Package org.hl7.fhir.r5.model

Class MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent

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.MolecularSequenceRelativeStartingSequenceComponent

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

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.hl7.fhir.r5.model.Base

Base.ProfileSource, Base.ValidationInfo, Base.ValidationMode, Base.ValidationReason

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 CodeableConcept	genomeAssembly	The genome assembly used for starting sequence, e.g.
protected Enumeration<MolecularSequence.OrientationType>	orientation	A relative reference to a DNA strand based on gene orientation.
protected DataType	sequence	The reference sequence that represents the starting sequence.
protected Enumeration<MolecularSequence.StrandType>	strand	An absolute reference to a strand.
protected IntegerType	windowEnd	End position of the window on the starting sequence.
protected IntegerType	windowStart	Start position of the window on the starting sequence.

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
MolecularSequenceRelativeStartingSequenceComponent()	Constructor

Method Summary

Modifier and Type	Method	Description
Base	addChild(String name)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	copy()
void	copyValues(MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent dst)
boolean	equalsDeep(Base other_)
boolean	equalsShallow(Base other_)
String	fhirType()
CodeableConcept	getChromosome()
CodeableConcept	getGenomeAssembly()
Property	getNamedProperty(int _hash, String _name, boolean _checkValid)
MolecularSequence.OrientationType	getOrientation()
Enumeration<MolecularSequence.OrientationType>	getOrientationElement()
Base[]	getProperty(int hash, String name, boolean checkValid)
DataType	getSequence()
CodeableConcept	getSequenceCodeableConcept()
Reference	getSequenceReference()
StringType	getSequenceStringType()
MolecularSequence.StrandType	getStrand()
Enumeration<MolecularSequence.StrandType>	getStrandElement()
String[]	getTypesForProperty(int hash, String name)
int	getWindowEnd()
IntegerType	getWindowEndElement()
int	getWindowStart()
IntegerType	getWindowStartElement()
boolean	hasChromosome()
boolean	hasGenomeAssembly()
boolean	hasOrientation()
boolean	hasOrientationElement()
boolean	hasSequence()
boolean	hasSequenceCodeableConcept()
boolean	hasSequenceReference()
boolean	hasSequenceStringType()
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.MolecularSequenceRelativeStartingSequenceComponent	setChromosome(CodeableConcept value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setGenomeAssembly(CodeableConcept value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setOrientation(MolecularSequence.OrientationType value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setOrientationElement(Enumeration<MolecularSequence.OrientationType> value)
Base	setProperty(int hash, String name, Base value)
Base	setProperty(String name, Base value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setSequence(DataType value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setStrand(MolecularSequence.StrandType value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setStrandElement(Enumeration<MolecularSequence.StrandType> value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setWindowEnd(int value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setWindowEndElement(IntegerType value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setWindowStart(int value)
MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent	setWindowStartElement(IntegerType value)

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

addExtension, addExtension, addExtension, copyExtensions, copyNewExtensions, copyValues, getExtension, getExtensionFirstRep, getExtensionString, getExtensionString, getFHIRPublicationVersion, getId, getIdBase, getIdElement, getStandardsStatus, hasExtension, hasExtension, hasId, hasIdElement, isDisallowExtensions, noExtensions, setDisallowExtensions, setExtension, setId, setIdBase, setIdElement, setStandardsStatus

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

addDefinition, addFormatCommentsPost, addFormatCommentsPre, addValidationMessage, canHavePrimitiveValue, children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, copyFormatComments, copyUserData, copyValues, dateTimeValue, equals, getChildByName, getChildValueByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, getValidationInfo, getValidationMessages, getXhtml, hasFormatComment, hasFormatCommentPost, hasFormatCommentPre, hasPrimitiveValue, hasType, hasUserData, hasValidated, hasValidationInfo, hasValidationMessages, isBooleanPrimitive, isCopyUserData, isDateTime, isMetadataBased, isPrimitive, isResource, listChildrenByName, listChildrenByName, primitiveValue, setCopyUserData, 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

genomeAssembly

protected CodeableConcept genomeAssembly

The genome assembly used for starting sequence, e.g. GRCh38.

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)).

sequence

protected DataType sequence

The reference sequence that represents the starting sequence.

windowStart

protected IntegerType windowStart

Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

windowEnd

protected IntegerType windowEnd

End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

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.

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.

Constructor Details

MolecularSequenceRelativeStartingSequenceComponent

public MolecularSequenceRelativeStartingSequenceComponent()

Constructor

Method Details

getGenomeAssembly

public CodeableConcept getGenomeAssembly()

Returns:

genomeAssembly (The genome assembly used for starting sequence, e.g. GRCh38.)

hasGenomeAssembly

public boolean hasGenomeAssembly()

setGenomeAssembly

public MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent setGenomeAssembly(CodeableConcept value)

Parameters:

value - genomeAssembly (The genome assembly used for starting sequence, e.g. GRCh38.)

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.MolecularSequenceRelativeStartingSequenceComponent 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)).)

getSequence

public DataType getSequence()

Returns:

sequence (The reference sequence that represents the starting sequence.)

getSequenceCodeableConcept

public CodeableConcept getSequenceCodeableConcept()
                                           throws org.hl7.fhir.exceptions.FHIRException

Returns:

sequence (The reference sequence that represents the starting sequence.)

Throws:

org.hl7.fhir.exceptions.FHIRException

hasSequenceCodeableConcept

public boolean hasSequenceCodeableConcept()

getSequenceStringType

public StringType getSequenceStringType()
                                 throws org.hl7.fhir.exceptions.FHIRException

Returns:

sequence (The reference sequence that represents the starting sequence.)

Throws:

org.hl7.fhir.exceptions.FHIRException

hasSequenceStringType

public boolean hasSequenceStringType()

getSequenceReference

public Reference getSequenceReference()
                               throws org.hl7.fhir.exceptions.FHIRException

Returns:

sequence (The reference sequence that represents the starting sequence.)

Throws:

org.hl7.fhir.exceptions.FHIRException

hasSequenceReference

public boolean hasSequenceReference()

hasSequence

public boolean hasSequence()

setSequence

public MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent setSequence(DataType value)

Parameters:

value - sequence (The reference sequence that represents the starting sequence.)

getWindowStartElement

public IntegerType getWindowStartElement()

Returns:

windowStart (Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.). 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.MolecularSequenceRelativeStartingSequenceComponent setWindowStartElement(IntegerType value)

Parameters:

value - windowStart (Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.). 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 starting sequence. This value should honor the rules of the coordinateSystem.

setWindowStart

public MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent setWindowStart(int value)

Parameters:

value - Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

getWindowEndElement

public IntegerType getWindowEndElement()

Returns:

windowEnd (End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.). 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.MolecularSequenceRelativeStartingSequenceComponent setWindowEndElement(IntegerType value)

Parameters:

value - windowEnd (End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.). 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 starting sequence. This value should honor the rules of the coordinateSystem.

setWindowEnd

public MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent setWindowEnd(int value)

Parameters:

value - End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

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.MolecularSequenceRelativeStartingSequenceComponent 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.MolecularSequenceRelativeStartingSequenceComponent 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.

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.MolecularSequenceRelativeStartingSequenceComponent 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.MolecularSequenceRelativeStartingSequenceComponent 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.

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.MolecularSequenceRelativeStartingSequenceComponent copy()

Specified by:

copy in class BackboneElement

copyValues

public void copyValues(MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent 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

Returns:

the FHIR type name of the instance (not the java class name)