HS.FHIRModel.R4.MolecularSequenceX.Variant
class HS.FHIRModel.R4.MolecularSequenceX.Variant extends HS.FHIRModel.FHIRClassSuper
******************************************* MolecularSequenceX.Variant generated class schema
*****************************************
Raw data describing a biological sequence.
Property Inventory
- _cigar
- _end
- _observedAllele
- _referenceAllele
- _start
- cigar
- end
- extension
- fhirID
- modifierExtension
- observedAllele
- referenceAllele
- start
- variantPointer
Method Inventory
- IncludeExtension()
- IncludeModifierExtension()
- IncludeVariantPointer()
- _getProperties()
- fromDao()
- toDao()
Parameters
parameter XMLTYPE = R4_MOLECULARSEQUENCEX_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.FHIRModel.R4.Element;
Extensions for cigar
Property methods: _cigarGet(), _cigarGetSwizzled(), _cigarIsValid(), _cigarNewObject(), _cigarSet()
property _end as HS.FHIRModel.R4.Element;
Extensions for end
Property methods: _endGet(), _endGetSwizzled(), _endIsValid(), _endNewObject(), _endSet()
property _observedAllele as HS.FHIRModel.R4.Element;
Extensions for observedAllele
Property methods: _observedAlleleGet(), _observedAlleleGetSwizzled(), _observedAlleleIsValid(), _observedAlleleNewObject(), _observedAlleleSet()
property _referenceAllele as HS.FHIRModel.R4.Element;
Extensions for referenceAllele
Property methods: _referenceAlleleGet(), _referenceAlleleGetSwizzled(), _referenceAlleleIsValid(), _referenceAlleleNewObject(), _referenceAlleleSet()
property _start as HS.FHIRModel.R4.Element;
Extensions for start
Property methods: _startGet(), _startGetSwizzled(), _startIsValid(), _startNewObject(), _startSet()
property cigar as %String;
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: cigarDisplayToLogical(), cigarGet(), cigarIsValid(), cigarLogicalToDisplay(), cigarLogicalToOdbc(), cigarNormalize(), cigarSet()
property end as %Integer;
End position of the variant on the reference sequence. If the coordinate
system is 0-based then end 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: endDisplayToLogical(), endGet(), endIsValid(), endLogicalToDisplay(), endNormalize(), endSet(), endXSDToLogical()
property extension as HS.FHIRModel.R4.SeqOfExtension;
May be used to represent additional information that is not part
of the basic definition of the element. 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;
Unique id for the element within a resource (for internal references).
This may be any string value that does not contain spaces.
Property methods: fhirIDDisplayToLogical(), fhirIDGet(), fhirIDIsValid(), fhirIDLogicalToDisplay(), fhirIDLogicalToOdbc(), fhirIDNormalize(), fhirIDSet()
property modifierExtension as HS.FHIRModel.R4.SeqOfExtension;
May be used to represent additional information that is not part
of the basic definition of the element and that modifies the understanding
of the element in which it is contained 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
can 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 observedAllele as %String;
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: observedAlleleDisplayToLogical(), observedAlleleGet(), observedAlleleIsValid(), observedAlleleLogicalToDisplay(), observedAlleleLogicalToOdbc(), observedAlleleNormalize(), observedAlleleSet()
property referenceAllele as %String;
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: referenceAlleleDisplayToLogical(), referenceAlleleGet(), referenceAlleleIsValid(), referenceAlleleLogicalToDisplay(), referenceAlleleLogicalToOdbc(), referenceAlleleNormalize(), referenceAlleleSet()
property start as %Integer;
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: startDisplayToLogical(), startGet(), startIsValid(), startLogicalToDisplay(), startNormalize(), startSet(), startXSDToLogical()
property variantPointer as HS.FHIRModel.R4.Reference;
A pointer to an Observation containing variant information.
Property methods: variantPointerGet(), variantPointerGetSwizzled(), variantPointerIsValid(), variantPointerNewObject(), variantPointerSet()
Methods
method IncludeExtension()
method IncludeModifierExtension()
method IncludeVariantPointer()
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.MolecularSequenceX.Variant
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()