Class VariantBnd

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable

    public class VariantBnd
    extends Variant
    A 'BND' variant (i.e. translocation) consisting of two endpoints
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • VariantBnd

        public VariantBnd()
      • VariantBnd

        public VariantBnd​(Marker parent,
                          int start,
                          java.lang.String ref,
                          java.lang.String alt,
                          Chromosome chrTr,
                          int startTr,
                          boolean left,
                          boolean before)
    • Method Detail

      • getEndPoint

        public Marker getEndPoint()
      • isBefore

        public boolean isBefore()
      • isBnd

        public boolean isBnd()
        Overrides:
        isBnd in class Variant
      • isLeft

        public boolean isLeft()
      • query

        public Markers query​(IntervalForest intervalForest)
        Return a collection of intervals that intersect both ends of this variant
        Overrides:
        query in class Marker
      • realignLeft

        public Variant realignLeft()
        Description copied from class: Variant
        Create a new variant realigning it towards the leftmost position
        Overrides:
        realignLeft in class Variant
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Variant