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Class Details

Parameters (5)
Properties (15)
Inherited Members

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HS.FHIR.DTL.vSTU3.Model.Resource.Sequence

class HS.FHIR.DTL.vSTU3.Model.Resource.Sequence extends HS.FHIR.DTL.vSTU3.Model.Base.DomainResource

Raw data describing a biological sequence.

Parameters

parameter ELEMENTQUALIFIED = 1;

Inherited description: ELEMENTQUALIFIED controls the format of exported XML. The ELEMENTQUALIFIED specification should be based on the elementFormDefault attribute of the schema that defines the type. To maintain compatibility, ELEMENTQUALIFIED will default to 1 (true) for literal format export and will default to 0 (false) for encoded or encoded12 format export. These were the values always previously assumed for the elementFormDefault attribute.

NOTE: Direct use of XMLExport method does not support the ELEMENTQUALIFIED. The export must be done using %XML.Writer or SOAP support.

parameter XMLNAME = Sequence;

Inherited description: This parameter provides the default XMLNAME for the class. If it is empty then the class name will be used to construct a default XML name. The default XMLNAME is used as the top level tag when exporting objects and the export context did not provide an XML container name.

parameter XMLPROJECTION = ELEMENT;

parameter XMLSEQUENCE = 1;

Inherited description: If the XMLSEQUENCE = 1, then the order of the XML elements must match the order of the class properties. This allows us to deal with XML where the same field appears multiple times and is distinguished by the order.

parameter XMLTYPE = Sequence;

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 %Integer (XMLNAME = "coordinateSystem", XMLPROJECTION = "ATTRIBUTE") [ Required ];

integer

Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)

Property methods: coordinateSystemDisplayToLogical(), coordinateSystemGet(), coordinateSystemIsValid(), coordinateSystemLogicalToDisplay(), coordinateSystemNormalize(), coordinateSystemSet(), coordinateSystemXSDToLogical()

property device as HS.FHIR.DTL.vSTU3.Model.Base.Reference (XMLNAME = "device", XMLPROJECTION = "ELEMENT");

Reference

The method for sequencing.

Device

Property methods: deviceGet(), deviceGetSwizzled(), deviceIsValid(), deviceNewObject(), deviceSet()

property identifier as list of HS.FHIR.DTL.vSTU3.Model.Datatype.Identifier (XMLNAME = "identifier", XMLPROJECTION = "ELEMENT");

Identifier

Unique ID for this particular sequence. This is a FHIR-defined id.

Property methods: identifierBuildValueArray(), identifierCollectionToDisplay(), identifierCollectionToOdbc(), identifierDisplayToCollection(), identifierGet(), identifierGetObject(), identifierGetObjectId(), identifierGetSwizzled(), identifierIsValid(), identifierOdbcToCollection(), identifierSet(), identifierSetObject(), identifierSetObjectId()

property observedSeq as %String (MAXLEN = 1000000, XMLNAME = "observedSeq", XMLPROJECTION = "ATTRIBUTE");

string

Sequence that was observed.

Property methods: observedSeqDisplayToLogical(), observedSeqGet(), observedSeqIsValid(), observedSeqLogicalToDisplay(), observedSeqLogicalToOdbc(), observedSeqNormalize(), observedSeqSet()

property patient as HS.FHIR.DTL.vSTU3.Model.Base.Reference (XMLNAME = "patient", XMLPROJECTION = "ELEMENT");

Reference

Who and/or what this is about.

Patient

Property methods: patientGet(), patientGetSwizzled(), patientIsValid(), patientNewObject(), patientSet()

property performer as HS.FHIR.DTL.vSTU3.Model.Base.Reference (XMLNAME = "performer", XMLPROJECTION = "ELEMENT");

Reference

Who should be responsible for test result.

Organization

Property methods: performerGet(), performerGetSwizzled(), performerIsValid(), performerNewObject(), performerSet()

property pointer as list of HS.FHIR.DTL.vSTU3.Model.Base.Reference (XMLNAME = "pointer", XMLPROJECTION = "ELEMENT");

Reference

Pointer to next atomic sequence.

Sequence

Property methods: pointerBuildValueArray(), pointerCollectionToDisplay(), pointerCollectionToOdbc(), pointerDisplayToCollection(), pointerGet(), pointerGetObject(), pointerGetObjectId(), pointerGetSwizzled(), pointerIsValid(), pointerOdbcToCollection(), pointerSet(), pointerSetObject(), pointerSetObjectId()

property quality as list of HS.FHIR.DTL.vSTU3.Model.Element.Sequence.quality (XMLNAME = "quality", XMLPROJECTION = "ELEMENT");

BackboneElement

An set of value as quality of sequence.

Property methods: qualityBuildValueArray(), qualityCollectionToDisplay(), qualityCollectionToOdbc(), qualityDisplayToCollection(), qualityGet(), qualityGetObject(), qualityGetObjectId(), qualityGetSwizzled(), qualityIsValid(), qualityOdbcToCollection(), qualitySet(), qualitySetObject(), qualitySetObjectId()

property quantity as HS.FHIR.DTL.vSTU3.Model.Datatype.Quantity (XMLNAME = "quantity", XMLPROJECTION = "ELEMENT");

Quantity

The number of copies of the seqeunce of interest. (RNASeq)

Property methods: quantityGet(), quantityGetSwizzled(), quantityIsValid(), quantityNewObject(), quantitySet()

property readCoverage as %Integer (XMLNAME = "readCoverage", XMLPROJECTION = "ATTRIBUTE");

integer

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.FHIR.DTL.vSTU3.Model.Element.Sequence.referenceSeq (XMLNAME = "referenceSeq", XMLPROJECTION = "ELEMENT");

BackboneElement

A sequence used as reference.

Property methods: referenceSeqGet(), referenceSeqGetSwizzled(), referenceSeqIsValid(), referenceSeqNewObject(), referenceSeqSet()

property repository as list of HS.FHIR.DTL.vSTU3.Model.Element.Sequence.repository (XMLNAME = "repository", XMLPROJECTION = "ELEMENT");

BackboneElement

External repository which contains detailed report related with observedSeq in this resource.

Property methods: repositoryBuildValueArray(), repositoryCollectionToDisplay(), repositoryCollectionToOdbc(), repositoryDisplayToCollection(), repositoryGet(), repositoryGetObject(), repositoryGetObjectId(), repositoryGetSwizzled(), repositoryIsValid(), repositoryOdbcToCollection(), repositorySet(), repositorySetObject(), repositorySetObjectId()

property specimen as HS.FHIR.DTL.vSTU3.Model.Base.Reference (XMLNAME = "specimen", XMLPROJECTION = "ELEMENT");

Reference

Specimen used for sequencing.

Specimen

Property methods: specimenGet(), specimenGetSwizzled(), specimenIsValid(), specimenNewObject(), specimenSet()

property type as %String (MAXLEN = 1000000, XMLNAME = "type", XMLPROJECTION = "ATTRIBUTE");

code

aa | dna | rna

any FHIR3 code may be used; sequence-type shows EXAMPLE codes, but you may use codes from any ValueSet.

Property methods: typeDisplayToLogical(), typeGet(), typeIsValid(), typeLogicalToDisplay(), typeLogicalToOdbc(), typeNormalize(), typeSet()

property variant as list of HS.FHIR.DTL.vSTU3.Model.Element.Sequence.variant (XMLNAME = "variant", XMLPROJECTION = "ELEMENT");

BackboneElement

Variant in sequence.

Property methods: variantBuildValueArray(), variantCollectionToDisplay(), variantCollectionToOdbc(), variantDisplayToCollection(), variantGet(), variantGetObject(), variantGetObjectId(), variantGetSwizzled(), variantIsValid(), variantOdbcToCollection(), variantSet(), variantSetObject(), variantSetObjectId()

Inherited Members

Inherited Properties

Inherited Methods

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