Package com.ibm.fhir.model.resource

Class MolecularSequence.Variant

  • 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.

    • Method Detail

      • 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.

      • 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.

      • 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.

      • 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.

      • 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.

      • getVariantPointer

        public Reference getVariantPointer()
        A pointer to an Observation containing variant information.
        Returns:
        An immutable object of type Reference 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