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HS.FHIR.vSTU3.Model.Resource.Sequence.Quality

deprecated class HS.FHIR.vSTU3.Model.Resource.Sequence.Quality 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.Quality;
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.Quality;
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 end as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "end", XMLPROJECTION = "ELEMENT");
End position of the 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 fScore as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "fScore", XMLPROJECTION = "ELEMENT");
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
Property methods: fScoreGet(), fScoreGetSwizzled(), fScoreIsValid(), fScoreNewObject(), fScoreSet()
property gtFP as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "gtFP", XMLPROJECTION = "ELEMENT");
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).
Property methods: gtFPGet(), gtFPGetSwizzled(), gtFPIsValid(), gtFPNewObject(), gtFPSet()
property method as HS.FHIR.vSTU3.Model.Base.CodeableConcept (XMLNAME = "method", XMLPROJECTION = "ELEMENT");
Which method is used to get sequence quality.
Property methods: methodGet(), methodGetSwizzled(), methodIsValid(), methodNewObject(), methodSet()
property precision as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "precision", XMLPROJECTION = "ELEMENT");
QUERY.TP / (QUERY.TP + QUERY.FP).
Property methods: precisionGet(), precisionGetSwizzled(), precisionIsValid(), precisionNewObject(), precisionSet()
property queryFP as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "queryFP", XMLPROJECTION = "ELEMENT");
False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.
Property methods: queryFPGet(), queryFPGetSwizzled(), queryFPIsValid(), queryFPNewObject(), queryFPSet()
property queryTP as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "queryTP", XMLPROJECTION = "ELEMENT");
True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
Property methods: queryTPGet(), queryTPGetSwizzled(), queryTPIsValid(), queryTPNewObject(), queryTPSet()
property recall as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "recall", XMLPROJECTION = "ELEMENT");
TRUTH.TP / (TRUTH.TP + TRUTH.FN).
Property methods: recallGet(), recallGetSwizzled(), recallIsValid(), recallNewObject(), recallSet()
property score as HS.FHIR.vSTU3.Model.Base.Quantity (XMLNAME = "score", XMLPROJECTION = "ELEMENT");
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
Property methods: scoreGet(), scoreGetSwizzled(), scoreIsValid(), scoreNewObject(), scoreSet()
property standardSequence as HS.FHIR.vSTU3.Model.Base.CodeableConcept (XMLNAME = "standardSequence", XMLPROJECTION = "ELEMENT");
Gold standard sequence used for comparing against.
Property methods: standardSequenceGet(), standardSequenceGetSwizzled(), standardSequenceIsValid(), standardSequenceNewObject(), standardSequenceSet()
property start as HS.FHIR.vSTU3.Model.Datatype.Integer (XMLNAME = "start", XMLPROJECTION = "ELEMENT");
Start position of the 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 truthFN as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "truthFN", XMLPROJECTION = "ELEMENT");
False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.
Property methods: truthFNGet(), truthFNGetSwizzled(), truthFNIsValid(), truthFNNewObject(), truthFNSet()
property truthTP as HS.FHIR.vSTU3.Model.Datatype.Decimal (XMLNAME = "truthTP", XMLPROJECTION = "ELEMENT");
True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
Property methods: truthTPGet(), truthTPGetSwizzled(), truthTPIsValid(), truthTPNewObject(), truthTPSet()
property type as HS.FHIR.vSTU3.Model.Base.qualityType (XMLNAME = "type", XMLPROJECTION = "ELEMENT") [ Required ];
INDEL / SNP / Undefined variant.
Property methods: typeGet(), typeGetSwizzled(), typeIsValid(), typeNewObject(), typeSet()

Methods

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 SetFScore(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 "fScore" property.
deprecated method SetGtFP(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 "gtFP" property.
deprecated method SetMethod(pCode As %String = "", pDisplay As %String = "", pSystem As %String = "", pText As %String = "", pVersion As %String = "", pUserSelected As %String = "", pId As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "method" property.
deprecated method SetPrecision(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 "precision" property.
deprecated method SetQueryFP(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 "queryFP" property.
deprecated method SetQueryTP(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 "queryTP" property.
deprecated method SetRecall(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 "recall" property.
deprecated method SetScore(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 "score" property.
deprecated method SetStandardSequence(pCode As %String = "", pDisplay As %String = "", pSystem As %String = "", pText As %String = "", pVersion As %String = "", pUserSelected As %String = "", pId As %String = "", pExtension As %RegisteredObject = "") as %Status
THIS DATA OBJECT MODEL CLASS IS DEPRECATED - Use %DynamicObject or HS.FHIRObject.* instead.
Set method for the "standardSequence" 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 SetTruthFN(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 "truthFN" property.
deprecated method SetTruthTP(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 "truthTP" 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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