Sequence.SequenceReferenceSeqComponent (HAPI FHIR Structures

java.lang.Object
- org.hl7.fhir.dstu3.model.Base
- - org.hl7.fhir.dstu3.model.Element
  - - org.hl7.fhir.dstu3.model.BackboneElement
    - - org.hl7.fhir.dstu3.model.Sequence.SequenceReferenceSeqComponent

All Implemented Interfaces:

IElement, Serializable, IBase, IBaseBackboneElement, IBaseElement, IBaseHasExtensions, IBaseHasModifierExtensions

Enclosing class:

Sequence
```
public static class Sequence.SequenceReferenceSeqComponent
extends BackboneElement
implements IBaseBackboneElement
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected CodeableConcept`	`chromosome` Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
`protected StringType`	`genomeBuild` The Genome Build used for reference, following GRCh build versions e.g.
`protected CodeableConcept`	`referenceSeqId` Reference identifier of reference sequence submitted to NCBI.
`protected Reference`	`referenceSeqPointer` A Pointer to another Sequence entity as reference sequence.
`protected Sequence`	`referenceSeqPointerTarget` The actual object that is the target of the reference (A Pointer to another Sequence entity as reference sequence.)
`protected StringType`	`referenceSeqString` A string like "ACGT".
`protected IntegerType`	`strand` Directionality of DNA sequence.
`protected IntegerType`	`windowEnd` End position of the window on the reference sequence.
`protected IntegerType`	`windowStart` Start position of the window on the reference sequence.

Fields inherited from class org.hl7.fhir.dstu3.model.BackboneElement
modifierExtension

Fields inherited from class org.hl7.fhir.dstu3.model.Element
extension, id

Constructor Summary

Constructors
Constructor and Description
`SequenceReferenceSeqComponent()` Constructor
`SequenceReferenceSeqComponent(IntegerType windowStart, IntegerType windowEnd)` Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Base`	`addChild(String name)`
`Sequence.SequenceReferenceSeqComponent`	`copy()`
`boolean`	`equalsDeep(Base other)`
`boolean`	`equalsShallow(Base other)`
`String`	`fhirType()`
`CodeableConcept`	`getChromosome()`
`String`	`getGenomeBuild()`
`StringType`	`getGenomeBuildElement()`
`Base[]`	`getProperty(int hash, String name, boolean checkValid)`
`CodeableConcept`	`getReferenceSeqId()`
`Reference`	`getReferenceSeqPointer()`
`Sequence`	`getReferenceSeqPointerTarget()`
`String`	`getReferenceSeqString()`
`StringType`	`getReferenceSeqStringElement()`
`int`	`getStrand()`
`IntegerType`	`getStrandElement()`
`String[]`	`getTypesForProperty(int hash, String name)`
`int`	`getWindowEnd()`
`IntegerType`	`getWindowEndElement()`
`int`	`getWindowStart()`
`IntegerType`	`getWindowStartElement()`
`boolean`	`hasChromosome()`
`boolean`	`hasGenomeBuild()`
`boolean`	`hasGenomeBuildElement()`
`boolean`	`hasReferenceSeqId()`
`boolean`	`hasReferenceSeqPointer()`
`boolean`	`hasReferenceSeqString()`
`boolean`	`hasReferenceSeqStringElement()`
`boolean`	`hasStrand()`
`boolean`	`hasStrandElement()`
`boolean`	`hasWindowEnd()`
`boolean`	`hasWindowEndElement()`
`boolean`	`hasWindowStart()`
`boolean`	`hasWindowStartElement()`
`boolean`	`isEmpty()`
`protected void`	`listChildren(List<Property> childrenList)`
`Base`	`makeProperty(int hash, String name)`
`Sequence.SequenceReferenceSeqComponent`	`setChromosome(CodeableConcept value)`
`Sequence.SequenceReferenceSeqComponent`	`setGenomeBuild(String value)`
`Sequence.SequenceReferenceSeqComponent`	`setGenomeBuildElement(StringType value)`
`Base`	`setProperty(int hash, String name, Base value)`
`Base`	`setProperty(String name, Base value)`
`Sequence.SequenceReferenceSeqComponent`	`setReferenceSeqId(CodeableConcept value)`
`Sequence.SequenceReferenceSeqComponent`	`setReferenceSeqPointer(Reference value)`
`Sequence.SequenceReferenceSeqComponent`	`setReferenceSeqPointerTarget(Sequence value)`
`Sequence.SequenceReferenceSeqComponent`	`setReferenceSeqString(String value)`
`Sequence.SequenceReferenceSeqComponent`	`setReferenceSeqStringElement(StringType value)`
`Sequence.SequenceReferenceSeqComponent`	`setStrand(int value)`
`Sequence.SequenceReferenceSeqComponent`	`setStrandElement(IntegerType value)`
`Sequence.SequenceReferenceSeqComponent`	`setWindowEnd(int value)`
`Sequence.SequenceReferenceSeqComponent`	`setWindowEndElement(IntegerType value)`
`Sequence.SequenceReferenceSeqComponent`	`setWindowStart(int value)`
`Sequence.SequenceReferenceSeqComponent`	`setWindowStartElement(IntegerType value)`

Methods inherited from class org.hl7.fhir.dstu3.model.BackboneElement
addModifierExtension, addModifierExtension, copyValues, getModifierExtension, getModifierExtensionFirstRep, hasModifierExtension, setModifierExtension

Methods inherited from class org.hl7.fhir.dstu3.model.Element
addExtension, addExtension, addExtension, copyValues, getExtension, getExtensionFirstRep, getExtensionsByUrl, getExtensionString, getId, getIdBase, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, setExtension, setId, setIdBase, setIdElement

Methods inherited from class org.hl7.fhir.dstu3.model.Base
castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, 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, hasFormatComment

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
  - chromosome
```
protected CodeableConcept chromosome
```
    Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
  - genomeBuild
```
protected StringType genomeBuild
```
    The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
  - referenceSeqId
```
protected CodeableConcept referenceSeqId
```
    Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.
  - referenceSeqPointer
```
protected Reference referenceSeqPointer
```
    A Pointer to another Sequence entity as reference sequence.
  - referenceSeqPointerTarget
```
protected Sequence referenceSeqPointerTarget
```
    The actual object that is the target of the reference (A Pointer to another Sequence entity as reference sequence.)
  - referenceSeqString
```
protected StringType referenceSeqString
```
    A string like "ACGT".
  - strand
```
protected IntegerType strand
```
    Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.
  - windowStart
```
protected IntegerType windowStart
```
    Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - windowEnd
```
protected IntegerType windowEnd
```
    End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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.
- Constructor Detail
  - SequenceReferenceSeqComponent
```
public SequenceReferenceSeqComponent()
```
    Constructor
  - SequenceReferenceSeqComponent
```
public SequenceReferenceSeqComponent(IntegerType windowStart,
                                     IntegerType windowEnd)
```
    Constructor
- Method Detail
  - getChromosome
```
public CodeableConcept getChromosome()
```
    Returns:
    
    chromosome (Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).)
  - hasChromosome
```
public boolean hasChromosome()
```
  - setChromosome
```
public Sequence.SequenceReferenceSeqComponent setChromosome(CodeableConcept value)
```
    Parameters:
    
    value - chromosome (Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).)
  - getGenomeBuildElement
```
public StringType getGenomeBuildElement()
```
    Returns:
    
    genomeBuild (The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.). This is the underlying object with id, value and extensions. The accessor "getGenomeBuild" gives direct access to the value
  - hasGenomeBuildElement
```
public boolean hasGenomeBuildElement()
```
  - hasGenomeBuild
```
public boolean hasGenomeBuild()
```
  - setGenomeBuildElement
```
public Sequence.SequenceReferenceSeqComponent setGenomeBuildElement(StringType value)
```
    Parameters:
    
    value - genomeBuild (The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.). This is the underlying object with id, value and extensions. The accessor "getGenomeBuild" gives direct access to the value
  - getGenomeBuild
```
public String getGenomeBuild()
```
    Returns:
    
    The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
  - setGenomeBuild
```
public Sequence.SequenceReferenceSeqComponent setGenomeBuild(String value)
```
    Parameters:
    
    value - The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
  - getReferenceSeqId
```
public CodeableConcept getReferenceSeqId()
```
    Returns:
    
    referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.)
  - hasReferenceSeqId
```
public boolean hasReferenceSeqId()
```
  - setReferenceSeqId
```
public Sequence.SequenceReferenceSeqComponent setReferenceSeqId(CodeableConcept value)
```
    Parameters:
    
    value - referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.)
  - getReferenceSeqPointer
```
public Reference getReferenceSeqPointer()
```
    Returns:
    
    referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)
  - hasReferenceSeqPointer
```
public boolean hasReferenceSeqPointer()
```
  - setReferenceSeqPointer
```
public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointer(Reference value)
```
    Parameters:
    
    value - referenceSeqPointer (A Pointer to another Sequence entity as reference sequence.)
  - getReferenceSeqPointerTarget
```
public Sequence getReferenceSeqPointerTarget()
```
    Returns:
    
    referenceSeqPointer The actual object that is the target of the reference. The reference library doesn't populate this, but you can use it to hold the resource if you resolve it. (A Pointer to another Sequence entity as reference sequence.)
  - setReferenceSeqPointerTarget
```
public Sequence.SequenceReferenceSeqComponent setReferenceSeqPointerTarget(Sequence value)
```
    Parameters:
    
    value - referenceSeqPointer The actual object that is the target of the reference. The reference library doesn't use these, but you can use it to hold the resource if you resolve it. (A Pointer to another Sequence entity as reference sequence.)
  - getReferenceSeqStringElement
```
public StringType getReferenceSeqStringElement()
```
    Returns:
    
    referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the value
  - hasReferenceSeqStringElement
```
public boolean hasReferenceSeqStringElement()
```
  - hasReferenceSeqString
```
public boolean hasReferenceSeqString()
```
  - setReferenceSeqStringElement
```
public Sequence.SequenceReferenceSeqComponent setReferenceSeqStringElement(StringType value)
```
    Parameters:
    
    value - referenceSeqString (A string like "ACGT".). This is the underlying object with id, value and extensions. The accessor "getReferenceSeqString" gives direct access to the value
  - getReferenceSeqString
```
public String getReferenceSeqString()
```
    Returns:
    
    A string like "ACGT".
  - setReferenceSeqString
```
public Sequence.SequenceReferenceSeqComponent setReferenceSeqString(String value)
```
    Parameters:
    
    value - A string like "ACGT".
  - getStrandElement
```
public IntegerType getStrandElement()
```
    Returns:
    
    strand (Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the value
  - hasStrandElement
```
public boolean hasStrandElement()
```
  - hasStrand
```
public boolean hasStrand()
```
  - setStrandElement
```
public Sequence.SequenceReferenceSeqComponent setStrandElement(IntegerType value)
```
    Parameters:
    
    value - strand (Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the value
  - getStrand
```
public int getStrand()
```
    Returns:
    
    Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.
  - setStrand
```
public Sequence.SequenceReferenceSeqComponent setStrand(int value)
```
    Parameters:
    
    value - Directionality of DNA sequence. Available values are "1" for the plus strand (5' to 3')/Watson/Sense/positive and "-1" for the minus strand(3' to 5')/Crick/Antisense/negative.
  - getWindowStartElement
```
public IntegerType getWindowStartElement()
```
    Returns:
    
    windowStart (Start position of the window 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 "getWindowStart" gives direct access to the value
  - hasWindowStartElement
```
public boolean hasWindowStartElement()
```
  - hasWindowStart
```
public boolean hasWindowStart()
```
  - setWindowStartElement
```
public Sequence.SequenceReferenceSeqComponent setWindowStartElement(IntegerType value)
```
    Parameters:
    
    value - windowStart (Start position of the window 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 "getWindowStart" gives direct access to the value
  - getWindowStart
```
public int getWindowStart()
```
    Returns:
    
    Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - setWindowStart
```
public Sequence.SequenceReferenceSeqComponent setWindowStart(int value)
```
    Parameters:
    
    value - Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
  - getWindowEndElement
```
public IntegerType getWindowEndElement()
```
    Returns:
    
    windowEnd (End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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 "getWindowEnd" gives direct access to the value
  - hasWindowEndElement
```
public boolean hasWindowEndElement()
```
  - hasWindowEnd
```
public boolean hasWindowEnd()
```
  - setWindowEndElement
```
public Sequence.SequenceReferenceSeqComponent setWindowEndElement(IntegerType value)
```
    Parameters:
    
    value - windowEnd (End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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 "getWindowEnd" gives direct access to the value
  - getWindowEnd
```
public int getWindowEnd()
```
    Returns:
    
    End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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.
  - setWindowEnd
```
public Sequence.SequenceReferenceSeqComponent setWindowEnd(int value)
```
    Parameters:
    
    value - End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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.
  - listChildren
```
protected void listChildren(List<Property> childrenList)
```
    Overrides:
    
    listChildren in class BackboneElement
  - getProperty
```
public Base[] getProperty(int hash,
                          String name,
                          boolean checkValid)
                   throws FHIRException
```
    Overrides:
    
    getProperty in class BackboneElement
    
    Throws:
    
    FHIRException
  - setProperty
```
public Base setProperty(int hash,
                        String name,
                        Base value)
                 throws FHIRException
```
    Overrides:
    
    setProperty in class BackboneElement
    
    Throws:
    
    FHIRException
  - setProperty
```
public Base setProperty(String name,
                        Base value)
                 throws FHIRException
```
    Overrides:
    
    setProperty in class BackboneElement
    
    Throws:
    
    FHIRException
  - makeProperty
```
public Base makeProperty(int hash,
                         String name)
                  throws FHIRException
```
    Overrides:
    
    makeProperty in class BackboneElement
    
    Throws:
    
    FHIRException
  - getTypesForProperty
```
public String[] getTypesForProperty(int hash,
                                    String name)
                             throws FHIRException
```
    Overrides:
    
    getTypesForProperty in class BackboneElement
    
    Throws:
    
    FHIRException
  - addChild
```
public Base addChild(String name)
              throws FHIRException
```
    Overrides:
    
    addChild in class BackboneElement
    
    Throws:
    
    FHIRException
  - copy
```
public Sequence.SequenceReferenceSeqComponent 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 IBase
    
    Overrides:
    
    isEmpty in class BackboneElement
  - fhirType
```
public String fhirType()
```
    Overrides:
    
    fhirType in class BackboneElement

Class Sequence.SequenceReferenceSeqComponent

Field Summary

Fields inherited from class org.hl7.fhir.dstu3.model.BackboneElement

Fields inherited from class org.hl7.fhir.dstu3.model.Element

Constructor Summary

Method Summary

Methods inherited from class org.hl7.fhir.dstu3.model.BackboneElement

Methods inherited from class org.hl7.fhir.dstu3.model.Element

Methods inherited from class org.hl7.fhir.dstu3.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.IBaseHasExtensions

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

Field Detail

chromosome

genomeBuild

referenceSeqId

referenceSeqPointer

referenceSeqPointerTarget

referenceSeqString

strand

windowStart

windowEnd

Constructor Detail

SequenceReferenceSeqComponent

SequenceReferenceSeqComponent

Method Detail

getChromosome

hasChromosome

setChromosome

getGenomeBuildElement

hasGenomeBuildElement

hasGenomeBuild

setGenomeBuildElement

getGenomeBuild

setGenomeBuild

getReferenceSeqId

hasReferenceSeqId

setReferenceSeqId

getReferenceSeqPointer

hasReferenceSeqPointer

setReferenceSeqPointer

getReferenceSeqPointerTarget

setReferenceSeqPointerTarget

getReferenceSeqStringElement

hasReferenceSeqStringElement

hasReferenceSeqString

setReferenceSeqStringElement

getReferenceSeqString

setReferenceSeqString

getStrandElement

hasStrandElement

hasStrand

setStrandElement

getStrand

setStrand

getWindowStartElement

hasWindowStartElement

hasWindowStart

setWindowStartElement

getWindowStart

setWindowStart

getWindowEndElement

hasWindowEndElement

hasWindowEnd

setWindowEndElement

getWindowEnd

setWindowEnd

listChildren

getProperty

setProperty

setProperty

makeProperty

getTypesForProperty

addChild

copy

equalsDeep

equalsShallow

isEmpty

fhirType