Package org.hl7.fhir.r5.model

Class MolecularSequence.MolecularSequenceRelativeEditComponent

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.MolecularSequenceRelativeEditComponent

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.MolecularSequenceRelativeEditComponent
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 IntegerType	end	End position of the edit on the starting sequence.
protected StringType	replacedSequence	Allele in the starting sequence.
protected StringType	replacementSequence	Allele that was observed.
protected IntegerType	start	Start position of the edit 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
MolecularSequenceRelativeEditComponent()	Constructor

Method Summary

Modifier and Type	Method	Description
Base	addChild(String name)
MolecularSequence.MolecularSequenceRelativeEditComponent	copy()
void	copyValues(MolecularSequence.MolecularSequenceRelativeEditComponent dst)
boolean	equalsDeep(Base other_)
boolean	equalsShallow(Base other_)
String	fhirType()
int	getEnd()
IntegerType	getEndElement()
Property	getNamedProperty(int _hash, String _name, boolean _checkValid)
Base[]	getProperty(int hash, String name, boolean checkValid)
String	getReplacedSequence()
StringType	getReplacedSequenceElement()
String	getReplacementSequence()
StringType	getReplacementSequenceElement()
int	getStart()
IntegerType	getStartElement()
String[]	getTypesForProperty(int hash, String name)
boolean	hasEnd()
boolean	hasEndElement()
boolean	hasReplacedSequence()
boolean	hasReplacedSequenceElement()
boolean	hasReplacementSequence()
boolean	hasReplacementSequenceElement()
boolean	hasStart()
boolean	hasStartElement()
boolean	isEmpty()
protected void	listChildren(List<Property> children)
Base	makeProperty(int hash, String name)
void	removeChild(String name, Base value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setEnd(int value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setEndElement(IntegerType value)
Base	setProperty(int hash, String name, Base value)
Base	setProperty(String name, Base value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setReplacedSequence(String value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setReplacedSequenceElement(StringType value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setReplacementSequence(String value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setReplacementSequenceElement(StringType value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setStart(int value)
MolecularSequence.MolecularSequenceRelativeEditComponent	setStartElement(IntegerType value)

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

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

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

addExtension, addExtension, addExtension, copyExtensions, copyNewExtensions, copyValues, getExtension, getExtensionByUrl, 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, executeFunction, 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, setXhtml

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

start

protected IntegerType start

Start position of the edit on the starting 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 edit on the starting 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.

replacementSequence

protected StringType replacementSequence

Allele that was observed. 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.

replacedSequence

protected StringType replacedSequence

Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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.

Constructor Details

MolecularSequenceRelativeEditComponent

public MolecularSequenceRelativeEditComponent()

Constructor

Method Details

getStartElement

public IntegerType getStartElement()

Returns:

start (Start position of the edit on the starting 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.MolecularSequenceRelativeEditComponent setStartElement(IntegerType value)

Parameters:

value - start (Start position of the edit on the starting 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 edit on the starting sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

setStart

public MolecularSequence.MolecularSequenceRelativeEditComponent setStart(int value)

Parameters:

value - Start position of the edit on the starting 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 edit on the starting 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.MolecularSequenceRelativeEditComponent setEndElement(IntegerType value)

Parameters:

value - end (End position of the edit on the starting 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 edit on the starting 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.MolecularSequenceRelativeEditComponent setEnd(int value)

Parameters:

value - End position of the edit on the starting 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.

getReplacementSequenceElement

public StringType getReplacementSequenceElement()

Returns:

replacementSequence (Allele that was observed. 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 "getReplacementSequence" gives direct access to the value

hasReplacementSequenceElement

public boolean hasReplacementSequenceElement()

hasReplacementSequence

public boolean hasReplacementSequence()

setReplacementSequenceElement

public MolecularSequence.MolecularSequenceRelativeEditComponent setReplacementSequenceElement(StringType value)

Parameters:

value - replacementSequence (Allele that was observed. 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 "getReplacementSequence" gives direct access to the value

getReplacementSequence

public String getReplacementSequence()

Returns:

Allele that was observed. 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.

setReplacementSequence

public MolecularSequence.MolecularSequenceRelativeEditComponent setReplacementSequence(String value)

Parameters:

value - Allele that was observed. 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.

getReplacedSequenceElement

public StringType getReplacedSequenceElement()

Returns:

replacedSequence (Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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 "getReplacedSequence" gives direct access to the value

hasReplacedSequenceElement

public boolean hasReplacedSequenceElement()

hasReplacedSequence

public boolean hasReplacedSequence()

setReplacedSequenceElement

public MolecularSequence.MolecularSequenceRelativeEditComponent setReplacedSequenceElement(StringType value)

Parameters:

value - replacedSequence (Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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 "getReplacedSequence" gives direct access to the value

getReplacedSequence

public String getReplacedSequence()

Returns:

Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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.

setReplacedSequence

public MolecularSequence.MolecularSequenceRelativeEditComponent setReplacedSequence(String value)

Parameters:

value - Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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.

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.MolecularSequenceRelativeEditComponent copy()

Specified by:

copy in class BackboneElement

copyValues

public void copyValues(MolecularSequence.MolecularSequenceRelativeEditComponent 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)