HS.FHIRModel.R4.MolecularSequence
class HS.FHIRModel.R4.MolecularSequence extends HS.FHIRModel.FHIRClassSuper
******************************************* MolecularSequence generated class schema
*****************************************
Raw data describing a biological sequence.
Property Inventory
- _coordinateSystem
- _implicitRules
- _language
- _observedSeq
- _readCoverage
- _type
- contained
- coordinateSystem
- device
- extension
- fhirID
- identifier
- implicitRules
- language
- meta
- modifierExtension
- observedSeq
- patient
- performer
- pointer
- quality
- quantity
- readCoverage
- referenceSeq
- repository
- resourceType
- specimen
- structureVariant
- text
- type
- variant
Method Inventory
- IncludeContained()
- IncludeDevice()
- IncludeExtension()
- IncludeIdentifier()
- IncludeMeta()
- IncludeModifierExtension()
- IncludePatient()
- IncludePerformer()
- IncludePointer()
- IncludeQuality()
- IncludeQuantity()
- IncludeReferenceSeq()
- IncludeRepository()
- IncludeSpecimen()
- IncludeStructureVariant()
- IncludeText()
- IncludeVariant()
- _getProperties()
- fromDao()
- toDao()
Parameters
parameter XMLTYPE = R4_MOLECULARSEQUENCE;
Inherited description: This parameter provides the default XMLTYPE for the class. If it is
empty then the class name will be used to construct a default XML type.
The default XMLTYPE is used when naming and referencing this type in a schema and the schema context did not provide an XML type name.
Properties
property _coordinateSystem as HS.FHIRModel.R4.Element;
Extensions for coordinateSystem
Property methods: _coordinateSystemGet(), _coordinateSystemGetSwizzled(), _coordinateSystemIsValid(), _coordinateSystemNewObject(), _coordinateSystemSet()
property _implicitRules as HS.FHIRModel.R4.Element;
Extensions for implicitRules
Property methods: _implicitRulesGet(), _implicitRulesGetSwizzled(), _implicitRulesIsValid(), _implicitRulesNewObject(), _implicitRulesSet()
property _language as HS.FHIRModel.R4.Element;
Extensions for language
Property methods: _languageGet(), _languageGetSwizzled(), _languageIsValid(), _languageNewObject(), _languageSet()
property _observedSeq as HS.FHIRModel.R4.Element;
Extensions for observedSeq
Property methods: _observedSeqGet(), _observedSeqGetSwizzled(), _observedSeqIsValid(), _observedSeqNewObject(), _observedSeqSet()
property _readCoverage as HS.FHIRModel.R4.Element;
Extensions for readCoverage
Property methods: _readCoverageGet(), _readCoverageGetSwizzled(), _readCoverageIsValid(), _readCoverageNewObject(), _readCoverageSet()
property _type as HS.FHIRModel.R4.Element;
Extensions for type
Property methods: _typeGet(), _typeGetSwizzled(), _typeIsValid(), _typeNewObject(), _typeSet()
property contained as HS.FHIRModel.R4.SeqOfResourceList;
These resources do not have an independent existence apart from the
resource that contains them - they cannot be identified independently,
and nor can they have their own independent transaction scope.
Property methods: containedGet(), containedGetSwizzled(), containedIsValid(), containedNewObject(), containedSet()
property coordinateSystem as %Integer;
Whether the sequence is numbered starting at 0 (0-based numbering
or coordinates, inclusive start, exclusive end) or starting at 1
(1-based numbering, inclusive start and inclusive end).
Property methods: coordinateSystemDisplayToLogical(), coordinateSystemGet(), coordinateSystemIsValid(), coordinateSystemLogicalToDisplay(), coordinateSystemNormalize(), coordinateSystemSet(), coordinateSystemXSDToLogical()
property device as HS.FHIRModel.R4.Reference;
The method for sequencing, for example, chip information.
Property methods: deviceGet(), deviceGetSwizzled(), deviceIsValid(), deviceNewObject(), deviceSet()
property extension as HS.FHIRModel.R4.SeqOfExtension;
May be used to represent additional information that is not part
of the basic definition of the resource. To make the use of extensions
safe and manageable, there is a strict set of governance applied
to the definition and use of extensions. Though any implementer
can define an extension, there is a set of requirements that SHALL
be met as part of the definition of the extension.
Property methods: extensionGet(), extensionGetSwizzled(), extensionIsValid(), extensionNewObject(), extensionSet()
property fhirID as %String;
The logical id of the resource, as used in the URL for the resource.
Once assigned, this value never changes.
Property methods: fhirIDDisplayToLogical(), fhirIDGet(), fhirIDIsValid(), fhirIDLogicalToDisplay(), fhirIDLogicalToOdbc(), fhirIDNormalize(), fhirIDSet()
property identifier as HS.FHIRModel.R4.SeqOfIdentifier;
A unique identifier for this particular sequence instance. This is
a FHIR-defined id.
Property methods: identifierGet(), identifierGetSwizzled(), identifierIsValid(), identifierNewObject(), identifierSet()
property implicitRules as %String;
A reference to a set of rules that were followed when the resource
was constructed, and which must be understood when processing the
content. Often, this is a reference to an implementation guide that
defines the special rules along with other profiles etc.
Property methods: implicitRulesDisplayToLogical(), implicitRulesGet(), implicitRulesIsValid(), implicitRulesLogicalToDisplay(), implicitRulesLogicalToOdbc(), implicitRulesNormalize(), implicitRulesSet()
property language as %String;
The base language in which the resource is written.
Property methods: languageDisplayToLogical(), languageGet(), languageIsValid(), languageLogicalToDisplay(), languageLogicalToOdbc(), languageNormalize(), languageSet()
property meta as HS.FHIRModel.R4.Meta;
The metadata about the resource. This is content that is maintained
by the infrastructure. Changes to the content might not always be
associated with version changes to the resource.
Property methods: metaGet(), metaGetSwizzled(), metaIsValid(), metaNewObject(), metaSet()
property modifierExtension as HS.FHIRModel.R4.SeqOfExtension;
May be used to represent additional information that is not part
of the basic definition of the resource and that modifies the understanding
of the element that contains it and/or the understanding of the
containing element's descendants. Usually modifier elements provide
negation or qualification. To make the use of extensions safe and
manageable, there is a strict set of governance applied to the definition
and use of extensions. Though any implementer is allowed to define
an extension, there is a set of requirements that SHALL be met as
part of the definition of the extension. Applications processing
a resource are required to check for modifier extensions. Modifier
extensions SHALL NOT change the meaning of any elements on Resource
or DomainResource (including cannot change the meaning of modifierExtension
itself).
Property methods: modifierExtensionGet(), modifierExtensionGetSwizzled(), modifierExtensionIsValid(), modifierExtensionNewObject(), modifierExtensionSet()
property observedSeq as %String;
Sequence that was observed. It is the result marked by referenceSeq
along with variant records on referenceSeq. This shall start from
referenceSeq.windowStart and end by referenceSeq.windowEnd.
Property methods: observedSeqDisplayToLogical(), observedSeqGet(), observedSeqIsValid(), observedSeqLogicalToDisplay(), observedSeqLogicalToOdbc(), observedSeqNormalize(), observedSeqSet()
property patient as HS.FHIRModel.R4.Reference;
The patient whose sequencing results are described by this resource.
Property methods: patientGet(), patientGetSwizzled(), patientIsValid(), patientNewObject(), patientSet()
property performer as HS.FHIRModel.R4.Reference;
The organization or lab that should be responsible for this result.
Property methods: performerGet(), performerGetSwizzled(), performerIsValid(), performerNewObject(), performerSet()
property pointer as HS.FHIRModel.R4.SeqOfReference;
Pointer to next atomic sequence which at most contains one variant.
Property methods: pointerGet(), pointerGetSwizzled(), pointerIsValid(), pointerNewObject(), pointerSet()
property quality as HS.FHIRModel.R4.MolecularSequenceX.SeqOfMolecularSequenceXQuality;
An experimental feature attribute that defines the quality of the
feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
Property methods: qualityGet(), qualityGetSwizzled(), qualityIsValid(), qualityNewObject(), qualitySet()
property quantity as HS.FHIRModel.R4.Quantity;
The number of copies of the sequence of interest. (RNASeq).
Property methods: quantityGet(), quantityGetSwizzled(), quantityIsValid(), quantityNewObject(), quantitySet()
property readCoverage as %Integer;
Coverage (read depth or depth) is the average number of reads representing
a given nucleotide in the reconstructed sequence.
Property methods: readCoverageDisplayToLogical(), readCoverageGet(), readCoverageIsValid(), readCoverageLogicalToDisplay(), readCoverageNormalize(), readCoverageSet(), readCoverageXSDToLogical()
property referenceSeq as HS.FHIRModel.R4.MolecularSequenceX.ReferenceSeq;
A sequence that is used as a reference to describe variants that
are present in a sequence analyzed.
Property methods: referenceSeqGet(), referenceSeqGetSwizzled(), referenceSeqIsValid(), referenceSeqNewObject(), referenceSeqSet()
property repository as HS.FHIRModel.R4.MolecularSequenceX.SeqOfMolecularSequenceXRepository;
Configurations of the external repository. The repository shall store
target's observedSeq or records related with target's observedSeq.
Property methods: repositoryGet(), repositoryGetSwizzled(), repositoryIsValid(), repositoryNewObject(), repositorySet()
property resourceType as %String [ InitialExpression = "MolecularSequence" , Required ];
This is a MolecularSequence resource
Property methods: resourceTypeDisplayToLogical(), resourceTypeGet(), resourceTypeIsValid(), resourceTypeLogicalToDisplay(), resourceTypeLogicalToOdbc(), resourceTypeNormalize(), resourceTypeSet()
property specimen as HS.FHIRModel.R4.Reference;
Specimen used for sequencing.
Property methods: specimenGet(), specimenGetSwizzled(), specimenIsValid(), specimenNewObject(), specimenSet()
property structureVariant as HS.FHIRModel.R4.MolecularSequenceX.SeqOfMolecularSequenceXStructureVariant;
Information about chromosome structure variation.
Property methods: structureVariantGet(), structureVariantGetSwizzled(), structureVariantIsValid(), structureVariantNewObject(), structureVariantSet()
property text as HS.FHIRModel.R4.Narrative;
A human-readable narrative that contains a summary of the resource
and can be used to represent the content of the resource to a human.
The narrative need not encode all the structured data, but is required
to contain sufficient detail to make it "clinically safe" for a
human to just read the narrative. Resource definitions may define
what content should be represented in the narrative to ensure clinical
safety.
Property methods: textGet(), textGetSwizzled(), textIsValid(), textNewObject(), textSet()
property type as %String (VALUELIST = ",aa,dna,rna");
Amino Acid Sequence/ DNA Sequence / RNA Sequence.
Property methods: typeDisplayToLogical(), typeGet(), typeIsValid(), typeLogicalToDisplay(), typeLogicalToOdbc(), typeNormalize(), typeSet()
property variant as HS.FHIRModel.R4.MolecularSequenceX.SeqOfMolecularSequenceXVariant;
The definition of variant here originates from Sequence ontology
([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).
This element can represent amino acid or nucleic sequence change(including
insertion,deletion,SNP,etc.) It can represent some complex mutation
or segment variation with the assist of CIGAR string.
Property methods: variantGet(), variantGetSwizzled(), variantIsValid(), variantNewObject(), variantSet()
Methods
method IncludeContained()
method IncludeDevice()
method IncludeExtension()
method IncludeIdentifier()
method IncludeMeta()
method IncludeModifierExtension()
method IncludePatient()
method IncludePerformer()
method IncludePointer()
method IncludeQuality()
method IncludeQuantity()
method IncludeReferenceSeq()
method IncludeRepository()
method IncludeSpecimen()
method IncludeStructureVariant()
method IncludeText()
method IncludeVariant()
method _getProperties() as %DynamicArray
Inherited description: Return an array of the defined properties of this class
in the definition order that they were discovered in the
the HL7FHIR JSchema document
classmethod fromDao(dao As %Library.DynamicAbstractObject) as HS.FHIRModel.R4.MolecularSequence
method toDao() as %DynamicAbstractObject
Inherited description: >
The toDao() method casts the set to a DAO.
Inherited Members
Inherited Methods
- %AddToSaveSet()
- %ClassIsLatestVersion()
- %ClassName()
- %ConstructClone()
- %DispatchClassMethod()
- %DispatchGetModified()
- %DispatchGetProperty()
- %DispatchMethod()
- %DispatchSetModified()
- %DispatchSetMultidimProperty()
- %DispatchSetProperty()
- %Extends()
- %GetParameter()
- %IsA()
- %IsModified()
- %New()
- %NormalizeObject()
- %ObjectModified()
- %OriginalNamespace()
- %PackageName()
- %RemoveFromSaveSet()
- %SerializeObject()
- %SetModified()
- %ValidateObject()
- XMLDTD()
- XMLExport()
- XMLExportToStream()
- XMLExportToString()
- XMLNew()
- XMLSchema()
- XMLSchemaNamespace()
- XMLSchemaType()
- add()
- addAll()
- apply()
- clear()
- contains()
- containsAll()
- get()
- iterator()
- put()
- putAll()
- putAllIfAbsent()
- putIfAbsent()
- remove()
- removeAll()
- removeIf()
- rename()
- replace()
- replaceAll()
- size()
- toString()