java.lang.Object
- org.hl7.fhir.r5.model.Base
- - org.hl7.fhir.r5.model.Element
  - - org.hl7.fhir.r5.model.BackboneElement
    - - org.hl7.fhir.r5.model.MolecularSequence.MolecularSequenceVariantComponent

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:

MolecularSequence
```
public static class MolecularSequence.MolecularSequenceVariantComponent
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`	End position of the variant on the reference sequence.
`protected StringType`	`observedAllele`	An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).
`protected StringType`	`referenceAllele`	An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).
`protected IntegerType`	`start`	Start position of the variant on the reference sequence.
`protected Reference`	`variantPointer`	A pointer to an Observation containing variant information.

Fields inherited from class org.hl7.fhir.r5.model.BackboneElement
modifierExtension

Fields inherited from class org.hl7.fhir.r5.model.Element
extension, id

Constructor Summary

Constructors
Constructor Description

MolecularSequenceVariantComponent()
Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Base`	`addChild(String name)`
`MolecularSequence.MolecularSequenceVariantComponent`	`copy()`
`void`	`copyValues(MolecularSequence.MolecularSequenceVariantComponent dst)`
`boolean`	`equalsDeep(Base other_)`
`boolean`	`equalsShallow(Base other_)`
`String`	`fhirType()`
`String`	`getCigar()`
`StringType`	`getCigarElement()`
`int`	`getEnd()`
`IntegerType`	`getEndElement()`
`Property`	`getNamedProperty(int _hash, String _name, boolean _checkValid)`
`String`	`getObservedAllele()`
`StringType`	`getObservedAlleleElement()`
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`String`	`getReferenceAllele()`
`StringType`	`getReferenceAlleleElement()`
`int`	`getStart()`
`IntegerType`	`getStartElement()`
`String[]`	`getTypesForProperty(int hash, String name)`
`Reference`	`getVariantPointer()`
`boolean`	`hasCigar()`
`boolean`	`hasCigarElement()`
`boolean`	`hasEnd()`
`boolean`	`hasEndElement()`
`boolean`	`hasObservedAllele()`
`boolean`	`hasObservedAlleleElement()`
`boolean`	`hasReferenceAllele()`
`boolean`	`hasReferenceAlleleElement()`
`boolean`	`hasStart()`
`boolean`	`hasStartElement()`
`boolean`	`hasVariantPointer()`
`boolean`	`isEmpty()`
`protected void`	`listChildren(List<Property> children)`
`Base`	`makeProperty(int hash, String name)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setCigar(String value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setCigarElement(StringType value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setEnd(int value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setEndElement(IntegerType value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setObservedAllele(String value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setObservedAlleleElement(StringType value)`
`Base`	`setProperty(int hash, String name, Base value)`
`Base`	`setProperty(String name, Base value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setReferenceAllele(String value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setReferenceAlleleElement(StringType value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setStart(int value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setStartElement(IntegerType value)`
`MolecularSequence.MolecularSequenceVariantComponent`	`setVariantPointer(Reference value)`

Methods inherited from class org.hl7.fhir.r5.model.BackboneElement
addModifierExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyValues, getExtensionByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionFirstRep, hasModifierExtension, removeExtension, setModifierExtension

Methods inherited from class org.hl7.fhir.r5.model.Element
addExtension, addExtension, addExtension, copyValues, getExtension, getExtensionFirstRep, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, setDisallowExtensions, setExtension, setId, setIdBase, setIdElement

Methods inherited from class org.hl7.fhir.r5.model.Base
children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, copyUserData, copyValues, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, getXhtml, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, isResource, 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
```
    Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - end
```
protected IntegerType end
```
    End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
  - observedAllele
```
protected StringType observedAllele
```
    An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - referenceAllele
```
protected StringType referenceAllele
```
    An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - 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).
  - variantPointer
```
protected Reference variantPointer
```
    A pointer to an Observation containing variant information.
- Constructor Detail
  - MolecularSequenceVariantComponent
```
public MolecularSequenceVariantComponent()
```
    Constructor
- Method Detail
  - getStartElement
```
public IntegerType getStartElement()
```
    Returns:
    
    start (Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.). 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 MolecularSequence.MolecularSequenceVariantComponent setStartElement(IntegerType value)
```
    Parameters:
    
    value - start (Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value
  - getStart
```
public int getStart()
```
    Returns:
    
    Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - setStart
```
public MolecularSequence.MolecularSequenceVariantComponent setStart(int value)
```
    Parameters:
    
    value - Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - getEndElement
```
public IntegerType getEndElement()
```
    Returns:
    
    end (End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.). 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 MolecularSequence.MolecularSequenceVariantComponent setEndElement(IntegerType value)
```
    Parameters:
    
    value - end (End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value
  - getEnd
```
public int getEnd()
```
    Returns:
    
    End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
  - setEnd
```
public MolecularSequence.MolecularSequenceVariantComponent setEnd(int value)
```
    Parameters:
    
    value - End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
  - getObservedAlleleElement
```
public StringType getObservedAlleleElement()
```
    Returns:
    
    observedAllele (An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.). 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 MolecularSequence.MolecularSequenceVariantComponent setObservedAlleleElement(StringType value)
```
    Parameters:
    
    value - observedAllele (An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.). This is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value
  - getObservedAllele
```
public String getObservedAllele()
```
    Returns:
    
    An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - setObservedAllele
```
public MolecularSequence.MolecularSequenceVariantComponent setObservedAllele(String value)
```
    Parameters:
    
    value - An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - getReferenceAlleleElement
```
public StringType getReferenceAlleleElement()
```
    Returns:
    
    referenceAllele (An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.). 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 MolecularSequence.MolecularSequenceVariantComponent setReferenceAlleleElement(StringType value)
```
    Parameters:
    
    value - referenceAllele (An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.). This is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value
  - getReferenceAllele
```
public String getReferenceAllele()
```
    Returns:
    
    An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - setReferenceAllele
```
public MolecularSequence.MolecularSequenceVariantComponent setReferenceAllele(String value)
```
    Parameters:
    
    value - An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 will lay in the range between variant.start and variant.end.
  - 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 MolecularSequence.MolecularSequenceVariantComponent 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 MolecularSequence.MolecularSequenceVariantComponent 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).
  - getVariantPointer
```
public Reference getVariantPointer()
```
    Returns:
    
    variantPointer (A pointer to an Observation containing variant information.)
  - hasVariantPointer
```
public boolean hasVariantPointer()
```
  - setVariantPointer
```
public MolecularSequence.MolecularSequenceVariantComponent setVariantPointer(Reference value)
```
    Parameters:
    
    value - variantPointer (A pointer to an Observation containing variant information.)
  - listChildren
```
protected void listChildren(List<Property> children)
```
    Overrides:
    
    listChildren in class BackboneElement
  - getNamedProperty
```
public Property getNamedProperty(int _hash,
                                 String _name,
                                 boolean _checkValid)
                          throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    getNamedProperty in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - 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 Base 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 Base 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
```
    Overrides:
    
    makeProperty in class BackboneElement
    
    Throws:
    
    org.hl7.fhir.exceptions.FHIRException
  - getTypesForProperty
```
public String[] getTypesForProperty(int hash,
                                    String name)
                             throws org.hl7.fhir.exceptions.FHIRException
```
    Overrides:
    
    getTypesForProperty in class BackboneElement
    
    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 MolecularSequence.MolecularSequenceVariantComponent copy()
```
    Specified by:
    
    copy in class BackboneElement
  - copyValues
```
public void copyValues(MolecularSequence.MolecularSequenceVariantComponent dst)
```
  - 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 MolecularSequence.MolecularSequenceVariantComponent

Field Summary

Fields inherited from class org.hl7.fhir.r5.model.BackboneElement

Fields inherited from class org.hl7.fhir.r5.model.Element

Constructor Summary

Method Summary

Methods inherited from class org.hl7.fhir.r5.model.BackboneElement

Methods inherited from class org.hl7.fhir.r5.model.Element

Methods inherited from class org.hl7.fhir.r5.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

variantPointer

Constructor Detail

MolecularSequenceVariantComponent

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

getVariantPointer

hasVariantPointer

setVariantPointer

listChildren

getNamedProperty

getProperty

setProperty

setProperty

makeProperty

getTypesForProperty

addChild

copy

copyValues

equalsDeep

equalsShallow

isEmpty

fhirType