Class MolecularSequence.ReferenceSeq
- 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.ReferenceSeq
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- All Implemented Interfaces:
Visitable
- Enclosing class:
- MolecularSequence
public static class MolecularSequence.ReferenceSeq extends BackboneElement
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MolecularSequence.ReferenceSeq.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.ReferenceSeq.Builder
builder()
boolean
equals(java.lang.Object obj)
CodeableConcept
getChromosome()
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.String
getGenomeBuild()
The Genome Build used for reference, following GRCh build versions e.g.OrientationType
getOrientation()
A relative reference to a DNA strand based on gene orientation.CodeableConcept
getReferenceSeqId()
Reference identifier of reference sequence submitted to NCBI.Reference
getReferenceSeqPointer()
A pointer to another MolecularSequence entity as reference sequence.String
getReferenceSeqString()
A string like "ACGT".StrandType
getStrand()
An absolute reference to a strand.Integer
getWindowEnd()
End position of the window on the reference sequence.Integer
getWindowStart()
Start position of the window on the reference sequence.boolean
hasChildren()
int
hashCode()
MolecularSequence.ReferenceSeq.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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getChromosome
public CodeableConcept getChromosome()
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology. org/browser/current_svn/term/SO:0000340)).- Returns:
- An immutable object of type
CodeableConcept
that may be null.
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getGenomeBuild
public String getGenomeBuild()
The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.- Returns:
- An immutable object of type
String
that may be null.
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getOrientation
public OrientationType getOrientation()
A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.- Returns:
- An immutable object of type
OrientationType
that may be null.
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getReferenceSeqId
public CodeableConcept getReferenceSeqId()
Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.- Returns:
- An immutable object of type
CodeableConcept
that may be null.
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getReferenceSeqPointer
public Reference getReferenceSeqPointer()
A pointer to another MolecularSequence entity as reference sequence.- Returns:
- An immutable object of type
Reference
that may be null.
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getReferenceSeqString
public String getReferenceSeqString()
A string like "ACGT".- Returns:
- An immutable object of type
String
that may be null.
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getStrand
public StrandType getStrand()
An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.- Returns:
- An immutable object of type
StrandType
that may be null.
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getWindowStart
public Integer getWindowStart()
Start position of the window 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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getWindowEnd
public Integer getWindowEnd()
End position of the window 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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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.ReferenceSeq.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.ReferenceSeq.Builder builder()
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