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HS.FHIR.vSTU3.Model.Resource.Sequence.Variant

deprecated class HS.FHIR.vSTU3.Model.Resource.Sequence.Variant extends HS.FHIR.vSTU3.Model.Base.BackboneElement

THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Raw data describing a biological sequence.

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 JSONTYPEFIELD;
Inherited description: Type property name for JSON export.
parameter XMLNAME = Sequence.Variant;
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.
parameter XMLTYPE = Sequence.Variant;
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 cigar as HS.FHIR.vSTU3.Model.Datatype.String (XMLNAME = "cigar", XMLPROJECTION = "ELEMENT");
Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
Property methods: cigarGet(), cigarGetSwizzled(), cigarIsValid(), cigarNewObject(), cigarSet()
property end as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "end", XMLPROJECTION = "ELEMENT");
End position of the variant on the reference sequence.If the coordinate system is 0-based then end is 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.
Property methods: endGet(), endGetSwizzled(), endIsValid(), endNewObject(), endSet()
property observedAllele as HS.FHIR.vSTU3.Model.Datatype.String (XMLNAME = "observedAllele", XMLPROJECTION = "ELEMENT");
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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.
Property methods: observedAlleleGet(), observedAlleleGetSwizzled(), observedAlleleIsValid(), observedAlleleNewObject(), observedAlleleSet()
property referenceAllele as HS.FHIR.vSTU3.Model.Datatype.String (XMLNAME = "referenceAllele", XMLPROJECTION = "ELEMENT");
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference 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.
Property methods: referenceAlleleGet(), referenceAlleleGetSwizzled(), referenceAlleleIsValid(), referenceAlleleNewObject(), referenceAlleleSet()
property start as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "start", XMLPROJECTION = "ELEMENT");
Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Property methods: startGet(), startGetSwizzled(), startIsValid(), startNewObject(), startSet()
property variantPointer as HS.FHIR.vSTU3.Model.Base.Reference (XMLNAME = "variantPointer", XMLPROJECTION = "ELEMENT");
A pointer to an Observation containing variant information.
Property methods: variantPointerGet(), variantPointerGetSwizzled(), variantPointerIsValid(), variantPointerNewObject(), variantPointerSet()

Methods

deprecated method SetCigar(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 "cigar" property.
deprecated method SetEnd(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 "end" property.
deprecated method SetObservedAllele(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 "observedAllele" property.
deprecated method SetReferenceAllele(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 "referenceAllele" property.
deprecated method SetStart(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 "start" property.
deprecated method SetVariantPointer(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 "variantPointer" property.

Inherited Members

Inherited Properties

Inherited Methods

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