Class SpliceSiteDonor

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

    public class SpliceSiteDonor
    extends SpliceSite
    Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • SpliceSiteDonor

        public SpliceSiteDonor()
      • SpliceSiteDonor

        public SpliceSiteDonor​(Intron parent,
                               int start,
                               int end,
                               boolean strandMinus,
                               java.lang.String id)
    • Method Detail

      • intersectsCoreSpliceSite

        public boolean intersectsCoreSpliceSite​(Marker marker)
        Description copied from class: SpliceSite
        Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins. Usually CORE_SPLICE_SITE_SIZE is 2 bases. Other spice sites are considered "non-core".
        Specified by:
        intersectsCoreSpliceSite in class SpliceSite