java.lang.Object
- org.hl7.fhir.dstu2016may.model.Base
- - org.hl7.fhir.dstu2016may.model.Element
  - - org.hl7.fhir.dstu2016may.model.BackboneElement
    - - org.hl7.fhir.dstu2016may.model.Sequence.SequenceVariationComponent

All Implemented Interfaces:

ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseBackboneElement, org.hl7.fhir.instance.model.api.IBaseElement, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

Enclosing class:

Sequence
```
public static class Sequence.SequenceVariationComponent
extends BackboneElement
implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`protected StringType`	`cigar`	Extended CIGAR string for aligning the sequence with reference bases.
`protected IntegerType`	`end`	0-based end position (exclusive) of the variation on the reference sequence.
`protected StringType`	`observedAllele`	Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence.
`protected StringType`	`referenceAllele`	Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence.
`protected IntegerType`	`start`	0-based start position (inclusive) of the variation on the reference sequence.

Fields inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement
modifierExtension

Fields inherited from class org.hl7.fhir.dstu2016may.model.Element
extension, id

Constructor Summary

Constructors
Constructor Description

SequenceVariationComponent()
Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Base`	`addChild(String name)`
`Sequence.SequenceVariationComponent`	`copy()`
`boolean`	`equalsDeep(Base other)`
`boolean`	`equalsShallow(Base other)`
`String`	`fhirType()`
`String`	`getCigar()`
`StringType`	`getCigarElement()`
`int`	`getEnd()`
`IntegerType`	`getEndElement()`
`String`	`getObservedAllele()`
`StringType`	`getObservedAlleleElement()`
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`String`	`getReferenceAllele()`
`StringType`	`getReferenceAlleleElement()`
`int`	`getStart()`
`IntegerType`	`getStartElement()`
`boolean`	`hasCigar()`
`boolean`	`hasCigarElement()`
`boolean`	`hasEnd()`
`boolean`	`hasEndElement()`
`boolean`	`hasObservedAllele()`
`boolean`	`hasObservedAlleleElement()`
`boolean`	`hasReferenceAllele()`
`boolean`	`hasReferenceAlleleElement()`
`boolean`	`hasStart()`
`boolean`	`hasStartElement()`
`boolean`	`isEmpty()`
`protected void`	`listChildren(List<Property> childrenList)`
`Base`	`makeProperty(int hash, String name)`	make an instance of a property.
`Sequence.SequenceVariationComponent`	`setCigar(String value)`
`Sequence.SequenceVariationComponent`	`setCigarElement(StringType value)`
`Sequence.SequenceVariationComponent`	`setEnd(int value)`
`Sequence.SequenceVariationComponent`	`setEndElement(IntegerType value)`
`Sequence.SequenceVariationComponent`	`setObservedAllele(String value)`
`Sequence.SequenceVariationComponent`	`setObservedAlleleElement(StringType value)`
`void`	`setProperty(int hash, String name, Base value)`
`void`	`setProperty(String name, Base value)`
`Sequence.SequenceVariationComponent`	`setReferenceAllele(String value)`
`Sequence.SequenceVariationComponent`	`setReferenceAlleleElement(StringType value)`
`Sequence.SequenceVariationComponent`	`setStart(int value)`
`Sequence.SequenceVariationComponent`	`setStartElement(IntegerType value)`

Methods inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement
addModifierExtension, addModifierExtension, copyValues, getModifierExtension, hasModifierExtension

Methods inherited from class org.hl7.fhir.dstu2016may.model.Element
addExtension, addExtension, copyValues, getExtension, getExtensionsByUrl, getExtensionString, getId, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, setId, setIdElement

Methods inherited from class org.hl7.fhir.dstu2016may.model.Base
castToActionDefinition, castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactPoint, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToModuleMetadata, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToUnsignedInt, castToUri, children, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isMetadataBased, isPrimitive, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN

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

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase
getFormatCommentsPost, getFormatCommentsPre, getUserData, hasFormatComment, setUserData

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseElement
getUserData, setUserData

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasExtensions
addExtension, getExtension, hasExtension

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions
addModifierExtension, getModifierExtension, hasModifierExtension

- Field Detail
  - start
```
protected IntegerType start
```
    0-based start position (inclusive) of the variation on the reference sequence.
  - end
```
protected IntegerType end
```
    0-based end position (exclusive) of the variation on the reference sequence.
  - observedAllele
```
protected StringType observedAllele
```
    Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - referenceAllele
```
protected StringType referenceAllele
```
    Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - cigar
```
protected StringType cigar
```
    Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
- Constructor Detail
  - SequenceVariationComponent
```
public SequenceVariationComponent()
```
    Constructor
- Method Detail
  - getStartElement
```
public IntegerType getStartElement()
```
    Returns:
    
    start (0-based start position (inclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value
  - hasStartElement
```
public boolean hasStartElement()
```
  - hasStart
```
public boolean hasStart()
```
  - setStartElement
```
public Sequence.SequenceVariationComponent setStartElement(IntegerType value)
```
    Parameters:
    
    value - start (0-based start position (inclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value
  - getStart
```
public int getStart()
```
    Returns:
    
    0-based start position (inclusive) of the variation on the reference sequence.
  - setStart
```
public Sequence.SequenceVariationComponent setStart(int value)
```
    Parameters:
    
    value - 0-based start position (inclusive) of the variation on the reference sequence.
  - getEndElement
```
public IntegerType getEndElement()
```
    Returns:
    
    end (0-based end position (exclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value
  - hasEndElement
```
public boolean hasEndElement()
```
  - hasEnd
```
public boolean hasEnd()
```
  - setEndElement
```
public Sequence.SequenceVariationComponent setEndElement(IntegerType value)
```
    Parameters:
    
    value - end (0-based end position (exclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value
  - getEnd
```
public int getEnd()
```
    Returns:
    
    0-based end position (exclusive) of the variation on the reference sequence.
  - setEnd
```
public Sequence.SequenceVariationComponent setEnd(int value)
```
    Parameters:
    
    value - 0-based end position (exclusive) of the variation on the reference sequence.
  - getObservedAlleleElement
```
public StringType getObservedAlleleElement()
```
    Returns:
    
    observedAllele (Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.). This is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value
  - hasObservedAlleleElement
```
public boolean hasObservedAlleleElement()
```
  - hasObservedAllele
```
public boolean hasObservedAllele()
```
  - setObservedAlleleElement
```
public Sequence.SequenceVariationComponent setObservedAlleleElement(StringType value)
```
    Parameters:
    
    value - observedAllele (Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.). This is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value
  - getObservedAllele
```
public String getObservedAllele()
```
    Returns:
    
    Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - setObservedAllele
```
public Sequence.SequenceVariationComponent setObservedAllele(String value)
```
    Parameters:
    
    value - Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - getReferenceAlleleElement
```
public StringType getReferenceAlleleElement()
```
    Returns:
    
    referenceAllele (Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.). This is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value
  - hasReferenceAlleleElement
```
public boolean hasReferenceAlleleElement()
```
  - hasReferenceAllele
```
public boolean hasReferenceAllele()
```
  - setReferenceAlleleElement
```
public Sequence.SequenceVariationComponent setReferenceAlleleElement(StringType value)
```
    Parameters:
    
    value - referenceAllele (Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.). This is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value
  - getReferenceAllele
```
public String getReferenceAllele()
```
    Returns:
    
    Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - setReferenceAllele
```
public Sequence.SequenceVariationComponent setReferenceAllele(String value)
```
    Parameters:
    
    value - Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.
  - getCigarElement
```
public StringType getCigarElement()
```
    Returns:
    
    cigar (Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value
  - hasCigarElement
```
public boolean hasCigarElement()
```
  - hasCigar
```
public boolean hasCigar()
```
  - setCigarElement
```
public Sequence.SequenceVariationComponent setCigarElement(StringType value)
```
    Parameters:
    
    value - cigar (Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value
  - getCigar
```
public String getCigar()
```
    Returns:
    
    Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
  - setCigar
```
public Sequence.SequenceVariationComponent setCigar(String value)
```
    Parameters:
    
    value - Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
  - listChildren
```
protected void listChildren(List<Property> childrenList)
```
    Overrides:
    
    listChildren in class BackboneElement
  - getProperty
```
public Base[] getProperty(int hash,
                          String name,
                          boolean checkValid)
                   throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    getProperty in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - setProperty
```
public void setProperty(int hash,
                        String name,
                        Base value)
                 throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    setProperty in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - setProperty
```
public void setProperty(String name,
                        Base value)
                 throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    setProperty in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - makeProperty
```
public Base makeProperty(int hash,
                         String name)
                  throws org.hl7.fhir.exceptions.FHIRException
```
    Description copied from class: Base
    
    make an instance of a property. If the property is a repeating property, make a new instance. if the property is not repeating, return the property
    
    Overrides:
    
    makeProperty in class BackboneElement
    
    Returns:
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - addChild
```
public Base addChild(String name)
              throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    addChild in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - copy
```
public Sequence.SequenceVariationComponent copy()
```
    Specified by:
    
    copy in class BackboneElement
  - equalsDeep
```
public boolean equalsDeep(Base other)
```
    Overrides:
    
    equalsDeep in class BackboneElement
  - equalsShallow
```
public boolean equalsShallow(Base other)
```
    Overrides:
    
    equalsShallow in class BackboneElement
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface org.hl7.fhir.instance.model.api.IBase
    
    Overrides:
    
    isEmpty in class BackboneElement
  - fhirType
```
public String fhirType()
```
    Specified by:
    
    fhirType in interface org.hl7.fhir.instance.model.api.IBase
    
    Overrides:
    
    fhirType in class BackboneElement

Class Sequence.SequenceVariationComponent

Field Summary

Fields inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement

Fields inherited from class org.hl7.fhir.dstu2016may.model.Element

Constructor Summary

Method Summary

Methods inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement

Methods inherited from class org.hl7.fhir.dstu2016may.model.Element

Methods inherited from class org.hl7.fhir.dstu2016may.model.Base

Methods inherited from class java.lang.Object

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseElement

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasExtensions

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

Field Detail

start

end

observedAllele

referenceAllele

cigar

Constructor Detail

SequenceVariationComponent

Method Detail

getStartElement

hasStartElement

hasStart

setStartElement

getStart

setStart

getEndElement

hasEndElement

hasEnd

setEndElement

getEnd

setEnd

getObservedAlleleElement

hasObservedAlleleElement

hasObservedAllele

setObservedAlleleElement

getObservedAllele

setObservedAllele

getReferenceAlleleElement

hasReferenceAlleleElement

hasReferenceAllele

setReferenceAlleleElement

getReferenceAllele

setReferenceAllele

getCigarElement

hasCigarElement

hasCigar

setCigarElement

getCigar

setCigar

listChildren

getProperty

setProperty

setProperty

makeProperty

addChild

copy

equalsDeep

equalsShallow

isEmpty

fhirType