a sequence
* </p>
*/
public java.util.List<StringDt> getPhased() {
if (myPhased == null) {
myPhased = new java.util.ArrayList<StringDt>();
}
return myPhased;
}
/**
* Sets the value(s) for <b>phased</b> (Phase status of the sequence)
*
* <p>
* <b>Definition:</b>
* Attribute describing the phasing of a sequence
* </p>
*/
public Sample setPhased(java.util.List<StringDt> theValue) {
myPhased = theValue;
return this;
}
/**
* Adds and returns a new value for <b>phased</b> (Phase status of the sequence)
*
* <p>
* <b>Definition:</b>
* Attribute describing the phasing of a sequence
* </p>
*/
public StringDt addPhased() {
StringDt newType = new StringDt();
getPhased().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>phased</b> (Phase status of the sequence),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Attribute describing the phasing of a sequence
* </p>
*/
public StringDt getPhasedFirstRep() {
if (getPhased().isEmpty()) {
return addPhased();
}
return getPhased().get(0);
}
/**
* Adds a new value for <b>phased</b> (Phase status of the sequence)
*
* <p>
* <b>Definition:</b>
* Attribute describing the phasing of a sequence
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public Sample addPhased( String theString) {
if (myPhased == null) {
myPhased = new java.util.ArrayList<StringDt>();
}
myPhased.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>genotype</b> (Genotype of individuals).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Genotypes of the individual
* </p>
*/
public java.util.List<StringDt> getGenotype() {
if (myGenotype == null) {
myGenotype = new java.util.ArrayList<StringDt>();
}
return myGenotype;
}
/**
* Sets the value(s) for <b>genotype</b> (Genotype of individuals)
*
* <p>
* <b>Definition:</b>
* Genotypes of the individual
* </p>
*/
public Sample setGenotype(java.util.List<StringDt> theValue) {
myGenotype = theValue;
return this;
}
/**
* Adds and returns a new value for <b>genotype</b> (Genotype of individuals)
*
* <p>
* <b>Definition:</b>
* Genotypes of the individual
* </p>
*/
public StringDt addGenotype() {
StringDt newType = new StringDt();
getGenotype().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>genotype</b> (Genotype of individuals),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Genotypes of the individual
* </p>
*/
public StringDt getGenotypeFirstRep() {
if (getGenotype().isEmpty()) {
return addGenotype();
}
return getGenotype().get(0);
}
/**
* Adds a new value for <b>genotype</b> (Genotype of individuals)
*
* <p>
* <b>Definition:</b>
* Genotypes of the individual
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public Sample addGenotype( String theString) {
if (myGenotype == null) {
myGenotype = new java.util.ArrayList<StringDt>();
}
myGenotype.add(new StringDt(theString));
return this;
}
/**
* Gets the value(s) for <b>variantReads</b> (Read number of the sequence).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Renumber of the sequence
* </p>
*/
public java.util.List<IntegerDt> getVariantReads() {
if (myVariantReads == null) {
myVariantReads = new java.util.ArrayList<IntegerDt>();
}
return myVariantReads;
}
/**
* Sets the value(s) for <b>variantReads</b> (Read number of the sequence)
*
* <p>
* <b>Definition:</b>
* Renumber of the sequence
* </p>
*/
public Sample setVariantReads(java.util.List<IntegerDt> theValue) {
myVariantReads = theValue;
return this;
}
/**
* Adds and returns a new value for <b>variantReads</b> (Read number of the sequence)
*
* <p>
* <b>Definition:</b>
* Renumber of the sequence
* </p>
*/
public IntegerDt addVariantReads() {
IntegerDt newType = new IntegerDt();
getVariantReads().add(newType);
return newType;
}
/**
* Gets the first repetition for <b>variantReads</b> (Read number of the sequence),
* creating it if it does not already exist.
*
* <p>
* <b>Definition:</b>
* Renumber of the sequence
* </p>
*/
public IntegerDt getVariantReadsFirstRep() {
if (getVariantReads().isEmpty()) {
return addVariantReads();
}
return getVariantReads().get(0);
}
/**
* Adds a new value for <b>variantReads</b> (Read number of the sequence)
*
* <p>
* <b>Definition:</b>
* Renumber of the sequence
* </p>
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public Sample addVariantReads( int theInteger) {
if (myVariantReads == null) {
myVariantReads = new java.util.ArrayList<IntegerDt>();
}
myVariantReads.add(new IntegerDt(theInteger));
return this;
}
/**
* Gets the value(s) for <b>totalReads</b> (Total reads).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Total reads of all sequence present in the sample
* </p>
*/
public IntegerDt getTotalReads() {
if (myTotalReads == null) {
myTotalReads = new IntegerDt();
}
return myTotalReads;
}
/**
* Sets the value(s) for <b>totalReads</b> (Total reads)
*
* <p>
* <b>Definition:</b>
* Total reads of all sequence present in the sample
* </p>
*/
public Sample setTotalReads(IntegerDt theValue) {
myTotalReads = theValue;
return this;
}
/**
* Sets the value for <b>totalReads</b> (Total reads)
*
* <p>
* <b>Definition:</b>
* Total reads of all sequence present in the sample
* </p>
*/
public Sample setTotalReads( int theInteger) {
myTotalReads = new IntegerDt(theInteger);
return this;
}
/**
* Gets the value(s) for <b>zygosity</b> (Zygosity).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* Zygosity of the sequences
* </p>
*/
public CodeDt getZygosity() {
if (myZygosity == null) {
myZygosity = new CodeDt();
}
return myZygosity;
}
/**
* Sets the value(s) for <b>zygosity</b> (Zygosity)
*
* <p>
* <b>Definition:</b>
* Zygosity of the sequences
* </p>
*/
public Sample setZygosity(CodeDt theValue) {
myZygosity = theValue;
return this;
}
/**
* Sets the value for <b>zygosity</b> (Zygosity)
*
* <p>
* <b>Definition:</b>
* Zygosity of the sequences
* </p>
*/
public Sample setZygosity( String theCode) {
myZygosity = new CodeDt(theCode);
return this;
}
}
}