Package com.ibm.fhir.model.resource

Class MolecularSequence.ReferenceSeq

  • 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.

    • Method Detail

      • 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.

      • 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.

      • 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.

      • 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.

      • getReferenceSeqPointer

        public Reference getReferenceSeqPointer()
        A pointer to another MolecularSequence entity as reference sequence.
        Returns:
        An immutable object of type Reference that may be null.

      • getReferenceSeqString

        public String getReferenceSeqString()
        A string like "ACGT".
        Returns:
        An immutable object of type String that may be null.

      • 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.

      • 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.

      • 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.

      • 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