Class MolecularSequence.Variant
- java.lang.Object
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- org.linuxforhealth.fhir.model.visitor.AbstractVisitable
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- org.linuxforhealth.fhir.model.type.Element
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- org.linuxforhealth.fhir.model.type.BackboneElement
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- org.linuxforhealth.fhir.model.resource.MolecularSequence.Variant
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- All Implemented Interfaces:
Visitable
- Enclosing class:
- MolecularSequence
public static class MolecularSequence.Variant extends BackboneElement
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.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MolecularSequence.Variant.Builder
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Field Summary
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Fields inherited from class org.linuxforhealth.fhir.model.type.BackboneElement
modifierExtension
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
accept(java.lang.String elementName, int elementIndex, Visitor visitor)
Accept a Visitor and invoke the appropriate visit methods.static MolecularSequence.Variant.Builder
builder()
boolean
equals(java.lang.Object obj)
String
getCigar()
Extended CIGAR string for aligning the sequence with reference bases.Integer
getEnd()
End position of the variant on the reference sequence.String
getObservedAllele()
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.String
getReferenceAllele()
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.Integer
getStart()
Start position of the variant on the reference sequence.Reference
getVariantPointer()
A pointer to an Observation containing variant information.boolean
hasChildren()
int
hashCode()
MolecularSequence.Variant.Builder
toBuilder()
Create a new Builder from the contents of this Element-
Methods inherited from class org.linuxforhealth.fhir.model.type.BackboneElement
getModifierExtension
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Methods inherited from class org.linuxforhealth.fhir.model.type.Element
as, getExtension, getId, hasValue, is
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Method Detail
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getStart
public Integer getStart()
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.- Returns:
- An immutable object of type
Integer
that may be null.
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getEnd
public Integer getEnd()
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.- Returns:
- An immutable object of type
Integer
that may be null.
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getObservedAllele
public String getObservedAllele()
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.- Returns:
- An immutable object of type
String
that may be null.
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getReferenceAllele
public String getReferenceAllele()
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.- Returns:
- An immutable object of type
String
that may be null.
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getCigar
public String getCigar()
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).- Returns:
- An immutable object of type
String
that may be null.
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getVariantPointer
public Reference getVariantPointer()
A pointer to an Observation containing variant information.- Returns:
- An immutable object of type
Reference
that may be null.
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hasChildren
public boolean hasChildren()
- Overrides:
hasChildren
in classBackboneElement
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accept
public void accept(java.lang.String elementName, int elementIndex, Visitor visitor)
Description copied from interface:Visitable
Accept a Visitor and invoke the appropriate visit methods. A typical implementation would look like this:if (visitor.preVisit(this)) { visitor.visitStart(elementName, elementIndex, this); if (visitor.visit(elementName, elementIndex, this)) { // visit children } visitor.visitEnd(elementName, elementIndex, this); visitor.postVisit(this); }
- Specified by:
accept
in interfaceVisitable
- Specified by:
accept
in classAbstractVisitable
- Parameters:
elementName
- the name of the element in the context of this visitelementIndex
- the index of the element in a list or -1 if it is not contained within a Listvisitor
- the visitor to use
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equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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toBuilder
public MolecularSequence.Variant.Builder toBuilder()
Description copied from class:Element
Create a new Builder from the contents of this Element- Specified by:
toBuilder
in classBackboneElement
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builder
public static MolecularSequence.Variant.Builder builder()
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