Class MolecularSequence
- java.lang.Object
-
- org.linuxforhealth.fhir.model.visitor.AbstractVisitable
-
- org.linuxforhealth.fhir.model.resource.Resource
-
- org.linuxforhealth.fhir.model.resource.DomainResource
-
- org.linuxforhealth.fhir.model.resource.MolecularSequence
-
- All Implemented Interfaces:
Visitable
@Generated("org.linuxforhealth.fhir.tools.CodeGenerator") public class MolecularSequence extends DomainResource
Raw data describing a biological sequence.Maturity level: FMM1 (Trial Use)
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MolecularSequence.Builder
static class
MolecularSequence.Quality
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).static class
MolecularSequence.ReferenceSeq
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.static class
MolecularSequence.Repository
Configurations of the external repository.static class
MolecularSequence.StructureVariant
Information about chromosome structure variation.static class
MolecularSequence.Variant
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.
-
Field Summary
-
Fields inherited from class org.linuxforhealth.fhir.model.resource.DomainResource
contained, extension, modifierExtension, text
-
-
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.Builder
builder()
boolean
equals(java.lang.Object obj)
Integer
getCoordinateSystem()
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).Reference
getDevice()
The method for sequencing, for example, chip information.java.util.List<Identifier>
getIdentifier()
A unique identifier for this particular sequence instance.String
getObservedSeq()
Sequence that was observed.Reference
getPatient()
The patient whose sequencing results are described by this resource.Reference
getPerformer()
The organization or lab that should be responsible for this result.java.util.List<Reference>
getPointer()
Pointer to next atomic sequence which at most contains one variant.java.util.List<MolecularSequence.Quality>
getQuality()
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).Quantity
getQuantity()
The number of copies of the sequence of interest.Integer
getReadCoverage()
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.MolecularSequence.ReferenceSeq
getReferenceSeq()
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.java.util.List<MolecularSequence.Repository>
getRepository()
Configurations of the external repository.Reference
getSpecimen()
Specimen used for sequencing.java.util.List<MolecularSequence.StructureVariant>
getStructureVariant()
Information about chromosome structure variation.SequenceType
getType()
Amino Acid Sequence/ DNA Sequence / RNA Sequence.java.util.List<MolecularSequence.Variant>
getVariant()
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.boolean
hasChildren()
int
hashCode()
MolecularSequence.Builder
toBuilder()
Create a new Builder from the contents of this Resource-
Methods inherited from class org.linuxforhealth.fhir.model.resource.DomainResource
getContained, getExtension, getModifierExtension, getText
-
Methods inherited from class org.linuxforhealth.fhir.model.resource.Resource
as, getId, getImplicitRules, getLanguage, getMeta, is
-
-
-
-
Method Detail
-
getIdentifier
public java.util.List<Identifier> getIdentifier()
A unique identifier for this particular sequence instance. This is a FHIR-defined id.- Returns:
- An unmodifiable list containing immutable objects of type
Identifier
that may be empty.
-
getType
public SequenceType getType()
Amino Acid Sequence/ DNA Sequence / RNA Sequence.- Returns:
- An immutable object of type
SequenceType
that may be null.
-
getCoordinateSystem
public Integer getCoordinateSystem()
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).- Returns:
- An immutable object of type
Integer
that is non-null.
-
getPatient
public Reference getPatient()
The patient whose sequencing results are described by this resource.- Returns:
- An immutable object of type
Reference
that may be null.
-
getSpecimen
public Reference getSpecimen()
Specimen used for sequencing.- Returns:
- An immutable object of type
Reference
that may be null.
-
getDevice
public Reference getDevice()
The method for sequencing, for example, chip information.- Returns:
- An immutable object of type
Reference
that may be null.
-
getPerformer
public Reference getPerformer()
The organization or lab that should be responsible for this result.- Returns:
- An immutable object of type
Reference
that may be null.
-
getQuantity
public Quantity getQuantity()
The number of copies of the sequence of interest. (RNASeq).- Returns:
- An immutable object of type
Quantity
that may be null.
-
getReferenceSeq
public MolecularSequence.ReferenceSeq getReferenceSeq()
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.- Returns:
- An immutable object of type
MolecularSequence.ReferenceSeq
that may be null.
-
getVariant
public java.util.List<MolecularSequence.Variant> getVariant()
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.- Returns:
- An unmodifiable list containing immutable objects of type
MolecularSequence.Variant
that may be empty.
-
getObservedSeq
public String getObservedSeq()
Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.- Returns:
- An immutable object of type
String
that may be null.
-
getQuality
public java.util.List<MolecularSequence.Quality> getQuality()
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).- Returns:
- An unmodifiable list containing immutable objects of type
MolecularSequence.Quality
that may be empty.
-
getReadCoverage
public Integer getReadCoverage()
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.- Returns:
- An immutable object of type
Integer
that may be null.
-
getRepository
public java.util.List<MolecularSequence.Repository> getRepository()
Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.- Returns:
- An unmodifiable list containing immutable objects of type
MolecularSequence.Repository
that may be empty.
-
getPointer
public java.util.List<Reference> getPointer()
Pointer to next atomic sequence which at most contains one variant.- Returns:
- An unmodifiable list containing immutable objects of type
Reference
that may be empty.
-
getStructureVariant
public java.util.List<MolecularSequence.StructureVariant> getStructureVariant()
Information about chromosome structure variation.- Returns:
- An unmodifiable list containing immutable objects of type
MolecularSequence.StructureVariant
that may be empty.
-
hasChildren
public boolean hasChildren()
- Overrides:
hasChildren
in classDomainResource
-
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
-
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
-
hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
-
toBuilder
public MolecularSequence.Builder toBuilder()
Description copied from class:Resource
Create a new Builder from the contents of this Resource- Specified by:
toBuilder
in classDomainResource
-
builder
public static MolecularSequence.Builder builder()
-
-