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HS.FHIR.vSTU3.Model.Resource.Sequence

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

THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Raw data describing a biological sequence.
If the element is present, it must have either a @value, an @id, or extensions

Property Inventory

Method Inventory

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 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.

Properties

property coordinateSystem as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "coordinateSystem", XMLPROJECTION = "ELEMENT") [ Required ];
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: coordinateSystemGet(), coordinateSystemGetSwizzled(), coordinateSystemIsValid(), coordinateSystemNewObject(), coordinateSystemSet()
property device as HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "device", XMLPROJECTION = "ELEMENT");
The method for sequencing, for example, chip information.
Property methods: deviceGet(), deviceGetSwizzled(), deviceIsValid(), deviceNewObject(), deviceSet()
property identifier as list of HS.FHIR.vSTU3.Model.Base.Identifier (XMLNAME = "identifier", XMLPROJECTION = "ELEMENT");
A unique identifier for this particular sequence instance. This is a FHIR-defined id.
Property methods: identifierBuildValueArray(), identifierCollectionToDisplay(), identifierCollectionToOdbc(), identifierDisplayToCollection(), identifierGet(), identifierGetObject(), identifierGetObjectId(), identifierGetSwizzled(), identifierIsValid(), identifierOdbcToCollection(), identifierSet(), identifierSetObject(), identifierSetObjectId()
property observedSeq as HS.FHIR.vSTU3.Model.Datatype.String (XMLNAME = "observedSeq", XMLPROJECTION = "ELEMENT");
Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
Property methods: observedSeqGet(), observedSeqGetSwizzled(), observedSeqIsValid(), observedSeqNewObject(), observedSeqSet()
property patient as HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "patient", XMLPROJECTION = "ELEMENT");
The patient whose sequencing results are described by this resource.
Property methods: patientGet(), patientGetSwizzled(), patientIsValid(), patientNewObject(), patientSet()
property performer as HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "performer", XMLPROJECTION = "ELEMENT");
The organization or lab that should be responsible for this result.
Property methods: performerGet(), performerGetSwizzled(), performerIsValid(), performerNewObject(), performerSet()
property pointer as list of HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "pointer", XMLPROJECTION = "ELEMENT");
Pointer to next atomic sequence which at most contains one variant.
Property methods: pointerBuildValueArray(), pointerCollectionToDisplay(), pointerCollectionToOdbc(), pointerDisplayToCollection(), pointerGet(), pointerGetObject(), pointerGetObjectId(), pointerGetSwizzled(), pointerIsValid(), pointerOdbcToCollection(), pointerSet(), pointerSetObject(), pointerSetObjectId()
property quality as list of HS.FHIR.vSTU3.Model.Resource.Sequence.Quality (XMLNAME = "quality", XMLPROJECTION = "ELEMENT");
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: qualityBuildValueArray(), qualityCollectionToDisplay(), qualityCollectionToOdbc(), qualityDisplayToCollection(), qualityGet(), qualityGetObject(), qualityGetObjectId(), qualityGetSwizzled(), qualityIsValid(), qualityOdbcToCollection(), qualitySet(), qualitySetObject(), qualitySetObjectId()
property quantity as HS.FHIR.vSTU3.Model.Base.Quantity (XMLNAME = "quantity", XMLPROJECTION = "ELEMENT");
The number of copies of the seqeunce of interest. (RNASeq).
Property methods: quantityGet(), quantityGetSwizzled(), quantityIsValid(), quantityNewObject(), quantitySet()
property readCoverage as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "readCoverage", XMLPROJECTION = "ELEMENT");
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
Property methods: readCoverageGet(), readCoverageGetSwizzled(), readCoverageIsValid(), readCoverageNewObject(), readCoverageSet()
property referenceSeq as HS.FHIR.vSTU3.Model.Resource.Sequence.ReferenceSeq (XMLNAME = "referenceSeq", XMLPROJECTION = "ELEMENT");
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 list of HS.FHIR.vSTU3.Model.Resource.Sequence.Repository (XMLNAME = "repository", XMLPROJECTION = "ELEMENT");
Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Property methods: repositoryBuildValueArray(), repositoryCollectionToDisplay(), repositoryCollectionToOdbc(), repositoryDisplayToCollection(), repositoryGet(), repositoryGetObject(), repositoryGetObjectId(), repositoryGetSwizzled(), repositoryIsValid(), repositoryOdbcToCollection(), repositorySet(), repositorySetObject(), repositorySetObjectId()
property specimen as HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "specimen", XMLPROJECTION = "ELEMENT");
Specimen used for sequencing.
Property methods: specimenGet(), specimenGetSwizzled(), specimenIsValid(), specimenNewObject(), specimenSet()
property type as HS.FHIR.vSTU3.Model.Datatype.Code (XMLNAME = "type", XMLPROJECTION = "ELEMENT");
Amino Acid Sequence/ DNA Sequence / RNA Sequence.
Property methods: typeGet(), typeGetSwizzled(), typeIsValid(), typeNewObject(), typeSet()
property variant as list of HS.FHIR.vSTU3.Model.Resource.Sequence.Variant (XMLNAME = "variant", XMLPROJECTION = "ELEMENT");
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: variantBuildValueArray(), variantCollectionToDisplay(), variantCollectionToOdbc(), variantDisplayToCollection(), variantGet(), variantGetObject(), variantGetObjectId(), variantGetSwizzled(), variantIsValid(), variantOdbcToCollection(), variantSet(), variantSetObject(), variantSetObjectId()

Methods

deprecated method SetCoordinateSystem(pValue As %String = "", pExtension As %RegisteredObject = "", pId As %String = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "coordinateSystem" property.
deprecated method SetDevice(pReference As %String = "", pDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "device" property.
deprecated method SetIdentifier(pValue As %String = "", pSystem As %String = "", pUse As %String = "", pTypeCode As %String = "", pTypeSystem As %String = "", pTypeDisplay As %String = "", pTypeText As %String = "", pId As %String = "", pStart As %String = "", pEnd As %String = "", pAssignerReference As %String = "", pAssignerDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Insert method for the "identifier" property.
deprecated method SetObservedSeq(pValue As %String = "", pExtension As %RegisteredObject = "", pId As %String = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "observedSeq" property.
deprecated method SetPatient(pReference As %String = "", pDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "patient" property.
deprecated method SetPerformer(pReference As %String = "", pDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "performer" property.
deprecated method SetPointer(pReference As %String = "", pDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Insert method for the "pointer" property.
deprecated method SetQuantity(pValue As %String = "", pComparator As %String = "", pUnit As %String = "", pSystem As %String = "", pCode As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "quantity" property.
deprecated method SetReadCoverage(pValue As %String = "", pExtension As %RegisteredObject = "", pId As %String = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "readCoverage" property.
deprecated method SetSpecimen(pReference As %String = "", pDisplay As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "specimen" property.
deprecated method SetType(pValue As %String = "", pExtension As %RegisteredObject = "", pId As %String = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "type" property.

Inherited Members

Inherited Properties

Inherited Methods

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