Package org.hl7.fhir.r4.model

Class MolecularSequence.MolecularSequenceReferenceSeqComponent

java.lang.Object

org.hl7.fhir.r4.model.Base

org.hl7.fhir.r4.model.Element

org.hl7.fhir.r4.model.BackboneElement

org.hl7.fhir.r4.model.MolecularSequence.MolecularSequenceReferenceSeqComponent

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.MolecularSequenceReferenceSeqComponent
extends BackboneElement
implements org.hl7.fhir.instance.model.api.IBaseBackboneElement

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	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 Enumeration<MolecularSequence.OrientationType>	orientation	A relative reference to a DNA strand based on gene orientation.
protected CodeableConcept	referenceSeqId	Reference identifier of reference sequence submitted to NCBI.
protected Reference	referenceSeqPointer	A pointer to another MolecularSequence entity as reference sequence.
protected MolecularSequence	referenceSeqPointerTarget	The actual object that is the target of the reference (A pointer to another MolecularSequence entity as reference sequence.)
protected StringType	referenceSeqString	A string like "ACGT".
protected Enumeration<MolecularSequence.StrandType>	strand	An absolute reference to a strand.
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.r4.model.BackboneElement

modifierExtension

Fields inherited from class org.hl7.fhir.r4.model.Element

extension, id

Constructor Summary

Constructors

Constructor	Description
MolecularSequenceReferenceSeqComponent()	Constructor

Method Summary

Modifier and Type	Method	Description
Base	addChild(String name)
MolecularSequence.MolecularSequenceReferenceSeqComponent	copy()
void	copyValues(MolecularSequence.MolecularSequenceReferenceSeqComponent dst)
boolean	equalsDeep(Base other_)
boolean	equalsShallow(Base other_)
String	fhirType()
CodeableConcept	getChromosome()
String	getGenomeBuild()
StringType	getGenomeBuildElement()
Property	getNamedProperty(int _hash, String _name, boolean _checkValid)
MolecularSequence.OrientationType	getOrientation()
Enumeration<MolecularSequence.OrientationType>	getOrientationElement()
Base[]	getProperty(int hash, String name, boolean checkValid)
CodeableConcept	getReferenceSeqId()
Reference	getReferenceSeqPointer()
MolecularSequence	getReferenceSeqPointerTarget()
String	getReferenceSeqString()
StringType	getReferenceSeqStringElement()
MolecularSequence.StrandType	getStrand()
Enumeration<MolecularSequence.StrandType>	getStrandElement()
String[]	getTypesForProperty(int hash, String name)
int	getWindowEnd()
IntegerType	getWindowEndElement()
int	getWindowStart()
IntegerType	getWindowStartElement()
boolean	hasChromosome()
boolean	hasGenomeBuild()
boolean	hasGenomeBuildElement()
boolean	hasOrientation()
boolean	hasOrientationElement()
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> children)
Base	makeProperty(int hash, String name)
void	removeChild(String name, Base value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setChromosome(CodeableConcept value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setGenomeBuild(String value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setGenomeBuildElement(StringType value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setOrientation(MolecularSequence.OrientationType value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setOrientationElement(Enumeration<MolecularSequence.OrientationType> value)
Base	setProperty(int hash, String name, Base value)
Base	setProperty(String name, Base value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setReferenceSeqId(CodeableConcept value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setReferenceSeqPointer(Reference value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setReferenceSeqPointerTarget(MolecularSequence value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setReferenceSeqString(String value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setReferenceSeqStringElement(StringType value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setStrand(MolecularSequence.StrandType value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setStrandElement(Enumeration<MolecularSequence.StrandType> value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setWindowEnd(int value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setWindowEndElement(IntegerType value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setWindowStart(int value)
MolecularSequence.MolecularSequenceReferenceSeqComponent	setWindowStartElement(IntegerType value)

Methods inherited from class org.hl7.fhir.r4.model.BackboneElement

addModifierExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyExtensions, copyNewExtensions, copyValues, getExtensionByUrl, getExtensionsByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionFirstRep, hasExtension, hasExtension, hasModifierExtension, removeExtension, setModifierExtension

Methods inherited from class org.hl7.fhir.r4.model.Element

addExtension, addExtension, addExtension, copyExtensions, copyNewExtensions, 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.r4.model.Base

castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCanonical, castToCode, castToCodeableConcept, castToCoding, castToContactDetail, castToContactPoint, castToContributor, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDosage, castToDuration, castToElementDefinition, castToExpression, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMarketingStatus, castToMeta, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPopulation, castToPositiveInt, castToProdCharacteristic, castToProductShelfLife, castToQuantity, castToRange, castToRatio, castToReference, castToRelatedArtifact, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToSubstanceAmount, castToTime, castToTiming, castToTriggerDefinition, castToType, castToUnsignedInt, castToUri, castToUrl, castToUsageContext, castToXhtml, castToXhtmlString, children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, 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 Details

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.

orientation

protected Enumeration<MolecularSequence.OrientationType> orientation

A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

referenceSeqId

protected CodeableConcept referenceSeqId

Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.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 MolecularSequence entity as reference sequence.

referenceSeqPointerTarget

protected MolecularSequence referenceSeqPointerTarget

The actual object that is the target of the reference (A pointer to another MolecularSequence entity as reference sequence.)

referenceSeqString

protected StringType referenceSeqString

A string like "ACGT".

strand

protected Enumeration<MolecularSequence.StrandType> strand

An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

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 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 Details

MolecularSequenceReferenceSeqComponent

public MolecularSequenceReferenceSeqComponent()

Constructor

Method Details

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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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.

getOrientationElement

public Enumeration<MolecularSequence.OrientationType> getOrientationElement()

Returns:

orientation (A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.). This is the underlying object with id, value and extensions. The accessor "getOrientation" gives direct access to the value

hasOrientationElement

public boolean hasOrientationElement()

hasOrientation

public boolean hasOrientation()

setOrientationElement

public MolecularSequence.MolecularSequenceReferenceSeqComponent setOrientationElement(Enumeration<MolecularSequence.OrientationType> value)

Parameters:

value - orientation (A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.). This is the underlying object with id, value and extensions. The accessor "getOrientation" gives direct access to the value

getOrientation

public MolecularSequence.OrientationType getOrientation()

Returns:

A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

setOrientation

public MolecularSequence.MolecularSequenceReferenceSeqComponent setOrientation(MolecularSequence.OrientationType value)

Parameters:

value - A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

getReferenceSeqId

public CodeableConcept getReferenceSeqId()

Returns:

referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.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 MolecularSequence.MolecularSequenceReferenceSeqComponent setReferenceSeqId(CodeableConcept value)

Parameters:

value - referenceSeqId (Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.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 MolecularSequence entity as reference sequence.)

hasReferenceSeqPointer

public boolean hasReferenceSeqPointer()

setReferenceSeqPointer

public MolecularSequence.MolecularSequenceReferenceSeqComponent setReferenceSeqPointer(Reference value)

Parameters:

value - referenceSeqPointer (A pointer to another MolecularSequence entity as reference sequence.)

getReferenceSeqPointerTarget

public MolecularSequence 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 MolecularSequence entity as reference sequence.)

setReferenceSeqPointerTarget

public MolecularSequence.MolecularSequenceReferenceSeqComponent setReferenceSeqPointerTarget(MolecularSequence 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 MolecularSequence 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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 MolecularSequence.MolecularSequenceReferenceSeqComponent setReferenceSeqString(String value)

Parameters:

value - A string like "ACGT".

getStrandElement

public Enumeration<MolecularSequence.StrandType> getStrandElement()

Returns:

strand (An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.). 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 MolecularSequence.MolecularSequenceReferenceSeqComponent setStrandElement(Enumeration<MolecularSequence.StrandType> value)

Parameters:

value - strand (An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.). This is the underlying object with id, value and extensions. The accessor "getStrand" gives direct access to the value

getStrand

public MolecularSequence.StrandType getStrand()

Returns:

An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

setStrand

public MolecularSequence.MolecularSequenceReferenceSeqComponent setStrand(MolecularSequence.StrandType value)

Parameters:

value - An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 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 MolecularSequence.MolecularSequenceReferenceSeqComponent 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 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 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 MolecularSequence.MolecularSequenceReferenceSeqComponent setWindowEnd(int value)

Parameters:

value - End position of the window 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.

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

removeChild

public void removeChild(String name,
 Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

removeChild 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.MolecularSequenceReferenceSeqComponent copy()

Specified by:

copy in class BackboneElement

copyValues

public void copyValues(MolecularSequence.MolecularSequenceReferenceSeqComponent 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