GVFVariant (HAPI FHIR - Core Library 0.7 API)

java.lang.Object
- ca.uhn.fhir.model.api.BaseElement
- - ca.uhn.fhir.model.api.BaseResource
  - - ca.uhn.fhir.model.dstu.resource.GVFVariant

All Implemented Interfaces:

ICompositeElement, IElement, IResource, ISupportsUndeclaredExtensions
```
public class GVFVariant
extends BaseResource
implements IResource
```
HAPI/FHIR GVFVariant Resource (GVF Variant)
Definition: A segment of a GVF file

Requirements:

Profile Definition: http://hl7.org/fhir/profiles/GVFVariant

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`GVFVariant.BreakpointDetail` Block class for child element: GVFVariant.breakpointDetail (Coordinate of a variant with zero length)
`static class`	`GVFVariant.Dbxref` Block class for child element: GVFVariant.dbxref (Reference of the feature in a database)
`static class`	`GVFVariant.EndRange` Block class for child element: GVFVariant.endRange (End range)
`static class`	`GVFVariant.Sample` Block class for child element: GVFVariant.sample (Individual genotypic information)
`static class`	`GVFVariant.SequenceContext` Block class for child element: GVFVariant.sequenceContext (Context of features being described)
`static class`	`GVFVariant.StartRange` Block class for child element: GVFVariant.startRange (Start range)
`static class`	`GVFVariant.Subject` Block class for child element: GVFVariant.subject (Subject described by this segment of GVF file)
`static class`	`GVFVariant.VariantEffect` Block class for child element: GVFVariant.variantEffect (Variant effect)

Field Summary

Fields
Modifier and Type	Field and Description
`static StringClientParam`	`COORDINATE` Fluent Client search parameter constant for coordinate
`static Include`	`INCLUDE_SUBJECT_PATIENT` Constant for fluent queries to be used to add include statements.
`static ReferenceClientParam`	`PATIENT` Fluent Client search parameter constant for patient
`static String`	`SP_COORDINATE` Search parameter constant for coordinate
`static String`	`SP_PATIENT` Search parameter constant for patient

Fields inherited from class ca.uhn.fhir.model.api.BaseResource
SP_RES_ID, SP_RES_LANGUAGE

Constructor Summary

Constructors
Constructor and Description

GVFVariant()

Constructors
Constructor and Description
`GVFVariant()`

Method Summary

Methods
Modifier and Type	Method and Description
`StringDt`	`addIndividual()` Adds and returns a new value for individual (Individuals being described)
`GVFVariant`	`addIndividual(String theString)` Adds a new value for individual (Individuals being described)
`StringDt`	`addReferenceAA()` Adds and returns a new value for referenceAA (Amino acids that overlaps with the reference sequence)
`GVFVariant`	`addReferenceAA(String theString)` Adds a new value for referenceAA (Amino acids that overlaps with the reference sequence)
`GVFVariant.Sample`	`addSample()` Adds and returns a new value for sample (Individual genotypic information)
`StringDt`	`addVariantAA()` Adds and returns a new value for variantAA (Amino acids that overlap with the features being described)
`GVFVariant`	`addVariantAA(String theString)` Adds a new value for variantAA (Amino acids that overlap with the features being described)
`StringDt`	`addVariantCodon()` Adds and returns a new value for variantCodon (Codons that overlap with feature being described)
`GVFVariant`	`addVariantCodon(String theString)` Adds a new value for variantCodon (Codons that overlap with feature being described)
`GVFVariant.VariantEffect`	`addVariantEffect()` Adds and returns a new value for variantEffect (Variant effect)
`DecimalDt`	`addVariantFreq()` Adds and returns a new value for variantFreq (Variant frequency)
`GVFVariant`	`addVariantFreq(BigDecimal theValue)` Adds a new value for variantFreq (Variant frequency)
`GVFVariant`	`addVariantFreq(double theValue)` Adds a new value for variantFreq (Variant frequency)
`GVFVariant`	`addVariantFreq(long theValue)` Adds a new value for variantFreq (Variant frequency)
`StringDt`	`addVariantSeq()` Adds and returns a new value for variantSeq (Sequence presents in the variant)
`GVFVariant`	`addVariantSeq(String theString)` Adds a new value for variantSeq (Sequence presents in the variant)
`StringDt`	`getAlias()` Gets the value(s) for alias (Alias of the feature).
`<T extends IElement> List<T>`	`getAllPopulatedChildElementsOfType(Class<T> theType)` Returns a list containing all child elements matching a given type
`GVFVariant.BreakpointDetail`	`getBreakpointDetail()` Gets the value(s) for breakpointDetail (Coordinate of a variant with zero length).
`GVFVariant.Dbxref`	`getDbxref()` Gets the value(s) for dbxref (Reference of the feature in a database).
`IntegerDt`	`getEnd()` Gets the value(s) for end (End position).
`GVFVariant.EndRange`	`getEndRange()` Gets the value(s) for endRange (End range).
`StringDt`	`getFeatureId()` Gets the value(s) for featureId (Id of the feature).
`List<StringDt>`	`getIndividual()` Gets the value(s) for individual (Individuals being described).
`StringDt`	`getIndividualFirstRep()` Gets the first repetition for individual (Individuals being described), creating it if it does not already exist.
`ResourceReferenceDt`	`getMeta()` Gets the value(s) for meta (GVF Meta).
`List<StringDt>`	`getReferenceAA()` Gets the value(s) for referenceAA (Amino acids that overlaps with the reference sequence).
`StringDt`	`getReferenceAAFirstRep()` Gets the first repetition for referenceAA (Amino acids that overlaps with the reference sequence), creating it if it does not already exist.
`StringDt`	`getReferenceCodon()` Gets the value(s) for referenceCodon (Codon that overlap with the reference sequence).
`StringDt`	`getReferenceSeq()` Gets the value(s) for referenceSeq (Reference sequence).
`List<GVFVariant.Sample>`	`getSample()` Gets the value(s) for sample (Individual genotypic information).
`GVFVariant.Sample`	`getSampleFirstRep()` Gets the first repetition for sample (Individual genotypic information), creating it if it does not already exist.
`IntegerDt`	`getScore()` Gets the value(s) for score (Sequence score).
`StringDt`	`getSeqid()` Gets the value(s) for seqid (Sequence Id).
`GVFVariant.SequenceContext`	`getSequenceContext()` Gets the value(s) for sequenceContext (Context of features being described).
`StringDt`	`getSource()` Gets the value(s) for source (Data source).
`AttachmentDt`	`getSourceFile()` Gets the value(s) for sourceFile (Source file).
`IntegerDt`	`getStart()` Gets the value(s) for start (Start position).
`GVFVariant.StartRange`	`getStartRange()` Gets the value(s) for startRange (Start range).
`CodeDt`	`getStrand()` Gets the value(s) for strand (Strand).
`GVFVariant.Subject`	`getSubject()` Gets the value(s) for subject (Subject described by this segment of GVF file).
`CodeDt`	`getType()` Gets the value(s) for type (Feature type).
`List<StringDt>`	`getVariantAA()` Gets the value(s) for variantAA (Amino acids that overlap with the features being described).
`StringDt`	`getVariantAAFirstRep()` Gets the first repetition for variantAA (Amino acids that overlap with the features being described), creating it if it does not already exist.
`List<StringDt>`	`getVariantCodon()` Gets the value(s) for variantCodon (Codons that overlap with feature being described).
`StringDt`	`getVariantCodonFirstRep()` Gets the first repetition for variantCodon (Codons that overlap with feature being described), creating it if it does not already exist.
`List<GVFVariant.VariantEffect>`	`getVariantEffect()` Gets the value(s) for variantEffect (Variant effect).
`GVFVariant.VariantEffect`	`getVariantEffectFirstRep()` Gets the first repetition for variantEffect (Variant effect), creating it if it does not already exist.
`List<DecimalDt>`	`getVariantFreq()` Gets the value(s) for variantFreq (Variant frequency).
`DecimalDt`	`getVariantFreqFirstRep()` Gets the first repetition for variantFreq (Variant frequency), creating it if it does not already exist.
`List<StringDt>`	`getVariantSeq()` Gets the value(s) for variantSeq (Sequence presents in the variant).
`StringDt`	`getVariantSeqFirstRep()` Gets the first repetition for variantSeq (Sequence presents in the variant), creating it if it does not already exist.
`boolean`	`isEmpty()`
`GVFVariant`	`setAlias(String theString)` Sets the value for alias (Alias of the feature)
`GVFVariant`	`setAlias(StringDt theValue)` Sets the value(s) for alias (Alias of the feature)
`GVFVariant`	`setBreakpointDetail(GVFVariant.BreakpointDetail theValue)` Sets the value(s) for breakpointDetail (Coordinate of a variant with zero length)
`GVFVariant`	`setDbxref(GVFVariant.Dbxref theValue)` Sets the value(s) for dbxref (Reference of the feature in a database)
`GVFVariant`	`setEnd(int theInteger)` Sets the value for end (End position)
`GVFVariant`	`setEnd(IntegerDt theValue)` Sets the value(s) for end (End position)
`GVFVariant`	`setEndRange(GVFVariant.EndRange theValue)` Sets the value(s) for endRange (End range)
`GVFVariant`	`setFeatureId(String theString)` Sets the value for featureId (Id of the feature)
`GVFVariant`	`setFeatureId(StringDt theValue)` Sets the value(s) for featureId (Id of the feature)
`GVFVariant`	`setIndividual(List<StringDt> theValue)` Sets the value(s) for individual (Individuals being described)
`GVFVariant`	`setMeta(ResourceReferenceDt theValue)` Sets the value(s) for meta (GVF Meta)
`GVFVariant`	`setReferenceAA(List<StringDt> theValue)` Sets the value(s) for referenceAA (Amino acids that overlaps with the reference sequence)
`GVFVariant`	`setReferenceCodon(String theString)` Sets the value for referenceCodon (Codon that overlap with the reference sequence)
`GVFVariant`	`setReferenceCodon(StringDt theValue)` Sets the value(s) for referenceCodon (Codon that overlap with the reference sequence)
`GVFVariant`	`setReferenceSeq(String theString)` Sets the value for referenceSeq (Reference sequence)
`GVFVariant`	`setReferenceSeq(StringDt theValue)` Sets the value(s) for referenceSeq (Reference sequence)
`GVFVariant`	`setSample(List<GVFVariant.Sample> theValue)` Sets the value(s) for sample (Individual genotypic information)
`GVFVariant`	`setScore(int theInteger)` Sets the value for score (Sequence score)
`GVFVariant`	`setScore(IntegerDt theValue)` Sets the value(s) for score (Sequence score)
`GVFVariant`	`setSeqid(String theString)` Sets the value for seqid (Sequence Id)
`GVFVariant`	`setSeqid(StringDt theValue)` Sets the value(s) for seqid (Sequence Id)
`GVFVariant`	`setSequenceContext(GVFVariant.SequenceContext theValue)` Sets the value(s) for sequenceContext (Context of features being described)
`GVFVariant`	`setSource(String theString)` Sets the value for source (Data source)
`GVFVariant`	`setSource(StringDt theValue)` Sets the value(s) for source (Data source)
`GVFVariant`	`setSourceFile(AttachmentDt theValue)` Sets the value(s) for sourceFile (Source file)
`GVFVariant`	`setStart(int theInteger)` Sets the value for start (Start position)
`GVFVariant`	`setStart(IntegerDt theValue)` Sets the value(s) for start (Start position)
`GVFVariant`	`setStartRange(GVFVariant.StartRange theValue)` Sets the value(s) for startRange (Start range)
`GVFVariant`	`setStrand(CodeDt theValue)` Sets the value(s) for strand (Strand)
`GVFVariant`	`setStrand(String theCode)` Sets the value for strand (Strand)
`GVFVariant`	`setSubject(GVFVariant.Subject theValue)` Sets the value(s) for subject (Subject described by this segment of GVF file)
`GVFVariant`	`setType(CodeDt theValue)` Sets the value(s) for type (Feature type)
`GVFVariant`	`setType(String theCode)` Sets the value for type (Feature type)
`GVFVariant`	`setVariantAA(List<StringDt> theValue)` Sets the value(s) for variantAA (Amino acids that overlap with the features being described)
`GVFVariant`	`setVariantCodon(List<StringDt> theValue)` Sets the value(s) for variantCodon (Codons that overlap with feature being described)
`GVFVariant`	`setVariantEffect(List<GVFVariant.VariantEffect> theValue)` Sets the value(s) for variantEffect (Variant effect)
`GVFVariant`	`setVariantFreq(List<DecimalDt> theValue)` Sets the value(s) for variantFreq (Variant frequency)
`GVFVariant`	`setVariantSeq(List<StringDt> theValue)` Sets the value(s) for variantSeq (Sequence presents in the variant)

Methods inherited from class ca.uhn.fhir.model.api.BaseResource
getContained, getId, getLanguage, getResourceMetadata, getText, isBaseEmpty, setContained, setId, setId, setLanguage, setResourceMetadata, setText, toString

Methods inherited from class ca.uhn.fhir.model.api.BaseElement
addUndeclaredExtension, addUndeclaredExtension, addUndeclaredExtension, getAllUndeclaredExtensions, getUndeclaredExtensions, getUndeclaredExtensionsByUrl, getUndeclaredModifierExtensions

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

Methods inherited from interface ca.uhn.fhir.model.api.IResource
getContained, getId, getLanguage, getResourceMetadata, getText, setId, setLanguage, setResourceMetadata

- Field Detail
  - SP_PATIENT
```
public static final String SP_PATIENT
```
    Search parameter constant for patient
    Description: Patient being described
    Type: reference
    Path: GVFVariant.subject.patient
    
    See Also:
    Constant Field Values
  - PATIENT
```
public static final ReferenceClientParam PATIENT
```
    Fluent Client search parameter constant for patient
    Description: Patient being described
    Type: reference
    Path: GVFVariant.subject.patient
  - INCLUDE_SUBJECT_PATIENT
```
public static final Include INCLUDE_SUBJECT_PATIENT
```
    Constant for fluent queries to be used to add include statements. Specifies the path value of "GVFVariant.subject.patient".
  - SP_COORDINATE
```
public static final String SP_COORDINATE
```
    Search parameter constant for coordinate
    Description: Coordinate of the variant being studied
    Type: string
    Path:
    
    See Also:
    Constant Field Values
  - COORDINATE
```
public static final StringClientParam COORDINATE
```
    Fluent Client search parameter constant for coordinate
    Description: Coordinate of the variant being studied
    Type: string
    Path:
- Constructor Detail
  - GVFVariant
```
public GVFVariant()
```
- Method Detail
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface IElement
  - getAllPopulatedChildElementsOfType
```
public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType)
```
    Description copied from interface: ICompositeElement
    
    Returns a list containing all child elements matching a given type
    
    Specified by:
    
    getAllPopulatedChildElementsOfType in interface ICompositeElement
    
    Parameters:
    theType - The type to match. If set to null, all child elements will be returned
  - getSubject
```
public GVFVariant.Subject getSubject()
```
    Gets the value(s) for subject (Subject described by this segment of GVF file). creating it if it does not exist. Will not return null.
    Definition: Subject described by this segment of GVF file
  - setSubject
```
public GVFVariant setSubject(GVFVariant.Subject theValue)
```
    Sets the value(s) for subject (Subject described by this segment of GVF file)
    Definition: Subject described by this segment of GVF file
  - getMeta
```
public ResourceReferenceDt getMeta()
```
    Gets the value(s) for meta (GVF Meta). creating it if it does not exist. Will not return null.
    Definition: Meta information of a GVF file
  - setMeta
```
public GVFVariant setMeta(ResourceReferenceDt theValue)
```
    Sets the value(s) for meta (GVF Meta)
    Definition: Meta information of a GVF file
  - getSourceFile
```
public AttachmentDt getSourceFile()
```
    Gets the value(s) for sourceFile (Source file). creating it if it does not exist. Will not return null.
    Definition: Source GVF file
  - setSourceFile
```
public GVFVariant setSourceFile(AttachmentDt theValue)
```
    Sets the value(s) for sourceFile (Source file)
    Definition: Source GVF file
  - getSeqid
```
public StringDt getSeqid()
```
    Gets the value(s) for seqid (Sequence Id). creating it if it does not exist. Will not return null.
    Definition: Id the sequence being described
  - setSeqid
```
public GVFVariant setSeqid(StringDt theValue)
```
    Sets the value(s) for seqid (Sequence Id)
    Definition: Id the sequence being described
  - setSeqid
```
public GVFVariant setSeqid(String theString)
```
    Sets the value for seqid (Sequence Id)
    Definition: Id the sequence being described
  - getSource
```
public StringDt getSource()
```
    Gets the value(s) for source (Data source). creating it if it does not exist. Will not return null.
    Definition: Algorithm or software used to generate the data
  - setSource
```
public GVFVariant setSource(StringDt theValue)
```
    Sets the value(s) for source (Data source)
    Definition: Algorithm or software used to generate the data
  - setSource
```
public GVFVariant setSource(String theString)
```
    Sets the value for source (Data source)
    Definition: Algorithm or software used to generate the data
  - getType
```
public CodeDt getType()
```
    Gets the value(s) for type (Feature type). creating it if it does not exist. Will not return null.
    Definition: Type of the feature being described
  - setType
```
public GVFVariant setType(CodeDt theValue)
```
    Sets the value(s) for type (Feature type)
    Definition: Type of the feature being described
  - setType
```
public GVFVariant setType(String theCode)
```
    Sets the value for type (Feature type)
    Definition: Type of the feature being described
  - getStart
```
public IntegerDt getStart()
```
    Gets the value(s) for start (Start position). creating it if it does not exist. Will not return null.
    Definition: Start position
  - setStart
```
public GVFVariant setStart(IntegerDt theValue)
```
    Sets the value(s) for start (Start position)
    Definition: Start position
  - setStart
```
public GVFVariant setStart(int theInteger)
```
    Sets the value for start (Start position)
    Definition: Start position
  - getEnd
```
public IntegerDt getEnd()
```
    Gets the value(s) for end (End position). creating it if it does not exist. Will not return null.
    Definition: End position
  - setEnd
```
public GVFVariant setEnd(IntegerDt theValue)
```
    Sets the value(s) for end (End position)
    Definition: End position
  - setEnd
```
public GVFVariant setEnd(int theInteger)
```
    Sets the value for end (End position)
    Definition: End position
  - getScore
```
public IntegerDt getScore()
```
    Gets the value(s) for score (Sequence score). creating it if it does not exist. Will not return null.
    Definition: Phred scaled score of the sequence
  - setScore
```
public GVFVariant setScore(IntegerDt theValue)
```
    Sets the value(s) for score (Sequence score)
    Definition: Phred scaled score of the sequence
  - setScore
```
public GVFVariant setScore(int theInteger)
```
    Sets the value for score (Sequence score)
    Definition: Phred scaled score of the sequence
  - getStrand
```
public CodeDt getStrand()
```
    Gets the value(s) for strand (Strand). creating it if it does not exist. Will not return null.
    Definition: Direction of the strand
  - setStrand
```
public GVFVariant setStrand(CodeDt theValue)
```
    Sets the value(s) for strand (Strand)
    Definition: Direction of the strand
  - setStrand
```
public GVFVariant setStrand(String theCode)
```
    Sets the value for strand (Strand)
    Definition: Direction of the strand
  - getFeatureId
```
public StringDt getFeatureId()
```
    Gets the value(s) for featureId (Id of the feature). creating it if it does not exist. Will not return null.
    Definition: Id of the attribute, unique to other segments in the same source file
  - setFeatureId
```
public GVFVariant setFeatureId(StringDt theValue)
```
    Sets the value(s) for featureId (Id of the feature)
    Definition: Id of the attribute, unique to other segments in the same source file
  - setFeatureId
```
public GVFVariant setFeatureId(String theString)
```
    Sets the value for featureId (Id of the feature)
    Definition: Id of the attribute, unique to other segments in the same source file
  - getAlias
```
public StringDt getAlias()
```
    Gets the value(s) for alias (Alias of the feature). creating it if it does not exist. Will not return null.
    Definition: Alias of the feature being described
  - setAlias
```
public GVFVariant setAlias(StringDt theValue)
```
    Sets the value(s) for alias (Alias of the feature)
    Definition: Alias of the feature being described
  - setAlias
```
public GVFVariant setAlias(String theString)
```
    Sets the value for alias (Alias of the feature)
    Definition: Alias of the feature being described
  - getDbxref
```
public GVFVariant.Dbxref getDbxref()
```
    Gets the value(s) for dbxref (Reference of the feature in a database). creating it if it does not exist. Will not return null.
    Definition: Reference of the feature in a database
  - setDbxref
```
public GVFVariant setDbxref(GVFVariant.Dbxref theValue)
```
    Sets the value(s) for dbxref (Reference of the feature in a database)
    Definition: Reference of the feature in a database
  - getVariantSeq
```
public List<StringDt> getVariantSeq()
```
    Gets the value(s) for variantSeq (Sequence presents in the variant). creating it if it does not exist. Will not return null.
    Definition: Sequence presents in the variant
  - setVariantSeq
```
public GVFVariant setVariantSeq(List<StringDt> theValue)
```
    Sets the value(s) for variantSeq (Sequence presents in the variant)
    Definition: Sequence presents in the variant
  - addVariantSeq
```
public StringDt addVariantSeq()
```
    Adds and returns a new value for variantSeq (Sequence presents in the variant)
    Definition: Sequence presents in the variant
  - getVariantSeqFirstRep
```
public StringDt getVariantSeqFirstRep()
```
    Gets the first repetition for variantSeq (Sequence presents in the variant), creating it if it does not already exist.
    Definition: Sequence presents in the variant
  - addVariantSeq
```
public GVFVariant addVariantSeq(String theString)
```
    Adds a new value for variantSeq (Sequence presents in the variant)
    Definition: Sequence presents in the variant
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getReferenceSeq
```
public StringDt getReferenceSeq()
```
    Gets the value(s) for referenceSeq (Reference sequence). creating it if it does not exist. Will not return null.
    Definition: Reference sequence
  - setReferenceSeq
```
public GVFVariant setReferenceSeq(StringDt theValue)
```
    Sets the value(s) for referenceSeq (Reference sequence)
    Definition: Reference sequence
  - setReferenceSeq
```
public GVFVariant setReferenceSeq(String theString)
```
    Sets the value for referenceSeq (Reference sequence)
    Definition: Reference sequence
  - getVariantFreq
```
public List<DecimalDt> getVariantFreq()
```
    Gets the value(s) for variantFreq (Variant frequency). creating it if it does not exist. Will not return null.
    Definition: Frequency of the variant
  - setVariantFreq
```
public GVFVariant setVariantFreq(List<DecimalDt> theValue)
```
    Sets the value(s) for variantFreq (Variant frequency)
    Definition: Frequency of the variant
  - addVariantFreq
```
public DecimalDt addVariantFreq()
```
    Adds and returns a new value for variantFreq (Variant frequency)
    Definition: Frequency of the variant
  - getVariantFreqFirstRep
```
public DecimalDt getVariantFreqFirstRep()
```
    Gets the first repetition for variantFreq (Variant frequency), creating it if it does not already exist.
    Definition: Frequency of the variant
  - addVariantFreq
```
public GVFVariant addVariantFreq(long theValue)
```
    Adds a new value for variantFreq (Variant frequency)
    Definition: Frequency of the variant
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - addVariantFreq
```
public GVFVariant addVariantFreq(double theValue)
```
    Adds a new value for variantFreq (Variant frequency)
    Definition: Frequency of the variant
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - addVariantFreq
```
public GVFVariant addVariantFreq(BigDecimal theValue)
```
    Adds a new value for variantFreq (Variant frequency)
    Definition: Frequency of the variant
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getVariantEffect
```
public List<GVFVariant.VariantEffect> getVariantEffect()
```
    Gets the value(s) for variantEffect (Variant effect). creating it if it does not exist. Will not return null.
    Definition: Effect of the variant
  - setVariantEffect
```
public GVFVariant setVariantEffect(List<GVFVariant.VariantEffect> theValue)
```
    Sets the value(s) for variantEffect (Variant effect)
    Definition: Effect of the variant
  - addVariantEffect
```
public GVFVariant.VariantEffect addVariantEffect()
```
    Adds and returns a new value for variantEffect (Variant effect)
    Definition: Effect of the variant
  - getVariantEffectFirstRep
```
public GVFVariant.VariantEffect getVariantEffectFirstRep()
```
    Gets the first repetition for variantEffect (Variant effect), creating it if it does not already exist.
    Definition: Effect of the variant
  - getStartRange
```
public GVFVariant.StartRange getStartRange()
```
    Gets the value(s) for startRange (Start range). creating it if it does not exist. Will not return null.
    Definition: Attribute describing ambiguity of the start position of the feature
  - setStartRange
```
public GVFVariant setStartRange(GVFVariant.StartRange theValue)
```
    Sets the value(s) for startRange (Start range)
    Definition: Attribute describing ambiguity of the start position of the feature
  - getEndRange
```
public GVFVariant.EndRange getEndRange()
```
    Gets the value(s) for endRange (End range). creating it if it does not exist. Will not return null.
    Definition: Attribute describing ambiguity of the end position of the feature
  - setEndRange
```
public GVFVariant setEndRange(GVFVariant.EndRange theValue)
```
    Sets the value(s) for endRange (End range)
    Definition: Attribute describing ambiguity of the end position of the feature
  - getVariantCodon
```
public List<StringDt> getVariantCodon()
```
    Gets the value(s) for variantCodon (Codons that overlap with feature being described). creating it if it does not exist. Will not return null.
    Definition: Codons that overlap with the feature being described
  - setVariantCodon
```
public GVFVariant setVariantCodon(List<StringDt> theValue)
```
    Sets the value(s) for variantCodon (Codons that overlap with feature being described)
    Definition: Codons that overlap with the feature being described
  - addVariantCodon
```
public StringDt addVariantCodon()
```
    Adds and returns a new value for variantCodon (Codons that overlap with feature being described)
    Definition: Codons that overlap with the feature being described
  - getVariantCodonFirstRep
```
public StringDt getVariantCodonFirstRep()
```
    Gets the first repetition for variantCodon (Codons that overlap with feature being described), creating it if it does not already exist.
    Definition: Codons that overlap with the feature being described
  - addVariantCodon
```
public GVFVariant addVariantCodon(String theString)
```
    Adds a new value for variantCodon (Codons that overlap with feature being described)
    Definition: Codons that overlap with the feature being described
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getReferenceCodon
```
public StringDt getReferenceCodon()
```
    Gets the value(s) for referenceCodon (Codon that overlap with the reference sequence). creating it if it does not exist. Will not return null.
    Definition: Codon that overlap with the reference sequence
  - setReferenceCodon
```
public GVFVariant setReferenceCodon(StringDt theValue)
```
    Sets the value(s) for referenceCodon (Codon that overlap with the reference sequence)
    Definition: Codon that overlap with the reference sequence
  - setReferenceCodon
```
public GVFVariant setReferenceCodon(String theString)
```
    Sets the value for referenceCodon (Codon that overlap with the reference sequence)
    Definition: Codon that overlap with the reference sequence
  - getVariantAA
```
public List<StringDt> getVariantAA()
```
    Gets the value(s) for variantAA (Amino acids that overlap with the features being described). creating it if it does not exist. Will not return null.
    Definition: Amino acids that overlap with the features being described
  - setVariantAA
```
public GVFVariant setVariantAA(List<StringDt> theValue)
```
    Sets the value(s) for variantAA (Amino acids that overlap with the features being described)
    Definition: Amino acids that overlap with the features being described
  - addVariantAA
```
public StringDt addVariantAA()
```
    Adds and returns a new value for variantAA (Amino acids that overlap with the features being described)
    Definition: Amino acids that overlap with the features being described
  - getVariantAAFirstRep
```
public StringDt getVariantAAFirstRep()
```
    Gets the first repetition for variantAA (Amino acids that overlap with the features being described), creating it if it does not already exist.
    Definition: Amino acids that overlap with the features being described
  - addVariantAA
```
public GVFVariant addVariantAA(String theString)
```
    Adds a new value for variantAA (Amino acids that overlap with the features being described)
    Definition: Amino acids that overlap with the features being described
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getReferenceAA
```
public List<StringDt> getReferenceAA()
```
    Gets the value(s) for referenceAA (Amino acids that overlaps with the reference sequence). creating it if it does not exist. Will not return null.
    Definition: Amino acids that overlaps with the reference sequence
  - setReferenceAA
```
public GVFVariant setReferenceAA(List<StringDt> theValue)
```
    Sets the value(s) for referenceAA (Amino acids that overlaps with the reference sequence)
    Definition: Amino acids that overlaps with the reference sequence
  - addReferenceAA
```
public StringDt addReferenceAA()
```
    Adds and returns a new value for referenceAA (Amino acids that overlaps with the reference sequence)
    Definition: Amino acids that overlaps with the reference sequence
  - getReferenceAAFirstRep
```
public StringDt getReferenceAAFirstRep()
```
    Gets the first repetition for referenceAA (Amino acids that overlaps with the reference sequence), creating it if it does not already exist.
    Definition: Amino acids that overlaps with the reference sequence
  - addReferenceAA
```
public GVFVariant addReferenceAA(String theString)
```
    Adds a new value for referenceAA (Amino acids that overlaps with the reference sequence)
    Definition: Amino acids that overlaps with the reference sequence
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getBreakpointDetail
```
public GVFVariant.BreakpointDetail getBreakpointDetail()
```
    Gets the value(s) for breakpointDetail (Coordinate of a variant with zero length). creating it if it does not exist. Will not return null.
    Definition: Coordinate of a variant with zero length
  - setBreakpointDetail
```
public GVFVariant setBreakpointDetail(GVFVariant.BreakpointDetail theValue)
```
    Sets the value(s) for breakpointDetail (Coordinate of a variant with zero length)
    Definition: Coordinate of a variant with zero length
  - getSequenceContext
```
public GVFVariant.SequenceContext getSequenceContext()
```
    Gets the value(s) for sequenceContext (Context of features being described). creating it if it does not exist. Will not return null.
    Definition: Sequences adjacent to the feature
  - setSequenceContext
```
public GVFVariant setSequenceContext(GVFVariant.SequenceContext theValue)
```
    Sets the value(s) for sequenceContext (Context of features being described)
    Definition: Sequences adjacent to the feature
  - getIndividual
```
public List<StringDt> getIndividual()
```
    Gets the value(s) for individual (Individuals being described). creating it if it does not exist. Will not return null.
    Definition: Individuals for whom the feature is described
  - setIndividual
```
public GVFVariant setIndividual(List<StringDt> theValue)
```
    Sets the value(s) for individual (Individuals being described)
    Definition: Individuals for whom the feature is described
  - addIndividual
```
public StringDt addIndividual()
```
    Adds and returns a new value for individual (Individuals being described)
    Definition: Individuals for whom the feature is described
  - getIndividualFirstRep
```
public StringDt getIndividualFirstRep()
```
    Gets the first repetition for individual (Individuals being described), creating it if it does not already exist.
    Definition: Individuals for whom the feature is described
  - addIndividual
```
public GVFVariant addIndividual(String theString)
```
    Adds a new value for individual (Individuals being described)
    Definition: Individuals for whom the feature is described
    
    Returns:
    Returns a reference to this object, to allow for simple chaining.
  - getSample
```
public List<GVFVariant.Sample> getSample()
```
    Gets the value(s) for sample (Individual genotypic information). creating it if it does not exist. Will not return null.
    Definition: Individual genotypic information
  - setSample
```
public GVFVariant setSample(List<GVFVariant.Sample> theValue)
```
    Sets the value(s) for sample (Individual genotypic information)
    Definition: Individual genotypic information
  - addSample
```
public GVFVariant.Sample addSample()
```
    Adds and returns a new value for sample (Individual genotypic information)
    Definition: Individual genotypic information
  - getSampleFirstRep
```
public GVFVariant.Sample getSampleFirstRep()
```
    Gets the first repetition for sample (Individual genotypic information), creating it if it does not already exist.
    Definition: Individual genotypic information

Class GVFVariant

Nested Class Summary

Field Summary

Fields inherited from class ca.uhn.fhir.model.api.BaseResource

Constructor Summary

Method Summary

Methods inherited from class ca.uhn.fhir.model.api.BaseResource

Methods inherited from class ca.uhn.fhir.model.api.BaseElement

Methods inherited from class java.lang.Object

Methods inherited from interface ca.uhn.fhir.model.api.IResource

Field Detail

SP_PATIENT

PATIENT

INCLUDE_SUBJECT_PATIENT

SP_COORDINATE

COORDINATE

Constructor Detail

GVFVariant

Method Detail

isEmpty

getAllPopulatedChildElementsOfType

getSubject

setSubject

getMeta

setMeta

getSourceFile

setSourceFile

getSeqid

setSeqid

setSeqid

getSource

setSource

setSource

getType

setType

setType

getStart

setStart

setStart

getEnd

setEnd

setEnd

getScore

setScore

setScore

getStrand

setStrand

setStrand

getFeatureId

setFeatureId

setFeatureId

getAlias

setAlias

setAlias

getDbxref

setDbxref

getVariantSeq

setVariantSeq

addVariantSeq

getVariantSeqFirstRep

addVariantSeq

getReferenceSeq

setReferenceSeq

setReferenceSeq

getVariantFreq

setVariantFreq

addVariantFreq

getVariantFreqFirstRep

addVariantFreq

addVariantFreq

addVariantFreq

getVariantEffect

setVariantEffect

addVariantEffect

getVariantEffectFirstRep

getStartRange

setStartRange

getEndRange

setEndRange

getVariantCodon