Package com.ibm.fhir.model.resource

Class MolecularSequence

  • All Implemented Interfaces:
    Visitable
    @Generated("com.ibm.fhir.tools.CodeGenerator")
public class MolecularSequence
extends DomainResource
    Raw data describing a biological sequence.

    Maturity level: FMM1 (Trial Use)

    • Method Detail

      • getIdentifier

        public 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.

      • getVariant

        public 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 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 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 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.

      • accept

        public void accept​(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 interface Visitable
        Specified by:
        accept in class AbstractVisitable
        Parameters:
        elementName - the name of the element in the context of this visit
        elementIndex - the index of the element in a list or -1 if it is not contained within a List
        visitor - the visitor to use

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object