Package org.hl7.fhir.r5.model

Class MolecularSequence

java.lang.Object

org.hl7.fhir.r5.model.Base

org.hl7.fhir.r5.model.BaseResource

org.hl7.fhir.r5.model.Resource

org.hl7.fhir.r5.model.DomainResource

org.hl7.fhir.r5.model.MolecularSequence

All Implemented Interfaces:

ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IAnyResource, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions, org.hl7.fhir.instance.model.api.IBaseResource, org.hl7.fhir.instance.model.api.IDomainResource

public class MolecularSequence
extends DomainResource

Representation of a molecular sequence.

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MolecularSequence.MolecularSequenceRelativeComponent
static class	MolecularSequence.MolecularSequenceRelativeEditComponent
static class	MolecularSequence.MolecularSequenceRelativeStartingSequenceComponent
static enum	MolecularSequence.OrientationType
static class	MolecularSequence.OrientationTypeEnumFactory
static enum	MolecularSequence.SequenceType
static class	MolecularSequence.SequenceTypeEnumFactory
static enum	MolecularSequence.StrandType
static class	MolecularSequence.StrandTypeEnumFactory

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 Reference	device	The method for sequencing, for example, chip information.
protected List<Attachment>	formatted	Sequence that was observed as file content.
protected List<Identifier>	identifier	A unique identifier for this particular sequence instance.
static final ca.uhn.fhir.rest.gclient.TokenClientParam	IDENTIFIER	Fluent Client search parameter constant for identifier
static final ca.uhn.fhir.model.api.Include	INCLUDE_PATIENT	Constant for fluent queries to be used to add include statements.
static final ca.uhn.fhir.model.api.Include	INCLUDE_SUBJECT	Constant for fluent queries to be used to add include statements.
protected StringType	literal	Sequence that was observed.
static final ca.uhn.fhir.rest.gclient.ReferenceClientParam	PATIENT	Fluent Client search parameter constant for patient
protected Reference	performer	The organization or lab that should be responsible for this result.
protected List<MolecularSequence.MolecularSequenceRelativeComponent>	relative	A sequence defined relative to another sequence.
static final String	SP_IDENTIFIER	Search parameter: identifier
static final String	SP_PATIENT	Search parameter: patient
static final String	SP_SUBJECT	Search parameter: subject
static final String	SP_TYPE	Search parameter: type
protected Reference	specimen	Specimen used for sequencing.
protected Reference	subject	Indicates the subject this sequence is associated too.
static final ca.uhn.fhir.rest.gclient.ReferenceClientParam	SUBJECT	Fluent Client search parameter constant for subject
protected Enumeration<MolecularSequence.SequenceType>	type	Amino Acid Sequence/ DNA Sequence / RNA Sequence.
static final ca.uhn.fhir.rest.gclient.TokenClientParam	TYPE	Fluent Client search parameter constant for type

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

contained, extension, modifierExtension, SP_TEXT, text, TEXT

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

id, implicitRules, language, meta

Fields inherited from interface org.hl7.fhir.instance.model.api.IAnyResource

RES_ID, SP_RES_ID

Fields inherited from interface org.hl7.fhir.instance.model.api.IBaseResource

INCLUDE_ALL, WILDCARD_ALL_SET

Constructor Summary

Constructors

Constructor	Description
MolecularSequence()	Constructor

Method Summary

Modifier and Type	Method	Description
Base	addChild(String name)
Attachment	addFormatted()
MolecularSequence	addFormatted(Attachment t)
Identifier	addIdentifier()
MolecularSequence	addIdentifier(Identifier t)
MolecularSequence.MolecularSequenceRelativeComponent	addRelative()
MolecularSequence	addRelative(MolecularSequence.MolecularSequenceRelativeComponent t)
MolecularSequence	copy()
void	copyValues(MolecularSequence dst)
boolean	equalsDeep(Base other_)
boolean	equalsShallow(Base other_)
String	fhirType()
Reference	getDevice()
List<Attachment>	getFormatted()
Attachment	getFormattedFirstRep()
List<Identifier>	getIdentifier()
Identifier	getIdentifierFirstRep()
String	getLiteral()
StringType	getLiteralElement()
Property	getNamedProperty(int _hash, String _name, boolean _checkValid)
Reference	getPerformer()
Base[]	getProperty(int hash, String name, boolean checkValid)
List<MolecularSequence.MolecularSequenceRelativeComponent>	getRelative()
MolecularSequence.MolecularSequenceRelativeComponent	getRelativeFirstRep()
ResourceType	getResourceType()
Reference	getSpecimen()
Reference	getSubject()
MolecularSequence.SequenceType	getType()
Enumeration<MolecularSequence.SequenceType>	getTypeElement()
String[]	getTypesForProperty(int hash, String name)
boolean	hasDevice()
boolean	hasFormatted()
boolean	hasIdentifier()
boolean	hasLiteral()
boolean	hasLiteralElement()
boolean	hasPerformer()
boolean	hasRelative()
boolean	hasSpecimen()
boolean	hasSubject()
boolean	hasType()
boolean	hasTypeElement()
boolean	isEmpty()
protected void	listChildren(List<Property> children)
Base	makeProperty(int hash, String name)
MolecularSequence	setDevice(Reference value)
MolecularSequence	setFormatted(List<Attachment> theFormatted)
MolecularSequence	setIdentifier(List<Identifier> theIdentifier)
MolecularSequence	setLiteral(String value)
MolecularSequence	setLiteralElement(StringType value)
MolecularSequence	setPerformer(Reference value)
Base	setProperty(int hash, String name, Base value)
Base	setProperty(String name, Base value)
MolecularSequence	setRelative(List<MolecularSequence.MolecularSequenceRelativeComponent> theRelative)
MolecularSequence	setSpecimen(Reference value)
MolecularSequence	setSubject(Reference value)
MolecularSequence	setType(MolecularSequence.SequenceType value)
MolecularSequence	setTypeElement(Enumeration<MolecularSequence.SequenceType> value)
protected MolecularSequence	typedCopy()

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

addContained, addExtension, addExtension, addExtension, addModifierExtension, addModifierExtension, checkNoModifiers, copyValues, getContained, getContained, getExtension, getExtensionByUrl, getExtensionsByUrl, getModifierExtension, getModifierExtensionsByUrl, getText, hasContained, hasExtension, hasExtension, hasModifierExtension, hasText, setContained, setExtension, setModifierExtension, setText

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

copyValues, getId, getIdBase, getIdElement, getIdPart, getImplicitRules, getImplicitRulesElement, getLanguage, getLanguage, getLanguageElement, getMeta, getSourcePackage, hasId, hasIdElement, hasImplicitRules, hasImplicitRulesElement, hasLanguage, hasLanguageElement, hasMeta, hasSourcePackage, setId, setIdBase, setIdElement, setImplicitRules, setImplicitRulesElement, setLanguage, setLanguageElement, setMeta, setSourcePackage

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

getStructureFhirVersionEnum, isResource, setId

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

addDefinition, children, clearUserData, compareDeep, compareDeep, compareDeep, compareDeep, compareValues, compareValues, copyUserData, copyValues, dateTimeValue, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getNamedProperty, getUserData, getUserInt, getUserString, getValidationInfo, getXhtml, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, hasValidationInfo, isBooleanPrimitive, isDateTime, isMetadataBased, isPrimitive, listChildrenByName, listChildrenByName, primitiveValue, removeChild, 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.IAnyResource

getId, getIdElement, getLanguageElement, getUserData, setId, setUserData

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

getFormatCommentsPost, getFormatCommentsPre, hasFormatComment

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

getMeta, getStructureFhirVersionEnum, setId

Field Details

identifier

protected List<Identifier> identifier

A unique identifier for this particular sequence instance.

type

protected Enumeration<MolecularSequence.SequenceType> type

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

subject

protected Reference subject

Indicates the subject this sequence is associated too.

specimen

protected Reference specimen

Specimen used for sequencing.

device

protected Reference device

The method for sequencing, for example, chip information.

performer

protected Reference performer

The organization or lab that should be responsible for this result.

literal

protected StringType literal

Sequence that was observed.

formatted

protected List<Attachment> formatted

Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.

relative

protected List<MolecularSequence.MolecularSequenceRelativeComponent> relative

A sequence defined relative to another sequence.

SP_IDENTIFIER

public static final String SP_IDENTIFIER

Search parameter: identifier

Description: The unique identity for a particular sequence
Type: token
Path: MolecularSequence.identifier

See Also:

• Constant Field Values

IDENTIFIER

public static final ca.uhn.fhir.rest.gclient.TokenClientParam IDENTIFIER

Fluent Client search parameter constant for identifier

Description: The unique identity for a particular sequence
Type: token
Path: MolecularSequence.identifier

SP_PATIENT

public static final String SP_PATIENT

Search parameter: patient

Description: The subject that the sequence is about
Type: reference
Path: MolecularSequence.subject

See Also:

• Constant Field Values

PATIENT

public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam PATIENT

Fluent Client search parameter constant for patient

Description: The subject that the sequence is about
Type: reference
Path: MolecularSequence.subject

INCLUDE_PATIENT

public static final ca.uhn.fhir.model.api.Include INCLUDE_PATIENT

Constant for fluent queries to be used to add include statements. Specifies the path value of "MolecularSequence:patient".

SP_SUBJECT

public static final String SP_SUBJECT

Search parameter: subject

Description: The subject that the sequence is about
Type: reference
Path: MolecularSequence.subject

See Also:

• Constant Field Values

SUBJECT

public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam SUBJECT

Fluent Client search parameter constant for subject

Description: The subject that the sequence is about
Type: reference
Path: MolecularSequence.subject

INCLUDE_SUBJECT

public static final ca.uhn.fhir.model.api.Include INCLUDE_SUBJECT

Constant for fluent queries to be used to add include statements. Specifies the path value of "MolecularSequence:subject".

SP_TYPE

public static final String SP_TYPE

Search parameter: type

Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: MolecularSequence.type

See Also:

• Constant Field Values

TYPE

public static final ca.uhn.fhir.rest.gclient.TokenClientParam TYPE

Fluent Client search parameter constant for type

Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
Type: token
Path: MolecularSequence.type

Constructor Details

MolecularSequence

public MolecularSequence()

Constructor

Method Details

getIdentifier

public List<Identifier> getIdentifier()

Returns:

identifier (A unique identifier for this particular sequence instance.)

setIdentifier

public MolecularSequence setIdentifier(List<Identifier> theIdentifier)

Returns:

Returns a reference to this for easy method chaining

hasIdentifier

public boolean hasIdentifier()

addIdentifier

public Identifier addIdentifier()

addIdentifier

public MolecularSequence addIdentifier(Identifier t)

getIdentifierFirstRep

public Identifier getIdentifierFirstRep()

Returns:

The first repetition of repeating field identifier, creating it if it does not already exist {3}

getTypeElement

public Enumeration<MolecularSequence.SequenceType> getTypeElement()

Returns:

type (Amino Acid Sequence/ DNA Sequence / RNA Sequence.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value

hasTypeElement

public boolean hasTypeElement()

hasType

public boolean hasType()

setTypeElement

public MolecularSequence setTypeElement(Enumeration<MolecularSequence.SequenceType> value)

Parameters:

value - type (Amino Acid Sequence/ DNA Sequence / RNA Sequence.). This is the underlying object with id, value and extensions. The accessor "getType" gives direct access to the value

getType

public MolecularSequence.SequenceType getType()

Returns:

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

setType

public MolecularSequence setType(MolecularSequence.SequenceType value)

Parameters:

value - Amino Acid Sequence/ DNA Sequence / RNA Sequence.

getSubject

public Reference getSubject()

Returns:

subject (Indicates the subject this sequence is associated too.)

hasSubject

public boolean hasSubject()

setSubject

public MolecularSequence setSubject(Reference value)

Parameters:

value - subject (Indicates the subject this sequence is associated too.)

getSpecimen

public Reference getSpecimen()

Returns:

specimen (Specimen used for sequencing.)

hasSpecimen

public boolean hasSpecimen()

setSpecimen

public MolecularSequence setSpecimen(Reference value)

Parameters:

value - specimen (Specimen used for sequencing.)

getDevice

public Reference getDevice()

Returns:

device (The method for sequencing, for example, chip information.)

hasDevice

public boolean hasDevice()

setDevice

public MolecularSequence setDevice(Reference value)

Parameters:

value - device (The method for sequencing, for example, chip information.)

getPerformer

public Reference getPerformer()

Returns:

performer (The organization or lab that should be responsible for this result.)

hasPerformer

public boolean hasPerformer()

setPerformer

public MolecularSequence setPerformer(Reference value)

Parameters:

value - performer (The organization or lab that should be responsible for this result.)

getLiteralElement

public StringType getLiteralElement()

Returns:

literal (Sequence that was observed.). This is the underlying object with id, value and extensions. The accessor "getLiteral" gives direct access to the value

hasLiteralElement

public boolean hasLiteralElement()

hasLiteral

public boolean hasLiteral()

setLiteralElement

public MolecularSequence setLiteralElement(StringType value)

Parameters:

value - literal (Sequence that was observed.). This is the underlying object with id, value and extensions. The accessor "getLiteral" gives direct access to the value

getLiteral

public String getLiteral()

Returns:

Sequence that was observed.

setLiteral

public MolecularSequence setLiteral(String value)

Parameters:

value - Sequence that was observed.

getFormatted

public List<Attachment> getFormatted()

Returns:

formatted (Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.)

setFormatted

public MolecularSequence setFormatted(List<Attachment> theFormatted)

Returns:

Returns a reference to this for easy method chaining

hasFormatted

public boolean hasFormatted()

addFormatted

public Attachment addFormatted()

addFormatted

public MolecularSequence addFormatted(Attachment t)

getFormattedFirstRep

public Attachment getFormattedFirstRep()

Returns:

The first repetition of repeating field formatted, creating it if it does not already exist {3}

getRelative

public List<MolecularSequence.MolecularSequenceRelativeComponent> getRelative()

Returns:

relative (A sequence defined relative to another sequence.)

setRelative

public MolecularSequence setRelative(List<MolecularSequence.MolecularSequenceRelativeComponent> theRelative)

Returns:

Returns a reference to this for easy method chaining

hasRelative

public boolean hasRelative()

addRelative

public MolecularSequence.MolecularSequenceRelativeComponent addRelative()

addRelative

public MolecularSequence addRelative(MolecularSequence.MolecularSequenceRelativeComponent t)

getRelativeFirstRep

public MolecularSequence.MolecularSequenceRelativeComponent getRelativeFirstRep()

Returns:

The first repetition of repeating field relative, creating it if it does not already exist {3}

listChildren

protected void listChildren(List<Property> children)

Overrides:

listChildren in class DomainResource

getNamedProperty

public Property getNamedProperty(int _hash,
 String _name,
 boolean _checkValid)
                          throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getNamedProperty in class DomainResource

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 DomainResource

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 DomainResource

Throws:

org.hl7.fhir.exceptions.FHIRException

setProperty

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

Overrides:

setProperty in class DomainResource

Throws:

org.hl7.fhir.exceptions.FHIRException

makeProperty

public Base makeProperty(int hash,
 String name)
                  throws org.hl7.fhir.exceptions.FHIRException

Overrides:

makeProperty in class DomainResource

Throws:

org.hl7.fhir.exceptions.FHIRException

getTypesForProperty

public String[] getTypesForProperty(int hash,
 String name)
                             throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getTypesForProperty in class DomainResource

Throws:

org.hl7.fhir.exceptions.FHIRException

addChild

public Base addChild(String name)
              throws org.hl7.fhir.exceptions.FHIRException

Overrides:

addChild in class DomainResource

Throws:

org.hl7.fhir.exceptions.FHIRException

fhirType

public String fhirType()

Specified by:

fhirType in interface org.hl7.fhir.instance.model.api.IBase

Overrides:

fhirType in class DomainResource

copy

public MolecularSequence copy()

Specified by:

copy in class DomainResource

copyValues

public void copyValues(MolecularSequence dst)

typedCopy

protected MolecularSequence typedCopy()

equalsDeep

public boolean equalsDeep(Base other_)

Overrides:

equalsDeep in class DomainResource

equalsShallow

public boolean equalsShallow(Base other_)

Overrides:

equalsShallow in class DomainResource

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface org.hl7.fhir.instance.model.api.IBase

Overrides:

isEmpty in class DomainResource

getResourceType

public ResourceType getResourceType()

Specified by:

getResourceType in class Resource